Refinement of protein termini in template-based modeling using conformational space annealing

Proteins: Structure, Function and Bioinformatics

Volumn 79, Issue 9, 2011, Pages 2725-2734

  Park, Hahnbeom ^a   Ko, Junsu ^a   Joo, Keehyoung ^b   Lee, Julian ^c   Seok, Chaok ^a   Lee, Jooyoung ^b  

^a Seoul National University   (South Korea)

^b Korea Institute for Advanced Study   (South Korea)

^c Soongsil University   (South Korea)

Author keywords

CASP; Fragment assembly; Protein structure prediction; Protein structure refinement; Protein terminus modeling

Indexed keywords

CASPASE 8; PROTEIN;

ARTICLE; ENERGY; MOLECULAR DOCKING; MOLECULAR MODEL; PHYSICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; PROTEIN TERMINUS MODELING; WEIGHT;

COMPUTATIONAL BIOLOGY; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS;

EID: 80051556272     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23101     Document Type: Article

References (43)

1. Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D. High-resolution structure prediction and the crystallographic phase problem. Nature 2007; 450: 259-264.
2. Keedy DA, Williams CJ, Headd JJ, Arendall WBIII, Chen VB, Kapral GJ, Gillespie RA, Block JN, Zemla A, Richardson DC, Richardson JS. The other 90% of the protein: assessment beyond the Cαs for CASP8 template-based and high-accuracy models. Proteins 2009; 77: 29-49.
3. Kopp J, Borddoli L, Battey JN, Kiefer F, Schwede T. Assessment of CASP7 predictions for template-based modeling targets. Proteins 2007; 69: 38-56.
4. MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA. Assessment of the protein-structure refinement category in CASP8. Proteins 2009; 77: 66-80.
5. Feig M, Rotkiewwicz P, Kolinski A, Skolnick J, Brooks CL, III. Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models. Proteins 2000; 41: 86-97.
6. Krivov GG, Shapovalov MV, Dunbrack RL, Jr. Improved prediction of protein side-chain conformations with SCWRL4. Proteins 2009; 77: 778-795.
7. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. Comparative protein structure modeling using MODELLER. Curr Protoc Bioinformatics 2006; 5.6: 1-30.
8. Summa CM, Levitt M. Near-native structure refinement using in vacuo energy minimization. Proc Natl Acad Sci USA 2007; 104: 3177-3182.
9. Chopra G, Kalisman N, Levitt M. Consistent refinement of submitted models at CASP using a knowledge-based potential. Proteins 2010; 78: 2668-2678.
10. Fan H, Mark AE. Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sci 2004; 13: 211-220.
11. Flohil JA, Vriend G, Berendsen HJC. Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 11 in the CASP modeling competition and posterior analysis. Proteins 2002; 48: 593-604.
12. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008; 9: 40.
13. Zhang Y. I-TASSER: fully automated protein structure prediction in CASP8. Proteins 2009; 77: 100-113.
14. Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim B-H, Das R, Grishin NV, Baker D. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins 2009; 77: 89-99.
15. Rohl CA, Strauss CEM, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with Rosetta. Proteins 2004; 55: 656-677.
16. Soto CS, Fasnacht M, Zhu J, Forrest L, Honig B. Loop modeling: sampling, filtering and scoring. Proteins 2008; 70: 834-843.
17. Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins 2004; 55: 351-367.
18. Joo K, Lee J, Seo JH, Lee K, Kim BG, Lee J. All-atom chain-building by optimizing MODELLER energy function using conformational space annealing. Proteins 2009; 75: 1010-1023.
19. Polevoda B, Sherman F. N-terminal acetyltransferases and sequence requirements for N-terminal acetylation of eukaryotic proteins. J Mol Biol 2003; 325: 595-622.
20. Chung JJ, Shikano S, Hanyu Y, Li M. Functional diversity of protein C-termini: more than zipcoding? Trends Cell Biol 2002; 12: 146-150.
21. Lee J, Liwo A, Scheraga HA. Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and apo calbindin d9k. Proc Natl Acad Sci USA 1999; 96: 2025-2030.
22. Cozzetto D, Kryshtafovych A, Krzysztof F, Moult J, Rost B, Tramontano A. Evaluation of template-based models in CASP8 with standard measures. Proteins 2009; 77: 18-28.
23. Wallner B, Elofsson A. Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci 2006; 15: 900-913.
24. Wang Z, Eickholt J, Cheng J. MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8. Bioinformatics 2010; 26: 882-888.
25. Sali A, Blundell T. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993; 234: 779-815.
26. MacKerell AD, Jr, Bashford D, Bellott M, Dunbrack RL, Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WEIII, Roux B, Schienkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 2002; 102: 3586-3616.
27. Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002; 11: 2714-2726.
28. Yang Y, Zhou Y. Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely-related all-atom statistical energy functions. Protein Sci 2008; 17: 1212-1219.
29. Yang Y, Zhou Y. Specific interactions for ab initio folding of protein termini with secondary structures. Proteins 2008; 72: 793-803.
30. Zhu J, Xie L, Honig B. Structural refinement of protein segments containing secondary structure elements: local sampling, knowledge-based potentials and clustering. Proteins 2006; 65: 463-479.
31. Zhou Y, Zhou H, Zhang C, Liu S. What is a desirable statistical energy function for proteins and how can it be obtained? Cell Biochem Biophys 2006; 46: 165-174.
32. Shen M, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci 2006; 15: 2507-2525.
33. Sasaki TN, Cetin H, Sasai M. A coarse-grained Langevin molecular dynamics approach to de novo protein structure prediction. Biochem Biophys Res Commun 2008; 369: 500-506.
34. Zhang Y, Kolinski A, Skolnick J. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 2003; 85: 1145-1164.
35. Rohl CA, Strauss CEM, Misura KMS, Baker D. Proteins structure prediction using Rosetta. Methods Enzymol 2004; 383: 66-93.
36. Lee J, Lee D, Park H, Coutsias EA, Seok C. Protein loop modeling by using fragment assembly and analytical loop closure. Proteins 2010; 78: 3426-3436.
37. Liu D, Nocedal J. On the limited memory BFGS method for large scale optimization. Math Programming B 1989; 45: 503-528.
38. Press WH. Numerical recipes, 2nd ed. Cambridge: Cambridge University Press; 1992.
39. Wang G, Dunbrack RL, Jr. PISCES: a protein sequence culling server. Bioinformatics 2003; 19: 1589-1591.
40. Joo K, Lee J, Lee S, Seo JH, Lee SJ, Lee J. High accuracy template based modeling by global optimization. Proteins 2007; 69: 83-89.
41. Joo K, Lee J, Kim I, Lee SJ, Lee J. Multiple sequence alignment by conformational space annealing. Biophys J 2008; 95: 4813-4819.
42. 2B-domain: synaptotagmin 1 as a phospholipid binding machine. Neuron 2001; 32: 1057-1069.
43. Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004; 57: 702-710.