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  • Protein Conformation  (53)
  • American Association for the Advancement of Science (AAAS)  (53)
  • American Geophysical Union (AGU)
  • American Institute of Physics (AIP)
  • 2005-2009  (53)
  • 1995-1999
  • 2008  (53)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (53)
  • American Geophysical Union (AGU)
  • American Institute of Physics (AIP)
  • Nature Publishing Group (NPG)  (21)
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  • 2005-2009  (53)
  • 1995-1999
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  • 1
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    Atomic-level models of the bacterial carboxysome shell (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-02-23
    Description: The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diameter and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into molecular layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolutions of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary atomic models for the carboxysome shell.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tanaka, Shiho -- Kerfeld, Cheryl A -- Sawaya, Michael R -- Cai, Fei -- Heinhorst, Sabine -- Cannon, Gordon C -- Yeates, Todd O -- New York, N.Y. -- Science. 2008 Feb 22;319(5866):1083-6. doi: 10.1126/science.1151458.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California at Los Angeles (UCLA), Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18292340" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/physiology ; Crystallography, X-Ray ; Cytoplasmic Structures/*chemistry/ultrastructure ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Synechocystis/*chemistry/ultrastructure
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Designed protein-protein association (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-01-12
    Description: The analysis of natural contact interfaces between protein subunits and between proteins has disclosed some general rules governing their association. We have applied these rules to produce a number of novel assemblies, demonstrating that a given protein can be engineered to form contacts at various points of its surface. Symmetry plays an important role because it defines the multiplicity of a designed contact and therefore the number of required mutations. Some of the proteins needed only a single side-chain alteration in order to associate to a higher-order complex. The mobility of the buried side chains has to be taken into account. Four assemblies have been structurally elucidated. Comparisons between the designed contacts and the results will provide useful guidelines for the development of future architectures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grueninger, Dirk -- Treiber, Nora -- Ziegler, Mathias O P -- Koetter, Jochen W A -- Schulze, Monika-Sarah -- Schulz, Georg E -- New York, N.Y. -- Science. 2008 Jan 11;319(5860):206-9. doi: 10.1126/science.1150421.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18187656" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde-Lyases/*chemistry/genetics ; Bacterial Proteins/*chemistry/genetics ; Crystallization ; Crystallography, X-Ray ; Cysteine Synthase/*chemistry/genetics ; Dimerization ; Glycoside Hydrolases/*chemistry/genetics ; Models, Molecular ; Mutagenesis, Site-Directed ; Mutant Proteins/chemistry ; Point Mutation ; Porins/*chemistry/genetics ; Protein Conformation ; *Protein Engineering ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/*chemistry/genetics ; Urocanate Hydratase/*chemistry/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 3
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    Tight regulation of unstructured proteins: from transcript synthesis to protein degradation (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-29
    Description: Altered abundance of several intrinsically unstructured proteins (IUPs) has been associated with perturbed cellular signaling that may lead to pathological conditions such as cancer. Therefore, it is important to understand how cells precisely regulate the availability of IUPs. We observed that regulation of transcript clearance, proteolytic degradation, and translational rate contribute to controlling the abundance of IUPs, some of which are present in low amounts and for short periods of time. Abundant phosphorylation and low stochasticity in transcription and translation indicate that the availability of IUPs can be finely tuned. Fidelity in signaling may require that most IUPs be available in appropriate amounts and not present longer than needed.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803065/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803065/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gsponer, Jorg -- Futschik, Matthias E -- Teichmann, Sarah A -- Babu, M Madan -- G0600158/Medical Research Council/United Kingdom -- MC_U105161047/Medical Research Council/United Kingdom -- MC_U105185859/Medical Research Council/United Kingdom -- U.1051.04.027.00001.01 (85859)/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Nov 28;322(5906):1365-8. doi: 10.1126/science.1163581.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK. jgsponer@mrc-lmb.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19039133" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Cycle ; Computational Biology ; Genes, Fungal ; Humans ; Phosphorylation ; Protein Biosynthesis ; Protein Conformation ; Protein Kinases/metabolism ; Proteome/chemistry ; RNA, Fungal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Saccharomyces cerevisiae/chemistry/cytology/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Schizosaccharomyces pombe Proteins/chemistry/metabolism ; Signal Transduction ; Transcription, Genetic
    Print ISSN: 0036-8075
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  • 4
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    Structural basis of toll-like receptor 3 signaling with double-stranded RNA (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-04-19
    Description: Toll-like receptor 3 (TLR3) recognizes double-stranded RNA (dsRNA), a molecular signature of most viruses, and triggers inflammatory responses that prevent viral spread. TLR3 ectodomains (ECDs) dimerize on oligonucleotides of at least 40 to 50 base pairs in length, the minimal length required for signal transduction. To establish the molecular basis for ligand binding and signaling, we determined the crystal structure of a complex between two mouse TLR3-ECDs and dsRNA at 3.4 angstrom resolution. Each TLR3-ECD binds dsRNA at two sites located at opposite ends of the TLR3 horseshoe, and an intermolecular contact between the two TLR3-ECD C-terminal domains coordinates and stabilizes the dimer. This juxtaposition could mediate downstream signaling by dimerizing the cytoplasmic Toll interleukin-1 receptor (TIR) domains. The overall shape of the TLR3-ECD does not change upon binding to dsRNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761030/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761030/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Lin -- Botos, Istvan -- Wang, Yan -- Leonard, Joshua N -- Shiloach, Joseph -- Segal, David M -- Davies, David R -- Z01 BC009254-33/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 18;320(5874):379-81. doi: 10.1126/science.1155406.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18420935" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Humans ; Ligands ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/genetics/metabolism ; NF-kappa B/metabolism ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Double-Stranded/*chemistry/*metabolism ; *Signal Transduction ; Toll-Like Receptor 3/*chemistry/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Architecture of a charge-transfer state regulating light harvesting in a plant antenna protein (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-10
    Description: Energy-dependent quenching of excess absorbed light energy (qE) is a vital mechanism for regulating photosynthetic light harvesting in higher plants. All of the physiological characteristics of qE have been positively correlated with charge transfer between coupled chlorophyll and zeaxanthin molecules in the light-harvesting antenna of photosystem II (PSII). We found evidence for charge-transfer quenching in all three of the individual minor antenna complexes of PSII (CP29, CP26, and CP24), and we conclude that charge-transfer quenching in CP29 involves a delocalized state of an excitonically coupled chlorophyll dimer. We propose that reversible conformational changes in CP29 can "tune" the electronic coupling between the chlorophylls in this dimer, thereby modulating the energy of the chlorophyll-zeaxanthin charge-transfer state and switching on and off the charge-transfer quenching during qE.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ahn, Tae Kyu -- Avenson, Thomas J -- Ballottari, Matteo -- Cheng, Yuan-Chung -- Niyogi, Krishna K -- Bassi, Roberto -- Fleming, Graham R -- New York, N.Y. -- Science. 2008 May 9;320(5877):794-7. doi: 10.1126/science.1154800.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18467588" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis Proteins/chemistry/genetics/*physiology ; Chlorophyll/physiology ; Chlorophyll Binding Proteins ; Chloroplast Proteins ; Electron Transport ; Electrophysiology ; Light ; Light-Harvesting Protein Complexes/chemistry/genetics/*physiology ; Lutein/metabolism ; Models, Molecular ; Photosystem II Protein Complex/chemistry/genetics/*physiology ; Protein Conformation ; Recombinant Proteins/metabolism ; Ribonucleoproteins ; Structure-Activity Relationship ; Xanthophylls/metabolism ; Zeaxanthins
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  • 6
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    Structural evidence for common ancestry of the nuclear pore complex and vesicle coats (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-01
    Description: Nuclear pore complexes (NPCs) facilitate nucleocytoplasmic transport. These massive assemblies comprise an eightfold symmetric scaffold of architectural proteins and central-channel phenylalanine-glycine-repeat proteins forming the transport barrier. We determined the nucleoporin 85 (Nup85)*Seh1 structure, a module in the heptameric Nup84 complex, at 3.5 angstroms resolution. Structural, biochemical, and genetic analyses position the Nup84 complex in two peripheral NPC rings. We establish a conserved tripartite element, the ancestral coatomer element ACE1, that reoccurs in several nucleoporins and vesicle coat proteins, providing structural evidence of coevolution from a common ancestor. We identified interactions that define the organization of the Nup84 complex on the basis of comparison with vesicle coats and confirmed the sites by mutagenesis. We propose that the NPC scaffold, like vesicle coats, is composed of polygons with vertices and edges forming a membrane-proximal lattice that provides docking sites for additional nucleoporins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680690/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680690/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brohawn, Stephen G -- Leksa, Nina C -- Spear, Eric D -- Rajashankar, Kanagalaghatta R -- Schwartz, Thomas U -- GM68762/GM/NIGMS NIH HHS/ -- GM77537/GM/NIGMS NIH HHS/ -- R01 GM077537/GM/NIGMS NIH HHS/ -- R01 GM077537-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 28;322(5906):1369-73. doi: 10.1126/science.1165886. Epub 2008 Oct 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18974315" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Coated Vesicles/*chemistry ; Crystallography, X-Ray ; Dimerization ; Evolution, Molecular ; Membrane Proteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Nuclear Pore/*chemistry ; Nuclear Pore Complex Proteins/*chemistry/genetics/metabolism ; Nuclear Proteins/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism ; Vesicular Transport Proteins/*chemistry
    Print ISSN: 0036-8075
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  • 7
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    Structural basis for specific substrate recognition by the chloroplast signal recognition particle protein cpSRP43 (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-16
    Description: Secretory and membrane proteins carry amino-terminal signal sequences that, in cotranslational targeting, are recognized by the signal recognition particle protein SRP54 without sequence specificity. The most abundant membrane proteins on Earth are the light-harvesting chlorophyll a/b binding proteins (LHCPs). They are synthesized in the cytoplasm, imported into the chloroplast, and posttranslationally targeted to the thylakoid membrane by cpSRP, a heterodimer formed by cpSRP54 and cpSRP43. We present the 1.5 angstrom crystal structure of cpSRP43 characterized by a unique arrangement of chromodomains and ankyrin repeats. The overall shape and charge distribution of cpSRP43 resembles the SRP RNA, which is absent in chloroplasts. The complex with the internal signal sequence of LHCPs reveals that cpSRP43 specifically recognizes a DPLG peptide motif. We describe how cpSPR43 adapts the universally conserved SRP system to posttranslational targeting and insertion of the LHCP family of membrane proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stengel, Katharina F -- Holdermann, Iris -- Cain, Peter -- Robinson, Colin -- Wild, Klemens -- Sinning, Irmgard -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):253-6. doi: 10.1126/science.1158640.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemie-Zentrum der Universitat Heidelberg, INF328, D-69120 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18621669" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Ankyrin Repeat ; Arabidopsis/chemistry/*metabolism ; Arabidopsis Proteins/*chemistry/metabolism ; Calorimetry ; Chloroplast Proteins ; Crystallography, X-Ray ; Dimerization ; Hydrophobic and Hydrophilic Interactions ; Light-Harvesting Protein Complexes/chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits ; RNA, Plant/chemistry/metabolism ; Signal Recognition Particle/*chemistry/*metabolism ; Thylakoids/metabolism
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  • 8
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    The crystal structure of a sodium galactose transporter reveals mechanistic insights into Na+/sugar symport (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-05
    Description: Membrane transporters that use energy stored in sodium gradients to drive nutrients into cells constitute a major class of proteins. We report the crystal structure of a member of the solute sodium symporters (SSS), the Vibrio parahaemolyticus sodium/galactose symporter (vSGLT). The approximately 3.0 angstrom structure contains 14 transmembrane (TM) helices in an inward-facing conformation with a core structure of inverted repeats of 5 TM helices (TM2 to TM6 and TM7 to TM11). Galactose is bound in the center of the core, occluded from the outside solutions by hydrophobic residues. Surprisingly, the architecture of the core is similar to that of the leucine transporter (LeuT) from a different gene family. Modeling the outward-facing conformation based on the LeuT structure, in conjunction with biophysical data, provides insight into structural rearrangements for active transport.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654663/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654663/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Faham, Salem -- Watanabe, Akira -- Besserer, Gabriel Mercado -- Cascio, Duilio -- Specht, Alexandre -- Hirayama, Bruce A -- Wright, Ernest M -- Abramson, Jeff -- DK19567/DK/NIDDK NIH HHS/ -- DK44602/DK/NIDDK NIH HHS/ -- GM07844/GM/NIGMS NIH HHS/ -- R01 GM078844/GM/NIGMS NIH HHS/ -- R01 GM078844-01/GM/NIGMS NIH HHS/ -- R01 GM078844-02/GM/NIGMS NIH HHS/ -- R01 GM078844-03/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Aug 8;321(5890):810-4. doi: 10.1126/science.1160406. Epub 2008 Jul 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1751, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18599740" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Biological Transport ; Crystallography, X-Ray ; Dimerization ; Galactose/chemistry/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers/chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Sodium/chemistry/*metabolism ; Sodium-Glucose Transport Proteins/*chemistry/metabolism ; Vibrio parahaemolyticus/*chemistry/metabolism
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  • 9
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    Micelles protect membrane complexes from solution to vacuum (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-06-17
    Description: The ability to maintain interactions between soluble protein subunits in the gas phase of a mass spectrometer gives critical insight into the stoichiometry and interaction networks of protein complexes. Conversely, for membrane protein complexes in micelles, the transition into the gas phase usually leads to the disruption of interactions, particularly between cytoplasmic and membrane subunits, and a mass spectrum dominated by large aggregates of detergent molecules. We show that by applying nanoelectrospray to a micellar solution of a membrane protein complex, the heteromeric adenosine 5'-triphosphate (ATP)-binding cassette transporter BtuC2D2, we can maintain the complex intact in the gas phase of a mass spectrometer. Dissociation of either transmembrane (BtuC) or cytoplasmic (BtuD) subunits uncovers modifications to the transmembrane subunits and cooperative binding of ATP. By protecting a membrane protein complex within a n-dodecyl-beta-d-maltoside micelle, we demonstrated a powerful strategy that will enable the subunit stoichiometry and ligand-binding properties of membrane complexes to be determined directly, by precise determination of the masses of intact complexes and dissociated subunits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barrera, Nelson P -- Di Bartolo, Natalie -- Booth, Paula J -- Robinson, Carol V -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):243-6. doi: 10.1126/science.1159292. Epub 2008 Jun 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18556516" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Detergents ; Escherichia coli Proteins/*chemistry/metabolism ; Gases ; Glucosides ; Hydrophobic and Hydrophilic Interactions ; Ligands ; *Micelles ; Multiprotein Complexes/chemistry ; Nanotechnology ; Protein Conformation ; Protein Structure, Secondary ; Protein Subunits/chemistry/metabolism ; Solubility ; *Spectrometry, Mass, Electrospray Ionization ; Vacuum
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  • 10
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    Insights into translational termination from the structure of RF2 bound to the ribosome (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-08
    Description: The termination of protein synthesis occurs through the specific recognition of a stop codon in the A site of the ribosome by a release factor (RF), which then catalyzes the hydrolysis of the nascent protein chain from the P-site transfer RNA. Here we present, at a resolution of 3.5 angstroms, the crystal structure of RF2 in complex with its cognate UGA stop codon in the 70S ribosome. The structure provides insight into how RF2 specifically recognizes the stop codon; it also suggests a model for the role of a universally conserved GGQ motif in the catalysis of peptide release.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2642913/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2642913/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weixlbaumer, Albert -- Jin, Hong -- Neubauer, Cajetan -- Voorhees, Rebecca M -- Petry, Sabine -- Kelley, Ann C -- Ramakrishnan, Venki -- 082086/Wellcome Trust/United Kingdom -- MC_U105184332/Medical Research Council/United Kingdom -- U.1051.04.018(78935)/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2008 Nov 7;322(5903):953-6. doi: 10.1126/science.1164840.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18988853" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/chemistry/metabolism ; Biocatalysis ; *Codon, Terminator/chemistry/metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; *Peptide Chain Termination, Translational ; Peptide Termination Factors/*chemistry/metabolism ; Peptides/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Bacterial/metabolism ; RNA, Transfer/metabolism ; Ribosome Subunits/chemistry/metabolism ; Ribosomes/chemistry/*metabolism ; Thermus thermophilus/*chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 11
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    Large-scale molecular dynamics simulations of self-assembling systems (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-09
    Description: Relentless increases in the size and performance of multiprocessor computers, coupled with new algorithms and methods, have led to novel applications of simulations across chemistry. This Perspective focuses on the use of classical molecular dynamics and so-called coarse-grain models to explore phenomena involving self-assembly in complex fluids and biological systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Klein, Michael L -- Shinoda, Wataru -- GM 40712/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Aug 8;321(5890):798-800. doi: 10.1126/science.1157834.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA. klein@lrsm.upenn.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18687954" target="_blank"〉PubMed〈/a〉
    Keywords: *Computer Simulation ; Macromolecular Substances/*chemistry ; Membrane Lipids/chemistry ; Membrane Proteins/*chemistry ; *Membranes, Artificial ; *Models, Molecular ; Nerve Tissue Proteins/chemistry ; Protein Conformation ; Protein Structure, Tertiary ; Surface-Active Agents/*chemistry
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  • 12
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    Biochemistry. An enzyme assembly line (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-09-06
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936446/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936446/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Janet L -- Sherman, David H -- R01 DK042303/DK/NIDDK NIH HHS/ -- R01 DK042303-20/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2008 Sep 5;321(5894):1304-5. doi: 10.1126/science.1163785.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA. janetsmith@umich.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18772425" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Catalytic Domain ; Crystallography, X-Ray ; Dimerization ; Evolution, Molecular ; Fatty Acid Synthase, Type I/*chemistry/genetics/metabolism ; Fatty Acids/biosynthesis ; Peptide Synthases/*chemistry ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Swine/*metabolism
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  • 13
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    Coiled-coil irregularities and instabilities in group A Streptococcus M1 are required for virulence (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-03-08
    Description: Antigenically variable M proteins are major virulence factors and immunogens of the human pathogen group A Streptococcus (GAS). Here, we report the approximately 3 angstrom resolution structure of a GAS M1 fragment containing the regions responsible for eliciting type-specific, protective immunity and for binding fibrinogen, which promotes M1 proinflammatory and antiphagocytic functions. The structure revealed substantial irregularities and instabilities throughout the coiled coil of the M1 fragment. Similar structural irregularities occur in myosin and tropomyosin, explaining the patterns of cross-reactivity seen in autoimmune sequelae of GAS infection. Sequence idealization of a large segment of the M1 coiled coil enhanced stability but diminished fibrinogen binding, proinflammatory effects, and antibody cross-reactivity, whereas it left protective immunogenicity undiminished. Idealized M proteins appear to have promise as vaccine immunogens.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2288698/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2288698/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McNamara, Case -- Zinkernagel, Annelies S -- Macheboeuf, Pauline -- Cunningham, Madeleine W -- Nizet, Victor -- Ghosh, Partho -- R01 AI048694/AI/NIAID NIH HHS/ -- R01 AI052453/AI/NIAID NIH HHS/ -- R01 AI052453-08/AI/NIAID NIH HHS/ -- R21 AI071167/AI/NIAID NIH HHS/ -- R21 AI071167-01A1/AI/NIAID NIH HHS/ -- T32 GM008326/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Mar 7;319(5868):1405-8. doi: 10.1126/science.1154470.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18323455" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Antibodies, Bacterial/immunology ; Antigens, Bacterial/*chemistry/genetics/immunology/metabolism ; Bacterial Outer Membrane Proteins/*chemistry/genetics/immunology/metabolism ; Carrier Proteins/*chemistry/genetics/immunology/metabolism ; Circular Dichroism ; Cross Reactions ; Crystallography, X-Ray ; Dimerization ; Fibrinogen/metabolism ; Humans ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry ; Protein Conformation ; Protein Structure, Secondary ; Repetitive Sequences, Amino Acid ; Streptococcal Infections/immunology/microbiology ; Streptococcus pyogenes/*chemistry/immunology/*pathogenicity ; Virulence
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 14
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    Helical structures of ESCRT-III are disassembled by VPS4 (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-09
    Description: During intracellular membrane trafficking and remodeling, protein complexes known as the ESCRTs (endosomal sorting complexes required for transport) interact with membranes and are required for budding processes directed away from the cytosol, including the budding of intralumenal vesicles to form multivesicular bodies; for the budding of some enveloped viruses; and for daughter cell scission in cytokinesis. We found that the ESCRT-III proteins CHMP2A and CHMP3 (charged multivesicular body proteins 2A and 3) could assemble in vitro into helical tubular structures that expose their membrane interaction sites on the outside of the tubule, whereas the AAA-type adenosine triphosphatase VPS4 could bind on the inside of the tubule and disassemble the tubes upon adenosine triphosphate hydrolysis. CHMP2A and CHMP3 copolymerized in solution, and their membrane targeting was cooperatively enhanced on planar lipid bilayers. Such helical CHMP structures could thus assemble within the neck of an inwardly budding vesicle, catalyzing late steps in budding under the control of VPS4.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758909/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758909/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lata, Suman -- Schoehn, Guy -- Jain, Ankur -- Pires, Ricardo -- Piehler, Jacob -- Gottlinger, Heinrich G -- Weissenhorn, Winfried -- AI29873/AI/NIAID NIH HHS/ -- R37 AI029873/AI/NIAID NIH HHS/ -- R37 AI029873-20/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2008 Sep 5;321(5894):1354-7. doi: 10.1126/science.1161070. Epub 2008 Aug 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Unit for Virus Host Cell Interaction, UMR 5233 UJF (Universite Joseph Fourier)-EMBL (European Molecular Biology Laboratory)-CNRS, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18687924" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*metabolism ; Adenosine Triphosphate/metabolism ; Biomarkers, Tumor/*chemistry/*metabolism ; Centrifugation, Density Gradient ; Dimerization ; Endosomal Sorting Complexes Required for Transport ; Humans ; Lipid Bilayers/chemistry ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Unilamellar Liposomes/chemistry ; Vesicular Transport Proteins/chemistry/*metabolism
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  • 15
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    Biochemistry. Dicey assemblies (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-01-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Janin, Joel -- New York, N.Y. -- Science. 2008 Jan 11;319(5860):165-6. doi: 10.1126/science.1152930.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Yeast Structural Genomics, Institut de Biochimie et Biophysique Moleculaire et Cellulaire, Bat. 430 UMR 8619 CNRS, Universite Paris-Sud, 91405 Orsay, France. joel.janin@u-psud.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18187645" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/genetics ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Evolution, Molecular ; Molecular Weight ; Mutagenesis, Site-Directed ; Mutant Proteins/chemistry ; Point Mutation ; Protein Conformation ; *Protein Engineering ; Protein Folding ; Protein Structure, Quaternary ; Protein Subunits/*chemistry/genetics
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  • 16
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    De novo computational design of retro-aldol enzymes (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-03-08
    Description: The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431203/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431203/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Lin -- Althoff, Eric A -- Clemente, Fernando R -- Doyle, Lindsey -- Rothlisberger, Daniela -- Zanghellini, Alexandre -- Gallaher, Jasmine L -- Betker, Jamie L -- Tanaka, Fujie -- Barbas, Carlos F 3rd -- Hilvert, Donald -- Houk, Kendall N -- Stoddard, Barry L -- Baker, David -- R01 CA097328/CA/NCI NIH HHS/ -- R01 GM049857/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Mar 7;319(5868):1387-91. doi: 10.1126/science.1152692.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18323453" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde-Lyases/*chemistry/metabolism ; *Algorithms ; Binding Sites ; Catalysis ; Catalytic Domain ; Computer Simulation ; Crystallography, X-Ray ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Protein Conformation ; Protein Engineering
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  • 17
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    Axle-less F1-ATPase rotates in the correct direction (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-02-16
    Description: F1-adenosine triphosphatase (ATPase) is an ATP-driven rotary molecular motor in which the central gamma subunit rotates inside a cylinder made of three alpha and three beta subunits alternately arranged. The rotor shaft, an antiparallel alpha-helical coiled coil of the amino and carboxyl termini of the gamma subunit, deeply penetrates the central cavity of the stator cylinder. We truncated the shaft step by step until the remaining rotor head would be outside the cavity and simply sat on the concave entrance of the stator orifice. All truncation mutants rotated in the correct direction, implying torque generation, although the average rotary speeds were low and short mutants exhibited moments of irregular motion. Neither a fixed pivot nor a rigid axle was needed for rotation of F1-ATPase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Furuike, Shou -- Hossain, Mohammad Delawar -- Maki, Yasushi -- Adachi, Kengo -- Suzuki, Toshiharu -- Kohori, Ayako -- Itoh, Hiroyasu -- Yoshida, Masasuke -- Kinosita, Kazuhiko Jr -- New York, N.Y. -- Science. 2008 Feb 15;319(5865):955-8. doi: 10.1126/science.1151343.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18276891" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Hydrolysis ; Microspheres ; Molecular Motor Proteins/*chemistry/metabolism ; Molecular Sequence Data ; Mutant Proteins/chemistry ; Mutation ; Protein Conformation ; Protein Subunits/chemistry/metabolism ; Proton-Translocating ATPases/*chemistry/genetics/*metabolism ; Rotation ; Torque
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  • 18
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    Structural insights into a circadian oscillator (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-11-01
    Description: An endogenous circadian system in cyanobacteria exerts pervasive control over cellular processes, including global gene expression. Indeed, the entire chromosome undergoes daily cycles of topological changes and compaction. The biochemical machinery underlying a circadian oscillator can be reconstituted in vitro with just three cyanobacterial proteins, KaiA, KaiB, and KaiC. These proteins interact to promote conformational changes and phosphorylation events that determine the phase of the in vitro oscillation. The high-resolution structures of these proteins suggest a ratcheting mechanism by which the KaiABC oscillator ticks unidirectionally. This posttranslational oscillator may interact with transcriptional and translational feedback loops to generate the emergent circadian behavior in vivo. The conjunction of structural, biophysical, and biochemical approaches to this system reveals molecular mechanisms of biological timekeeping.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588432/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588432/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnson, Carl Hirschie -- Egli, Martin -- Stewart, Phoebe L -- F32 GM71276/GM/NIGMS NIH HHS/ -- GM067152/GM/NIGMS NIH HHS/ -- GM073845/GM/NIGMS NIH HHS/ -- R01 GM067152/GM/NIGMS NIH HHS/ -- R01 GM067152-06/GM/NIGMS NIH HHS/ -- R01 GM073845/GM/NIGMS NIH HHS/ -- R01 GM073845-03/GM/NIGMS NIH HHS/ -- R01 MH043836/MH/NIMH NIH HHS/ -- R01 MH043836-17/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 31;322(5902):697-701. doi: 10.1126/science.1150451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Box 35-1634, Vanderbilt University, Nashville, TN 37235-1634, USA. carl.h.johnson@vanderbilt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18974343" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; *Biological Clocks ; Cell Division ; Chromosomes, Bacterial/physiology ; *Circadian Rhythm ; Circadian Rhythm Signaling Peptides and Proteins ; Dimerization ; Models, Molecular ; Phosphorylation ; Promoter Regions, Genetic ; Protein Biosynthesis ; Protein Conformation ; Synechococcus/chemistry/genetics/*physiology ; Transcription, Genetic
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  • 19
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    Biochemistry. How enzymes work (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-06-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ringe, Dagmar -- Petsko, Gregory A -- R37 GM032415/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Jun 13;320(5882):1428-9. doi: 10.1126/science.1159747.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA. petsko@brandeis.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18556536" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Catalytic Domain ; Crystallography, X-Ray ; Enzymes/chemistry/*metabolism ; Models, Molecular ; Muramidase/chemistry/metabolism ; Protein Conformation ; Substrate Specificity
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  • 20
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    The high-affinity E. coli methionine ABC transporter: structure and allosteric regulation (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-16
    Description: The crystal structure of the high-affinity Escherichia coli MetNI methionine uptake transporter, a member of the adenosine triphosphate (ATP)-binding cassette (ABC) family, has been solved to 3.7 angstrom resolution. The overall architecture of MetNI reveals two copies of the adenosine triphosphatase (ATPase) MetN in complex with two copies of the transmembrane domain MetI, with the transporter adopting an inward-facing conformation exhibiting widely separated nucleotide binding domains. Each MetI subunit is organized around a core of five transmembrane helices that correspond to a subset of the helices observed in the larger membrane-spanning subunits of the molybdate (ModBC) and maltose (MalFGK) ABC transporters. In addition to the conserved nucleotide binding domain of the ABC family, MetN contains a carboxyl-terminal extension with a ferredoxin-like fold previously assigned to a conserved family of regulatory ligand-binding domains. These domains separate the nucleotide binding domains and would interfere with their association required for ATP binding and hydrolysis. Methionine binds to the dimerized carboxyl-terminal domain and is shown to inhibit ATPase activity. These observations are consistent with an allosteric regulatory mechanism operating at the level of transport activity, where increased intracellular levels of the transported ligand stabilize an inward-facing, ATPase-inactive state of MetNI to inhibit further ligand translocation into the cell.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527972/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527972/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kadaba, Neena S -- Kaiser, Jens T -- Johnson, Eric -- Lee, Allen -- Rees, Douglas C -- GM45162/GM/NIGMS NIH HHS/ -- R37 GM045162/GM/NIGMS NIH HHS/ -- R37 GM045162-18/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):250-3. doi: 10.1126/science.1157987.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, Mail Code 114-96, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18621668" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry/metabolism ; Adenosine Triphosphatases/*chemistry/*metabolism ; Allosteric Regulation ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Escherichia coli Proteins/*chemistry/*metabolism ; Membrane Transport Proteins/*chemistry/*metabolism ; Methionine/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism
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    Biochemistry. Opening the molecular floodgates (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gandhi, Chris S -- Rees, Douglas C -- New York, N.Y. -- Science. 2008 Aug 29;321(5893):1166-7. doi: 10.1126/science.1162963.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18755963" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Cell Membrane/*chemistry/physiology ; *Cell Membrane Permeability ; Crystallography, X-Ray ; Escherichia coli/*chemistry/physiology ; Escherichia coli Proteins/*chemistry/genetics/*physiology ; Hydrophobic and Hydrophilic Interactions ; *Ion Channel Gating ; Ion Channels/*chemistry/genetics/*physiology ; Lipid Bilayers ; Protein Conformation ; Protein Structure, Secondary
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  • 22
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    Midbody targeting of the ESCRT machinery by a noncanonical coiled coil in CEP55 (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-25
    Description: The ESCRT (endosomal sorting complex required for transport) machinery is required for the scission of membrane necks in processes including the budding of HIV-1 and cytokinesis. An essential step in cytokinesis is recruitment of the ESCRT-I complex and the ESCRT-associated protein ALIX to the midbody (the structure that tethers two daughter cells) by the protein CEP55. Biochemical experiments show that peptides from ALIX and the ESCRT-I subunit TSG101 compete for binding to the ESCRT and ALIX-binding region (EABR) of CEP55. We solved the crystal structure of EABR bound to an ALIX peptide at a resolution of 2.0 angstroms. The structure shows that EABR forms an aberrant dimeric parallel coiled coil. Bulky and charged residues at the interface of the two central heptad repeats create asymmetry and a single binding site for an ALIX or TSG101 peptide. Both ALIX and ESCRT-I are required for cytokinesis, which suggests that multiple CEP55 dimers are required for function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720046/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720046/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Hyung Ho -- Elia, Natalie -- Ghirlando, Rodolfo -- Lippincott-Schwartz, Jennifer -- Hurley, James H -- Z01 DK036125-01/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 24;322(5901):576-80. doi: 10.1126/science.1162042.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18948538" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Calcium-Binding Proteins/*chemistry/*metabolism ; Cell Cycle Proteins/*chemistry/*metabolism ; Cellular Structures/metabolism ; Crystallography, X-Ray ; *Cytokinesis ; DNA-Binding Proteins/chemistry/metabolism ; Dimerization ; Endosomal Sorting Complexes Required for Transport ; Endosomes/metabolism ; HeLa Cells ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Biological ; Models, Molecular ; Nuclear Proteins/*chemistry/*metabolism ; Peptide Fragments/chemistry/metabolism ; Protein Binding ; Protein Conformation ; Transcription Factors/chemistry/metabolism ; Transfection
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  • 23
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    Surface sites for engineering allosteric control in proteins (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-18
    Description: Statistical analyses of protein families reveal networks of coevolving amino acids that functionally link distantly positioned functional surfaces. Such linkages suggest a concept for engineering allosteric control into proteins: The intramolecular networks of two proteins could be joined across their surface sites such that the activity of one protein might control the activity of the other. We tested this idea by creating PAS-DHFR, a designed chimeric protein that connects a light-sensing signaling domain from a plant member of the Per/Arnt/Sim (PAS) family of proteins with Escherichia coli dihydrofolate reductase (DHFR). With no optimization, PAS-DHFR exhibited light-dependent catalytic activity that depended on the site of connection and on known signaling mechanisms in both proteins. PAS-DHFR serves as a proof of concept for engineering regulatory activities into proteins through interface design at conserved allosteric sites.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071530/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071530/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Jeeyeon -- Natarajan, Madhusudan -- Nashine, Vishal C -- Socolich, Michael -- Vo, Tina -- Russ, William P -- Benkovic, Stephen J -- Ranganathan, Rama -- R01 EY018720/EY/NEI NIH HHS/ -- R01 EY018720-01/EY/NEI NIH HHS/ -- R01 EY018720-02/EY/NEI NIH HHS/ -- R01 EY018720-03/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 17;322(5900):438-42. doi: 10.1126/science.1159052.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18927392" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Allosteric Site ; Binding Sites ; Catalysis ; Cryptochromes ; Escherichia coli/enzymology ; Flavoproteins/*chemistry/metabolism ; Kinetics ; Ligands ; Light ; Models, Molecular ; NADP/metabolism ; Protein Conformation ; *Protein Engineering ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/*chemistry/*metabolism ; Tetrahydrofolate Dehydrogenase/*chemistry/metabolism
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  • 24
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    Plant immunity requires conformational changes [corrected] of NPR1 via S-nitrosylation and thioredoxins (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-19
    Description: Changes in redox status have been observed during immune responses in different organisms, but the associated signaling mechanisms are poorly understood. In plants, these redox changes regulate the conformation of NPR1, a master regulator of salicylic acid (SA)-mediated defense genes. NPR1 is sequestered in the cytoplasm as an oligomer through intermolecular disulfide bonds. We report that S-nitrosylation of NPR1 by S-nitrosoglutathione (GSNO) at cysteine-156 facilitates its oligomerization, which maintains protein homeostasis upon SA induction. Conversely, the SA-induced NPR1 oligomer-to-monomer reaction is catalyzed by thioredoxins (TRXs). Mutations in both NPR1 cysteine-156 and TRX compromised NPR1-mediated disease resistance. Thus, the regulation of NPR1 is through the opposing action of GSNO and TRX. These findings suggest a link between pathogen-triggered redox changes and gene regulation in plant immunity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833675/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833675/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tada, Yasuomi -- Spoel, Steven H -- Pajerowska-Mukhtar, Karolina -- Mou, Zhonglin -- Song, Junqi -- Wang, Chun -- Zuo, Jianru -- Dong, Xinnian -- 1R01-GM69594/GM/NIGMS NIH HHS/ -- R01 GM069594/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Aug 15;321(5891):952-6. doi: 10.1126/science.1156970. Epub 2008 Jul 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Post Office Box 90338, Duke University, Durham, NC 27708, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18635760" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/chemistry/*immunology/*metabolism/microbiology ; Arabidopsis Proteins/*chemistry/genetics/metabolism ; Cysteine/metabolism ; Gene Expression Regulation, Plant ; Homeostasis ; Immunity, Innate ; Mutation ; Nitric Oxide/metabolism ; Oxidation-Reduction ; Plant Diseases/*immunology ; Protein Conformation ; Protein Structure, Quaternary ; Pseudomonas syringae/immunology ; Recombinant Fusion Proteins/chemistry/metabolism ; S-Nitrosoglutathione/*metabolism/pharmacology ; Salicylic Acid/metabolism/pharmacology ; Thioredoxin h/*metabolism
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  • 25
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    Crystal structure of the termination module of a nonribosomal peptide synthetase (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-06-28
    Description: Nonribosomal peptide synthetases (NRPSs) are modular multidomain enzymes that act as an assembly line to catalyze the biosynthesis of complex natural products. The crystal structure of the 144-kilodalton Bacillus subtilis termination module SrfA-C was solved at 2.6 angstrom resolution. The adenylation and condensation domains of SrfA-C associate closely to form a catalytic platform, with their active sites on the same side of the platform. The peptidyl carrier protein domain is flexibly tethered to this platform and thus can move with its substrate-loaded 4'-phosphopantetheine arm between the active site of the adenylation domain and the donor side of the condensation domain. The SrfA-C crystal structure has implications for the rational redesign of NRPSs as a means of producing novel bioactive peptides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tanovic, Alan -- Samel, Stefan A -- Essen, Lars-Oliver -- Marahiel, Mohamed A -- New York, N.Y. -- Science. 2008 Aug 1;321(5889):659-63. doi: 10.1126/science.1159850. Epub 2008 Jun 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein-Strasse, D35032 Marburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18583577" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacillus subtilis/*enzymology ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Peptide Synthases/*chemistry/metabolism ; Protein Conformation ; Protein Engineering ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism
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  • 26
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    The flavivirus precursor membrane-envelope protein complex: structure and maturation (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-03-29
    Description: Many viruses go through a maturation step in the final stages of assembly before being transmitted to another host. The maturation process of flaviviruses is directed by the proteolytic cleavage of the precursor membrane protein (prM), turning inert virus into infectious particles. We have determined the 2.2 angstrom resolution crystal structure of a recombinant protein in which the dengue virus prM is linked to the envelope glycoprotein E. The structure represents the prM-E heterodimer and fits well into the cryo-electron microscopy density of immature virus at neutral pH. The pr peptide beta-barrel structure covers the fusion loop in E, preventing fusion with host cell membranes. The structure provides a basis for identifying the stages of its pH-directed conformational metamorphosis during maturation, ending with release of pr when budding from the host.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Long -- Lok, Shee-Mei -- Yu, I-Mei -- Zhang, Ying -- Kuhn, Richard J -- Chen, Jue -- Rossmann, Michael G -- 1-U54-AI-057153/AI/NIAID NIH HHS/ -- AI055672/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2008 Mar 28;319(5871):1830-4. doi: 10.1126/science.1153263.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18369147" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Dengue Virus/*chemistry/growth & development ; Dimerization ; Hydrogen-Ion Concentration ; Models, Molecular ; Protein Conformation ; Protein Precursors/chemistry/metabolism ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Viral Envelope Proteins/*chemistry/metabolism ; Viral Matrix Proteins/*chemistry/metabolism ; Virus Assembly
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  • 27
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    Structural biology. Symmetric transporters for asymmetric transport (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-09
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2630483/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2630483/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Karpowich, Nathan K -- Wang, Da-Neng -- DK053973/DK/NIDDK NIH HHS/ -- GM075026/GM/NIGMS NIH HHS/ -- GM075936/GM/NIGMS NIH HHS/ -- MH083840/MH/NIMH NIH HHS/ -- R01 DK053973/DK/NIDDK NIH HHS/ -- R01 DK053973-09/DK/NIDDK NIH HHS/ -- R01 MH083840/MH/NIMH NIH HHS/ -- R01 MH083840-01/MH/NIMH NIH HHS/ -- R21 GM075936/GM/NIGMS NIH HHS/ -- R21 GM075936-02S1/GM/NIGMS NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM075026-040010/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Aug 8;321(5890):781-2. doi: 10.1126/science.1161495.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA. karpowic@saturn.med.nyu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18687947" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Cell Membrane/*metabolism ; Galactose/*metabolism ; Glucose/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Intestinal Absorption ; Intestinal Mucosa/metabolism ; Kidney/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sodium/metabolism ; Sodium-Glucose Transport Proteins/*chemistry/metabolism ; Sodium-Glucose Transporter 1/metabolism ; Sodium-Glucose Transporter 2/*metabolism ; Vibrio parahaemolyticus/*chemistry/metabolism
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  • 28
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    Biochemistry. Getting close to termination (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liljas, Anders -- New York, N.Y. -- Science. 2008 Nov 7;322(5903):863-5. doi: 10.1126/science.1166913.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics, Lund University, Sweden. anders.liljas@mbfys.lu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18988828" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/chemistry/metabolism ; Codon, Terminator ; Crystallography, X-Ray ; Hydrogen Bonding ; *Peptide Chain Termination, Translational ; Peptide Termination Factors/*chemistry/metabolism ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Ribosomal/chemistry/metabolism ; RNA, Transfer/chemistry/metabolism ; Ribosomes/*metabolism ; Thermus thermophilus/*chemistry/genetics/metabolism
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  • 29
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    Biochemistry. RT slides home (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sarafianos, Stefan G -- Arnold, Eddy -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1059-60. doi: 10.1126/science.1167454.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA. sarafianoss@missouri.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19008434" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; DNA, Viral/*metabolism ; Fluorescence Resonance Energy Transfer ; HIV Reverse Transcriptase/chemistry/*metabolism ; HIV-1/*enzymology ; Models, Molecular ; Nevirapine/metabolism/pharmacology ; Oligonucleotides/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Viral/*metabolism ; Reverse Transcriptase Inhibitors/metabolism/pharmacology
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    Biochemistry. Controlled chaos (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-11-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Uversky, Vladimir N -- Dunker, A Keith -- GM071714-01A2/GM/NIGMS NIH HHS/ -- R01 LM007688-01A1/LM/NLM NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 28;322(5906):1340-1. doi: 10.1126/science.1167453.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. vuversky@iupui.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19039128" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Computational Biology ; Escherichia coli Proteins/chemistry/metabolism ; Evolution, Molecular ; Humans ; Protein Conformation ; Protein Structure, Secondary ; Proteins/*chemistry/*metabolism ; Proteome/chemistry ; RNA, Fungal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Schizosaccharomyces pombe Proteins/chemistry/metabolism
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    Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-15
    Description: The reverse transcriptase (RT) of human immunodeficiency virus (HIV) catalyzes a series of reactions to convert single-stranded viral RNA into double-stranded DNA for host cell integration. This process requires a variety of enzymatic activities, including DNA polymerization, RNA cleavage, strand transfer, and strand displacement synthesis. We used single-molecule fluorescence resonance energy transfer to probe the interactions between RT and nucleic acid substrates in real time. RT was observed to slide on nucleic acid duplexes, rapidly shuttling between opposite termini of the duplex. Upon reaching the DNA 3' terminus, RT can spontaneously flip into a polymerization orientation. Sliding kinetics were regulated by cognate nucleotides and anti-HIV drugs, which stabilized and destabilized the polymerization mode, respectively. These long-range translocation activities facilitate multiple stages of the reverse transcription pathway, including normal DNA polymerization and strand displacement synthesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717043/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717043/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Shixin -- Abbondanzieri, Elio A -- Rausch, Jason W -- Le Grice, Stuart F J -- Zhuang, Xiaowei -- GM 068518/GM/NIGMS NIH HHS/ -- R01 GM068518/GM/NIGMS NIH HHS/ -- R01 GM068518-05/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1092-7. doi: 10.1126/science.1163108.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19008444" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbocyanines ; DNA Primers/metabolism ; DNA, Viral/biosynthesis/*metabolism ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes ; HIV Reverse Transcriptase/chemistry/*metabolism ; HIV-1/*enzymology ; Kinetics ; Models, Molecular ; Nevirapine/metabolism/pharmacology ; Nucleic Acid Hybridization ; Nucleotides/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Viral/*metabolism ; Reverse Transcriptase Inhibitors/metabolism/pharmacology ; Reverse Transcription ; Ribonuclease H/chemistry/metabolism
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    A structural mechanism for MscS gating in lipid bilayers (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-30
    Description: The mechanosensitive channel of small conductance (MscS) is a key determinant in the prokaryotic response to osmotic challenges. We determined the structural rearrangements associated with MscS activation in membranes, using functorial measurements, electron paramagnetic resonance spectroscopy, and computational analyses. MscS was trapped in its open conformation after the transbilayer pressure profile was modified through the asymmetric incorporation of lysophospholipids. The transition from the closed to the open state is accompanied by the downward tilting of the transmembrane TM1-TM2 hairpin and by the expansion, tilt, and rotation of the TM3 helices. These movements expand the permeation pathway, leading to an increase in accessibility to water around TM3. Our open MscS model is compatible with single-channel conductance measurements and supports the notion that helix tilting is associated with efficient pore widening in mechanosensitive channels.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897165/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897165/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vasquez, Valeria -- Sotomayor, Marcos -- Cordero-Morales, Julio -- Schulten, Klaus -- Perozo, Eduardo -- 1 R01 GM067887/GM/NIGMS NIH HHS/ -- GM063617/GM/NIGMS NIH HHS/ -- P41 RR005969/RR/NCRR NIH HHS/ -- P41 RR005969-19/RR/NCRR NIH HHS/ -- P41-RR05969/RR/NCRR NIH HHS/ -- R01 GM067887/GM/NIGMS NIH HHS/ -- R01 GM067887-05/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Aug 29;321(5893):1210-4. doi: 10.1126/science.1159674.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18755978" target="_blank"〉PubMed〈/a〉
    Keywords: Electron Spin Resonance Spectroscopy ; Escherichia coli Proteins/*chemistry/genetics/*physiology ; *Ion Channel Gating ; Ion Channels/*chemistry/genetics/*physiology ; *Lipid Bilayers ; Lysophosphatidylcholines ; Micelles ; Models, Molecular ; Mutant Proteins/chemistry/metabolism ; Patch-Clamp Techniques ; Pressure ; Protein Conformation ; Protein Structure, Secondary
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    Biochemistry. An almost-complete movie (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Diallinas, George -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1644-5. doi: 10.1126/science.1168107.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Faculty of Biology, University of Athens, Panepistimioupolis 15781, Athens, Greece. diallina@biol.uoa.gr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074336" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Transport System X-AG/chemistry/metabolism ; Amino Acid Transport Systems/chemistry/metabolism ; Bacterial Proteins/*chemistry/*metabolism ; Binding Sites ; Cation Transport Proteins/chemistry/metabolism ; Computer Simulation ; Crystallography, X-Ray ; Ion Channel Gating ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Molecular ; Protein Conformation ; Protein Structure, Tertiary ; Sodium-Glucose Transport Proteins/chemistry/metabolism ; Symporters/chemistry/metabolism
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    The crystal structure of a mammalian fatty acid synthase (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-09-06
    Description: Mammalian fatty acid synthase is a large multienzyme that catalyzes all steps of fatty acid synthesis. We have determined its crystal structure at 3.2 angstrom resolution covering five catalytic domains, whereas the flexibly tethered terminal acyl carrier protein and thioesterase domains remain unresolved. The structure reveals a complex architecture of alternating linkers and enzymatic domains. Substrate shuttling is facilitated by flexible tethering of the acyl carrier protein domain and by the limited contact between the condensing and modifying portions of the multienzyme, which are mainly connected by linkers rather than direct interaction. The structure identifies two additional nonenzymatic domains: (i) a pseudo-ketoreductase and (ii) a peripheral pseudo-methyltransferase that is probably a remnant of an ancestral methyltransferase domain maintained in some related polyketide synthases. The structural comparison of mammalian fatty acid synthase with modular polyketide synthases shows how their segmental construction allows the variation of domain composition to achieve diverse product synthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maier, Timm -- Leibundgut, Marc -- Ban, Nenad -- New York, N.Y. -- Science. 2008 Sep 5;321(5894):1315-22. doi: 10.1126/science.1161269.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, 8092 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18772430" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Carrier Protein/chemistry/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Dimerization ; Evolution, Molecular ; Fatty Acid Synthase, Type I/*chemistry ; Fatty Acids/biosynthesis ; Methyltransferases/chemistry ; Models, Molecular ; Molecular Sequence Data ; NADP/chemistry/metabolism ; Polyketide Synthases/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Swine/*metabolism
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    Antigen recognition by variable lymphocyte receptors (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-09-27
    Description: Variable lymphocyte receptors (VLRs) rather than antibodies play the primary role in recognition of antigens in the adaptive immune system of jawless vertebrates. Combinatorial assembly of leucine-rich repeat (LRR) gene segments achieves the required repertoire for antigen recognition. We have determined a crystal structure for a VLR-antigen complex, VLR RBC36 in complex with the H-antigen trisaccharide from human blood type O erythrocytes, at 1.67 angstrom resolution. RBC36 binds the H-trisaccharide on the concave surface of the LRR modules of the solenoid structure where three key hydrophilic residues, multiple van der Waals interactions, and the highly variable insert of the carboxyl-terminal LRR module determine antigen recognition and specificity. The concave surface assembled from the most highly variable regions of the LRRs, along with diversity in the sequence and length of the highly variable insert, can account for the recognition of diverse antigens by VLRs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581502/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581502/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Han, Byung Woo -- Herrin, Brantley R -- Cooper, Max D -- Wilson, Ian A -- AI072435/AI/NIAID NIH HHS/ -- AI42266/AI/NIAID NIH HHS/ -- R37 AI042266/AI/NIAID NIH HHS/ -- R37 AI042266-11/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2008 Sep 26;321(5897):1834-7. doi: 10.1126/science.1162484.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18818359" target="_blank"〉PubMed〈/a〉
    Keywords: ABO Blood-Group System/chemistry/*immunology/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lampreys/*immunology ; Lymphocytes/*immunology ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Antigen/*chemistry/*immunology/metabolism ; Trisaccharides/chemistry/*immunology/metabolism
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  • 36
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    Detection of GTP-tubulin conformation in vivo reveals a role for GTP remnants in microtubule rescues (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-18
    Description: Microtubules display dynamic instability, with alternating phases of growth and shrinkage separated by catastrophe and rescue events. The guanosine triphosphate (GTP) cap at the growing end of microtubules, whose presence is essential to prevent microtubule catastrophes in vitro, has been difficult to observe in vivo. We selected a recombinant antibody that specifically recognizes GTP-bound tubulin in microtubules and found that GTP-tubulin was indeed present at the plus end of growing microtubules. Unexpectedly, GTP-tubulin remnants were also present in older parts of microtubules, which suggests that GTP hydrolysis is sometimes incomplete during polymerization. Observations in living cells suggested that these GTP remnants may be responsible for the rescue events in which microtubules recover from catastrophe.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dimitrov, Ariane -- Quesnoit, Melanie -- Moutel, Sandrine -- Cantaloube, Isabelle -- Pous, Christian -- Perez, Franck -- New York, N.Y. -- Science. 2008 Nov 28;322(5906):1353-6. doi: 10.1126/science.1165401. Epub 2008 Oct 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS UMR144, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18927356" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies/immunology ; Cell Line ; Computer Simulation ; Dimerization ; Fluorescent Antibody Technique ; Guanosine Triphosphate/*analysis/metabolism ; HeLa Cells ; Humans ; Microtubules/*chemistry/metabolism/ultrastructure ; Models, Biological ; Monte Carlo Method ; Protein Conformation ; Recombinant Fusion Proteins/metabolism ; Tubulin/analysis/*chemistry/immunology/metabolism
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    An inhibitor of FtsZ with potent and selective anti-staphylococcal activity (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-09-20
    Description: FtsZ is an essential bacterial guanosine triphosphatase and homolog of mammalian beta-tubulin that polymerizes and assembles into a ring to initiate cell division. We have created a class of small synthetic antibacterials, exemplified by PC190723, which inhibits FtsZ and prevents cell division. PC190723 has potent and selective in vitro bactericidal activity against staphylococci, including methicillin- and multi-drug-resistant Staphylococcus aureus. The putative inhibitor-binding site of PC190723 was mapped to a region of FtsZ that is analogous to the Taxol-binding site of tubulin. PC190723 was efficacious in an in vivo model of infection, curing mice infected with a lethal dose of S. aureus. The data validate FtsZ as a target for antibacterial intervention and identify PC190723 as suitable for optimization into a new anti-staphylococcal therapy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haydon, David J -- Stokes, Neil R -- Ure, Rebecca -- Galbraith, Greta -- Bennett, James M -- Brown, David R -- Baker, Patrick J -- Barynin, Vladimir V -- Rice, David W -- Sedelnikova, Sveta E -- Heal, Jonathan R -- Sheridan, Joseph M -- Aiwale, Sachin T -- Chauhan, Pramod K -- Srivastava, Anil -- Taneja, Amit -- Collins, Ian -- Errington, Jeff -- Czaplewski, Lloyd G -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2008 Sep 19;321(5896):1673-5. doi: 10.1126/science.1159961.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Prolysis, Begbroke Science Park, Oxfordshire OX5 1PF, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18801997" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacillus subtilis/chemistry/*drug effects/genetics ; Bacterial Proteins/*antagonists & inhibitors/chemistry/genetics/metabolism ; Binding Sites ; Cell Division/drug effects ; Crystallography, X-Ray ; Cytoskeletal Proteins/*antagonists & inhibitors/chemistry/genetics/metabolism ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial ; Ligands ; Methicillin Resistance ; Mice ; Microbial Sensitivity Tests ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Pyridines/chemistry/metabolism/*pharmacology/therapeutic use ; Staphylococcal Infections/*drug therapy ; Staphylococcus aureus/chemistry/*drug effects ; Thiazoles/chemistry/metabolism/*pharmacology/therapeutic use ; Tubulin/chemistry/metabolism
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    The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-10-25
    Description: Structural studies of the T7 bacteriophage DNA-dependent RNA polymerase (T7 RNAP) have shown that the conformation of the amino-terminal domain changes substantially between the initiation and elongation phases of transcription, but how this transition is achieved remains unclear. We report crystal structures of T7 RNAP bound to promoter DNA containing either a 7- or an 8-nucleotide (nt) RNA transcript that illuminate intermediate states along the transition pathway. The amino-terminal domain comprises the C-helix subdomain and the promoter binding domain (PBD), which consists of two segments separated by subdomain H. The structures of the intermediate complex reveal that the PBD and the bound promoter rotate by approximately 45 degrees upon synthesis of an 8-nt RNA transcript. This allows the promoter contacts to be maintained while the active site is expanded to accommodate a growing heteroduplex. The C-helix subdomain moves modestly toward its elongation conformation, whereas subdomain H remains in its initiation- rather than its elongation-phase location, more than 70 angstroms away.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892258/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892258/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Durniak, Kimberly J -- Bailey, Scott -- Steitz, Thomas A -- GM57510/GM/NIGMS NIH HHS/ -- R01 GM057510/GM/NIGMS NIH HHS/ -- R01 GM057510-10/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 24;322(5901):553-7. doi: 10.1126/science.1163433.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18948533" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T7/*enzymology ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; DNA-Directed RNA Polymerases/*chemistry/genetics/*metabolism ; Models, Genetic ; Models, Molecular ; Mutant Proteins/chemistry/metabolism ; *Promoter Regions, Genetic ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Transcription, Genetic ; Viral Proteins/*chemistry/genetics/*metabolism
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    Adapting proteostasis for disease intervention (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-02-16
    Description: The protein components of eukaryotic cells face acute and chronic challenges to their integrity. Eukaryotic protein homeostasis, or proteostasis, enables healthy cell and organismal development and aging and protects against disease. Here, we describe the proteostasis network, a set of interacting activities that maintain the health of proteome and the organism. Deficiencies in proteostasis lead to many metabolic, oncological, neurodegenerative, and cardiovascular disorders. Small-molecule or biological proteostasis regulators that manipulate the concentration, conformation, quaternary structure, and/or the location of protein(s) have the potential to ameliorate some of the most challenging diseases of our era.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balch, William E -- Morimoto, Richard I -- Dillin, Andrew -- Kelly, Jeffery W -- AG 18917/AG/NIA NIH HHS/ -- AG026647/AG/NIA NIH HHS/ -- AG04342/AG/NIA NIH HHS/ -- DK46336/DK/NIDDK NIH HHS/ -- DK75295/DK/NIDDK NIH HHS/ -- GM38109/GM/NIGMS NIH HHS/ -- NS50636/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2008 Feb 15;319(5865):916-9. doi: 10.1126/science.1141448.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology and Institute for Childhood and Neglected Diseases, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18276881" target="_blank"〉PubMed〈/a〉
    Keywords: *Aging ; Animals ; Cell Line ; *Cell Physiological Phenomena ; *Drug Therapy ; Homeostasis ; Humans ; Infection/drug therapy/metabolism ; Metabolic Diseases/drug therapy/metabolism ; Metabolic Networks and Pathways ; Neoplasms/drug therapy/metabolism ; Protein Conformation ; Protein Folding ; Protein Transport ; Proteins/*chemistry/*metabolism/therapeutic use ; Signal Transduction
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    The structure of an open form of an E. coli mechanosensitive channel at 3.45 A resolution (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-08-30
    Description: How ion channels are gated to regulate ion flux in and out of cells is the subject of intense interest. The Escherichia coli mechanosensitive channel, MscS, opens to allow rapid ion efflux, relieving the turgor pressure that would otherwise destroy the cell. We present a 3.45 angstrom-resolution structure for the MscS channel in an open conformation. This structure has a pore diameter of approximately 13 angstroms created by substantial rotational rearrangement of the three transmembrane helices. The structure suggests a molecular mechanism that underlies MscS gating and its decay of conductivity during prolonged activation. Support for this mechanism is provided by single-channel analysis of mutants with altered gating characteristics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299565/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299565/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Wenjian -- Black, Susan S -- Edwards, Michelle D -- Miller, Samantha -- Morrison, Emma L -- Bartlett, Wendy -- Dong, Changjiang -- Naismith, James H -- Booth, Ian R -- 040174/Wellcome Trust/United Kingdom -- 077564/Wellcome Trust/United Kingdom -- BB/F003455/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0400277/Medical Research Council/United Kingdom -- G0400277(70731)/Medical Research Council/United Kingdom -- GR077564MA/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2008 Aug 29;321(5893):1179-83. doi: 10.1126/science.1159262.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Biomolecular Sciences, The North Haugh, University of St. Andrews, KY16 9ST, Scotland, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18755969" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/*chemistry ; Crystallography, X-Ray ; Electric Conductivity ; Escherichia coli/*chemistry/physiology ; Escherichia coli Proteins/*chemistry/genetics/*physiology ; Hydrophobic and Hydrophilic Interactions ; *Ion Channel Gating ; Ion Channels/*chemistry/genetics/*physiology ; Models, Molecular ; Mutant Proteins/chemistry ; Mutation ; Patch-Clamp Techniques ; Pressure ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    Chemistry. An enlightening structure-function relationship (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-03-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Armitage, Bruce A -- Berget, Peter B -- New York, N.Y. -- Science. 2008 Feb 29;319(5867):1195-6. doi: 10.1126/science.1155093.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Molecular Biosensor and Imaging Center (MBIC), Carnegie Mellon University, Pittsburgh, PA 15213, USA. army@cmu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18309067" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Antibodies, Monoclonal/*chemistry/genetics ; Antigen-Antibody Complex ; Binding Sites, Antibody ; Crystallization ; Fluorescence ; Fluorescent Dyes ; Hydrophobic and Hydrophilic Interactions ; Luminescence ; Molecular Structure ; Mutation ; Protein Conformation ; Spectrometry, Fluorescence ; Stilbenes/*chemistry/immunology ; Structure-Activity Relationship
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 42
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    Amyloid fibrils of the HET-s(218-289) prion form a beta solenoid with a triangular hydrophobic core (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-03-15
    Description: Prion and nonprion forms of proteins are believed to differ solely in their three-dimensional structure, which is therefore of paramount importance for the prion function. However, no atomic-resolution structure of the fibrillar state that is likely infectious has been reported to date. We present a structural model based on solid-state nuclear magnetic resonance restraints for amyloid fibrils from the prion-forming domain (residues 218 to 289) of the HET-s protein from the filamentous fungus Podospora anserina. On the basis of 134 intra- and intermolecular experimental distance restraints, we find that HET-s(218-289) forms a left-handed beta solenoid, with each molecule forming two helical windings, a compact hydrophobic core, at least 23 hydrogen bonds, three salt bridges, and two asparagine ladders. The structure is likely to have broad implications for understanding the infectious amyloid state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wasmer, Christian -- Lange, Adam -- Van Melckebeke, Helene -- Siemer, Ansgar B -- Riek, Roland -- Meier, Beat H -- New York, N.Y. -- Science. 2008 Mar 14;319(5869):1523-6. doi: 10.1126/science.1151839.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18339938" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amyloid/*chemistry ; Fungal Proteins/*chemistry ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Peptides/chemistry ; Podospora/*chemistry ; Prions/*chemistry ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 43
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    A competitive inhibitor traps LeuT in an open-to-out conformation (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-12-17
    Description: Secondary transporters are workhorses of cellular membranes, catalyzing the movement of small molecules and ions across the bilayer and coupling substrate passage to ion gradients. However, the conformational changes that accompany substrate transport, the mechanism by which a substrate moves through the transporter, and principles of competitive inhibition remain unclear. We used crystallographic and functional studies on the leucine transporter (LeuT), a model for neurotransmitter sodium symporters, to show that various amino acid substrates induce the same occluded conformational state and that a competitive inhibitor, tryptophan (Trp), traps LeuT in an open-to-out conformation. In the Trp complex, the extracellular gate residues arginine 30 and aspartic acid 404 define a second weak binding site for substrates or inhibitors as they permeate from the extracellular solution to the primary substrate site, which demonstrates how residues that participate in gating also mediate permeation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832577/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832577/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Singh, Satinder K -- Piscitelli, Chayne L -- Yamashita, Atsuko -- Gouaux, Eric -- K99 MH083050-02/MH/NIMH NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 MH070039/MH/NIMH NIH HHS/ -- R01 MH070039-05/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1655-61. doi: 10.1126/science.1166777.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074341" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Transport Systems/antagonists & inhibitors/*chemistry/*metabolism ; Amino Acids/metabolism/pharmacology ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Binding, Competitive ; Biological Transport ; Crystallization ; Crystallography, X-Ray ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Leucine/*metabolism ; Ligands ; Models, Biological ; Models, Molecular ; Protein Conformation ; Protein Structure, Tertiary ; Sodium/metabolism ; Symporters/antagonists & inhibitors/*chemistry/*metabolism ; Tryptophan/metabolism/*pharmacology
    Print ISSN: 0036-8075
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  • 44
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    Solution structure of the integral human membrane protein VDAC-1 in detergent micelles (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-30
    Description: The voltage-dependent anion channel (VDAC) mediates trafficking of small molecules and ions across the eukaryotic outer mitochondrial membrane. VDAC also interacts with antiapoptotic proteins from the Bcl-2 family, and this interaction inhibits release of apoptogenic proteins from the mitochondrion. We present the nuclear magnetic resonance (NMR) solution structure of recombinant human VDAC-1 reconstituted in detergent micelles. It forms a 19-stranded beta barrel with the first and last strand parallel. The hydrophobic outside perimeter of the barrel is covered by detergent molecules in a beltlike fashion. In the presence of cholesterol, recombinant VDAC-1 can form voltage-gated channels in phospholipid bilayers similar to those of the native protein. NMR measurements revealed the binding sites of VDAC-1 for the Bcl-2 protein Bcl-x(L), for reduced beta-nicotinamide adenine dinucleotide, and for cholesterol. Bcl-x(L) interacts with the VDAC barrel laterally at strands 17 and 18.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2579273/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2579273/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hiller, Sebastian -- Garces, Robert G -- Malia, Thomas J -- Orekhov, Vladislav Y -- Colombini, Marco -- Wagner, Gerhard -- EB002026/EB/NIBIB NIH HHS/ -- GM066360/GM/NIGMS NIH HHS/ -- GM075879/GM/NIGMS NIH HHS/ -- GM47467/GM/NIGMS NIH HHS/ -- P01 GM047467/GM/NIGMS NIH HHS/ -- P01 GM047467-11/GM/NIGMS NIH HHS/ -- P01 GM047467-12/GM/NIGMS NIH HHS/ -- P01 GM047467-12S2/GM/NIGMS NIH HHS/ -- P01 GM047467-13/GM/NIGMS NIH HHS/ -- P01 GM047467-14/GM/NIGMS NIH HHS/ -- P01 GM047467-14S1/GM/NIGMS NIH HHS/ -- P01 GM047467-15/GM/NIGMS NIH HHS/ -- P01 GM047467-16/GM/NIGMS NIH HHS/ -- P01 GM047467-17/GM/NIGMS NIH HHS/ -- P41 EB002026/EB/NIBIB NIH HHS/ -- P41 EB002026-28/EB/NIBIB NIH HHS/ -- P41 EB002026-29/EB/NIBIB NIH HHS/ -- P41 EB002026-30/EB/NIBIB NIH HHS/ -- P41 EB002026-31/EB/NIBIB NIH HHS/ -- P41 EB002026-32/EB/NIBIB NIH HHS/ -- P41 EB002026-33/EB/NIBIB NIH HHS/ -- P41 GM066360/GM/NIGMS NIH HHS/ -- P41 GM066360-01/GM/NIGMS NIH HHS/ -- P41 GM066360-02/GM/NIGMS NIH HHS/ -- P41 GM066360-03/GM/NIGMS NIH HHS/ -- P41 GM066360-04/GM/NIGMS NIH HHS/ -- P41 GM066360-05/GM/NIGMS NIH HHS/ -- R01 GM075879/GM/NIGMS NIH HHS/ -- R01 GM075879-01/GM/NIGMS NIH HHS/ -- R01 GM075879-02/GM/NIGMS NIH HHS/ -- R01 GM075879-03/GM/NIGMS NIH HHS/ -- R01 GM075879-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Aug 29;321(5893):1206-10. doi: 10.1126/science.1161302.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18755977" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Cholesterol/metabolism ; Detergents ; Dimethylamines ; Humans ; Hydrophobic and Hydrophilic Interactions ; Ion Channel Gating ; Lipid Bilayers ; Micelles ; Molecular Sequence Data ; NAD/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/metabolism ; Static Electricity ; Voltage-Dependent Anion Channel 1/*chemistry/*metabolism ; bcl-X Protein/metabolism
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  • 45
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    A shared docking motif in TRF1 and TRF2 used for differential recruitment of telomeric proteins (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-01-19
    Description: Mammalian telomeres are protected by a six-protein complex: shelterin. Shelterin contains two closely related proteins (TRF1 and TRF2), which recruit various proteins to telomeres. We dissect the interactions of TRF1 and TRF2 with their shared binding partner (TIN2) and other shelterin accessory factors. TRF1 recognizes TIN2 using a conserved molecular surface in its TRF homology (TRFH) domain. However, this same surface does not act as a TIN2 binding site in TRF2, and TIN2 binding to TRF2 is mediated by a region outside the TRFH domain. Instead, the TRFH docking site of TRF2 binds a shelterin accessory factor (Apollo), which does not interact with the TRFH domain of TRF1. Conversely, the TRFH domain of TRF1, but not of TRF2, interacts with another shelterin-associated factor: PinX1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Yong -- Yang, Yuting -- van Overbeek, Megan -- Donigian, Jill R -- Baciu, Paul -- de Lange, Titia -- Lei, Ming -- New York, N.Y. -- Science. 2008 Feb 22;319(5866):1092-6. doi: 10.1126/science.1151804. Epub 2008 Jan 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202258" target="_blank"〉PubMed〈/a〉
    Keywords: *Amino Acid Motifs ; Amino Acid Sequence ; Crystallography, X-Ray ; Dimerization ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Inhibitor of Apoptosis Proteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Nuclear Proteins/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; TATA Box Binding Protein-Like Proteins/*chemistry/genetics/*metabolism ; Telomere-Binding Proteins/chemistry/genetics/*metabolism ; Telomeric Repeat Binding Protein 1/*chemistry/*metabolism ; Telomeric Repeat Binding Protein 2 ; Tumor Suppressor Proteins/chemistry/metabolism
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  • 46
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    Structure and molecular mechanism of a nucleobase-cation-symport-1 family transporter (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-18
    Description: The nucleobase-cation-symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Here, we report the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 transmembrane helices, 10 of which are arranged in two inverted repeats of five helices. The structures of the outward-facing open and substrate-bound occluded conformations were solved, showing how the outward-facing cavity closes upon binding of substrate. Comparisons with the leucine transporter LeuT(Aa) and the galactose transporter vSGLT reveal that the outward- and inward-facing cavities are symmetrically arranged on opposite sides of the membrane. The reciprocal opening and closing of these cavities is synchronized by the inverted repeat helices 3 and 8, providing the structural basis of the alternating access model for membrane transport.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885439/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885439/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weyand, Simone -- Shimamura, Tatsuro -- Yajima, Shunsuke -- Suzuki, Shun'ichi -- Mirza, Osman -- Krusong, Kuakarun -- Carpenter, Elisabeth P -- Rutherford, Nicholas G -- Hadden, Jonathan M -- O'Reilly, John -- Ma, Pikyee -- Saidijam, Massoud -- Patching, Simon G -- Hope, Ryan J -- Norbertczak, Halina T -- Roach, Peter C J -- Iwata, So -- Henderson, Peter J F -- Cameron, Alexander D -- 062164/Z/00/Z/Wellcome Trust/United Kingdom -- 079209/Wellcome Trust/United Kingdom -- B17935/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/C51725/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G020043/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Oct 31;322(5902):709-13. doi: 10.1126/science.1164440. Epub 2008 Oct 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Membrane Protein Laboratory, Diamond Light Source Limited, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18927357" target="_blank"〉PubMed〈/a〉
    Keywords: Actinomycetales/*chemistry/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Cations/chemistry/metabolism ; Cell Membrane/chemistry/metabolism ; Crystallography, X-Ray ; Hydantoins/chemistry/metabolism ; Ion Transport ; Models, Molecular ; Molecular Sequence Data ; Nucleobase Transport Proteins/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Sodium/metabolism ; Symporters/*chemistry/metabolism
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  • 47
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    Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-06-17
    Description: Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lange, Oliver F -- Lakomek, Nils-Alexander -- Fares, Christophe -- Schroder, Gunnar F -- Walter, Korvin F A -- Becker, Stefan -- Meiler, Jens -- Grubmuller, Helmut -- Griesinger, Christian -- de Groot, Bert L -- New York, N.Y. -- Science. 2008 Jun 13;320(5882):1471-5. doi: 10.1126/science.1157092.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18556554" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Anisotropy ; Chemistry, Physical ; Crystallography, X-Ray ; Entropy ; Kinetics ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Physicochemical Phenomena ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Solutions ; Ubiquitin/*chemistry/*metabolism ; Xenopus laevis
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  • 48
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    Structure of the immature dengue virus at low pH primes proteolytic maturation (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-03-29
    Description: Intracellular cleavage of immature flaviviruses is a critical step in assembly that generates the membrane fusion potential of the E glycoprotein. With cryo-electron microscopy we show that the immature dengue particles undergo a reversible conformational change at low pH that renders them accessible to furin cleavage. At a pH of 6.0, the E proteins are arranged in a herringbone pattern with the pr peptides docked onto the fusion loops, a configuration similar to that of the mature virion. After cleavage, the dissociation of pr is pH-dependent, suggesting that in the acidic environment of the trans-Golgi network pr is retained on the virion to prevent membrane fusion. These results suggest a mechanism by which flaviviruses are processed and stabilized in the host cell secretory pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, I-Mei -- Zhang, Wei -- Holdaway, Heather A -- Li, Long -- Kostyuchenko, Victor A -- Chipman, Paul R -- Kuhn, Richard J -- Rossmann, Michael G -- Chen, Jue -- 1-U54-AI-057153/AI/NIAID NIH HHS/ -- AI055672/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2008 Mar 28;319(5871):1834-7. doi: 10.1126/science.1153264.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, 915 West State Street, Purdue University, West Lafayette, IN 47907-2054, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18369148" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; Crystallography, X-Ray ; Dengue Virus/*chemistry/growth & development/metabolism/*ultrastructure ; Dimerization ; Endoplasmic Reticulum/virology ; Furin/metabolism ; Hydrogen-Ion Concentration ; Image Processing, Computer-Assisted ; Membrane Fusion ; Protein Conformation ; Viral Envelope Proteins/*chemistry/metabolism ; Viral Fusion Proteins/chemistry/metabolism ; Viral Matrix Proteins/*chemistry/metabolism ; Virion/metabolism/ultrastructure ; trans-Golgi Network/metabolism/virology
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  • 49
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    The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-10-04
    Description: The adenosine class of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) mediates the important role of extracellular adenosine in many physiological processes and is antagonized by caffeine. We have determined the crystal structure of the human A2A adenosine receptor, in complex with a high-affinity subtype-selective antagonist, ZM241385, to 2.6 angstrom resolution. Four disulfide bridges in the extracellular domain, combined with a subtle repacking of the transmembrane helices relative to the adrenergic and rhodopsin receptor structures, define a pocket distinct from that of other structurally determined GPCRs. The arrangement allows for the binding of the antagonist in an extended conformation, perpendicular to the membrane plane. The binding site highlights an integral role for the extracellular loops, together with the helical core, in ligand recognition by this class of GPCRs and suggests a role for ZM241385 in restricting the movement of a tryptophan residue important in the activation mechanism of the class A receptors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586971/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586971/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jaakola, Veli-Pekka -- Griffith, Mark T -- Hanson, Michael A -- Cherezov, Vadim -- Chien, Ellen Y T -- Lane, J Robert -- Ijzerman, Adriaan P -- Stevens, Raymond C -- GM075915/GM/NIGMS NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073197-04/GM/NIGMS NIH HHS/ -- R01 GM089857/GM/NIGMS NIH HHS/ -- U54 GM074961/GM/NIGMS NIH HHS/ -- U54 GM074961-04/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 21;322(5905):1211-7. doi: 10.1126/science.1164772. Epub 2008 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037 USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18832607" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine A2 Receptor Antagonists ; Animals ; Binding Sites ; Crystallography, X-Ray ; Humans ; Ligands ; Protein Binding ; Protein Conformation ; Receptor, Adenosine A2A/*chemistry ; Structure-Activity Relationship ; Triazines/chemistry ; Triazoles/chemistry ; Tryptophan/chemistry ; Turkeys
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    Biochemistry. How do proteins interact? (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-06-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boehr, David D -- Wright, Peter E -- New York, N.Y. -- Science. 2008 Jun 13;320(5882):1429-30. doi: 10.1126/science.1158818.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA. boehr@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18556537" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Evolution, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; *Protein Binding ; Protein Conformation ; Protein Folding ; Proteins/*chemistry/*metabolism ; Thermodynamics ; Ubiquitin/*chemistry/*metabolism
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    Structural basis of trans-inhibition in a molybdate/tungstate ABC transporter (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-05-31
    Description: Transport across cellular membranes is an essential process that is catalyzed by diverse membrane transport proteins. The turnover rates of certain transporters are inhibited by their substrates in a process termed trans-inhibition, whose structural basis is poorly understood. We present the crystal structure of a molybdate/tungstate ABC transporter (ModBC) from Methanosarcina acetivorans in a trans-inhibited state. The regulatory domains of the nucleotide-binding subunits are in close contact and provide two oxyanion binding pockets at the shared interface. By specifically binding to these pockets, molybdate or tungstate prevent adenosine triphosphatase activity and lock the transporter in an inward-facing conformation, with the catalytic motifs of the nucleotide-binding domains separated. This allosteric effect prevents the transporter from switching between the inward-facing and the outward-facing states, thus interfering with the alternating access and release mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gerber, Sabina -- Comellas-Bigler, Mireia -- Goetz, Birke A -- Locher, Kaspar P -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):246-50. doi: 10.1126/science.1156213. Epub 2008 May 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, HPK D14.3, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18511655" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*antagonists & inhibitors/*chemistry/metabolism ; Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Archaeal Proteins/antagonists & inhibitors/*chemistry/metabolism ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Methanosarcina/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Molybdenum/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Tungsten Compounds/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Conformational switch of syntaxin-1 controls synaptic vesicle fusion (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-16
    Description: During synaptic vesicle fusion, the soluble N-ethylmaleimide-sensitive factor-attachment protein receptor (SNARE) protein syntaxin-1 exhibits two conformations that both bind to Munc18-1: a "closed" conformation outside the SNARE complex and an "open" conformation in the SNARE complex. Although SNARE complexes containing open syntaxin-1 and Munc18-1 are essential for exocytosis, the function of closed syntaxin-1 is unknown. We generated knockin/knockout mice that expressed only open syntaxin-1B. Syntaxin-1B(Open) mice were viable but succumbed to generalized seizures at 2 to 3 months of age. Binding of Munc18-1 to syntaxin-1 was impaired in syntaxin-1B(Open) synapses, and the size of the readily releasable vesicle pool was decreased; however, the rate of synaptic vesicle fusion was dramatically enhanced. Thus, the closed conformation of syntaxin-1 gates the initiation of the synaptic vesicle fusion reaction, which is then mediated by SNARE-complex/Munc18-1 assemblies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3235364/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3235364/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gerber, Stefan H -- Rah, Jong-Cheol -- Min, Sang-Won -- Liu, Xinran -- de Wit, Heidi -- Dulubova, Irina -- Meyer, Alexander C -- Rizo, Josep -- Arancillo, Marife -- Hammer, Robert E -- Verhage, Matthijs -- Rosenmund, Christian -- Sudhof, Thomas C -- NS051262/NS/NINDS NIH HHS/ -- NS37200/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Sep 12;321(5895):1507-10. doi: 10.1126/science.1163174. Epub 2008 Aug 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18703708" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; Epilepsy/etiology ; Excitatory Postsynaptic Potentials ; Membrane Fusion ; Mice ; Mice, Knockout ; Munc18 Proteins/metabolism ; Mutation ; Protein Conformation ; Protein Structure, Tertiary ; SNARE Proteins/metabolism ; Sucrose/metabolism ; Synapses/physiology ; Synaptic Vesicles/*physiology/ultrastructure ; Syntaxin 1/*chemistry/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Rapid membrane disruption by a perforin-like protein facilitates parasite exit from host cells (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-20
    Description: Perforin-like proteins are expressed by many bacterial and protozoan pathogens, yet little is known about their function or mode of action. Here, we describe Toxoplasma perforin-like protein 1 (TgPLP1), a secreted perforin-like protein of the intracellular protozoan pathogen Toxoplasma gondii that displays structural features necessary for pore formation. After intracellular growth, TgPLP1-deficient parasites failed to exit normally, resulting in entrapment within host cells. We show that this defect is due to an inability to rapidly permeabilize the parasitophorous vacuole membrane and host plasma membrane during exit. TgPLP1 ablation had little effect on growth in culture but resulted in a reduction greater than five orders of magnitude of acute virulence in mice. Perforin-like proteins from other intracellular pathogens may play a similar role in microbial egress and virulence.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2662845/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2662845/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kafsack, Bjorn F C -- Pena, Janethe D O -- Coppens, Isabelle -- Ravindran, Sandeep -- Boothroyd, John C -- Carruthers, Vern B -- R01 AI021423/AI/NIAID NIH HHS/ -- R01 AI046675/AI/NIAID NIH HHS/ -- R01 AI046675-06/AI/NIAID NIH HHS/ -- R01 AI046675-07/AI/NIAID NIH HHS/ -- R01 AI046675-08/AI/NIAID NIH HHS/ -- R01 AI046675-09/AI/NIAID NIH HHS/ -- R01 AI46675/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2009 Jan 23;323(5913):530-3. doi: 10.1126/science.1165740. Epub 2008 Dec 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19095897" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Calcimycin/pharmacology ; Cell Membrane/*metabolism ; Cell Membrane Permeability ; Cells, Cultured ; Host-Parasite Interactions ; Humans ; Intracellular Membranes/*metabolism ; Ionophores/pharmacology ; Models, Molecular ; Molecular Sequence Data ; Perforin/chemistry/genetics/*metabolism ; Permeability ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protozoan Proteins/chemistry/genetics/*metabolism ; Toxoplasma/genetics/growth & development/*metabolism/pathogenicity ; Vacuoles/*metabolism/*parasitology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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