Understanding hierarchical protein evolution from first principles

Journal of Molecular Biology

Volumn 312, Issue 1, 2001, Pages 289-307

  Dokholyan, Nikolay V ^a   Shakhnovich, Eugene I ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

Energy gap model; Profile solution; Protein evolution

Indexed keywords

PROTEIN;

AMINO ACID COMPOSITION; ARTICLE; MOLECULAR DYNAMICS; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY;

EID: 0035823119     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4949     Document Type: Article

References (100)

1. The foldability landscape of model protein
2. Evolution of model proteins on a foldability landscape
3. Structural patterns in globular proteins
4. One thousand families for the molecular biologist
5. Why are some protein structures so common?
6. Protein superfamilies and domain superfolds
7. Folded proteins occur frequently in libraries of random amino acid sequences
8. Why are the same protein folds used to perform different functions?
9. Scop: A structural classification of proteins database for the investigation of sequences and structures
10. Emergence of preferred structures in a simple model of protein folding
11. Protein structures sustain evolutionary drift
12. Protein evolution - How far can sequences diverge?
13. Estimation of evolutionary distances from protein spatial structures
14. How far divergent evolution goes in proteins
15. Unification of protein families
16. Surveying determinants of protein structure designability across different energy models and amino-acid alphabets: A consensus
17. Database of homology-derived protein structures and the structural meaning of sequence alignment
18. Similarity of the three-dimensional structures of actin and the ATPase fragment of a 70k heat-shock cognate protein
19. A new ATP-binding fold in actin, hexokinase and Hsc70
20. Cath - A hierarchic classification of protein domain structures
21. The HSSP database of protein structure-sequence alignments and family profiles
22. Protein structure modeling for structural genomics
23. Assigning genomic sequences to CATH
24. Protein structure comparison by alignment of distance matrices
25. An evolutionary treasure: Unification of a broad set of amidohydrolases related to urease
26. "Homology" in proteins and nucleic acids: A terminology muddle and a way out of it
27. Optimal protein-folding codes from spinglass theory
28. Engineering of stable and fast folding sequences of model proteins
29. Improved design of stable and fast-folding model proteins
30. Theoretical studies of protein-folding thermodynamics and kinetics
31. Spin glasses and the statistical mechanics of protein folding
32. Theory of kinetic partitioning in protein folding with possible applications to prions
33. Protein design: A perspective from simple tractable models
34. Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
35. Coordinated amino acid changes in homologous protein families
36. The prediction of protein contacts from multiple sequence alignments
37. Temperature dependence of the folding rate in a simple protein model: Search for a "glass" transition
38. Universal correlation between energy gap and foldability for the random energy model and lattice proteins
39. Statistical significance of protein structure prediction by threading
40. Ground state of random copolymers and the discrete random energy model
41. The protein data bank: A computer-based archival file for macromolecular structures
42. Protein data bank
43. Statistical mechanics of proteins with evolutionary "selected" sequences
44. Kinetics of protein folding. A lattice model study for the requirements for folding to the native state
45. Freezing transition of random heteropolymers consisting of arbitrary sets of monomers
46. Statistical mechanics of the combinatorial synthesis and analysis of folding molecules
47. A method to identify protein sequences that fold into a known 3-dimensional structure
48. Formation of unique structure in polypeptide chains: Theoretical investigation with the aid of a replica approach
49. Implications of thermodynamics of protein folding for evolution of primary sequences
50. Statistical mechanics of simple models of protein folding and design
51. Error detecting and error correcting codes
52. When is it safe to use an oversimplified substitution model in tree-making?
53. Converting amino acid alignment scores into measures of evolutionary time: A simulation study of various relationships
54. Protein folding and protein evolution: Common folding nucleus in different subfamilies of c-type cytochromes?
55. How evolution makes proteins fold quickly
56. Non-functional conserved residues in globins and their possible role as a folding nucleus
57. Folding of homologous proteins
58. How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins
59. Evolutionary conservation and variation of protein folding pathways
60. A comparison of the folding kinetics and thermodynamics of two homologous fibronectin type III modules
61. Conservation of folding pathways in evolutionarily distant globin sequences
62. Effects of core mutations on the folding of a beta-sheet protein: Implications for backbone organization in the i-state
63. Surface-exposed phenylalanines in the rnp1/rnp2 motif stabilize the cold-shock protein cspb from Bacillus subtilis
64. Structure of the transition state for folding of the 129 aa protein chey resembles that of a smaller protein
65. Supersites within superfolds. Binding site similarity in the absence of homology
66. 2+, and conformation of the chemotaxis protein chey on its binding to the flagellar switch protein film
67. The three-dimensional structure of two mutants of the signal transduction protein chey suggests its molecular activation mechanism
68. Structure analysis of two chey mutants: Importance of the hydrogen bond contribution to protein stability
69. Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain
70. Slow folding of muscle acylphosphatase in the absence of intermediates
71. Slow cooperative folding of a small globular protein hpr
72. Nature of driving force for protein folding: A result from analyzing the statistical potential
73. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
74. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
75. Excluded volume in protein sidechain packing
76. The structure of the transition-state for folding of chymotrypsin inhibitor-2 analyzed by protein engineering methods - Evidence for a nucleation-condensation mechanism for protein folding
77. The folding of an immunoglobulin-like greek key protein is defined by a common-core nucleus and regions constrained by topology
78. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding
79. Identifying the protein folding nucleus using molecular dynamics
80. Structure of the adenylylcyclase catalytic core
81. A polymerase I palm in adenylyl cyclase
82. A polymerase I palm in adenylyl cyclase-reply
83. The sequences of small proteins are not extensively optimized for rapid folding by natural selection
84. Tolerance of a protein helix to multiple alanine and valine substitutions
85. Crystal structure of a pol α family replication DNA polymerase from bacteriophage RB69
86. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
87. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystals
88. A test of the "jigsaw puzzle" model for protein folding by multiple methionine substitutions within the core of T4 lysozyme
89. Active barnase variants with completely random hydrophobic core
90. Magnesium binding to the bacterial chemotaxis protein CheY results in large conformational changes involving its functional surface
91. Structural similarities between topoisomerases that cleave one or both DNA strands
92. Nucleation mechanisms in protein folding
93. Molecular dynamics studies of folding of a protein-like model
94. Thermodynamically important contacts in folding of model proteins
95. Distinguishing homologous from analogous proteins
96. Structure-derived potentials and protein simulations
97. Hiking in the energy landscape in sequence space: A bumpy road to good folders
98. Closed loops of nearly standard size: Common basic element of protein structure