Exploring the conformational space of protein loops using a mean field technique with MOLS sampling

Proteins: Structure, Function and Genetics

Volumn 67, Issue 4, 2007, Pages 908-921

  Kanagasabai, V ^a   Arunachalam, J ^a   Arun Prasad, P ^a   Gautham, N ^a  

^a UNIVERSITY OF MADRAS   (India)

Author keywords

Mean field technique; Mutually orthogonal Latin squares; Protein loop conformations

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; ATOM; LANDSCAPE; LATIN SQUARE DESIGN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN INTERACTION; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; GLYCINE; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOLVENTS;

EID: 34248562845     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21333     Document Type: Article

References (43)

1. Leszczynski JF, Rose GD. Loops in globular proteins: a novel category of secondary structure. Science 1986;234:849-855.
2. Fetrow JS. Omega loops: nonregular secondary structures significant in protein function and stability. FASEB J 1995;9: 708-717.
3. Yates SP, Merrill AR. A catalytic loop within pseudomonas aeruginosa exotoxin A modulates its transferase activity. J Biol Chem 2001;276:35029-35036.
4. Rost B, Sander C. Prediction of protein secondary structure at better than 70 % accuracy. J Mol Biol 1993;232:584-599.
5. Frishman D, Argos P. Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. Protein Eng 1996;9:133-142.
6. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
7. Fiser A, Gian Do KR, Sali R. Modeling of loops in protein structures. Protein Sci 2000;9:1753-1773.
8. DePristo MA, de Bakker PI, Lovell SC, Blundell TL. Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins: Struct Funct Genet 2003;51:41-55.
9. i dimer database. Protein Sci 1995; 4:1412-1420.
10. Wojcik J, Mornon J, Chomilier J. New efficient statistical sequence-dependant structure prediction of short to medium sized protein loops based on an exhaustive loop classification. J Mol Biol 1999;289:1469-1490.
11. Van Vlijmen TWH, Karplus M. PDB based protein loop prediction: parameters for selection and methods for optimization. J Mol Biol 1997;267:975-1001.
12. Deane MC, Blundell TL. A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins. Proteins: Struct Funct Genet 2000;40:135-144.
13. Ring CS, Kneller DG, Langridge R, Cohen FE. Taxonomy and conformational analysis of loops in proteins. J Mol Biol 1992; 224:685-699.
14. Efimov AV. Patterns of loop regions in proteins. Curr Opin Struct Biol 1993;3:379-384.
15. Vekatachalam CM. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 1968;6:1425-1436.
16. Sibanda BL, Blundell TL, Thornton JM. Conformation of β-hairpins in protein structures. A systematic classification with applications to modeling by homology, electron density fitting and protein engineering. J Mol Biol 1989;206:759-777.
17. Efimov A. Structure of coiled β-β-hairpins and β-β-corners. FEBS Lett 1991;284:288-292.
18. Sibanda BL, Thornton JM. Accommodating sequence changes in β-hairpins in proteins. J Mol Biol 1993;229:428-447.
19. Oliva B, Bates PA, Querol E, Aviles FX, Sternberg MJ. An automated classification of the structure of protein loops. J Mol Biol 1997;266:814-830.
20. Michalsky E, Goede A, Preissner R. Loops In Proteins (LIP) - A comprehensive loop database for homology modelling. Protein Eng 2003;16:979-985.
21. Vengadesan K, Gautham N. Enhanced sampling of the molecular potential energy surface using mutually orthogonal latin squares: application to peptide structures. Biophys J 2003;84: 2897-2906.
22. Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994;3:522-524.
23. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
24. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
25. Olszewski KA, Piela L, Scheraga HA. Mean field theory as a tool for intramolecular conformational optimization. III. Test on Melittin. J Phys Chem 1993;97:261-210.
26. Koehl P, Delarue M. A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modeling. Nat Struct Biol 1995;2:163-170.
27. Liu Z, Dominy BN, Shakhnovich EI. Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential. J Am Chem Soc 2004;126: 8515-8528.
28. Finney DJ. Experimental design and its statistical basis. London: Cambridge University Press; 1955. pp 56-67.
29. Vengadesan K, Gautham N. Conformational studies on enkephalins using the MOLS technique. Biopolymers 2004;74:476-494.
30. Betancourt MR, Skolnick J. Finding the needle in a haystack: deducing native folds from ambiguous ab initio protein structure predictions. J Comput Chem 2001;22:339-353.
31. Biosym/MSI. Biosym/MSI, release 95.0. San Diego, CA: Biosym, Molecular Simulations; 1995.
32. Nemethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA. Energy parameters in polypeptides. X. Improved geometric parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J Phys Chem 1992;96:6472-6484.
33. Ołziej S, Czaplewski C, Liwo A, Chinchio M, Nanias M, Vila JA, Khalili M, Arnautova YA, Jagielska A, Makowski M, Schafroth HD, Kazmierkiewicz R, Ripoll DR, Pillardy J, Saunders JA, Kang YK, Gibson KD, Scheraga HA. Physics based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. Proc Natl Acad Sci USA 2005;102:7547-7552.
34. Hutchinson EG, Thornton JM. PROMOTIF - A program to identify and analyze structural motifs in proteins. Protein Sci 1996; 5:212-220.
35. Vengadesan K, Gautham N. Energy landscape of Met-Enkephalin and Leu-Enkephalin drawn using mutually orthogonal latin squares sampling. J Phys Chem B 2004;108:11196-11205.
36. Levy Y, Becker OM. Energy landscapes of conformationally constrained peptides. J Chem Phys 2001;114:993-1009.
37. Levy Y, Jortner J, Becker OM. Dynamics of hierarchical folding on energy landscapes of hexapeptides. J Chem Phys 2001;115: 10533-10547.
38. Amadei A, Linssen AB, Berendsen HJ. Essential dynamics of proteins. Proteins: Struct Funct Genet 1993;17:412-425.
39. Elmaci N, Berry RS. Principal coordinate analysis on a protein model. J Chem Phys 1999;110:10606-10622.
40. Kriz Z, Carlsen PHJ, Koca J. Conformational features of linear and cyclic enkephalins. A computational study. J Mol Struct Theochem 2001;540:231-250.
41. Onuchic JN, Luthey-Schulten Z, Wolynes PG. Theory of protein folding: the energy landscape perspective. Annu Rev Phys Chem 1997;48:545-600.
42. Weiner SJ, Kollman PA. An all atom force field for simulations of proteins and nucleic acids. J Comp Chem 1986;7:230-252.
43. Ryser HJ. Combinatorial mathematics. Washington, DC: Mathematical Association of America; 1963. pp 79-84.