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  • 1
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    Structural biology: The gatekeepers revealed (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-06-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2010 Jun 10;465(7299):823-6. doi: 10.1038/465823a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20535212" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Computational Biology ; Computer Simulation ; Cryoelectron Microscopy ; Crystallization ; Crystallography, X-Ray ; Drug Design ; Humans ; Lipid Bilayers/chemistry/metabolism ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Membrane Proteins/*chemistry/isolation & purification/*metabolism ; Membranes, Artificial ; *Models, Molecular ; Movement ; Protein Conformation ; Receptors, G-Protein-Coupled/chemistry/isolation & purification/metabolism ; Solubility ; Structure-Activity Relationship
    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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  • 2
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    Computational design of proteins targeting the conserved stem region of influenza hemagglutinin (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-05-14
    Description: We describe a general computational method for designing proteins that bind a surface patch of interest on a target macromolecule. Favorable interactions between disembodied amino acid residues and the target surface are identified and used to anchor de novo designed interfaces. The method was used to design proteins that bind a conserved surface patch on the stem of the influenza hemagglutinin (HA) from the 1918 H1N1 pandemic virus. After affinity maturation, two of the designed proteins, HB36 and HB80, bind H1 and H5 HAs with low nanomolar affinity. Further, HB80 inhibits the HA fusogenic conformational changes induced at low pH. The crystal structure of HB36 in complex with 1918/H1 HA revealed that the actual binding interface is nearly identical to that in the computational design model. Such designed binding proteins may be useful for both diagnostics and therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164876/" 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/PMC3164876/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fleishman, Sarel J -- Whitehead, Timothy A -- Ekiert, Damian C -- Dreyfus, Cyrille -- Corn, Jacob E -- Strauch, Eva-Maria -- Wilson, Ian A -- Baker, David -- AI057141/AI/NIAID NIH HHS/ -- AI058113/AI/NIAID NIH HHS/ -- GM080209/GM/NIGMS NIH HHS/ -- P01 AI058113/AI/NIAID NIH HHS/ -- P01 AI058113-07/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 May 13;332(6031):816-21. doi: 10.1126/science.1202617.〈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/21566186" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Binding Sites ; Computational Biology ; *Computer Simulation ; Hemagglutinin Glycoproteins, Influenza Virus/chemistry/*metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; *Models, Molecular ; Molecular Sequence Data ; Mutation ; Peptide Library ; Protein Binding ; Protein Conformation ; *Protein Engineering ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Proteins/*chemistry/genetics/*metabolism ; Software
    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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    Solution structure of a minor and transiently formed state of a T4 lysozyme mutant (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-08-23
    Description: Proteins are inherently plastic molecules, whose function often critically depends on excursions between different molecular conformations (conformers). However, a rigorous understanding of the relation between a protein's structure, dynamics and function remains elusive. This is because many of the conformers on its energy landscape are only transiently formed and marginally populated (less than a few per cent of the total number of molecules), so that they cannot be individually characterized by most biophysical tools. Here we study a lysozyme mutant from phage T4 that binds hydrophobic molecules and populates an excited state transiently (about 1 ms) to about 3% at 25 degrees C (ref. 5). We show that such binding occurs only via the ground state, and present the atomic-level model of the 'invisible', excited state obtained using a combined strategy of relaxation-dispersion NMR (ref. 6) and CS-Rosetta model building that rationalizes this observation. The model was tested using structure-based design calculations identifying point mutants predicted to stabilize the excited state relative to the ground state. In this way a pair of mutations were introduced, inverting the relative populations of the ground and excited states and altering function. Our results suggest a mechanism for the evolution of a protein's function by changing the delicate balance between the states on its energy landscape. More generally, they show that our approach can generate and validate models of excited protein states.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706084/" 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/PMC3706084/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bouvignies, Guillaume -- Vallurupalli, Pramodh -- Hansen, D Flemming -- Correia, Bruno E -- Lange, Oliver -- Bah, Alaji -- Vernon, Robert M -- Dahlquist, Frederick W -- Baker, David -- Kay, Lewis E -- R01 GM092802/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Aug 21;477(7362):111-4. doi: 10.1038/nature10349.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5S 1A8, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21857680" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T4/*enzymology/*genetics ; Evolution, Molecular ; Hydrophobic and Hydrophilic Interactions ; Ligands ; *Models, Molecular ; Muramidase/*chemistry/*genetics ; *Mutation ; Protein Binding ; Temperature
    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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    Improved molecular replacement by density- and energy-guided protein structure optimization (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-05-03
    Description: Molecular replacement procedures, which search for placements of a starting model within the crystallographic unit cell that best account for the measured diffraction amplitudes, followed by automatic chain tracing methods, have allowed the rapid solution of large numbers of protein crystal structures. Despite extensive work, molecular replacement or the subsequent rebuilding usually fail with more divergent starting models based on remote homologues with less than 30% sequence identity. Here we show that this limitation can be substantially reduced by combining algorithms for protein structure modelling with those developed for crystallographic structure determination. An approach integrating Rosetta structure modelling with Autobuild chain tracing yielded high-resolution structures for 8 of 13 X-ray diffraction data sets that could not be solved in the laboratories of expert crystallographers and that remained unsolved after application of an extensive array of alternative approaches. We estimate that the new method should allow rapid structure determination without experimental phase information for over half the cases where current methods fail, given diffraction data sets of better than 3.2 A resolution, four or fewer copies in the asymmetric unit, and the availability of structures of homologous proteins with 〉20% sequence identity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365536/" 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/PMC3365536/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DiMaio, Frank -- Terwilliger, Thomas C -- Read, Randy J -- Wlodawer, Alexander -- Oberdorfer, Gustav -- Wagner, Ulrike -- Valkov, Eugene -- Alon, Assaf -- Fass, Deborah -- Axelrod, Herbert L -- Das, Debanu -- Vorobiev, Sergey M -- Iwai, Hideo -- Pokkuluri, P Raj -- Baker, David -- 082961/Wellcome Trust/United Kingdom -- 5R01GM092802/GM/NIGMS NIH HHS/ -- GM074898/GM/NIGMS NIH HHS/ -- P01 GM063210/GM/NIGMS NIH HHS/ -- P41RR002250/RR/NCRR NIH HHS/ -- R01 GM092802/GM/NIGMS NIH HHS/ -- U54 GM074898/GM/NIGMS NIH HHS/ -- U54 GM074958/GM/NIGMS NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- U54GM074958/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- Wellcome Trust/United Kingdom -- England -- Nature. 2011 May 26;473(7348):540-3. doi: 10.1038/nature09964. Epub 2011 May 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Washington, Department of Biochemistry and HHMI, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21532589" target="_blank"〉PubMed〈/a〉
    Keywords: Computational Biology/*methods ; Crystallography, X-Ray ; Databases, Protein ; Electrons ; *Models, Molecular ; Proteins/*chemistry ; Sequence Alignment ; Sequence Homology, Amino Acid ; *Structural Homology, Protein
    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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