Quantitative comparison of the ability of hydropathy scales to recognize surface β-strands in proteins

Proteins: Structure, Function and Genetics

Volumn 42, Issue 2, 2001, Pages 243-255

  Palliser, Christopher C ^a   Parry, David A D ^a  

^a MASSEY UNIVERSITY   (New Zealand)

Author keywords

Hydropathy profile; Prediction method; Secondary structure

Indexed keywords

ALPHA HELIX; AMINO ACID SEQUENCE; CONFERENCE PAPER; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; SCORING SYSTEM; STRUCTURE ANALYSIS; SURFACE PROPERTY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 0035255017     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0134(20010201)42:2<243::AID-PROT120>3.0.CO;2-B     Document Type: Conference Paper

References (134)

1. Some factors in the interpretation of protein denaturation
2. Dominant forces in protein folding
3. Guidelines for membrane protein engineering derived from de novo designed model peptides
4. The meaning of hydrophobicity
5. Which effective property of amino acids is best preserved by the genetic code?
6. The molecular structure of reptilian keratin
7. Hard α-keratin intermediate filament chains: Substructure of the N- and C-terminal domains and the predicted structure and function of the C-terminal domains of type I and II chains
8. Surface β-strands in proteins: Identification using an hydropathy technique
9. Hydrophobic parameters II of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides
10. Turns in peptides and proteins
11. Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins
12. Hydrophobicity indices for amino acid residues as determined by high-performance liquid chromatography
13. Environmental characteristics of residues in proteins: Three-dimensional molecular hydrophobicity potential approach
14. Physicochemical basis of amino acid hydrophobicity scales: Evaluation of four new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of peptides
15. Hydrophobic characteristics of folded proteins
16. The development of the prediction of protein structure
17. Prediction of secondary structure of proteins by means of hydrophobicity profiles
18. Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins
19. Empirical predictions of protein conformation
20. Secondary structure prediction: Combination of three different methods
21. A critical evaluation of the hydropathy profile of membrane proteins
22. Trans-membrane translocation of proteins. The direct transfer model
23. Hydrophobic moments and protein structure
24. A simple method for displaying the hydropathic character of a protein
25. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins
26. Amino acid side-chain partition energies and distribution of residues in soluble proteins
27. Prediction of transmembrane helices from hydrophobic characteristics of proteins
28. Protein secondary structure conformations and associated hydrophobicity scales
29. Prediction of protein secondary structures from their hydrophobic characteristics
30. Protein transmembrane structure: Recognition and prediction by using hydrophobicity scales through preference functions
31. WHAT IF: A molecular modeling and drug design program
32. The interpretation of protein structures: Estimation of static accessibility
33. Compartmentalization of amino acids in surfactant aggregates
34. Thermodynamic parameters of transfer of N-acetyl ethyl esters of different amino acids from organic solvents to water
35. Refined models for computer simulation of protein folding. Applications to the study of conserved secondary structure and flexible hinge points during the folding of pancreatic trypsin inhibitor
36. The behaviour of peptides on reverse-phase supports during high-pressure liquid chromatography
37. Affinities of amino acid chains for solvent water
38. Measurement and correlation of partition coefficients of polar amino acids
39. Measurement of relative hydrophobicity of amino acid side-chains by partition in an aqueous two-phase polymeric system: Hydrophobicity scale for non-polar and ionogenic side-chains
40. The role of solvent polarity in the free energy of transfer of amino acid side chains from water to organic solvents
41. Distribution of accessible surfaces of amino acids in globular proteins
42. Dependence of conformational stability on hydrophobicity of the amino acid residue in a series of variant proteins substituted at a unique position of tryptophan synthase α subunit
43. Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of Ile 3
44. Amino acids in AOT reversed micelles. 2. The hydrophobic effect and hydrogen bonding as driving forces for interfacial solubilization
45. Heat capacity of proteins. I. Partial molar heat capacity of individual amino acid residues in aqueous solution: Hydration effect
46. Amino acid side-chain contributions to free energy of transfer of tripeptides from water to octanol
47. An effective solvation term based on atomic occupancies for use in protein simulations
48. Protein stability for single substitution mutants and the extent of local compactness in the denatured state
49. Spatial and free energy distribution patterns of amino acid residues in water soluble proteins
50. Hydrophobic contribution constants of amino acid residues to the hydrophobicities of oligopeptides
51. Phase behaviour of α-amino acids in multicomponent aqueous alkanol solutions
52. Direct determination of the membrane affinities of individual amino acids
53. Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins
54. Prediction of the surface-interior diagram of globular proteins by an empirical method
55. Structural prediction of membrane-bound proteins
56. Prediction of chain flexibility in proteins
57. A statistical technique for predicting membrane protein structure
58. Prediction of sequential antigenic regions in proteins
59. A conformational preference parameter to predict helices in integral membrane proteins
60. Linear optimization of predictors for secondary structure. Application to transbilayer segments of membrane proteins
61. Thermodynamic β-sheet propensities measured using a zinc-finger host peptide
62. Measurement of the β-sheet-forming propensities of amino acids
63. Intrinsic secondary structure propensities of the amino acids, using statistical φ-ψ matrices: Comparison with experimental scales
64. A thermodynamic scale for the β-sheet forming tendencies of the amino acids
65. Hydrophobic bonding and accessible surface area in proteins
66. The nature of the accessible and buried surfaces in proteins
67. Interior and surface of monomeric proteins
68. Surface, subunit interfaces and interior of oligomeric proteins
69. Hydrophobicity of amino acid residues in globular proteins
70. Cluster analysis of amino acid indices for prediction of protein structure and function
71. On the hydrophobic nature of signal sequences
72. Algorithms for prediction of α-helical and β-structural regions in globular proteins
73. Hydrophobic character of amino acid residues in globular proteins
74. The light and medium subunits of the photosynthetic reaction centre from Rhodopseudomonas viridis: Isolation of the genes, nucleotide and amino acid sequence
75. Hydrophobicity and structural classes in proteins
76. Empirical studies of hydrophobicity. 1. Effect of protein size on the hydrophobic behavior of amino acids
77. Internal residue criteria for predicting three-dimensional protein structures
78. The characterization of amino acid sequences in proteins by statistical methods
79. An empirical hydrophobicity scale for α-aminoacids and some of its applications
80. Hydration of macromolecules. III. Hydration of polypeptides
81. Surface tension of amino acid solutions: A hydrophobicity scale of the amino acid residues
82. Amino acid properties and side-chain orientation in proteins: A cross correlation approach
83. A simplified representation of protein conformations for rapid simulation of protein folding
84. Influence of water on protein structure. An analysis of the preferences of amino acid residues for the inside or outside and for specific conformations in a protein molecule
85. Surface and inside volumes in globular proteins
86. Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition
87. Hydrophobic basis of packing in globular proteins
88. Prediction of protein antigenic determinants from amino acid sequences
89. Factors affecting retention and resolution of peptides in high-performance liquid chromatography
90. The isolation of peptides by high-performance liquid chromatography using prediction elution positions
91. Theoretical prediction of protein antigenic determinants from amino acid sequences
92. Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure
93. The apolar surface area of amino acids and its empirical correlation with hydrophobic free energy
94. Protein antigen conformation: Folding patterns and predictive algorithms; selection of antigenic and immunogenic peptides
95. A simple experimental model for hydrophobic interactions in proteins
96. Recognition of super-secondary structure in proteins
97. Statistical analysis of the physical properties of the 20 naturally occurring amino acids
98. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
99. Solvation energy in protein folding and binding
100. Prediction of peptide retention times in reversed-phase high-performance liquid chromatography I. Determination of retention coefficients of amino acid residues of model synthetic peptides
101. Protein surface analysis. Methods for identifying antigenic determinants and other interaction sites
102. New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: Correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites
103. Extension of the fragment method to calculate amino acid zwitterion and side chain partition coefficients
104. Effect of positional environmental domains on the variation of high-performance liquid chromatographic peptide retention coefficients
105. The transmembrane helices of beef heart cytochrome oxidase
106. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
107. Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds
108. The nature of the hydrophobic binding of small peptides at the bilayer interface: Implications for the insertion of transbilayer helices
109. Excluded volume approximation to protein-solvent interaction. The solvent contact model
110. Hydrophobicity of amino acid subgroups in proteins
111. Development of hydrophobicity parameters to analyze proteins which bear post- or cotranslational modifications
112. Extracting hydrophobic free energies from experimental data: Relationship to protein folding and theoretical models
113. Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds
114. A molecular thermodynamic approach to predict the secondary structure of homopolypeptides in aqueous systems
115. Hydrophobicity scale for proteins based on inverse temperature transitions
116. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule
117. Empirical scale of side-chain conformational entropy in protein folding
118. Reversed-phase chromatography of synthetic amphipathic α-helical peptides as a model for ligand/receptor interactions. Effect of changing hydrophobic environment on the relative hydrophilicity/hydrophobicity of amino acid side-chains
119. Atomic and residue hydrophilicity in the context of folded protein structures
120. Relationship of sidechain hydrophobicity and α-helical propensity on the stability of the single-stranded amphipathic α-helix
121. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides
122. Experimentally determined hydrophobicity scale for proteins at membrane interfaces
123. Hydrophobicity regained
124. Quantitative structure-function and structure-stability relationships of purposely modified proteins
125. Five axioms for the functional design of peptide-based polymers as molecular machines and materials: Principle for macromolecular assemblies
126. Three-dimensional structure of membrane and surface proteins
127. Hydrophobic moments as tools for analyzing protein sequences and structures
128. Prediction of the helix/strand of globular proteins based on their primary sequences
129. Hydrophobic distribution and spatial arrangement of amino acid residues in membrane proteins
130. Structural invariants in globular proteins
131. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions
132. Local interactions as a structure determinant for protein molecules: II
133. Structural invariants in protein folding
134. Contribution of hydrophobic interactions to the stability of the globular conformation of proteins