Iterative Assembly of Helical Proteins by Optimal Hydrophobic Packing

Structure

Volumn 16, Issue 8, 2008, Pages 1257-1266

  Wu, G Albert ^a   Coutsias, Evangelos A ^b   Dill, Ken A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

PROTEIN

Indexed keywords

ALGORITHM; ALPHA HELIX; ARTICLE; MATCHSTIX ALGORITHM; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN CONFORMATION; PROTEIN INTERACTION; PROTEIN TERTIARY STRUCTURE; STRUCTURE ANALYSIS;

ALGORITHMS; COMPUTER SIMULATION; DISULFIDES; HYDROPHOBICITY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOFTWARE;

EID: 48149105157     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2008.04.019     Document Type: Article

References (46)

1. Atilgan A.R., Durell S.R., Jernigan R.L., Demirel M.C., Keskin O., and Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80 (2001) 505-515
2. Bowie J.U., and Eisenberg D. An evolutionary approach to folding small α-helical proteins that uses sequence information and an empirical guiding fitness function. Proc. Natl. Acad. Sci. USA 91 (1994) 4436-4440
3. Bratley P., and Fox B.L. ALGORITHM 659: implementing Sobol's quasirandom sequence generator. ACM Trans. Math. Softw. 14 (1988) 88-100
4. Bromberg S., and Dill K.A. Side-chain entropy and packing in proteins. Protein Sci. 3 (1994) 997-1009
5. Case D.A., Cheatham III T.E., Darden T., Gohlke H., Luo R., Merz Jr. K.M., Onufriev A., Simmerling C., Wang B., and Woods R.J. The Amber biomolecular simulation programs. J. Comput. Chem. 26 (2005) 1668-1688
6. Cohen F.E., Richmond T.J., and Richards F.M. Protein folding: evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as an example. J. Mol. Biol. 132 (1979) 275-288
7. Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., and Kollman P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117 (1995) 5179-5197
8. Coutsias E.A., Seok C., Jacobson M.P., and Dill K.A. A kinematic view of loop closure. J. Comput. Chem. 25 (2004) 510-528
9. Coutsias E.A., Seok C., Wester M.J., and Dill K.A. Resultants and loop closure. Int. J. Quantum Chem. 106 (2005) 176-189
10. Crick F. The packing of α-helices: simple coiled-coils. Acta Crystallogr. 6 (1953) 689-697
11. Cuff J.A., and Barton G.J. Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins 34 (1999) 508-519
12. DeLano W.L. The PyMOL Molecular Graphics System (2002), DeLano Scientific, San Carlos, CA
13. Dodd L.R., Boone T.D., and Theodorou D.N. A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses. Molecular Physics 78 (1993) 961-996
14. Dunbrack Jr. R.L. Rotamer libraries in the 21st century. Curr. Opin. Struct. Biol. 12 (2002) 431-440
15. Dunbrack Jr. R.L., and Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J. Mol. Biol. 230 (1993) 543-574
16. Fain B., and Levitt M. A novel method for sampling α-helical protein backbones. J. Mol. Biol. 305 (2001) 191-201
17. Fain B., and Levitt M. Funnel sculpting for in silico assembly of secondary structure elements of proteins. Proc. Natl. Acad. Sci. USA 100 (2003) 10700-10705
18. Fleming P.J., Gong H., and Rose G.D. Secondary structure determines protein topology. Protein Sci. 15 (2006) 1829-1834
19. Go N., and Scheraga H.A. Ring closure and local conformational deformations of chain molecules. Macromolecules 3 (1970) 178-187
20. Ho B.K., and Dill K.A. Folding very short peptides using molecular dynamics. PLoS Comput. Biol. 2 (2006) e27
21. Hoang T.X., Seno F., Banavar J.R., Cieplak M., and Maritan A. Assembly of protein tertiary structures from secondary structures using optimized potentials. Proteins 52 (2003) 155-165
22. Huang E.S., Samudrala R., and Ponder J.W. Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions. J. Mol. Biol. 290 (1999) 267-281
23. Jones D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292 (1999) 195-202
24. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
25. Kohn W.D., Mant C.T., and Hodges R.S. α-Helical protein assembly motifs. J. Biol. Chem. 272 (1997) 2583-2586
26. Kolodny R., and Levitt M. Protein decoy assembly using short fragments under geometric constraints. Biopolymers 68 (2003) 278-285
27. Lee H., and Liang C. Displacement analysis of the general spatial 7-link 7 R mechanism. Mechanism and Machine Theory 23 (1988) 219-226
28. Lin M.S., Fawzi N.L., and Head-Gordon T. Hydrophobic potential of mean force as a solvation function for protein structure prediction. Structure 15 (2007) 727-740
29. Lovell S.C., Davis I.W., Arendall III W.B., de Bakker P.I., Word J.M., Prisant M.G., Richardson J.S., and Richardson D.C. Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins 50 (2003) 437-450
30. Lupas A., Van Dyke M., and Stock J. Predicting coiled coils from protein sequences. Science 252 (1991) 1162-1164
31. McAllister S.R., Mickus B.E., Klepeis J.L., and Floudas C.A. Novel approach for α-helical topology prediction in globular proteins: generation of interhelical restraints. Proteins 65 (2006) 930-952
32. Miyazawa S., and Jernigan R.L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 256 (1996) 623-644
33. Moult J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr. Opin. Struct. Biol. 15 (2005) 285-289
34. Mumenthaler C., and Braun W. Predicting the helix packing of globular proteins by self-correcting distance geometry. Protein Sci. 4 (1995) 863-871
35. Nanias M., Chinchio M., Pillardy J., Ripoll D.R., and Scheraga H.A. Packing helices in proteins by global optimization of a potential energy function. Proc. Natl. Acad. Sci. USA 100 (2003) 1706-1710
36. Narang P., Bhushan K., Bose S., and Jayaram B. A computational pathway for bracketing native-like structures for small α helical globular proteins. Phys. Chem. Chem. Phys. 7 (2005) 2364-2375
37. Onufriev A., Bashford D., and Case D.A. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 55 (2004) 383-394
38. Ozkan S.B., Wu G.A., Chodera J.D., and Dill K.A. Protein folding by zipping and assembly. Proc. Natl. Acad. Sci. USA 104 (2007) 11987-11992
39. Ramachandran G.N., Ramakrishnan C., and Sasisekharan V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7 (1963) 95-99
40. Rost B., Yachdav G., and Liu J. The PredictProtein server. Nucleic Acids Res. 32 (2004) W321-W326
41. Simons K.T., Kooperberg C., Huang E., and Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268 (1997) 209-225
42. Wedemeyer W.J., and Scheraga H.A. Exact analytical loop closure in proteins using polynomial equations. J. Comput. Chem. 20 (1999) 819-844
43. Wolf E., Kim P.S., and Berger B. MultiCoil: a program for predicting two- and three-stranded coiled coils. Protein Sci. 6 (1997) 1179-1189
44. Yue K., and Dill K.A. Constraint-based assembly of tertiary protein structures from secondary structure elements. Protein Sci. 9 (2000) 1935-1946
45. Zhang C., Hou J., and Kim S.H. Fold prediction of helical proteins using torsion angle dynamics and predicted restraints. Proc. Natl. Acad. Sci. USA 99 (2002) 3581-3585
46. Zhang J., and Liu J.S. On side-chain conformational entropy of proteins. PLoS Comput. Biol. 2 (2006) e168