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Protein Sci. Oct 1995; 4(10): 2107–2117.
PMCID: PMC2142984

Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets.

Abstract

Various existing derivations of the effective potentials of mean force for the two-body interactions between amino acid side chains in proteins are reviewed and compared to each other. The differences between different parameter sets can be traced to the reference state used to define the zero of energy. Depending on the reference state, the transfer free energy or other pseudo-one-body contributions can be present to various extents in two-body parameter sets. It is, however, possible to compare various derivations directly by concentrating on the "excess" energy-a term that describes the difference between a real protein and an ideal solution of amino acids. Furthermore, the number of protein structures available for analysis allows one to check the consistency of the derivation and the errors by comparing parameters derived from various subsets of the whole database. It is shown that pair interaction preferences are very consistent throughout the database. Independently derived parameter sets have correlation coefficients on the order of 0.8, with the mean difference between equivalent entries of 0.1 kT. Also, the low-quality (low resolution, little or no refinement) structures show similar regularities. There are, however, large differences between interaction parameters derived on the basis of crystallographic structures and structures obtained by the NMR refinement. The origin of the latter difference is not yet understood.

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Selected References

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  • Anfinsen CB. Principles that govern the folding of protein chains. Science. 1973 Jul 20;181(4096):223–230. [PubMed]
  • Barlow DJ, Thornton JM. Ion-pairs in proteins. J Mol Biol. 1983 Aug 25;168(4):867–885. [PubMed]
  • Bauer A, Beyer A. An improved pair potential to recognize native protein folds. Proteins. 1994 Mar;18(3):254–261. [PubMed]
  • Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. [PubMed]
  • Bowie JU, Clarke ND, Pabo CO, Sauer RT. Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins. 1990;7(3):257–264. [PubMed]
  • Bryant SH, Lawrence CE. The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: a statistical model for nonbonded interactions. Proteins. 1991;9(2):108–119. [PubMed]
  • Godzik A, Kolinski A, Skolnick J. De novo and inverse folding predictions of protein structure and dynamics. J Comput Aided Mol Des. 1993 Aug;7(4):397–438. [PubMed]
  • Godzik A, Kolinski A, Skolnick J. Topology fingerprint approach to the inverse protein folding problem. J Mol Biol. 1992 Sep 5;227(1):227–238. [PubMed]
  • Gregoret LM, Cohen FE. Novel method for the rapid evaluation of packing in protein structures. J Mol Biol. 1990 Feb 20;211(4):959–974. [PubMed]
  • Hendlich M, Lackner P, Weitckus S, Floeckner H, Froschauer R, Gottsbacher K, Casari G, Sippl MJ. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J Mol Biol. 1990 Nov 5;216(1):167–180. [PubMed]
  • Hinds DA, Levitt M. A lattice model for protein structure prediction at low resolution. Proc Natl Acad Sci U S A. 1992 Apr 1;89(7):2536–2540. [PMC free article] [PubMed]
  • Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci. 1994 Mar;3(3):522–524. [PMC free article] [PubMed]
  • Hobohm U, Scharf M, Schneider R, Sander C. Selection of representative protein data sets. Protein Sci. 1992 Mar;1(3):409–417. [PMC free article] [PubMed]
  • Holtzer A. Does Flory-Huggins theory help in interpreting solute partitioning experiments? Biopolymers. 1994 Mar;34(3):315–320. [PubMed]
  • Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature. 1992 Jul 2;358(6381):86–89. [PubMed]
  • Kolinski A, Skolnick J. Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin. Proteins. 1994 Apr;18(4):353–366. [PubMed]
  • Kolinski A, Skolnick J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins. 1994 Apr;18(4):338–352. [PubMed]
  • Levitt M. A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol. 1976 Jun 14;104(1):59–107. [PubMed]
  • Maiorov VN, Crippen GM. Contact potential that recognizes the correct folding of globular proteins. J Mol Biol. 1992 Oct 5;227(3):876–888. [PubMed]
  • Narayana SV, Argos P. Residue contacts in protein structures and implications for protein folding. Int J Pept Protein Res. 1984 Jul;24(1):25–39. [PubMed]
  • Novotný J, Bruccoleri R, Karplus M. An analysis of incorrectly folded protein models. Implications for structure predictions. J Mol Biol. 1984 Aug 25;177(4):787–818. [PubMed]
  • Rooman MJ, Wodak SJ. Identification of predictive sequence motifs limited by protein structure data base size. Nature. 1988 Sep 1;335(6185):45–49. [PubMed]
  • Sali A, Blundell TL. Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J Mol Biol. 1990 Mar 20;212(2):403–428. [PubMed]
  • Singh J, Thornton JM. SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups. J Mol Biol. 1990 Feb 5;211(3):595–615. [PubMed]
  • Tanaka S, Scheraga HA. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules. 1976 Nov-Dec;9(6):945–950. [PubMed]
  • Wallqvist A, Ullner M. A simplified amino acid potential for use in structure predictions of proteins. Proteins. 1994 Mar;18(3):267–280. [PubMed]
  • Warme PK, Morgan RS. A survey of amino acid side-chain interactions in 21 proteins. J Mol Biol. 1978 Jan 25;118(3):289–304. [PubMed]
  • Wilson C, Doniach S. A computer model to dynamically simulate protein folding: studies with crambin. Proteins. 1989;6(2):193–209. [PubMed]

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