Computational protein design and large-scale assessment by I-TASSER structure assembly simulations

Journal of Molecular Biology

Volumn 407, Issue 5, 2011, Pages 764-776

  Bazzoli, Andrea ^a   Tettamanzi, Andrea G B ^b   Zhang, Yang ^a,c  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF MILAN   (Italy)

^c UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

Monte Carlo minimization; protein design; protein structure prediction; sequence clustering

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER AIDED DESIGN; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN STRUCTURE; SIMULATION;

EID: 79952738527     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.02.017     Document Type: Article

References (44)

1. Drexler, K. E. (1981). Molecular engineering: an approach to the development of general capabilities for molecular manipulation. Proc. Natl Acad. Sci. USA, 78, 5275-5278.
2. Pabo, C. (1983). Molecular technology: designing proteins and peptides. Nature, 301, 200.
3. Alvizo, O., Allen, B. D. & Mayo, S. L. (2007). Computational protein design promises to revolutionize protein engineering. Biotechniques, 42, 31-39.
4. Voigt, C. A., Gordon, D. B. & Mayo, S. L. (2000). Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design. J. Mol. Biol. 299, 789-803.
5. Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. (1953). Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087-1092.
6. Shortle, D., Simons, K. T. & Baker, D. (1998). Clustering of low-energy conformations near the native structures of small proteins. Proc. Natl Acad. Sci. USA, 95, 11158-11162.
7. Zhang, Y. & Skolnick, J. (2004). SPICKER: a clustering approach to identify near-native protein folds. J. Comput. Chem. 25, 865-871.
8. Lorenzen, S. & Zhang, Y. (2007). Identification of near-native structures by clustering protein docking conformations. Proteins, 68, 187-194. (Pubitemid 46871592)
9. Kuhlman, B., Dantas, G., Ireton, G. C., Varani, G., Stoddard, B. L. & Baker, D. (2003). Design of a novel globular protein fold with atomic-level accuracy. Science, 302, 1364-1368.
10. Kuhlman, B. & Baker, D. (2000). Native protein sequences are close to optimal for their structures. Proc. Natl Acad. Sci. USA, 97, 10383-10388.
11. Larson, S. M., Garg, A., Desjarlais, J. R. & Pande, V. S. (2003). Increased detection of structural templates using alignments of designed sequences. Proteins, 51, 390-396. (Pubitemid 36528824)
12. Saunders, C. T. & Baker, D. (2005). Recapitulation of protein family divergence using flexible backbone protein design. J. Mol. Biol. 346, 631-644.
13. Ding, F. & Dokholyan, N. V. (2006). Emergence of protein fold families through rational design. PLoS Comput. Biol. 2, e85.
14. Dill, K. A. (1990). Dominant forces in protein folding. Biochemistry, 29, 7133-7155.
15. Ventura, S. & Serrano, L. (2004). Designing proteins from the inside out. Proteins, 56, 1-10. (Pubitemid 38720833)
16. Zhang, Y. (2008). Progress and challenges in protein structure prediction. Curr. Opin. Struct. Biol. 18, 342-348.
17. Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinf. 9, 40.
18. Roy, A., Kucukural, A. & Zhang, Y. (2010). I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc. 5, 725-738.
19. Battey, J. N., Kopp, J., Bordoli, L., Read, R. J., Clarke, N. D. & Schwede, T. (2007). Automated server predictions in CASP7. Proteins, 69, 68-82. (Pubitemid 350210114)
20. Cozzetto, D., Kryshtafovych, A., Fidelis, K., Moult, J., Rost, B. & Tramontano, A. (2009). Evaluation of template-based models in CASP8 with standard measures. Proteins, 77, 18-28.
21. Guerois, R., Nielsen, J. E. & Serrano, L. (2002). Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol. 320, 369-387.
22. Krivov, G. G., Shapovalov, M. V. & Dunbrack, R. L., Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins, 77, 778-795.
23. Henikoff, S. & Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
24. Koehl, P. & Levitt, M. (1999). De novo protein design: II. Plasticity in sequence space. J. Mol. Biol. 293, 1183-1193.
25. Kyte, J. & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132.
26. Spector, S., Wang, M., Carp, S. A., Robblee, J., Hendsch, Z. S., Fairman, R. et al. (2000). Rational modification of protein stability by the mutation of charged surface residues. Biochemistry, 39, 872-879. (Pubitemid 30075313)
27. The PyMOL Molecular Graphics System, Version 0.99, Schrödinger, LLC, San Diego, CA.
28. Dahiyat, B. I. & Mayo, S. L. (1997). De novo protein design: fully automated sequence selection. Science, 278, 82-87. (Pubitemid 27446279)
29. Dobson, N., Dantas, G., Baker, D. & Varani, G. (2006). High-resolution structural validation of the computational redesign of human U1A protein. Structure, 14, 847-856.
30. Dantas, G., Corrent, C., Reichow, S. L., Havranek, J. J., Eletr, Z. M., Isern, N. G. et al. (2007). High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. J. Mol. Biol. 366, 1209-1221.
31. Zhang, Y. (2007). Template-based modeling and free modeling by I-TASSER in CASP7. Proteins, 69, 108-117.
32. Zhang, Y. (2009). I-TASSER: fully automated protein structure prediction in CASP8. Proteins, 77, 100-113.
33. Needleman, S. B. & Wunsch, C. D. (1970). A general method applicable to search for similarities in amino acid sequence of 2 proteins. J. Mol. Biol. 48, 443-453.
34. Canutescu, A. A., Shelenkov, A. A. & Dunbrack, R. L. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 12, 2001-2014. (Pubitemid 37022822)
35. Bonneau, R., Tsai, J., Ruczinski, I., Chivian, D., Rohl, C., Strauss, C. E. M. & Baker, D. (2001). Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins, 45, 119-126.
36. Wu, S., Skolnick, J. & Zhang, Y. (2007). Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol. 5, 17.
37. Wu, S. & Zhang, Y. (2008). MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins, 72, 547-556. (Pubitemid 351928511)
38. Zhang, Y., Kihara, D. & Skolnick, J. (2002). Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins, 48, 192-201. (Pubitemid 34743409)
39. Zhang, Y., Arakaki, A. K. & Skolnick, J. (2005). TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins, 61, 91-98. (Pubitemid 43069961)
40. Zhang, Y. & Skolnick, J. (2005). TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 33, 2302-2309. (Pubitemid 41439897)
41. Li, Y. & Zhang, Y. (2009). REMO: a new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins, 76, 665-676.
42. Wang, G. L. & Dunbrack, R. L. (2005). PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res. 33, W94-W98.
43. Rost, B. & Sander, C. (1994). Conservation and prediction of solvent accessibility in protein families. Proteins, 20, 216-226. (Pubitemid 24378913)
44. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.