Statistical theory of combinatorial libraries of folding proteins: Energetic discrimination of a target structure

Journal of Molecular Biology

Volumn 296, Issue 1, 2000, Pages 281-294

  Zou, Jinming ^a   Saven, Jeffery G ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Combinatorial library; Protein design; Protein folding; Sequence profile; Stability gap

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; ENTROPY; PRIORITY JOURNAL; PROBABILITY; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; STATISTICS; THEORY; THERMODYNAMICS;

EID: 0034635349     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3426     Document Type: Article

References (88)

1. Improved design of stable and fast-folding model proteins
2. Active barnase variants with completely random hydrophobic cores
3. Crystallization of a designed peptide from a molten globule ensemble
4. A method to identify protein sequences that fold into a known three-dimensional structure
5. A quantitative methodology for the de novo design of proteins
6. When is a potential accurate enough for structure prediction theory and application to a random heteropolymer model of protein folding
7. Spin glasses and the statistical mechanics of protein folding
8. Protein design: A hierarchic approach
9. From coiled coils to small globular proteins: Design of a native-like three-helix bundle
10. Optimizing potentials for the inverse folding problem
11. De novo protein design: Fully automated sequence selection
12. Folded proteins occur frequently in libraries of random amino acid sequences
13. Random-energy model: An exactly solvable model of disordered systems
14. De novo design of the hydrophobic cores of proteins
15. New algorithm for protein design
16. Dominant forces in protein folding
17. Modeling protein stability as heteropolymer collapse
18. Factors that affect the folding ability of proteins
19. Protein engineering of man-made proteins
20. Enhanced sampling in molecular dynamics: Use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
21. A search for the most stable folds of protein chains
22. Why are the same protein folds used to perform different functions?
23. Boltzmann-like statistics of protein architectures origins and consequences
24. Why do protein architectures have boltzmann-like statistics?
25. Theoretical studies of protein folding
26. Topology fingerprint aproach folding problem
27. Protein tertiary structure recognition using optimized hamiltonians with local interactions
28. Optimal protein-folding codes from spin-glass theory
29. Searching for fast-folding proteins using optimized energy functions
30. Why are some protein structures so common?
31. High-resolution protein design with backbone freedom
32. Optimal sequence selection in proteins of known structure by simulated evolution
33. 2d, a nativelike de novo designed protein
34. From structure to sequence and back again
35. Monte carlo procedure for protein design
36. Design of sequence with good folding properties in coarse-grained protein models
37. De novo protein design using pair-wise potentials and a genetic algorithm
38. Protein design by binary patterning of polar and nonpolar amino acids
39. The sequences of small proteins are not extensively optimized for rapid folding by natural selection
40. Mean-field minimization methods for biological macromolecules
41. Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry
42. A strategy for the de novo design of helical proteins with stable folds
43. Libraries of random-sequence polypeptides produced with high yield as carboxy-terminal fusions with ubiquitin
44. A lattice statistical mechanics model of the conformational and sequence spaces of proteins
45. Protein folding funnels-a kinetic approach to the sequence structure relationship
46. Emergence of preferred structures in a simple model of protein folding
47. Designability, thermodynamic stability and dynamics in protein folding: A lattice model study
48. How to derive a protein folding potential? A new approach to an old problem
49. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
50. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
51. Design of proteins with selected thermal properties
52. Proposed mechanism for stability of proteins to evolutionary mutations
53. Toward an outline of the topography of a realistic protein-folding funnel
54. Protein superfamilies and domain super-folds
55. Folding thermodynamics and kinetics of imprinted renaturable heteropolymers
56. How accurate must potentials be for successful modeling of protein folding?
57. Energy functions that discriminate x-ray and near-native folds from well-constructed decoys
58. Monte carlo simulations of protein folding using inexact potentials: How accurate must parameters be in order to preserve the essential features of the energy landscape?
59. Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes
60. A new approach to the design of a sequence with the highest affinity for a molecular surface
61. Are database-derived potentials valid for scoring both forward and inverted protein folding?
62. Stabilizing the subtilisin bpn pro-domain by pjage display selection, how restrictive is the amino acid code for maximum protein stability?
63. Kinetics of protein folding. a lattice model study of the requirements for folding to the native state
64. Conformation, energy, and folding ability of selected amino acid sequences
65. Protein folding from a combinatorial perspective
66. Statistical mechanics of the combinatorial synthesis and analysis of folding macromolecules
67. Optimal protein design procedure
68. Theoretical studies of protein-folding thermodynamics and kinetics
69. Protein design: A perspective from simple tractable models
70. Implications of thermodynamics of protein folding for evolution of primary sequences
71. Enumeration of all compact conformations of copolymers with random sequence of links
72. A new approach to the design of stable proteins
73. Conserved residues and the mechanism of protein folding
74. Calculation of conformational ensembles from potentials of mean force
75. Folding kinetics of protein-like heteropolymers
76. Designing amino acid sequences to fold with good hydrophobic cores
77. Statistical potentials extracted from protein structures: How accurate are they?
78. Local interactions dominate folding in a simple protein model
79. Protein folding kinetics: Timescales, pathways and energy landscapes in terms of sequence-dependent properties
80. Treating sequence dependence of protein stability in a mean-field model
81. Solution structure and dynamics of a de novo designed three-helix bundle protein
82. A test of lattice protein folding algorithms