Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations

Journal of Molecular Biology

Volumn 320, Issue 2, 2002, Pages 369-387

  Guerois, Raphael ^a,b   Nielsen, Jens Erik ^a,c   Serrano, Luis ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b CEA SACLAY   (France)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Mutation; Prediction; Protein complex; Protein stability; Thermodynamic

Indexed keywords

ALGORITHM; ALPHA HELIX; ARTICLE; DATA BASE; ENERGY; MUTATION; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY;

EID: 0036291145     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00442-4     Document Type: Article

References (93)

1. Empirical potentials and functions for protein folding and binding
2. Protein docking along smooth association pathways
3. Effective energy functions for protein structure prediction
4. The SH3-fold family: Experimental evidence and prediction of variations in the folding pathways
5. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
6. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures
7. A simple model for calculating the kinetics of protein folding from three-dimensional structures
8. Thermodynamics of structural stability and cooperative folding behavior in proteins
9. Forces contributing to the conformational stability of proteins
10. Knowledge-based potentials for proteins
11. Are database-derived potentials valid for scoring both forward and inverted protein folding?
12. Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials
13. Predicting protein stability changes upon mutation using database-derived potentials: Solvent accessibility determines the importance of local versus non-local interactions along the sequence
14. Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables
15. Suggestions for safe residue substitutions in site-directed mutagenesis
16. Mutagenesis of a buried polar interaction in an SH3 domain: Sequence conservation provides the best prediction of stability effects
17. The identification of conserved interactions within the SH3 domain by alignment of sequences and structures
18. Contribution of the hydrophobic effect to protein stability: Analysis based on simulations of the Ile-96-Ala mutation in barnase
19. Exhaustive mutagenesis in silico: Multicoordinate free energy calculations on proteins and peptides
20. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
21. Elucidating the folding problem of alpha-helices: Local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters
22. Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: Comparison with Zimm-Bragg and Lifson-Roig formalisms
23. Experimental verification of the "stability profile of mutant protein" (SPMP) data using mutant human lysozymes
24. Stabilization of proteins by rational design of alpha-helix stability using helix/coil transition theory
25. Improving the refolding yield of interleukin-4 through the optimization of local interactions
26. Stabilisation of alpha-helices by site-directed mutagenesis reveals the importance of secondary structure in the transition state for acylphosphatase folding
27. ProTherm: Thermodynamic database for proteins and mutants
28. ProTherm, version 2.0: Thermodynamic database for proteins and mutants
29. Buried waters and internal cavities in monomeric proteins
30. Contribution of water molecules in the interior of a protein to the conformational stability
31. Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme
32. Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: Comparison with experimental scales
33. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
34. The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability
35. Studies on protein stability with T4 lysozyme
36. Excluded volume approximation to protein-solvent interaction. The solvent contact model
37. Evaluation of protein models by atomic solvation preference
38. An effective solvation term based on atomic occupancies for use in protein simulations
39. The interpretation of protein structures: Estimation of static accessibility
40. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding
41. Obligatory steps in protein folding and the conformational diversity of the transition state
42. Experiment and theory highlight role of native state topology in SH3 folding
43. The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology
44. Mapping the interactions present in the transition state for unfolding/folding of FKBP12
45. Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain
46. Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein CI-2
47. A single-point mutation in the extreme heat- and pressure-resistant sso7d protein from sulfolobus solfataricus leads to a major rearrangement of the hydrophobic core
48. The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme
49. Critical role of beta-hairpin formation in protein G folding
50. A breakdown of symmetry in the folding transition state of protein L
51. Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease
52. Contributions of the polar, uncharged amino acids to the stability of staphylococcal nuclease: Evidence for mutational effects on the free energy of the denatured state
53. Contributions of the ionizable amino acids to the stability of staphylococcal nuclease
54. Persistence of native-like topology in a denatured protein in 8 M urea
55. Staphylococcal nuclease: A showcase of m-value effects
56. WHAT IF: A molecular modeling and drug design program
57. Evaluation of direct and cooperative contributions towards the strength of buried hydrogen bonds and salt bridges
58. Flexibility and packing in proteins
59. Empirical correlation for the replacement of Ala by Gly: Importance of amino acid secondary intrinsic propensities
60. Are the parameters of various stabilization factors estimated from mutant human lysozymes compatible with other proteins?
61. Kinetic characterization of the chemotactic protein from Escherichia coli, CheY. Kinetic analysis of the inverse hydrophobic effect
62. Structure of a protein G helix variant suggests the importance of helix propensity and helix dipole interactions in protein design
63. Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution
64. Determination of atomic desolvation energies from the structures of crystallized proteins
65. Hydrophobic parameters of amino acid side-chains from the partitioning of N-acetyl-amino-acid amides
66. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale
67. A simplified representation of protein conformations for rapid simulation of protein folding
68. Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds
69. Contribution of hydrogen bonding to the conformational stability of ribonuclease T1
70. Contribution of buried hydrogen bonds to protein stability. The crystal structures of two barnase mutants
71. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
72. PoPMuSiC, an algorithm for predicting protein mutant stability changes: Application to prion proteins
73. Discrimination of the native from misfolded protein models with an energy function including implicit solvation
74. Discrimination of near-native protein structures from misfolded models by empirical free energy functions
75. Van der Waals volume fragmental constants
76. Hydrogen bond stereochemistry in protein structure and function
77. Flexible-geometry conformational energy maps for the amino acid residue preceding a proline
78. Long-range order in the src SH3 folding transition state
79. Core and surface mutations affect folding kinetics, stability and cooperativity in IL-1 beta: Does alteration in buried water play a role?
80. Modelling of solvent positions around polar groups in proteins
81. Patterns for prediction of hydration around polar residues in proteins
82. Local water bridges and protein conformational stability
83. Direct observation of better hydration at the N terminus of an alpha-helix with glycine rather than alanine as the N-cap residue
84. Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain
85. Nine hydrophobic side chains are key determinants of the thermodynamic stability and oligomerization status of tumour suppressor p53 tetramerization domain
86. A mixed-charge pair in human interleukin 4 dominates high-affinity interaction with the receptor alpha chain
87. Crystal structure of the interleukin-4/receptor alpha chain complex reveals a mosaic binding interface
88. The use of position-specific rotamers in model building by homology
89. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
90. Improving macromolecular electrostatics calculations
91. Structural analysis of a non-contiguous second-site revertant in T4 lysozyme shows that increasing the rigidity of a protein can enhance its stability
92. Contribution of intra- and intermolecular hydrogen bonds to the conformational stability of human lysozyme