Ideal architecture of residue packing and its observation in protein structures

Protein Science

Volumn 6, Issue 10, 1997, Pages 2072-2083

  Raghunathan, G ^a,b   Jernigan, R L ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b Structural Bioinformatics Inc   (United States)

Author keywords

Equivalent sphere packing model; Ideal packing; Long range interactions; Packing geometry; Protein lattices; Residue packing

Indexed keywords

ARTICLE; GEOMETRY; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE;

EID: 0030850226     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560061003     Document Type: Article

References (44)

1. Bahar I, Jernigan R. 1996a. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 266:195-214.
2. Bahar I, Jernigan R. 1996b. Coordination geometry of non-bonded residues in globular proteins. Folding & Design 1:357-370.
3. Bahar I, Kaplan M, Jernigan R. 1997. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins. Forthcoming.
4. Baldwin E, Matthews B. 1994. Core-packing constraints, hydrophobicity, and protein design. Curr Opin Biotechnol 5:396-402.
5. Behe M, Lattman E, Rose G. 1991. The protein-folding problem: The native fold determines packing, but does packing determine the native fold? Proc Natl Acad Sci USA 88:4195-4199.
6. Bryant SH, Lawrence CE. 1993. An empirical energy function for threading protein sequence through the folding motif. Proteins 16:92-112.
7. Casari G, Sippl MJ. 1992. Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. J Mol Biol 224:725-732.
8. Chandrasekaran R, Ramachandran G. 1970. Studies on the conformation of amino acids. XI. Analysis of the observed side group conformations in proteins. Int J Protein Res 2:223-233.
9. Cho J, Mattice W. 1997. Estimation of long-range interactions in coarse-grained rotational isomeric state polyethylene chains on a high-coordination lattice. Macromolecules350:637-644.
10. Covell DG, Jernigan RL. 1990. Conformations of folded proteins in restricted spaces. Biochemistry 29:3287-3294.
11. DeWitte R, Shakhnovich E. 1994. Pseudodihedrals: Simplified protein backbone representation with knowledge-based energy. Protein Sci 3:1570-1581.
12. Eriksson A, Baase W, Zhang X-J, Heinz D, Blaber M, Baldwin E, Matthews B. 1992. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science 255:178-183.
13. Flory P. 1969. Statistical mechanics of chain molecules. New York: Interscience Publishers.
14. Godzik A, Kolinski A, Skolnick J. 1995. Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets. Protein Sci 4:2107-2117.
15. Hinds D, Levitt M. 1992. A lattice model for protein structure prediction at low resolution. Proc Natl Acad Sci USA 89:2536-2540.
16. Janin J, Wodak S, Levitt M, Maigret B. 1978. Conformation of amino acid side-chains in proteins. J Mol Biol 125:357-386.
17. Jernigan R, Raghunathan G, Bahar I. 1994. Characterization of interactions and metal ion binding sites in proteins. Curr Opin Struct Biol 4:256-263.
18. Kappraff J. 1991. Connections. The geometric bridge between art and science. New York: McGraw-Hill, Inc.
19. Kauzmann W. 1959. Some factors in the interpretation of protein denaturation. Adv Prot Chem 14:1-63.
20. Kocher J-PA, Rooman MJ, Wodak S. 1994. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 235:1598-1613.
21. Kolinski A, Skolnick J. 1994. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 18:338-352.
22. Levitt M, Hirshberg M, Sharon R, Daggett V. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comp Phys Commun. Forthcoming.
23. Lim W, Model A, Sauer R, Richards F. 1994. The crystal structure of a mutant protein with altered but improved hydrophobic core packing. Proc Natl Acad Sci USA 91:423-427.
24. Miyazawa S, Jernigan R. 1985. Estimation of effective inter-residue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18:534-552.
25. Miyazawa S, Jernigan R. 1996. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256:623-644.
26. Munson M, Balasubramanian S, Fleming K, Nagi A, O'Brien R, Sturtevant J, Regan L. 1996. What makes a protein a protein? Hydrophobic core designs that specify stability and structural properties. Protein Sci 5:1584-1593.
27. Nishikawa K, Matsuo Y. 1993. Development of pseudoenergy potentials for assessing protein 3d-1d compatibility and detecting weak homologies. Protein Eng 6:811-820.
28. Nishikawa K, Moomany F, Scheraga H. 1974. Low-energy structures of two dipeptides and their relationship to bend conformations. Macromolecules 7:797-806.
29. Park BH, Levitt M. 1995. The complexity and accuracy of discrete state models of protein structure. J Mol Biol 249:493-507.
30. Ponnuswamy P, Sasisekharan V. 1971a. Studies on the conformation of amino acids. IV. Conformations of serine, threonine, cysteine, and valine. Int J Protein Res 3:1-8.
31. Ponnuswamy P, Sasisekharan V. 1971b. Studies on the conformation of amino acids. V. Conformation of amino acids with delta-atoms. Int J Protein Res 3:9-18.
32. Ramachandran G, Ramakrishnan C, Sasisekharan V. 1963. Stereochemistry of polypeptide chain configurations. J Mol Biol 7:95-99.
33. Rapold R, Mattice W. 1996. Introduction of short-and long-range energies to simulate real chains on the 2nd lattice. Macromolecules 29:2457-2466.
34. Reva BA, Finkelstein AV, Rykunov DS, Olson AJ. 1996. Building self-avoiding lattice models of proteins using a self-consistent field optimization. Proteins 26:1-8.
35. Reva BA, Rykunov DS, Olson AJ, Finkelstein AV. 1995. Constructing lattice models of protein chains with side groups. J Comput Biol 2:527-535.
36. Richards F. 1974. The interpretation of protein structures: Total volume, group volume distributions, and packing density. J Mol Biol 82:1-14.
37. Richards F, Lim W. 1993. An analysis of packing in the protein folding problem. Q Rev Biophys 26:423-498.
38. Singh J, Thornton J. 1992. Atlas of protein side-chain interactions. Oxford: IRL Press.
39. Sippl MJ. 1995. Knowledge-based potentials for proteins. Curr Opin Struct Biol 5:229-235.
40. Skolnick J, Kolinski A. 1991. Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure, and dynamics. J Mol Biol 221:499-531.
41. Srinivasan R, Balasubramanian R, Rajan S. 1975. Some new methods and general results of analysis of protein crystallographic structural data. J Mol Biol 98:739-747.
42. Wells A. 1956. The third dimension in chemistry. Oxford: Clarendon Press.
43. Wodak S, Rooman M. 1993. Generating and testing protein folds. Curr Opin Struct Biol 3:247-259.
44. Wynn R, Harkins P, Richards F, Fox R. 1996. Mobile unnatural amino acid side chains in the core of staphylococcal nuclease. Protein Sci 5:1026-1031.