Unified perspective on proteins: a physics approach.
暂无分享,去创建一个
Flavio Seno | Antonio Trovato | Jayanth R Banavar | Amos Maritan | A. Maritan | J. Banavar | F. Seno | A. Trovato | T. X. Hoang | Trinh X Hoang
[1] J. Thornton,et al. Diversity of protein–protein interactions , 2003, The EMBO journal.
[2] G. Rose. Getting to know u. , 2002, Advances in protein chemistry.
[3] K. Nishikawa,et al. Trifluoroethanol-induced Stabilization of the α-Helical Structure of β-Lactoglobulin: Implication for Non-hierarchical Protein Folding , 1995 .
[4] A M Lesk,et al. Interior and surface of monomeric proteins. , 1987, Journal of molecular biology.
[5] L. Schulman. In: Finite size scaling and numerical simulation of statistical systems , 1990 .
[6] H. Scheraga,et al. Influence of lysine content and pH on the stability of alanine-based copolypeptides. , 2001, Biopolymers.
[7] H. Stanley,et al. Direct molecular dynamics observation of protein folding transition state ensemble. , 2002, Biophysical journal.
[8] J R Banavar,et al. Protein threading by learning , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[9] Karl Sigmund,et al. Kepler’s conjecture: How some of the greatest minds in history helped solve one of the oldest math problems in the world , 2004 .
[10] J. Maddocks,et al. Global curvature, thickness, and the ideal shapes of knots. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[11] G. Rose,et al. Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[12] Stanley B. Prusiner,et al. Nobel Lecture: Prions , 1998 .
[13] Peter J Bickel,et al. Finding important sites in protein sequences , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[14] D. Engelman,et al. Mutations can cause large changes in the conformation of a denatured protein. , 1993, Biochemistry.
[15] Amos Maritan,et al. Colloquium: Geometrical approach to protein folding: a tube picture , 2003 .
[16] R. Sauer,et al. Folded proteins occur frequently in libraries of random amino acid sequences. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[17] W E Stites,et al. Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. , 1990, Biochemistry.
[18] Antonio Trovato,et al. Geometry and physics of proteins , 2002, Proteins.
[19] H. Orland,et al. Phase diagram of a semiflexible polymer chain in a θ solvent: Application to protein folding , 1995, cond-mat/9512058.
[20] Marek Cieplak,et al. Universality classes in folding times of proteins. , 2002, Biophysical journal.
[21] K. Dill,et al. From Levinthal to pathways to funnels , 1997, Nature Structural Biology.
[22] D. Baker,et al. Contact order, transition state placement and the refolding rates of single domain proteins. , 1998, Journal of molecular biology.
[23] W. H. Toliver,et al. Liquid Crystals , 1912, Nature.
[24] O. Lichtarge,et al. Evolutionary predictions of binding surfaces and interactions. , 2002, Current opinion in structural biology.
[25] A. R. Fresht. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding , 1999 .
[26] J. Onuchic,et al. Navigating the folding routes , 1995, Science.
[27] P. Flory,et al. Random coil configurations of polypeptide copolymers , 1967 .
[28] M. Karplus,et al. How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations , 2004, Science.
[29] P. Wolynes,et al. Spin glasses and the statistical mechanics of protein folding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[30] Alan M. Ferrenberg,et al. Optimized Monte Carlo data analysis. , 1989, Physical Review Letters.
[31] John Maynard Smith,et al. Natural Selection and the Concept of a Protein Space , 1970, Nature.
[32] D. Shortle. The expanded denatured state: an ensemble of conformations trapped in a locally encoded topological space. , 2002, Advances in protein chemistry.
[33] S. Rackovsky,et al. Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids , 1982 .
[34] Computational approach to the protein‐folding problem , 2001, Proteins.
[35] Guido Tiana,et al. Imprint of evolution on protein structures. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[36] L. Pauling,et al. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. , 1951, Proceedings of the National Academy of Sciences of the United States of America.
[37] B. Matthews,et al. Folding and function of a T4 lysozyme containing 10 consecutive alanines illustrate the redundancy of information in an amino acid sequence. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[38] D Baker,et al. The sequences of small proteins are not extensively optimized for rapid folding by natural selection. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[39] K. Dill,et al. Protein folding in the landscape perspective: Chevron plots and non‐arrhenius kinetics , 1998, Proteins.
[40] J. L. King,et al. Non-Darwinian evolution. , 1969, Science.
[41] Christopher M Dobson,et al. The behaviour of polyamino acids reveals an inverse side chain effect in amyloid structure formation , 2002, The EMBO journal.
[42] H. Chan. Protein folding: Matching speed and locality , 1998, Nature.
[43] W. DeGrado,et al. Protein design, a minimalist approach. , 1989, Science.
[44] P. B. Yale. Geometry and symmetry , 1969 .
[45] L. Pauling,et al. Configurations of Polypeptide Chains With Favored Orientations Around Single Bonds: Two New Pleated Sheets. , 1951, Proceedings of the National Academy of Sciences of the United States of America.
[46] A. P. Brunet,et al. The role of turns in the structure of an α-helical protein , 1993, Nature.
[47] C. Mannella,et al. Distribution of accessible surfaces of amino acids in globular proteins , 1987, Proteins.
[48] Zhengshuang Shi,et al. Contribution of hydrogen bonding to protein stability estimated from isotope effects. , 2002, Biochemistry.
[49] M. Kimura. Evolutionary Rate at the Molecular Level , 1968, Nature.
[50] D C Richardson,et al. The de novo design of protein structures. , 1989, Trends in biochemical sciences.
[51] Leslie A Kuhn,et al. Protein unfolding: Rigidity lost , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[52] Mohamed A. Marahiel,et al. Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins , 1998, Nature Structural Biology.
[53] Zhou,et al. First-Order Disorder-to-Order Transition in an Isolated Homopolymer Model. , 1996, Physical review letters.
[54] L A Mirny,et al. How evolution makes proteins fold quickly. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[55] Robert L. Baldwin,et al. NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A , 1988, Nature.
[56] H. Scheraga,et al. Conformational studies of poly‐L‐alanine in water , 1968, Biopolymers.
[57] Christopher M. Dobson,et al. A camelid antibody fragment inhibits the formation of amyloid fibrils by human lysozyme , 2003, Nature.
[58] D. Eisenberg. Proteins. Structures and molecular properties, T.E. Creighton. W. H. Freeman and Company, New York (1984), 515, $36.95 , 1985 .
[59] Vijay S. Pande,et al. Heteropolymer freezing and design: Towards physical models of protein folding , 2000 .
[60] Self-Interactions of Strands and Sheets , 2003, cond-mat/0301258.
[61] R. Srinivasan,et al. LINUS: A hierarchic procedure to predict the fold of a protein , 1995, Proteins.
[62] K. Wilkinson,et al. Alcohol-induced conformational changes of ubiquitin. , 1986, Archives of biochemistry and biophysics.
[63] K N Houk,et al. Kinetic and stereochemical evidence for the involvement of only one proline molecule in the transition states of proline-catalyzed intra- and intermolecular aldol reactions. , 2003, Journal of the American Chemical Society.
[64] Christopher M Dobson,et al. From Computer Simulations to Human Disease Emerging Themes in Protein Folding , 1999, Cell.
[65] P. Privalov. Stability of proteins. Proteins which do not present a single cooperative system. , 1982, Advances in protein chemistry.
[66] Annabel E. Todd,et al. From protein structure to function. , 1999, Current opinion in structural biology.
[67] A. Flammini,et al. Physics of thick polymers , 2005, cond-mat/0508446.
[68] M. Levitt,et al. Funnel sculpting for in silico assembly of secondary structure elements of proteins , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[69] S. Rackovsky,et al. Differential Geometry and Polymer Conformation. 2. Development of a Conformational Distance Function , 1980 .
[70] K. Dill,et al. Denatured states of proteins. , 1991, Annual review of biochemistry.
[71] K. Plaxco,et al. Unfolded, yes, but random? Never! , 2001, Nature Structural Biology.
[72] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[73] D. Shortle,et al. Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation , 1986, Proteins.
[74] C. Dobson,et al. Rationalization of the effects of mutations on peptide andprotein aggregation rates , 2003, Nature.
[75] B. Matthews,et al. Structural and genetic analysis of protein stability. , 1993, Annual review of biochemistry.
[76] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[77] Dudley H. Williams,et al. Characterization of a partially denatured state of a protein by two-dimensional NMR: reduction of the hydrophobic interactions in ubiquitin. , 1991, Biochemistry.
[78] D. T. Jones,et al. A new approach to protein fold recognition , 1992, Nature.
[79] Michael R. Shirts,et al. Native-like mean structure in the unfolded ensemble of small proteins. , 2002, Journal of molecular biology.
[80] Klimov,et al. Criterion that determines the foldability of proteins. , 1996, Physical review letters.
[81] J. D. Bernal. Structure of Proteins , 1939, Nature.
[82] C. Dobson,et al. Insights into protein folding using physical techniques: studies of lysozyme and alpha-lactalbumin. , 1995, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.
[83] Annabel E. Todd,et al. From structure to function: Approaches and limitations , 2000, Nature Structural Biology.
[84] V. B. Smocovitis. Population Genetics, Molecular Evolution, and the Neutral Theory: Selected Papers. Motoo Kimura , Naoyuki Takahata , 1995 .
[85] M. Karplus,et al. Three key residues form a critical contact network in a protein folding transition state , 2001, Nature.
[86] J. Onuchic,et al. Protein folding funnels: a kinetic approach to the sequence-structure relationship. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[87] B. Snel,et al. Comparative assessment of large-scale data sets of protein–protein interactions , 2002, Nature.
[88] Manfred Eigen,et al. The origin of genetic information. , 1981, Scientific American.
[89] P. W. Anderson,et al. Suggested model for prebiotic evolution: the use of chaos. , 1983, Proceedings of the National Academy of Sciences of the United States of America.
[90] R. L. Baldwin. A new perspective on unfolded proteins. , 2002, Advances in protein chemistry.
[91] J. Onuchic,et al. Funnels, pathways, and the energy landscape of protein folding: A synthesis , 1994, Proteins.
[92] A. Ginsburg,et al. Some Specific Ion Effects on the Conformation and Thermal Stability of Ribonuclease , 1965 .
[93] C Sander,et al. An evolutionary treasure: unification of a broad set of amidohydrolases related to urease , 1997, Proteins.
[94] O. Gonzalez,et al. Global curvature and self-contact of nonlinearly elastic curves and rods , 2002 .
[95] R. L. Baldwin,et al. Unusually stable helix formation in short alanine-based peptides. , 1989, Proceedings of the National Academy of Sciences of the United States of America.
[96] A. Flammini,et al. Geometry of Compact Tubes and Protein Structures , 2002, Complexus.
[97] M. Mézard,et al. Spin Glass Theory and Beyond , 1987 .
[98] E. Dufour,et al. Alcohol-induced changes of β-lactoglobulin - retinol-binding stoichiometry , 1990 .
[99] X. Daura,et al. Unfolded state of peptides. , 2002, Advances in protein chemistry.
[100] C. Chothia,et al. Evolution of the Protein Repertoire , 2003, Science.
[101] Alexei V. Finkelstein,et al. Protein Physics: A Course of Lectures , 2002 .
[102] D. Baker,et al. Functional rapidly folding proteins from simplified amino acid sequences , 1997, Nature Structural Biology.
[103] D. Baker,et al. A surprising simplicity to protein folding , 2000, Nature.
[104] Chern-Sing Goh,et al. Co-evolutionary analysis reveals insights into protein-protein interactions. , 2002, Journal of molecular biology.
[105] J. Trefil,et al. Great Ideas in Physics , 1992 .
[106] D. Bassett. Principles of polymer morphology , 1981 .
[107] J. Baum,et al. Structural characterization of monellin in the alcohol-denatured state by NMR: evidence for beta-sheet to alpha-helix conversion. , 1993, Biochemistry.
[108] J. Thoday. Population Genetics , 1956, Nature.
[109] C. Chothia. One thousand families for the molecular biologist , 1992, Nature.
[110] W. Lim,et al. The role of internal packing interactions in determining the structure and stability of a protein. , 1991, Journal of molecular biology.
[111] S. Rackovsky,et al. Differential Geometry and Polymer Conformation. 1. Comparison of Protein Conformations1a,b , 1978 .
[112] B. Fierz,et al. Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding. , 2003, Journal of molecular biology.
[113] C. Sander,et al. Database of homology‐derived protein structures and the structural meaning of sequence alignment , 1991, Proteins.
[114] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[115] C. Orengo,et al. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. , 2002, Journal of molecular biology.
[116] L. Looger,et al. Computational design of receptor and sensor proteins with novel functions , 2003, Nature.
[117] J. Kelly,et al. The alternative conformations of amyloidogenic proteins and their multi-step assembly pathways. , 1998, Current opinion in structural biology.
[118] G. Rose,et al. A simple model for polyproline II structure in unfolded states of alanine‐based peptides , 2002, Protein science : a publication of the Protein Society.
[119] D. Jacobs,et al. Protein flexibility predictions using graph theory , 2001, Proteins.
[120] E. Shakhnovich,et al. Conserved residues and the mechanism of protein folding , 1996, Nature.
[121] G. Rose,et al. Hydrophobicity of amino acid residues in globular proteins. , 1985, Science.
[122] A. Sokal. Monte Carlo methods for the self-avoiding walk , 1994, hep-lat/9509032.
[123] P. Bork,et al. Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.
[124] Zhengshuang Shi,et al. Alanine is an intrinsic α-helix stabilizing amino acid , 1999 .
[125] G. Fredrickson. The theory of polymer dynamics , 1996 .
[126] J. D. Bernal,et al. “The Origins of Life” , 1957, Nature.
[127] F. Crick,et al. Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1953, Nature.
[128] Gary D Bader,et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.
[129] L. H. Bradley,et al. Protein design by binary patterning of polar and nonpolar amino acids. , 1993, Methods in molecular biology.
[130] Christopher M. Dobson,et al. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding , 1999, Nature Structural Biology.
[131] G. N. Ramachandran,et al. Conformation of polypeptides and proteins. , 1968, Advances in protein chemistry.
[132] Amos Maritan,et al. Bethe approximation for a semiflexible polymer chain , 1998 .
[133] Andreas Matouschek,et al. Transient folding intermediates characterized by protein engineering , 1990, Nature.
[134] Arthur M. Lesk,et al. Introduction to protein architecture : the structural biologyof proteins , 2001 .
[135] Hiromi Yamakawa,et al. Modern Theory of Polymer Solutions , 1971 .
[136] L. Henderson. The Fitness of the Environment: An Inquiry Into the Biological Significance of the Properties of Matter , 1913 .
[137] J J Hopfield,et al. Neural networks and physical systems with emergent collective computational abilities. , 1982, Proceedings of the National Academy of Sciences of the United States of America.
[138] M. Denton,et al. Laws of form revisited , 2001, Nature.
[139] A V Finkelstein,et al. The classification and origins of protein folding patterns. , 1990, Annual review of biochemistry.
[140] S. Rackovsky,et al. Differential geometry and protein folding , 1984 .
[141] H. Dyson,et al. Coupling of folding and binding for unstructured proteins. , 2002, Current opinion in structural biology.
[142] Eric J. Rawdon,et al. Thickness of knots , 1999 .
[143] H. Eyring,et al. The Application of the Theory of Absolute Reacton Rates to Proteins. , 1939 .
[144] Antonio Trovato,et al. Optimal shapes of compact strings , 2000, Nature.
[145] P. Gennes,et al. The physics of liquid crystals , 1974 .
[146] Vladimir Privman,et al. Finite Size Scaling and Numerical Simulation of Statistical Systems , 1990 .
[147] J. Richardson,et al. De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. , 1990, Science.
[148] Luis Serrano,et al. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved , 1999, Nature Structural Biology.
[149] H. Orland,et al. Protein Folding, Anisotropic Collapse and Blue Phases , 1997, cond-mat/9706101.
[150] David Eisenberg,et al. The discovery of the α-helix and β-sheet, the principal structural features of proteins , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[151] Flavio Seno,et al. Geometry and symmetry presculpt the free-energy landscape of proteins. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[152] S. Jackson,et al. How do small single-domain proteins fold? , 1998, Folding & design.
[153] C. Woodward,et al. Hydrogen exchange kinetics and internal motions in proteins and nucleic acids. , 1979, Annual review of biophysics and bioengineering.
[154] David Baker,et al. Experiment and theory highlight role of native state topology in SH3 folding , 1999, Nature Structural Biology.
[155] A. Fersht,et al. Characterizing transition states in protein folding: an essential step in the puzzle. , 1995, Current opinion in structural biology.
[156] Ericka Stricklin-Parker,et al. Ann , 2005 .
[157] A. N. Semenov,et al. Hierarchical self-assembly of chiral rod-like molecules as a model for peptide β-sheet tapes, ribbons, fibrils, and fibers , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[158] C. Dobson. Protein Folding and Disease: a view from the first Horizon Symposium , 2003, Nature Reviews Drug Discovery.
[159] K. Binder,et al. Spin glasses: Experimental facts, theoretical concepts, and open questions , 1986 .
[160] R. Srinivasan,et al. The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[161] George D Rose,et al. Polyproline II structure in a sequence of seven alanine residues , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[162] G. Rose,et al. Is protein folding hierarchic? I. Local structure and peptide folding. , 1999, Trends in biochemical sciences.
[163] S. Rackovsky,et al. Differential geometry and polymer conformation. 3. Single-site and nearest-neighbor distribution and nucleation of protein folding , 1981 .
[164] C. Dobson,et al. Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases , 2002, Nature.
[165] A Scherer,et al. A microfabricated device for sizing and sorting DNA molecules. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[166] E. Koonin,et al. The structure of the protein universe and genome evolution , 2002, Nature.
[167] L Serrano,et al. Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain. , 1998, Journal of molecular biology.
[168] W. Lim,et al. Deciphering the message in protein sequences: tolerance to amino acid substitutions. , 1990, Science.
[169] R. L. Baldwin,et al. A neutral, water-soluble, .alpha.-helical peptide: the effect of ionic strength on the helix-coil equilibrium , 1991 .
[170] A. Horwich,et al. Chaperone rings in protein folding and degradation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[171] S. J. Campbell,et al. Ligand binding: functional site location, similarity and docking. , 2003, Current opinion in structural biology.