Interatomic potentials and solvation parameters from protein engineering data for buried residues

Protein Science

Volumn 11, Issue 8, 2002, Pages 1984-2000

  Lomize, Andrei L ^a   Reibarkh, Mikhail Y ^a   Pogozheva, Irina D ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Energy functions; Free energy; Protein engineering; Protein folding; Protein stability; Secondary structure; Solvation

Indexed keywords

ALIPHATIC COMPOUND; AROMATIC COMPOUND; CARBON; CYCLOHEXANE; LYSOZYME; NITROGEN; OCTANOL; OXYGEN; RIBONUCLEASE H; SULFUR; THYROXINE; WATER;

ALPHA HELIX; ARTICLE; ATOM; BETA SHEET; CRYSTAL STRUCTURE; ENERGY; HYDROGEN BOND; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; SOLVATION; THERMODYNAMICS; VAN DER WAALS INTERACTION;

AMINO ACID SUBSTITUTION; AMINO ACIDS; ANIMALS; CHICKENS; ELECTROSTATICS; HUMANS; HYDROPHOBICITY; MODELS, CHEMICAL; MURAMIDASE; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; RIBONUCLEASES; THERMODYNAMICS; WATER;

JONES;

EID: 0036070661     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0307002     Document Type: Article

References (147)

1. Hydrogen bonding. 32. An analysis of water-octanol and water-alkane partitioning and the ΔlogP parameter of Seiler
2. Hydrophobic core repacking and aromatic-aromatic interaction in the thermostable mutant of T4 lysozyme Ser 117 → Phe
3. Role of the molten globule state in protein folding
4. The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme
5. Thermodynamic and structural compensation in "size-switch" core repacking variants of bacteriophage T4 lysozyme
6. Temperature dependence of the hydrophobic interaction in protein folding
7. How does protein folding get started?
8. Tight packing of protein cores and interfaces
9. Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-Ser and Val-Thr substitutions in T4 lysozyme
10. Determination of α-helix propensity within the context of a folded protein. Sites 44 and 131 in bacteriophage T4 lysozyme
11. Alanine scanning mutagenesis of the alpha-helix 115-123 of phage T4 lysozyme effects on structure, stability and the binding of solvent
12. The meaning of component analysis: Decomposition of the free energy in terms of specific interactions
13. Decomposition of interaction free energies in proteins and other complex systems
14. Entropy in protein folding and in protein-protein interactions
15. Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations
16. Stability of α-helices
17. Structural invariants in protein folding
18. Heat capacity of hydrogen-bonding networks: An alternative view of protein folding thermodynamics
19. Side-chain conformational entropy in protein unfolded states
20. Modeling unfolded states of peptides and proteins
21. Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility
22. Structural and thermodynamic analysis of the packing of two alpha-helices in bacteriophage T4 lysozyme
23. Computer-aided design of β-sheet peptides
24. The entropic cost of bound water in crystals and biomolecules
25. Attractions and repulsions in molecular crystals: What can be learned from the crystal structures of condensed ring aromatic hydrocarbons?
26. High apparent dielectric constants in the interior of a protein reflect water penetration
27. A solvent model for simulations of peptides in bilayers. I. Membrane-promoting α-helix formation
28. Solvation energy in protein folding and binding
29. Empirical score functions: I. The development of a fast empirical score function to estimate the binding affinity of ligands in receptor complexes
30. Response of a protein structure to cavitycreating mutations and its relation to the hydrophobic effect
31. Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4-lysozyme have different structural and thermodynamic consequences
32. Derivation of class II force fields. 7. Nonbonded force field parameters for organic compounds
33. A mutant T4 lysozyme displays 5 different crystal conformations
34. Principles of protein stability derived from protein engineering experiments
35. Contribution of amino acid substitutions at two different interior positions to the conformational stability of human lysozyme
36. Are the parameters of various stabilization factors estimated from mutant human lysozymes compatible with other proteins?
37. Methionine and alanine substitutions show that the formation of wild-type-like structure in the carboxy-terminal domain of T4 lysozyme is a rate-limiting step in folding
38. Geometry of the intermolecular X-H ... Y (X, Y = N,O) hydrogen bond and the calibration of empirical hydrogen-bond potentials
39. Energetic aspects of crystal packing: Experiment and computer simulations
40. Stability changes upon mutation of solventaccessible residues in proteins evaluated by database-derived potentials
41. Predicting protein stability changes upon mutation using database-derived potentials: Solvent accessibility determines the importance of local versus non-local interactions along the sequence
42. Statistical potentials and scoring functions applied to protein-ligand binding
43. Energy functions for protein design
44. Thermodynamic stability of globular proteins: A reliable model from small molecule studies
45. Partition coefficients of indoles and betacarbolines
46. Potential energy functions
47. Designing potential energy functions for protein folding
48. A consistent empirical potential for water-protein interactions
49. Understanding hydrophobic behavior
50. α-helix stability in proteins. 2. Factors that influence stability at an internal position
51. Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme
52. Stabilization of Escherichia coli ribonuclease HI by cavity-filling mutations within a hydrophobic core
53. Cooperative stabilization of Escherichia coli ribonuclease HI by insertion of Gly-80B and Gly-77-Ala substitution
54. Effect of cavity-creating mutations in the hydrophobic core of chymotrypsin inhibitor 2
55. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
56. Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding
57. Energetics of complementary side-chain packing in a protein hydrophobic core
58. Crevice-forming mutants of bovine pancreatic trypsin inhibitor: Stability changes and new hydrophobic surface
59. De novo protein design. I. In search of stability and specificity
60. Free energy calculations: Applications to chemical and biochemical phenomena
61. Enthalpic contribution to protein stability: Insights from atom-based calculations and statistical mechanics
62. Effective energy functions for protein structure predictions
63. Intermolecular forces in biology
64. Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation
65. Context-dependent protein stabilization by methionine-to-leucine substitution shown in T4 lysozyme
66. The introduction of strain and its effects on the structure and stability of T4 lysozyme
67. Thermodynamic model of secondary structure for α-helical peptides and proteins
68. Prediction of protein structure: The problem of fold multiplicity
69. Structural organization of G protein-coupled receptors
70. Structure-based prediction of binding affinities and molecular design of peptide ligands
71. Side chain contributions to the stability of alpha-helical structure in peptides
72. Energetics of interactions of aromatic hydrocarbons with water
73. Energetics of protein structure
74. Decomposition of the free energy in terms of specific interactions. Implications for theoretical and experimental studies
75. Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of IIe-3
76. Structural and genetic analysis of protein stability
77. Can protein structure be turned inside-out?
78. Studies on protein stability with T4 lysozyme
79. Structural and genetic analysis of the folding and function of T4 lysozyme
80. Satisfying hydrogen bonding potential in proteins
81. Three-body dispersion forces
82. Additivity methods in molecular polarizability
83. Measurement of the β-sheet-forming propensities of amino acids
84. Context is the major determinant of β-sheet propensity
85. Protein stability for single substitution mutants and the extent of local compactness in the denatured state
86. Intermolecular potentials from crystal data. III. Determination of empirical potentials and application to the packing configurations and lattice energies in crystals of hydrocarbons, carboxylic acids, amines, and amides
87. Energy parameters in polypeptides. VII Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids
88. Automated docking using a Lamarkian generic algorithm and an empirical binding energy function
89. Hydrogen bonding stabilizes globular proteins
90. Parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids
91. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
92. Stabilization of hen egg white lysozyme by a cavity-filling mutation
93. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids
94. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
95. Contribution of the hydrophobic effect to globular protein stability
96. Polar group burial contributes more to protein stability than nonpolar group burial
97. Forces contributing to the conformational stability of proteins
98. Residue helix parameters obtained from dichroic analysis of peptides of defined sequence
99. Factors affecting the ability of energy functions to discriminate correct from incorrect folds
100. Empirical scale of side-chain conformational entropy in protein folding
101. Perturbation of Trp-138 in T4 lysozyme by mutations at Gln-105 used to correlate changes in structure, stability, solvation, and spectroscopic properties
102. Unfolded, yes, but random? Never!
103. The transmembrane 7-α-bundle of rhodopsin: Distance geometry calculation with hydrogen bonding constraints
104. Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, I-octanol, and neutral aqueous solution
105. Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics
106. Use of propensities of amino acids to the local structural environments to understand effect of substitution mutations on protein stability
107. Some thermodynamic implications for the thermostability of proteins
108. Areas, volumes, packing, and protein structure
109. Protein structure and energetics of protein stability
110. Hydrogen bonding, hydrophobicity, packing, and protein folding
111. Implicit solvation models
112. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
113. Calorimetric determination of the enthalpy change for the α-helix to coil transition of an alanine peptide in water
114. The energetics of ion-pair and hydrogen-bonding interactions in a helical peptide
115. The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability
116. Theory of cooperative transitions in protein molecules. I. Why denaturation of globular proteins is a firstorder phase transition
117. Mutational studies of protein structures and their stabilities
118. The denatured state (the other half of the folding equation) and its role in protein stability
119. Prospects for ab initio protein structural genomics
120. Knowledge-based potentials for proteins
121. Free energies of amino acid side-chain rotamers in α-helices, β-sheets and α-helix N-caps
122. Contribution of hydrophobic residues to the stability of human lysozyme-calorimetric studies and x-ray structural analysis of the 5 isoleucine to valine mutants
123. Contribution of water molecules in the interior of a protein to the conformational stability
124. Contribution of the hydrophobic effect to the stability of human lysozyme: Calorimetric studies and x-ray structural analyses of the nine Valine to Alanine mutants
125. A general rule for the relationship between hydrophobic effect and conformational stability of a protein: Stability and structure of a series of hydrophobic mutants of human lysozyme
126. Experimental verification of the "stability profile of mutant protein" (SPMP) data using mutant human lysozymes
127. Contribution of intra- and intermolecular hydrogen bonds to the conformational stability of human lysozyme
128. Contribution of hydrogen bonds to the conformational stability of human lysozyme: Calorimetry and x-ray analysis of six Ser → Ala mutants
129. Contribution of polar groups in the interior of a protein to the conformational stability
130. Analysis of hydrogen bonding strengths in proteins using unnatural amino acids
131. Prediction of protein mutants based on structural environment-dependent amino acid substitution and propensity tables
132. The packing density in proteins: Standard radii and volumes
133. Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments
134. Empirical potentials and functions for protein folding and binding
135. Side-chain interactions between sulfurcontaining amino-acid and phenylalanine in α-helices
136. Solvation model based on weighted solvent accessible surface area
137. Electrostatic effects in macromolecules: Fundamental concepts and practical modeling
138. Differences between pair and bulk hydrophobic interactions
139. Structural analysis of a non-contiguous second-site revertant in T4 lysozyme shows that increasing the rigidity of a protein can enhance its stability
140. The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect
141. Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme
142. Contribution of hydrogen bonds to the conformational stability of human lysozyme: Calorimetry and x-ray analysis of six tyrosine → phenylalanine mutants
143. Folding proteins with a simple energy function and extensive conformational searching