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  • 1
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    Implementation of accelerated molecular dynamics in NAMD (2011)
    Institute of Physics Publishing (IOP)
    Details
    Publication Date: 2011-03-02
    Description: Accelerated molecular dynamics (aMD) is an enhanced sampling method that improves the conformational space sampling by reducing energy barriers separating different states of a system. Here, we present the implementation of aMD in the parallel simulation program NAMD. We show that aMD simulations performed with NAMD have only a small overhead compared with classical MD simulations. Through example applications to the alanine dipeptide, we discuss the choice of acceleration parameters, the interpretation of aMD results, as well as the advantages and limitations of the aMD method.
    Print ISSN: 1749-4699
    Electronic ISSN: 1749-4680
    Topics: Computer Science
    Published by Institute of Physics Publishing (IOP)
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  • 2
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    Electron transfer. Exploiting thermal motion (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schulten, K -- New York, N.Y. -- Science. 2000 Oct 6;290(5489):61-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. kschulte@ks.uiuc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11183149" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriochlorophylls/chemistry/metabolism ; Chemistry, Physical ; *Electrons ; Light-Harvesting Protein Complexes ; Pheophytins/chemistry/metabolism ; Photosynthetic Reaction Center Complex Proteins/*chemistry/*metabolism ; Physicochemical Phenomena ; Quantum Theory ; Quinones/chemistry/metabolism ; Rhodobacter sphaeroides/metabolism ; Thermodynamics
    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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  • 3
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    Control of the selectivity of the aquaporin water channel family by global orientational tuning (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-04-20
    Description: Aquaporins are transmembrane channels found in cell membranes of all life forms. We examine their apparently paradoxical property, facilitation of efficient permeation of water while excluding protons, which is of critical importance to preserving the electrochemical potential across the cell membrane. We have determined the structure of the Escherichia coli aquaglyceroporin GlpF with bound water, in native (2.7 angstroms) and in W48F/F200T mutant (2.1 angstroms) forms, and carried out 12-nanosecond molecular dynamics simulations that define the spatial and temporal probability distribution and orientation of a single file of seven to nine water molecules inside the channel. Two conserved asparagines force a central water molecule to serve strictly as a hydrogen bond donor to its neighboring water molecules. Assisted by the electrostatic potential generated by two half-membrane spanning loops, this dictates opposite orientations of water molecules in the two halves of the channel, and thus prevents the formation of a "proton wire," while permitting rapid water diffusion. Both simulations and observations revealed a more regular distribution of channel water and an increased water permeability for the W48F/F200T mutant.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tajkhorshid, Emad -- Nollert, Peter -- Jensen, Morten O -- Miercke, Larry J W -- O'Connell, Joseph -- Stroud, Robert M -- Schulten, Klaus -- New York, N.Y. -- Science. 2002 Apr 19;296(5567):525-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Theoretical Biophysics Group, Beckman Institute, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11964478" target="_blank"〉PubMed〈/a〉
    Keywords: Aquaporins/*chemistry/genetics/metabolism ; Asparagine/chemistry ; Chemistry, Physical ; Computer Simulation ; Crystallography, X-Ray ; Diffusion ; Electrochemistry ; Escherichia coli ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Glycerol/metabolism ; Hydrogen Bonding ; Models, Molecular ; Mutation ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Secondary ; Protons ; Static Electricity ; Water/chemistry/*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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  • 4
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    Single-molecule experiments in vitro and in silico (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-26
    Description: Single-molecule force experiments in vitro enable the characterization of the mechanical response of biological matter at the nanometer scale. However, they do not reveal the molecular mechanisms underlying mechanical function. These can only be readily studied through molecular dynamics simulations of atomic structural models: "in silico" (by computer analysis) single-molecule experiments. Steered molecular dynamics simulations, in which external forces are used to explore the response and function of macromolecules, have become a powerful tool complementing and guiding in vitro single-molecule experiments. The insights provided by in silico experiments are illustrated here through a review of recent research in three areas of protein mechanics: elasticity of the muscle protein titin and the extracellular matrix protein fibronectin; linker-mediated elasticity of the cytoskeleton protein spectrin; and elasticity of ankyrin repeats, a protein module found ubiquitously in cells but with an as-yet unclear function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sotomayor, Marcos -- Schulten, Klaus -- 1 R01 GM073655/GM/NIGMS NIH HHS/ -- P41 RR05969/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2007 May 25;316(5828):1144-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, University of Illinois at Urbana-Champaign, and Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17525328" target="_blank"〉PubMed〈/a〉
    Keywords: Ankyrin Repeat/*physiology ; Computer Simulation ; Connectin ; Elasticity ; Fibronectins/*physiology ; Humans ; Models, Biological ; Muscle Proteins/*physiology ; Protein Kinases/*physiology ; Spectrin/*physiology ; Spectrum Analysis/*methods
    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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  • 5
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    Structural insight into nascent polypeptide chain-mediated translational stalling (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-11-26
    Description: Expression of the Escherichia coli tryptophanase operon depends on ribosome stalling during translation of the upstream TnaC leader peptide, a process for which interactions between the TnaC nascent chain and the ribosomal exit tunnel are critical. We determined a 5.8 angstrom-resolution cryo-electron microscopy and single-particle reconstruction of a ribosome stalled during translation of the tnaC leader gene. The nascent chain was extended within the exit tunnel, making contacts with ribosomal components at distinct sites. Upon stalling, two conserved residues within the peptidyltransferase center adopted conformations that preclude binding of release factors. We propose a model whereby interactions within the tunnel are relayed to the peptidyltransferase center to inhibit translation. Moreover, we show that nascent chains adopt distinct conformations within the ribosomal exit tunnel.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2920484/" 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/PMC2920484/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seidelt, Birgit -- Innis, C Axel -- Wilson, Daniel N -- Gartmann, Marco -- Armache, Jean-Paul -- Villa, Elizabeth -- Trabuco, Leonardo G -- Becker, Thomas -- Mielke, Thorsten -- Schulten, Klaus -- Steitz, Thomas A -- Beckmann, Roland -- GM022778/GM/NIGMS NIH HHS/ -- P41 RR005969/RR/NCRR NIH HHS/ -- P41 RR005969-19/RR/NCRR NIH HHS/ -- P41-RR05969/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Dec 4;326(5958):1412-5. doi: 10.1126/science.1177662. Epub 2009 Oct 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gene Center and Center for Integrated Protein Science Munich (CIPSM), Department for Chemistry and Biochemistry, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19933110" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cryoelectron Microscopy ; Escherichia coli/*genetics/metabolism ; Escherichia coli Proteins/*chemistry/genetics/*metabolism/ultrastructure ; Gene Expression Regulation, Bacterial ; Image Processing, Computer-Assisted ; Models, Biological ; Models, Molecular ; Operon ; Peptidyl Transferases/metabolism ; *Protein Biosynthesis ; Protein Conformation ; RNA-Binding Proteins/chemistry/metabolism/ultrastructure ; Ribosomal Proteins/chemistry/metabolism/ultrastructure ; Ribosomes/*metabolism/ultrastructure ; Tryptophanase/biosynthesis/*genetics
    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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  • 6
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    Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-05-31
    Description: Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven alpha-helices and a beta-hairpin, a carboxy-terminal domain (CTD) comprising four alpha-helices, and a flexible linker with a 310-helix connecting the two structural domains. Structures of the capsid-protein assembly units have been determined by X-ray crystallography; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 A resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3729984/" 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/PMC3729984/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhao, Gongpu -- Perilla, Juan R -- Yufenyuy, Ernest L -- Meng, Xin -- Chen, Bo -- Ning, Jiying -- Ahn, Jinwoo -- Gronenborn, Angela M -- Schulten, Klaus -- Aiken, Christopher -- Zhang, Peijun -- GM082251/GM/NIGMS NIH HHS/ -- GM085043/GM/NIGMS NIH HHS/ -- GM104601/GM/NIGMS NIH HHS/ -- P41 GM104601/GM/NIGMS NIH HHS/ -- P50 GM082251/GM/NIGMS NIH HHS/ -- R01 GM085043/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 May 30;497(7451):643-6. doi: 10.1038/nature12162.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23719463" target="_blank"〉PubMed〈/a〉
    Keywords: Capsid/*chemistry/*ultrastructure ; Capsid Proteins/chemistry/ultrastructure ; Cryoelectron Microscopy ; HIV-1/*chemistry/*ultrastructure ; Human Immunodeficiency Virus Proteins/chemistry/ultrastructure ; Hydrophobic and Hydrophilic Interactions ; *Molecular Dynamics Simulation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-13
    Description: Despite the recent advances in single-molecule manipulation techniques, purely mechanical approaches cannot detect subtle conformational changes in the biologically important regime of weak forces. We developed a hybrid scheme combining force and fluorescence that allowed us to examine the effect of subpiconewton forces on the nanometer scale motion of the Holliday junction (HJ) at 100-hertz bandwidth. The HJ is an exquisitely sensitive force sensor whose force response is amplified with an increase in its arm lengths, demonstrating a lever-arm effect at the nanometer-length scale. Mechanical interrogation of the HJ in three different directions helped elucidate the structures of the transient species populated during its conformational changes. This method of mapping two-dimensional reaction landscapes at low forces is readily applicable to other nucleic acid systems and their interactions with proteins and enzymes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558530/" 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/PMC3558530/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hohng, Sungchul -- Zhou, Ruobo -- Nahas, Michelle K -- Yu, Jin -- Schulten, Klaus -- Lilley, David M J -- Ha, Taekjip -- 11722/Cancer Research UK/United Kingdom -- GM065367/GM/NIGMS NIH HHS/ -- R01 GM065367/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 12;318(5848):279-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. tjha@uiuc.edgu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17932299" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda ; Biophysical Phenomena ; Biophysics ; DNA, Cruciform/*chemistry ; DNA, Viral/chemistry ; Fluorescence Resonance Energy Transfer ; *Nucleic Acid Conformation ; Optical Tweezers
    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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  • 8
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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
    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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  • 9
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    Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-11-26
    Description: The trimeric Sec61/SecY complex is a protein-conducting channel (PCC) for secretory and membrane proteins. Although Sec complexes can form oligomers, it has been suggested that a single copy may serve as an active PCC. We determined subnanometer-resolution cryo-electron microscopy structures of eukaryotic ribosome-Sec61 complexes. In combination with biochemical data, we found that in both idle and active states, the Sec complex is not oligomeric and interacts mainly via two cytoplasmic loops with the universal ribosomal adaptor site. In the active state, the ribosomal tunnel and a central pore of the monomeric PCC were occupied by the nascent chain, contacting loop 6 of the Sec complex. This provides a structural basis for the activity of a solitary Sec complex in cotranslational protein translocation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2920595/" 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/PMC2920595/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Becker, Thomas -- Bhushan, Shashi -- Jarasch, Alexander -- Armache, Jean-Paul -- Funes, Soledad -- Jossinet, Fabrice -- Gumbart, James -- Mielke, Thorsten -- Berninghausen, Otto -- Schulten, Klaus -- Westhof, Eric -- Gilmore, Reid -- Mandon, Elisabet C -- Beckmann, Roland -- GM35687/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/ -- New York, N.Y. -- Science. 2009 Dec 4;326(5958):1369-73. doi: 10.1126/science.1178535. Epub 2009 Oct 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gene Center Munich and Center for Integrated Protein Science, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universitat Munchen, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19933108" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cryoelectron Microscopy ; Dogs ; Image Processing, Computer-Assisted ; Membrane Proteins/*chemistry/*metabolism/ultrastructure ; Models, Molecular ; *Protein Biosynthesis ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; *Protein Transport ; Proteins/chemistry/*metabolism/ultrastructure ; Ribosomes/*metabolism/ultrastructure ; Saccharomyces cerevisiae Proteins/*chemistry/*metabolism/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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  • 10
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    Comparison of the early stages of forced unfolding for fibronectin type III modules (2001)
    National Academy of Sciences
    Details
    Publication Date: 2001-05-01
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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