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  • 1
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    Active sugar transport [Physiology] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-07-06
    Description: Secondary active transporters, such as those that adopt the leucine-transporter fold, are found in all domains of life, and they have the unique capability of harnessing the energy stored in ion gradients to accumulate small molecules essential for life as well as expel toxic and harmful compounds. How these proteins...
    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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  • 2
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    The mechanism of sodium and substrate release from the binding pocket of vSGLT (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-12-07
    Description: Membrane co-transport proteins that use a five-helix inverted repeat motif have recently emerged as one of the largest structural classes of secondary active transporters. However, despite many structural advances there is no clear evidence of how ion and substrate transport are coupled. Here we report a comprehensive study of the sodium/galactose transporter from Vibrio parahaemolyticus (vSGLT), consisting of molecular dynamics simulations, biochemical characterization and a new crystal structure of the inward-open conformation at a resolution of 2.7 A. Our data show that sodium exit causes a reorientation of transmembrane helix 1 that opens an inner gate required for substrate exit, and also triggers minor rigid-body movements in two sets of transmembrane helical bundles. This cascade of events, initiated by sodium release, ensures proper timing of ion and substrate release. Once set in motion, these molecular changes weaken substrate binding to the transporter and allow galactose readily to enter the intracellular space. Additionally, we identify an allosteric pathway between the sodium-binding sites, the unwound portion of transmembrane helix 1 and the substrate-binding site that is essential in the coupling of co-transport.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736980/" 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/PMC3736980/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Watanabe, Akira -- Choe, Seungho -- Chaptal, Vincent -- Rosenberg, John M -- Wright, Ernest M -- Grabe, Michael -- Abramson, Jeff -- DK19567/DK/NIDDK NIH HHS/ -- GM078844/GM/NIGMS NIH HHS/ -- R01 DK019567/DK/NIDDK NIH HHS/ -- R01 GM078844/GM/NIGMS NIH HHS/ -- RGY0069/PHS HHS/ -- England -- Nature. 2010 Dec 16;468(7326):988-91. doi: 10.1038/nature09580. Epub 2010 Dec 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, University of California, Los Angeles, Los Angeles, California 90095-1759, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21131949" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Binding Sites ; Biological Transport ; Crystallography, X-Ray ; Galactose/*metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Protein Conformation ; Sodium/*metabolism ; Symporters/*chemistry/*metabolism ; Vibrio parahaemolyticus/*chemistry
    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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  • 3
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    Antibacterial membrane attack by a pore-forming intestinal C-type lectin (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-11-22
    Description: Human body-surface epithelia coexist in close association with complex bacterial communities and are protected by a variety of antibacterial proteins. C-type lectins of the RegIII family are bactericidal proteins that limit direct contact between bacteria and the intestinal epithelium and thus promote tolerance to the intestinal microbiota. RegIII lectins recognize their bacterial targets by binding peptidoglycan carbohydrate, but the mechanism by which they kill bacteria is unknown. Here we elucidate the mechanistic basis for RegIII bactericidal activity. We show that human RegIIIalpha (also known as HIP/PAP) binds membrane phospholipids and kills bacteria by forming a hexameric membrane-permeabilizing oligomeric pore. We derive a three-dimensional model of the RegIIIalpha pore by docking the RegIIIalpha crystal structure into a cryo-electron microscopic map of the pore complex, and show that the model accords with experimentally determined properties of the pore. Lipopolysaccharide inhibits RegIIIalpha pore-forming activity, explaining why RegIIIalpha is bactericidal for Gram-positive but not Gram-negative bacteria. Our findings identify C-type lectins as mediators of membrane attack in the mucosal immune system, and provide detailed insight into an antibacterial mechanism that promotes mutualism with the resident microbiota.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160023/" 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/PMC4160023/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mukherjee, Sohini -- Zheng, Hui -- Derebe, Mehabaw G -- Callenberg, Keith M -- Partch, Carrie L -- Rollins, Darcy -- Propheter, Daniel C -- Rizo, Josep -- Grabe, Michael -- Jiang, Qiu-Xing -- Hooper, Lora V -- C06 RR30414/RR/NCRR NIH HHS/ -- F32 DK100074/DK/NIDDK NIH HHS/ -- GM093271/GM/NIGMS NIH HHS/ -- R01 DK070855/DK/NIDDK NIH HHS/ -- R01 NS040944/NS/NINDS NIH HHS/ -- R01 NS40944/NS/NINDS NIH HHS/ -- R01GM088745/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Jan 2;505(7481):103-7. doi: 10.1038/nature12729. Epub 2013 Nov 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. ; Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. ; Department of Biological Sciences, University of Pittsburgh, and Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania 15261, USA. ; Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. ; Department of Biochemistry and Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. ; 1] Department of Biological Sciences, University of Pittsburgh, and Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania 15261, USA [2] Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143, USA. ; 1] Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [2]. ; 1] Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [2] The Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [3].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24256734" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/chemistry/immunology/*metabolism/pharmacology ; Antigens, Neoplasm/chemistry/immunology/*metabolism ; Biomarkers, Tumor/antagonists & inhibitors/chemistry/immunology/*metabolism ; Cell Membrane Permeability/drug effects ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Gram-Negative Bacteria/drug effects/immunology/metabolism ; Humans ; Immunity, Mucosal/drug effects/immunology ; Intestines/*chemistry/immunology/microbiology ; Lectins, C-Type/antagonists & inhibitors/chemistry/immunology/*metabolism ; Lipopolysaccharides/pharmacology ; Listeria monocytogenes/drug effects/immunology/metabolism ; Microbial Viability/drug effects ; Models, Molecular ; Peptidoglycan/metabolism ; Phospholipids/metabolism ; Porins/antagonists & inhibitors/chemistry/*metabolism ; Symbiosis
    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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  • 4
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    De novo design of a transmembrane Zn(2)(+)-transporting four-helix bundle (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-12-20
    Description: The design of functional membrane proteins from first principles represents a grand challenge in chemistry and structural biology. Here, we report the design of a membrane-spanning, four-helical bundle that transports first-row transition metal ions Zn(2+) and Co(2+), but not Ca(2+), across membranes. The conduction path was designed to contain two di-metal binding sites that bind with negative cooperativity. X-ray crystallography and solid-state and solution nuclear magnetic resonance indicate that the overall helical bundle is formed from two tightly interacting pairs of helices, which form individual domains that interact weakly along a more dynamic interface. Vesicle flux experiments show that as Zn(2+) ions diffuse down their concentration gradients, protons are antiported. These experiments illustrate the feasibility of designing membrane proteins with predefined structural and dynamic properties.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4400864/" 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/PMC4400864/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joh, Nathan H -- Wang, Tuo -- Bhate, Manasi P -- Acharya, Rudresh -- Wu, Yibing -- Grabe, Michael -- Hong, Mei -- Grigoryan, Gevorg -- DeGrado, William F -- F32 GM096727/GM/NIGMS NIH HHS/ -- R01 GM054616/GM/NIGMS NIH HHS/ -- R01 GM088204/GM/NIGMS NIH HHS/ -- R01 GM089740/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Dec 19;346(6216):1520-4. doi: 10.1126/science.1261172.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA. ; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. ; School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India. ; Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA. william.degrado@ucsf.edu gevorg.grigoryan@dartmouth.edu meihong@mit.edu michael.grabe@ucsf.edu. ; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. william.degrado@ucsf.edu gevorg.grigoryan@dartmouth.edu meihong@mit.edu michael.grabe@ucsf.edu. ; Department of Computer Science and Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA. william.degrado@ucsf.edu gevorg.grigoryan@dartmouth.edu meihong@mit.edu michael.grabe@ucsf.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25525248" target="_blank"〉PubMed〈/a〉
    Keywords: Carrier Proteins/*chemistry ; Crystallography, X-Ray ; Ion Transport ; Lipid Bilayers ; Membrane Proteins/*chemistry ; Micelles ; Molecular Dynamics Simulation ; *Protein Engineering ; Protein Structure, Secondary ; Zinc/*chemistry
    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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    Direct observation of proton pumping by a eukaryotic P-type ATPase (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-03-26
    Description: In eukaryotes, P-type adenosine triphosphatases (ATPases) generate the plasma membrane potential and drive secondary transport systems; however, despite their importance, their regulation remains poorly understood. We monitored at the single-molecule level the activity of the prototypic proton-pumping P-type ATPase Arabidopsis thaliana isoform 2 (AHA2). Our measurements, combined with a physical nonequilibrium model of vesicle acidification, revealed that pumping is stochastically interrupted by long-lived (~100 seconds) inactive or leaky states. Allosteric regulation by pH gradients modulated the switch between these states but not the pumping or leakage rates. The autoinhibitory regulatory domain of AHA2 reduced the intrinsic pumping rates but increased the dwell time in the active pumping state. We anticipate that similar functional dynamics underlie the operation and regulation of many other active transporters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Veshaguri, Salome -- Christensen, Sune M -- Kemmer, Gerdi C -- Ghale, Garima -- Moller, Mads P -- Lohr, Christina -- Christensen, Andreas L -- Justesen, Bo H -- Jorgensen, Ida L -- Schiller, Jurgen -- Hatzakis, Nikos S -- Grabe, Michael -- Pomorski, Thomas Gunther -- Stamou, Dimitrios -- R21-GM100224/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2016 Mar 25;351(6280):1469-73. doi: 10.1126/science.aad6429.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bionanotecnology and Nanomedicine Laboratory, University of Copenhagen, Copenhagen, Denmark. Department of Chemistry, University of Copenhagen, Copenhagen, Denmark. Nano-Science Center, University of Copenhagen, Copenhagen, Denmark. Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark. ; Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg Denmark. ; Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, Leipzig, Germany. ; Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27013734" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Arabidopsis Proteins/antagonists & inhibitors/chemistry/*metabolism ; Hydrogen-Ion Concentration ; Ion Transport ; Membrane Potentials/drug effects/physiology ; Molecular Imaging ; Protein Structure, Tertiary ; Proton-Translocating ATPases/antagonists & inhibitors/chemistry/*metabolism ; *Protons ; Valinomycin/pharmacology
    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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  • 6
    Electronic Resource
    Electronic Resource
    Uncertainties, confidence ellipsoids and security polytopes in LSA
    Amsterdam : Elsevier
    Physics Letters A 165 (1992), S. 124-132 
    Details
    ISSN: 0375-9601
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0375-9601(92)90087-3
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  • 7
    Electronic Resource
    Electronic Resource
    Pathways, pathway tubes, pathway docking, and propagators in electron transfer proteins (1995)
    Springer
    Journal of bioenergetics and biomembranes 27 (1995), S. 285-293 
    Details
    ISSN: 1573-6881
    Keywords: Tunneling pathways ; protein electron transfer ; donor-acceptor interactions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Physics
    Notes: Abstract The simplest views of long-range electron transfer utilize flat one-dimensional barrier tunneling models, neglecting structural details of the protein medium. The pathway model of protein electron transfer reintroduces structure by distinguishing between covalent bonds, hydrogen bonds, and van der Waals contacts. These three kinds of interactions in a tunneling pathway each have distinctive decay factors associated with them. The distribution and arrangement of these bonded and nonbonded contacts in a folded protein varies tremendously between structures, adding a richness to the tunneling problem that is absent in simpler views. We review the pathway model and the predictions that it makes for protein electron transfer rates in small proteins, docked proteins, and the photosynthetic reactions center. We also review the formulation of the protein electron transfer problem as an effective two-level system. New multi-pathway approaches and improved electronic Hamiltonians are described briefly as well.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02110098
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  • 8
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    A quantitative assessment of models for voltage-dependent gating of ion channels (2004)
    National Academy of Sciences
    Details
    Publication Date: 2004-12-10
    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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  • 9
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    Energy transduction in the sodium F-ATPase of Propionigenium modestum (1999)
    National Academy of Sciences
    Details
    Publication Date: 1999-04-27
    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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  • 10
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    Electrostatic interactions in the channel cavity as an important determinant of potassium channel selectivity (2006)
    National Academy of Sciences
    Details
    Publication Date: 2006-09-18
    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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