Lessons from application of the UNRES force field to predictions of structures of CASP10 targets

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

Volumn 110, Issue 37, 2013, Pages 14936-14941

  He, Yi ^a   Mozolewska, Magdalena A ^a,b   Krupa, Paweł ^a,b   Sieradzan, Adam K ^b   Wirecki, Tomasz K ^a,b   Liwo, Adam ^b   Kachlishvili, Khatuna ^a   Rackovsky, Shalom ^a,c   Jagieła, Dawid ^b   Ślusarz, Rafał ^b   Czaplewski, Cezary R ^b   Ołdziej, Stanisław ^b   Scheraga, Harold A ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF GDA SK   (Poland)

^c MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

Multi domain packing; Protein folding; Structure symmetry

Indexed keywords

POLYPEPTIDE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CRITICAL ASSESSMENT OF TECHNIQUE FOR PROTEIN STRUCTURE PREDICTION; HUMAN; KNOWLEDGE; KNOWLEDGE BASE; LABORATORY TEST; MOLECULAR DYNAMICS; PHYSICS; PREDICTION; PREDICTIVE VALUE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEIN TARGETING; SIMULATION; STRUCTURAL BIOINFORMATICS; UNITED RESIDUE FORCE FIELD;

MULTI-DOMAIN PACKING; PROTEIN FOLDING; STRUCTURE SYMMETRY;

BIOPHYSICAL PHENOMENA; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEINS;

EID: 84883816396     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1313316110     Document Type: Article

References (50)

1. Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181(4096):223-230.
2. Tramontano A (2005) The Ten Most Wanted Solutions in Protein Bioinformatics (CRC, London), pp 69-88.
3. Warme PK, Momany FA, Rumball SV, Tuttle RW, Scheraga HA (1974) Computation of structures of homologous proteins. α-lactalbumin from lysozyme. Biochemistry 13(4): 768-782.
4. Jones TA, Thirup S (1986) Using known substructures in protein model building and crystallography. EMBO J 5(4):819-822.
5. Zhang Y (2008) Progress and challenges in protein structure prediction. Curr Opin Struct Biol 18(3):342-348.
6. Jones D, Thornton J (1993) Protein fold recognition. J Comput Aided Mol Des 7(4): 439-456.
7. Miller RT, Jones DT, Thornton JM (1996) Protein fold recognition by sequence threading: Tools and assessment techniques. FASEB J 10(1):171- 178.
8. Mirny LA, Shakhnovich EI (1998) Protein structure prediction by threading. Why it works and why it does not. J Mol Biol 283(2):507-526. (Pubitemid 28470425)
9. Bonneau R, et al. (2001) Rosetta in CASP4: Progress in ab initio protein structure prediction. Proteins (Suppl 5):119-126. (Pubitemid 34113174)
10. Rohl CA, Strauss CEM, Misura KMS, Baker D (2004) Protein structure prediction using Rosetta. Methods Enzymol 383:66-93. (Pubitemid 38401787)
11. Skolnick J, Kolinski A, Ortiz AR (1997) MONSSTER: A method for folding globular proteins with a small number of distance restraints. J Mol Biol 265(2):217-241. (Pubitemid 27110659)
12. Misura KM, Chivian D, Rohl CA, Kim DE, Baker D (2006) Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci USA 103(14):5361-5366.
13. Zhang Y, Kolinski A, Skolnick J (2003) TOUCHSTONE II: A new approach to ab initio protein structure prediction. Biophys J 85(2):1145-1164. (Pubitemid 36909676)
14. Zhang Y, Skolnick J (2005) The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci USA 102(4):1029-1034. (Pubitemid 40170720)
15. Jones DT (2001) Predicting novel protein folds by using FRAGFOLD. Proteins (Suppl 5): 127-132.
16. Grishin NV (2012) Predictive landscape of casp. 10th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction. Available at www. predictioncenter.org/casp10/docs.cgi?view= presentations. Accessed August 6, 2013.
17. He YA, Chen YH, Alexander PA, Bryan PN, Orban J (2012) Mutational tipping points for switching protein folds and functions. Structure 20(2):283-291.
18. Liwo A, Lee J, Ripoll DR, Pillardy J, Scheraga HA (1999) Protein structure prediction by global optimization of a potential energy function. Proc Natl Acad Sci USA 96(10): 5482-5485. (Pubitemid 29234643)
19. O?dziej S, et al. (2005) Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests. Proc Natl Acad Sci USA 102(21):7547-7552.
20. Pande VS, et al. (2003) Atomistic protein folding simulations on the submilli-second time scale using worldwide distributed computing. Biopolymers 68(1):91-109. (Pubitemid 36098310)
21. Friedrichs MS, et al. (2009) Accelerating molecular dynamic simulation on graphics processing units. J Comput Chem 30(6):864-872.
22. Shaw DE, et al. (2008) Anton, a special-purpose machine for molecular dynamics simulation. Commun ACM 51:91-97.
23. Kolinski A, Gront D, Pokarowski P, Skolnick J (2003) A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition. Biopolymers 69(3): 399-405. (Pubitemid 36841403)
24. Tozzini V (2005) Coarse-grained models for proteins. Curr Opin Struct Biol 15(2): 144-150.
25. Czaplewski C, Liwo A, Makowski M, O?dziej S, Scheraga HA (2010) Multiscale Approaches to Protein Modeling, ed Koliński A (Springer, Berlin), pp 35-83.
26. Khalili M, Liwo A, Jagielska A, Scheraga HA (2005) Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model α-helical systems. J Phys Chem B 109(28):13798-13810. (Pubitemid 41083972)
27. Liwo A, Czaplewski C, Pillardy J, Scheraga HA (2001) Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field. J Chem Phys 115:2323-2347. (Pubitemid 32742790)
28. Liwo A, et al. (2007) Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins. J Phys Chem B 111(1):260-285. (Pubitemid 46277990)
29. Liwo A, et al. (2008) Coarse-Graining of Condensed Phase and Biomolecular Systems, ed Voth GA (CRC, Boca Raton, FL) pp 107-122.
30. Koz?owska U, Maisuradze GG, Liwo A, Scheraga HA (2010) Determination of side-chain- rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field. J Comput Chem 31(6):1154-1167.
31. Hansmann UHE (1997) Parallel tempering algorithm for conformational studies of biological molecules. Chem Phys Lett 281:140-150.
32. Nanias M, Czaplewski C, Scheraga HA (2006) Replica exchange and multicanonical algorithms with the coarse-grained UNRES force field. J Chem Theory Comput 2(3): 513-528.
33. Czaplewski C, Kalinowski S, Liwo A, Scheraga HA (2009) Application of multiplexing replica exchange molecular dynamics method to the UNRES force field: Tests with alpha and alpha+beta proteins. J Chem Theory Comput 5:627-640.
34. Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J Comput Chem 13:1011-1021.
35. Späth H (1980) Cluster Analysis Algorithms (Halsted Press, New York).
36. Liwo A, et al. (2010) Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards milli-second-scale simulations of protein structure, dynamics, and thermodynamics. J Chem Theory Comput 6(3):890-909.
37. Liwo A, He Y, Scheraga HA (2011) Coarse-grained force field: General folding theory. Phys Chem Chem Phys 13(38):16890-16901.
38. Lee J, et al. (2000) Hierarchical energy-based approach to protein-structure prediction; blind-test evaluation with casp3 targets. Int J Quantum Chem 77:90-117.
39. Pillardy J, et al. (2001) Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proc Natl Acad Sci USA 98(5): 2329-2333. (Pubitemid 32209482)
40. Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25(17):3389-3402. (Pubitemid 27359211)
41. Taylor TJ, Bai H, Tai CH, Lee BK (2013) Score functions to evaluate casp10 predictions for free-modeling targets. Prot Struct Funct Bioinf 81(Suppl 11).
42. Lee BK (2012) Template free modeling assessment in casp10. 10th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction. Available at www.predictioncenter.org/casp10/docs.cgi?view= presentations. Accessed August 6, 2013.
43. Makowski M, et al. (2008) Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains. J Phys Chem B 112(36):11385-11395.
44. Makowski M, Liwo A, Scheraga HA (2011) Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains. J Phys Chem B 115(19):6130-6137.
45. KhaliliM, Liwo A, Rakowski F, Grochowski P, Scheraga HA (2005) Molecular dynamics with the united-residuemodel of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode. J Phys Chem B 109(28):13785-13797. (Pubitemid 41083971)
46. Kaźmierkiewicz R, Liwo A, Scheraga HA (2002) Energy-based reconstruction of a protein backbone from its α-carbon trace by a Monte-Carlo method. J Comput Chem 23(7):715-723. (Pubitemid 34504567)
47. Kaźmierkiewicz R, Liwo A, Scheraga HA (2003) Addition of side chains to a known backbone with defined side-chain centroids. Biophys Chem 100(1-3):261-280, and erratum. (2003) 106(1):91.
48. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-3690.
49. Rakowski F, Grochowski P, Lesyng B, Liwo A, Scheraga HA (2006) Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function. J Chem Phys 125(20):204107.
50. McGuffin LJ, Bryson K, Jones DT (2000) The PSIPRED protein structure prediction server. Bioinformatics 16(4):404-405. (Pubitemid 30417087)