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  • 1
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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
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  • 2
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    Design of a novel globular protein fold with atomic-level accuracy (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-25
    Description: A major challenge of computational protein design is the creation of novel proteins with arbitrarily chosen three-dimensional structures. Here, we used a general computational strategy that iterates between sequence design and structure prediction to design a 93-residue alpha/beta protein called Top7 with a novel sequence and topology. Top7 was found experimentally to be folded and extremely stable, and the x-ray crystal structure of Top7 is similar (root mean square deviation equals 1.2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuhlman, Brian -- Dantas, Gautam -- Ireton, Gregory C -- Varani, Gabriele -- Stoddard, Barry L -- Baker, David -- New York, N.Y. -- Science. 2003 Nov 21;302(5649):1364-8.〈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/14631033" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Circular Dichroism ; Computational Biology ; Computer Graphics ; Computer Simulation ; Crystallization ; Crystallography, X-Ray ; Databases, Protein ; Models, Molecular ; Molecular Sequence Data ; Monte Carlo Method ; Nuclear Magnetic Resonance, Biomolecular ; *Protein Conformation ; Protein Denaturation ; *Protein Engineering ; *Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry ; *Software ; Solubility ; Temperature ; Thermodynamics
    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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  • 3
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    Toward high-resolution de novo structure prediction for small proteins (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-17
    Description: The prediction of protein structure from amino acid sequence is a grand challenge of computational molecular biology. By using a combination of improved low- and high-resolution conformational sampling methods, improved atomically detailed potential functions that capture the jigsaw puzzle-like packing of protein cores, and high-performance computing, high-resolution structure prediction (〈1.5 angstroms) can be achieved for small protein domains (〈85 residues). The primary bottleneck to consistent high-resolution prediction appears to be conformational sampling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bradley, Philip -- Misura, Kira M S -- Baker, David -- New York, N.Y. -- Science. 2005 Sep 16;309(5742):1868-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Washington, Department of Biochemistry, and Howard Hughes Medical Institute, Box 357350, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16166519" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chemistry, Physical ; *Computational Biology ; Computer Simulation ; Hydrogen Bonding ; Models, Molecular ; Monte Carlo Method ; Physicochemical Phenomena ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry ; Sequence Alignment ; Thermodynamics
    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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  • 4
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    Computational thermostabilization of an enzyme (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-05-10
    Description: Thermostabilizing an enzyme while maintaining its activity for industrial or biomedical applications can be difficult with traditional selection methods. We describe a rapid computational approach that identified three mutations within a model enzyme that produced a 10 degrees C increase in apparent melting temperature T(m) and a 30-fold increase in half-life at 50 degrees C, with no reduction in catalytic efficiency. The effects of the mutations were synergistic, giving an increase in excess of the sum of their individual effects. The redesigned enzyme induced an increased, temperature-dependent bacterial growth rate under conditions that required its activity, thereby coupling molecular and metabolic engineering.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412875/" 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/PMC3412875/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korkegian, Aaron -- Black, Margaret E -- Baker, David -- Stoddard, Barry L -- CA85939/CA/NCI NIH HHS/ -- CA97328/CA/NCI NIH HHS/ -- GM49857/GM/NIGMS NIH HHS/ -- GM59224/GM/NIGMS NIH HHS/ -- R01 CA097328/CA/NCI NIH HHS/ -- R01 GM049857/GM/NIGMS NIH HHS/ -- T32-GM08268/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 May 6;308(5723):857-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Basic Sciences, Fred Hutchinson Cancer Research Center (FHCRC), 1100 Fairview Avenue North, Seattle, WA 98109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15879217" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Catalysis ; Circular Dichroism ; *Computer Simulation ; Crystallography, X-Ray ; Cytosine Deaminase/*chemistry/*metabolism ; Enzyme Stability ; Escherichia coli/genetics/metabolism ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Monte Carlo Method ; Mutagenesis, Site-Directed ; Point Mutation ; Protein Conformation ; Protein Denaturation ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; Software ; Temperature ; Thermodynamics ; Transformation, Genetic ; Yeasts/enzymology
    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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    Principles for designing ideal protein structures (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-11-09
    Description: Unlike random heteropolymers, natural proteins fold into unique ordered structures. Understanding how these are encoded in amino-acid sequences is complicated by energetically unfavourable non-ideal features--for example kinked alpha-helices, bulged beta-strands, strained loops and buried polar groups--that arise in proteins from evolutionary selection for biological function or from neutral drift. Here we describe an approach to designing ideal protein structures stabilized by completely consistent local and non-local interactions. The approach is based on a set of rules relating secondary structure patterns to protein tertiary motifs, which make possible the design of funnel-shaped protein folding energy landscapes leading into the target folded state. Guided by these rules, we designed sequences predicted to fold into ideal protein structures consisting of alpha-helices, beta-strands and minimal loops. Designs for five different topologies were found to be monomeric and very stable and to adopt structures in solution nearly identical to the computational models. These results illuminate how the folding funnels of natural proteins arise and provide the foundation for engineering a new generation of functional proteins free from natural evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705962/" 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/PMC3705962/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koga, Nobuyasu -- Tatsumi-Koga, Rie -- Liu, Gaohua -- Xiao, Rong -- Acton, Thomas B -- Montelione, Gaetano T -- Baker, David -- U54 GM094597/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Nov 8;491(7423):222-7. doi: 10.1038/nature11600.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Washington, Department of Biochemistry and Howard Hughes Medical Institute, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23135467" target="_blank"〉PubMed〈/a〉
    Keywords: *Computer Simulation ; *Models, Molecular ; *Protein Folding ; *Protein Stability ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry ; Thermodynamics
    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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  • 6
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    Atomic model of the type III secretion system needle (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-06-16
    Description: Pathogenic bacteria using a type III secretion system (T3SS) to manipulate host cells cause many different infections including Shigella dysentery, typhoid fever, enterohaemorrhagic colitis and bubonic plague. An essential part of the T3SS is a hollow needle-like protein filament through which effector proteins are injected into eukaryotic host cells. Currently, the three-dimensional structure of the needle is unknown because it is not amenable to X-ray crystallography and solution NMR, as a result of its inherent non-crystallinity and insolubility. Cryo-electron microscopy combined with crystal or solution NMR subunit structures has recently provided a powerful hybrid approach for studying supramolecular assemblies, resulting in low-resolution and medium-resolution models. However, such approaches cannot deliver atomic details, especially of the crucial subunit-subunit interfaces, because of the limited cryo-electron microscopic resolution obtained in these studies. Here we report an alternative approach combining recombinant wild-type needle production, solid-state NMR, electron microscopy and Rosetta modelling to reveal the supramolecular interfaces and ultimately the complete atomic structure of the Salmonella typhimurium T3SS needle. We show that the 80-residue subunits form a right-handed helical assembly with roughly 11 subunits per two turns, similar to that of the flagellar filament of S. typhimurium. In contrast to established models of the needle in which the amino terminus of the protein subunit was assumed to be alpha-helical and positioned inside the needle, our model reveals an extended amino-terminal domain that is positioned on the surface of the needle, while the highly conserved carboxy terminus points towards the lumen.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598588/" 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/PMC3598588/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Loquet, Antoine -- Sgourakis, Nikolaos G -- Gupta, Rashmi -- Giller, Karin -- Riedel, Dietmar -- Goosmann, Christian -- Griesinger, Christian -- Kolbe, Michael -- Baker, David -- Becker, Stefan -- Lange, Adam -- 1R01GM092802-01/GM/NIGMS NIH HHS/ -- R01 GM092802/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 May 20;486(7402):276-9. doi: 10.1038/nature11079.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22699623" target="_blank"〉PubMed〈/a〉
    Keywords: *Bacterial Secretion Systems ; HeLa Cells ; Humans ; Microscopy, Electron ; *Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Structure, Secondary ; Salmonella typhimurium/*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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  • 7
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    Computational design of self-assembling protein nanomaterials with atomic level accuracy (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-02
    Description: We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138882/" 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/PMC4138882/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉King, Neil P -- Sheffler, William -- Sawaya, Michael R -- Vollmar, Breanna S -- Sumida, John P -- Andre, Ingemar -- Gonen, Tamir -- Yeates, Todd O -- Baker, David -- RR-15301/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jun 1;336(6085):1171-4. doi: 10.1126/science.1219364.〈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/22654060" target="_blank"〉PubMed〈/a〉
    Keywords: Chromatography, Gel ; Cloning, Molecular ; Computational Biology ; Computer Simulation ; Crystallography, X-Ray ; Escherichia coli/genetics/metabolism ; Hydrogen Bonding ; Microscopy, Electron ; Models, Molecular ; Molecular Weight ; Mutation ; *Nanostructures ; *Protein Engineering ; *Protein Multimerization ; Protein Structure, Secondary ; Protein Subunits/*chemistry/genetics ; Proteins/*chemistry/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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  • 8
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    Transition states. Trapping a transition state in a computationally designed protein bottle (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-02-24
    Description: The fleeting lifetimes of the transition states (TSs) of chemical reactions make determination of their three-dimensional structures by diffraction methods a challenge. Here, we used packing interactions within the core of a protein to stabilize the planar TS conformation for rotation around the central carbon-carbon bond of biphenyl so that it could be directly observed by x-ray crystallography. The computational protein design software Rosetta was used to design a pocket within threonyl-transfer RNA synthetase from the thermophile Pyrococcus abyssi that forms complementary van der Waals interactions with a planar biphenyl. This latter moiety was introduced biosynthetically as the side chain of the noncanonical amino acid p-biphenylalanine. Through iterative rounds of computational design and structural analysis, we identified a protein in which the side chain of p-biphenylalanine is trapped in the energetically disfavored, coplanar conformation of the TS of the bond rotation reaction.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581533/" 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/PMC4581533/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pearson, Aaron D -- Mills, Jeremy H -- Song, Yifan -- Nasertorabi, Fariborz -- Han, Gye Won -- Baker, David -- Stevens, Raymond C -- Schultz, Peter G -- 2 R01 GM097206-05/GM/NIGMS NIH HHS/ -- F32 GM099210/GM/NIGMS NIH HHS/ -- F32GM099210/GM/NIGMS NIH HHS/ -- R01 GM097206/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Feb 20;347(6224):863-7. doi: 10.1126/science.aaa2424.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. ; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. ; Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA. ; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute (HHMI), University of Washington, Seattle, WA 98195, USA. ; Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. schultz@scripps.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25700516" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/*analogs & derivatives/chemistry ; Archaeal Proteins/*chemistry ; Biphenyl Compounds/*chemistry ; Computer Simulation ; Computer-Aided Design ; Crystallography, X-Ray ; Entropy ; Models, Chemical ; Protein Structure, Secondary ; Pyrococcus abyssi/*enzymology ; Software ; Threonine-tRNA Ligase/*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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