Ab initio prediction of the three-dimensional structure of a de novo designed protein: A double-blind case study

Proteins: Structure, Function and Genetics

Volumn 58, Issue 3, 2005, Pages 560-570

  Klepeis, John L ^a,c   Wei, Yinan ^b,d   Hecht, Michael H ^b   Floudas, Christodoulos A ^a  

^a Princeton University   (United States)

^b PRINCETON UNIVERSITY   (United States)

^c D E SHAW RESEARCH   (United States)

^d BROOKHAVEN NATIONAL LABORATORY   (United States)

Author keywords

Binary patterning; Four helix bundle; Optimization; Protein design; Protein folding; Structure prediction

Indexed keywords

AB INITIO CALCULATION; AMINO ACID SEQUENCE; ARTICLE; COMBINATORIAL LIBRARY; NUCLEAR MAGNETIC RESONANCE; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; STRUCTURE ANALYSIS;

ALGORITHMS; AMINO ACIDS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; DOUBLE-BLIND METHOD; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PEPTIDE LIBRARY; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTEOMICS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 12944263648     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20338     Document Type: Article

References (60)

1. Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181:223-230.
2. Moult J, Fidelis K, Zemla A, Hubbard T. Critical assessment of methods of protein structure prediction (CASP)-round 4. Proteins 2001;Suppl 5:2-7.
3. Klepeis JL, Floudas CA. Ab initio tertiary structure prediction of proteins. J Global Optim 2003;25:113-140.
4. Klepeis JL, Floudas CA. ASTRO-FOLD: a combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino-acid sequence. Biophysical J 2003;85:2119-2143.
5. Liwo A, Lee J, Ripoll D, Pillardy J, Scheraga H. Surmounting the multiple minima problem in protein folding. Proc Natl Acad Sci USA 1999;96:5482-5485.
6. Pillardy J, Czaplewski C, Liwo A, Wedemeyer W, Lee J, Ripoll D, Arlukowicz P, Oldziej S, Arnautova E, Scheraga H. Development of physics-based energy functions that predict medium resolution structure for proteins of α, β and α/β structural classes. J Phys Chem B 2001;105:7299-7311.
7. Klepeis JL, Floudas CA. Prediction of beta-sheet topology and disulfide bridges in polypeptides. J Comp Chem 2003;24:191-208.
8. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science 2003;302:1364-1368.
9. Klepeis JL, Floudas CA, Morikis D, Tsokos CG, Argyropoulos E, Spruce L, Lambris JD. Integrated computational and experimental approach for lead optimization and design of compstatin variants with improved activity. J Am Chem Soc 2003;125:8422-8423.
10. Wei Y, Kim S, Fela D, Baum J, Hecht M. Solution structure of a protein from a designed combinatorial. Proc Natl Acad Sci USA 2003;100(23):13270-13273.
11. Hill RB, Raleigh DP, Lombardi A, DeGrado WF. De novo design of helical bundles as models for understanding protein folding and function. Acc Chem Res 2000;33:745-754.
12. Hecht MH, Richardson DS, Richardson DC, Ogden RC. De novo design, expression and chracterisation of felix: a four helix bundle protein with native-like sequence. Science 1990;249:884-891.
13. Bowie JU, Reidhaar-Olson JF, Lim WA, Sauer RT. Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science 1990;247:1306-1310.
14. Moore JC, Arnold FH. Directed evolution of a para-nitrobenzyl esterase for aqueous-organic solvents. Nat Biotechnol 1996;14:458-467.
15. Dahiyat BI, Gordon DB, Mayo SL. Automated design of the surface positions of protein helices. Protein Sci 1997;6:1333-1337.
16. Dahiyat BI, Mayo SL. De novo protein design: fully automated sequence selection. Science 1997;278:82-87.
17. Skalicky JJ, Gibney BR, Rabanal F, Urbauer RJB, Dutton PL, Wand AJ. Solution structure of a designed four-r-helix bundle maquette scaffold. J Am Chem Soc 1999;121:4941-4951.
18. Baltzer L, Broo KS. De novo designed polypeptide catalysts with adopted folded structures. Biopolymers 1998;1:31-40.
19. Raha K, Wollacott AM, Italia MJ, Desjarlais JR. Prediction of amino acid sequence from structure. Protein Sci 2000;9:1106-1119.
20. Street AG, Mayo SL. Pairwise calculation of protein solvent-accessible surface areas. Fold Des 1998;3:253-258.
21. Nohaile MJ, Hendsch ZS, Tidor B, Sauer RT. Altering dimerization specificity by changes in surface electrostatics. Proc Natl Acad Sci USA 2001;98:3109-3114.
22. Wei Y, Hecht MH. Enzyme-like proteins from an unselected library of de novo sequences. Protein Engineering, Design and Selection (PEDS) 2004;17:65-75.
23. Wei Y, Liu T, Sazinsky SL, Moffet DA, Pelczer I, Hecht MH. Stably folded de novo proteins from a designed combinatorial library. Protein Sci 2003;12:92-102.
24. Kamtekar S, Schiffer JM, Xiong HY, Babik JM, Hecht MH. Protein design by binary patterning of polar and nonpolar amino-acids. Science 1993;262:1680-1685.
25. West MW, Wang WX, Patterson J, Mancias JD, Beasley JR, Hecht MH. De novo amyloid proteins from designed combinatorial libraries. Proc Natl Acad Sci USA 1999;96:11211-11216.
26. Wang W, Hecht MH. Rationally designed mutations convert de novo amyloid-like fibrils into soluble monomeric β-sheet proteins. Proc Natl Acad Sci USA 2002;99:2760-2765.
27. Dill KA. Polymer principles and protein folding. Prot Sci 1999;8: 1166-1180.
28. Baldwin RL, Rose GD. Is protein folding hierarchic?: I. Local structure and peptide folding. TIBS 1999;24:26-33.
29. Baldwin RL, Rose GD. Is protein folding hierarchic?: II. Folding intermediates and transition states. TIBS 1999;24:77-83.
30. Minor D, Kim P. Content dependent secondary structure formation of a designed peptide sequence. Nature 1996;380:730-734.
31. Némethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA. Energy parameters in polypeptides: 10. J Phys Chem 1992;96:6472-6484.
32. Klepeis JL, Floudas CA. Free energy calculations for peptides via deterministic global optimization. J Chem Phys 1999;110:7491-7512.
33. Lee J, Scheraga H, Rackovsky S. Conformational analysis of the 20-residue membrane bound portion of mellitin by conformational space annealing. Biopolymers 1998;46:103-115.
34. Gilson M, Sharp K, Honig B. Calculating electrostatic interactions in biomolecules: method and error assessment. J Comp Chem 1987;9:327-335.
35. Floudas CA. Nonlinear and mixed-integer optimization: fundamentals and applications. New York and Oxford: Oxford University Press; 1995.
36. Klepeis JL, Floudas CA, Morikis D, Lambris JD. Predicting peptide structures using NMR data and deterministic global optimization. J Comput Chem 1999;20:1354-1370.
37. Androulakis IP, Maranas CD, Floudas CA. αBB: a global optimization method for general constrained nonconvex problems. J Global Optim 1995;7:337-363.
38. Floudas CA. Deterministic global optimization: theory, methods and applications. Kluwer Academic; 2000.
39. Güntert P, Mumenthaler C, Wüthrich K. Torsion angle dynamics for NMR structure calculation with the new program dyana. J Mol Biol 1997;273:283-298.
40. Guex N, Peitsch MC. Swiss-model and the Swiss-pdbviewer: an environment for comparative protein modeling. Electrophoresis 1997;18:2714-2723.
41. Jones DT. Protein secondary structure prediction based on position specific scoring matrices. J Mol Biol 1999;292:195-202.
42. McGuffin LJ, Bryson K, Jones DT. The psipred protein structure prediction server. Bioinformatics 2000;16:404-405.
43. Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R. Combining local-structure, fold-recognition and new-fold methods for protein structure prediction. Proteins 2003;53:491-496.
44. Simons K, Kooperberg C, Huang C, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997;268:209-225.
45. Rost B, Liu JF. The prediction protein server. Nucleic Acids Res 2003;31:3300-3304.
46. McGuffin LJ, Jones DT. Targeting novel folds for structural genomics. Proteins 2002;48:44-52.
47. Rychlewski L, Fischer D, Elofsson A. Livebench-6: large scale automated evaluation of protein structure prediction servers. Proteins 2003;53:542-547.
48. Lundstrom J, Rychlewski L, Bujnicki J, Elofsson A. Pcons: a neural network based consensus predictor that improves fold recognition. Protein Sci 2001;10:2354-2362.
49. Fischer D. 3ds3 and 3ds5 3d-shotgun meta predictors in cafasp3. Proteins 2003;53:517-523.
50. Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3d-jury: a simple approach to improve protein structure predictions. Bioinformatics 2003;19:1015-1018.
51. Koehl P, Levitt M. De novo protein design: I. In search of stability and specificity. J Mol Biol 1999;293:1161-1181.
52. Skolnick J, Kolinski A, Ortiz A. Monsster: a method for folding globular proteins with a small number of distance restraints. J Mol Biol 1997;265:217-241.
53. Skolnick J, Kolinski A, Kihara D, Betancourt M, Rotkiewicz P, Boniecki M. Ab initio protein structure prediction via a combination of threading lattice folding, clustering and structure refinement. Proteins 2001;Suppl 5:149-156.
54. Eyrich V, Standley DM, Felts AK, Friesner RA. Protein tertiary structure prediction using a branch and bound algorithm. Proteins 1999;35:41-57.
55. Standley DM, Eyrich VA, Felts AK, Friesner RA, McDermott AE. A branch and bound algorithm for protein structure refinement from sparse NMR data sets. J Mol Biol 1999;285:1691-1710.
56. Nanias M, Chinchio M, Pillardy J, Ripoll DR, Scheraga HA. Packing helices in proteins by global optimization of a potential energy function. Proc Natl Acad Sci USA 2003;100:1706-1710.
57. van Gunsteren WF, Berendsen HJC. GROMOS. Groningen, the Netherlands: Groningen Molecular Simulation; 1987.
58. Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152.
59. Brooks B, Bruccoleri R, Olafson B, States D, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J Comp Chem 1983;4: 187-217.
60. Lazaridis T, Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 1999;288:477-487.