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  • 1
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    Solution structure of FKBP, a rotamase enzyme and receptor for FK506 and rapamycin (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-05-10
    Description: Immunophilins, when complexed to immunosuppressive ligands, appear to inhibit signal transduction pathways that result in exocytosis and transcription. The solution structure of one of these, the human FK506 and rapamycin binding protein (FKBP), has been determined by nuclear magnetic resonance (NMR). FKBP has a previously unobserved antiparallel beta-sheet folding topology that results in a novel loop crossing and produces a large cavity lined by a conserved array of aromatic residues; this cavity serves as the rotamase active site and drug-binding pocket. There are other significant structural features (such as a protruding positively charged loop and an apparently flexible loop) that may be involved in the biological activity of FKBP.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Michnick, S W -- Rosen, M K -- Wandless, T J -- Karplus, M -- Schreiber, S L -- GM-30804/GM/NIGMS NIH HHS/ -- GM-38627/GM/NIGMS NIH HHS/ -- I-S10-RR04870/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1991 May 10;252(5007):836-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1709301" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/metabolism ; Binding Sites ; Carrier Proteins/*ultrastructure ; Crystallography ; Humans ; Immunosuppressive Agents/metabolism ; Magnetic Resonance Spectroscopy ; Molecular Structure ; Polyenes/metabolism ; Sirolimus ; Tacrolimus ; Tacrolimus Binding Proteins
    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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    Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-09-21
    Description: Triosephosphate isomerase (TIM) is used as a model system for the study of how a localized conformational change in a protein structure is produced and related to enzyme reactivity. An 11-residue loop region moves more than 7 angstroms and closes over the active site when substrate binds. The loop acts like a "lid" in that it moves rigidly and is attached by two hinges to the remainder of the protein. The nature of the motion appears to be built into the loop by conserved residues; the hinge regions, in contrast, are not conserved. Results of molecular dynamics calculations confirm the structural analysis and suggest a possible ligand-induced mechanism for loop closure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joseph, D -- Petsko, G A -- Karplus, M -- New York, N.Y. -- Science. 1990 Sep 21;249(4975):1425-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2402636" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Carbohydrate Epimerases/*metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; *Protein Conformation ; Software ; Triose-Phosphate Isomerase/*metabolism
    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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  • 3
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    "New view" of protein folding reconciled with the old through multiple unfolding simulations (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-01-07
    Description: Twenty-four molecular dynamics trajectories of chymotrypsin inhibitor 2 provide a direct demonstration of the diversity of unfolding pathways. Comparison with experiments suggests that the transition state region for folding and unfolding occurs early with only 25 percent of the native contacts and that the root-mean-square deviations between contributing structures can be as large as 15 angstroms. Nevertheless, a statistically preferred unfolding pathway emerges from the simulations; disruption of tertiary interactions between the helix and a two-stranded portion of the beta sheet is the primary unfolding event. The results suggest a synthesis of the "new" and the classical view of protein folding with a preferred pathway on a funnel-like average energy surface.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lazaridis, T -- Karplus, M -- New York, N.Y. -- Science. 1997 Dec 12;278(5345):1928-31.〈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/9395391" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Simulation ; Models, Molecular ; Peptides/*chemistry ; Plant Proteins ; Protein Conformation ; Protein Denaturation ; *Protein Folding ; Protein Structure, Secondary ; Thermodynamics
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  • 4
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    How enzymes work: analysis by modern rate theory and computer simulations (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-13
    Description: Advances in transition state theory and computer simulations are providing new insights into the sources of enzyme catalysis. Both lowering of the activation free energy and changes in the generalized transmission coefficient (recrossing of the transition state, tunneling, and nonequilibrium contributions) can play a role. A framework for understanding these effects is presented, and the contributions of the different factors, as illustrated by specific enzymes, are identified and quantified by computer simulations. The resulting understanding of enzyme catalysis is used to comment on alternative proposals of how enzymes work.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia-Viloca, Mireia -- Gao, Jiali -- Karplus, Martin -- Truhlar, Donald G -- New York, N.Y. -- Science. 2004 Jan 9;303(5655):186-95.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14716003" target="_blank"〉PubMed〈/a〉
    Keywords: *Catalysis ; Computer Simulation ; Enzymes/*chemistry/*metabolism ; Kinetics ; Mathematics ; Models, Chemical ; Models, Molecular ; Protein Conformation ; Thermodynamics
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  • 5
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    Hidden thermodynamics of mutant proteins: a molecular dynamics analysis (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-06-02
    Description: A molecular dynamics simulation method is used to determine the contributions of individual amino acid residues and solvent molecules to free energy changes in proteins. Its application to the hemoglobin interface mutant Asp G1(99) beta----Ala shows that some of the contributions to the difference in the free energy of cooperativity are as large as 60 kilocalories (kcal) per mole. Since the overall free energy change is only -5.5 kcal/mole (versus the experimental value of -3.4 kcal/mole), essential elements of the thermodynamics are hidden in the measured results. By exposing the individual contributions, the free energy simulation provides new insights into the origin of thermodynamic changes in mutant proteins and demonstrates the role of effects beyond those usually considered in structural analyses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gao, J -- Kuczera, K -- Tidor, B -- Karplus, M -- New York, N.Y. -- Science. 1989 Jun 2;244(4908):1069-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2727695" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine ; Asparagine ; Hemoglobins/*genetics ; Hydrogen Bonding ; Macromolecular Substances ; Molecular Structure ; *Mutation ; Oxyhemoglobins ; Structure-Activity Relationship ; Thermodynamics
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  • 6
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    Effective coupling in biological electron transfer: exponential or complex distance dependence? (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-11-19
    Description: Calculations for a simple model electron transfer system and tuna cytochrome c demonstrate a dichotomy in the distance dependence of the effective coupling. In one regime, the effective coupling varies exponentially with distance and depends primarily on the average properties of the bridging material; in the other regime, the effective coupling has a complex distance dependence and is more sensitive to the details of the bridging material. Experiments and theory indicate that both regimes may occur in biological systems, providing a perspective on a recent controversy over the nature of the distance dependence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Evenson, J W -- Karplus, M -- New York, N.Y. -- Science. 1993 Nov 19;262(5137):1247-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8235654" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cytochrome c Group/chemistry/*metabolism ; *Electron Transport ; Heme/chemistry/*metabolism ; Mathematics ; Models, Biological ; Models, Chemical ; Tuna
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  • 7
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    Crystallographic R factor refinement by molecular dynamics (1987)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1987-01-23
    Description: Molecular dynamics was used to refine macromolecular structures by incorporating the difference between the observed crystallographic structure factor amplitude and that calculated from an assumed atomic model into the total energy of the system. The method has a radius of convergence that is larger than that of conventional restrained least-squares refinement. Test cases showed that the need for manual corrections during refinement of macromolecular crystal structures is reduced. In crambin, the dynamics calculation moved residues that were misplaced by more than 3 angstroms into the correct positions without human intervention.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brunger, A T -- Kuriyan, J -- Karplus, M -- New York, N.Y. -- Science. 1987 Jan 23;235(4787):458-60.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17810339" target="_blank"〉PubMed〈/a〉
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  • 8
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    Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin (1987)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1987-01-16
    Description: A molecular dynamics simulation of myoglobin provides the first direct demonstration that the potential energy surface of a protein is characterized by a large number of thermally accessible minima in the neighborhood of the native structure (for example, approximately 2000 minima were sampled in a 300-picosecond trajectory). This is expected to have important consequences for the interpretation of the activity of transport proteins and enzymes. Different minima correspond to changes in the relative orientation of the helices coupled with side-chain rearrangements that preserve the close packing of the protein interior. The conformational space sampled by the simulation is similar to that found in the evolutionary development of the globins. Glasslike behavior is expected at low temperatures. The minima obtained from the trajectory do not satisfy certain criteria for ultrametricity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elber, R -- Karplus, M -- New York, N.Y. -- Science. 1987 Jan 16;235(4786):318-21.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3798113" target="_blank"〉PubMed〈/a〉
    Keywords: Models, Structural ; Motion ; *Myoglobin ; Protein Conformation ; Thermodynamics
    Print ISSN: 0036-8075
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  • 9
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    Solution of a protein crystal structure with a model obtained from NMR interproton distance restraints (1987)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1987-02-27
    Description: Model calculations were performed to test the possibility of solving crystal structures of proteins by Patterson search techniques with three-dimensional structures obtained from nuclear magnetic resonance (NMR) interproton distance restraints. Structures for crambin obtained from simulated NMR data were used as the test system; the root-mean-square deviations of the NMR structures from the x-ray structure were 1.5 to 2.2 A for backbone atoms and 2.0 to 2.8 A for side-chain atoms. Patterson searches were made to determine the orientation and position of the NMR structures in the unit cell. The correct solution was obtained by comparing the rotation function results of several of the NMR structures and the average structure derived from them. Conventional refinement techniques reduced the R factor from 0.43 at 4 A resolution to 0.27 at 2 A resolution without inclusion of water molecules. The partially refined structure has root-mean-square backbone and side-chain atom deviations from the x-ray structure of 0.5 and 1.3 A, respectively.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brunger, A T -- Campbell, R L -- Clore, G M -- Gronenborn, A M -- Karplus, M -- Petsko, G A -- Teeter, M M -- New York, N.Y. -- Science. 1987 Feb 27;235(4792):1049-53.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17782253" target="_blank"〉PubMed〈/a〉
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  • 10
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    Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference (1985)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1985-08-09
    Description: The internal motions of the double-stranded DNA oligomer (dCdG)3 (dC, deoxycytidylate; dG, deoxyguanylate) in the B and Z forms have been calculated in the harmonic approximation. A complete vibrational analysis has been made, and the resulting normal mode frequencies have been used to evaluate the vibrational entropy of B and Z DNA. The greater flexibility of the B DNA hexamer leads to an entropic stabilization relative to the stiffer Z DNA hexamer of 22 calories per mole per kelvin at 300 K. The calculated value is of the same order as that (21 to 27 calories per mole per kelvin) obtained from nuclear magnetic resonance measurements on the methylated duplexes (m5dCdG)3 and (dCdGm5dCdGdCdG). This result demonstrates the importance of internal motions, which have been neglected in earlier studies of the transition from B to Z DNA, in the stability of different nucleic acid conformers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Irikura, K K -- Tidor, B -- Brooks, B R -- Karplus, M -- New York, N.Y. -- Science. 1985 Aug 9;229(4713):571-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3839596" target="_blank"〉PubMed〈/a〉
    Keywords: *Dna ; Methanol ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides ; Stereoisomerism ; Thermodynamics ; Vibration
    Print ISSN: 0036-8075
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