Mimicking the folding pathway to improve homology-free protein structure prediction

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 10, 2009, Pages 3734-3739

  DeBartolo, Joe ^a,b   Colubri, Andrés ^a,c   Jha, Abhishek K ^a,b,c   Fitzgerald, James E ^b,c   Freed, Karl F ^a,b,c   Sosnick, Tobin R ^a,b  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

Iterative fixing; Protein folding; Secondary structure prediction; Statistical potentials; Tertiary structure prediction

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PREDICTION; DIAGNOSTIC ACCURACY; MOLECULAR MIMICRY; MONTE CARLO METHOD; NONHUMAN; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SCORING SYSTEM; SEQUENCE HOMOLOGY; SURFACE PROPERTY; THREE DIMENSIONAL IMAGING;

ALGORITHMS; AMINO ACID SEQUENCE; MOLECULAR MIMICRY; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 62649111500     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0811363106     Document Type: Article

References (33)

1. Yooseph S, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families. PLoS Biol 5:e16.
2. Service RF (2008) Problem solved* (*sort of). Science 321:784-786.
3. Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
4. Pollastri G, Przybylski D, Rost B, Baldi P (2002) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 47:228-235.
5. Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195-202.
6. Kihara D (2005) The effect of long-range interactions on the secondary structure formation of proteins. Protein Sci 14:1955-1963.
7. Minor DL, Jr, Kim PS (1996) Context-dependent secondary structure formation of a designed protein sequence. Nature 380:730-734.
8. Alexander PA, He Y, Chen Y, Orban J, Bryan PN (2007) The design and characterization of two proteins with 88% sequence identity but different structure and function. Proc Natl Acad Sci USA 104:11963-11968.
9. Dor O, Zhou Y (2007) Achieving 80% 10-fold cross-validated accuracy for secondary structure prediction by large-scale training. Proteins 66:838-845.
10. Meiler J, Baker D (2003) Coupled prediction of protein secondary and tertiary structure. Proc Natl Acad Sci USA 100:12105-12110.
11. Yang JS, Chen WW, Skolnick J, Shakhnovich EI (2007) All-atom ab initio folding of a diverse set of proteins. Structure 15:53-63.
12. Liwo A, Khalili M, Scheraga HA (2005) Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc Natl Acad Sci USA 102:2362-2367.
13. Srinivasan R, Rose GD (1995) LINUS: A hierarchic procedure to predict the fold of a protein. Proteins 22:81-99.
14. Srinivasan R, Fleming PJ, Rose GD (2004) Ab initio protein folding using LINUS. Methods Enzymol 383:48-66.
15. Ozkan SB, Wu GA, Chodera JD, Dill KA (2007) Protein folding by zipping and assembly. Proc Natl Acad Sci USA 104:11987-11992.
16. Shen MY, Sali A (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci 15:2507-2524.
17. Eramian D, et al. (2006) A composite score for predicting errors in protein structure models. Protein Sci 15:1653-1666.
18. Colubri A, et al. (2006) Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. J Mol Biol 363:835-857.
19. Fitzgerald JE, Jha AK, Colubri A, Sosnick TR, Freed KF (2007) Reduced Cβ statistical potentials can outperform all-atom potentials in decoy identification. Protein Sci 16:2123-2139.
20. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
21. Doyle AC (1989) The Sign of the Four (Penguin Books, London).
22. Zaman MH, Shen MY, Berry RS, Freed KF, Sosnick TR (2003) Investigations into sequence and conformational dependence of backbone entropy, interbasin dynamics and the Flory isolated-pair hypothesis for peptides. J Mol Biol 331:693-711.
23. Jha AK, et al. (2005) Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. Biochemistry 44:9691-9702.
24. Jha AK, Colubri A, Freed KF, Sosnick TR (2005) Statistical coil model of the unfolded state: Resolving the reconciliation problem. Proc Natl Acad Sci USA 102:13099-13104.
25. Wu TT, Kabat EA (1973) An attempt to evaluate the influence of neighboring amino acids (n-1) and (n+1) on the backbone conformation of amino acid (n) in proteins: Use in predicting the three-dimensional structure of the polypeptide backbone of other proteins. J Mol Biol 75:13-31.
26. β statistical potentials can outperform all-atom potentials in decoy identification. Protein Sci 16:2123-2139.
27. Bradley P, Misura KM, Baker D (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309:1868-1871.
28. Bai Y, Englander SW (1996) Future directions in folding: The multi-state nature of protein structure. Proteins 24:145-151.
29. Maity H, Maity M, Krishna MM, Mayne L, Englander SW (2005) Protein folding: The stepwise assembly of foldon units. Proc Natl Acad Sci USA 102:4741-4746.
30. Krantz BA, Dothager RS, Sosnick TR (2004) Discerning the structure and energy of multiple transition states in protein folding using ψ analysis. J Mol Biol 337:463-475.
31. Sosnick TR, Krantz BA, Dothager RS, BaxaM(2006) Characterizing the protein folding transition state using ψ analysis. Chem Rev 106:1862-1876.
32. Cheng J, Randall AZ, Sweredoski MJ, Baldi P (2005) SCRATCH: A protein structure and structural feature prediction server. Nucleic Acids Res 33:W72-W76.
33. Bryson K, et al. (2005) Protein structure prediction servers at University College London. Nucleic Acids Res 33:W36-W38.