Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD

Journal of Chemical Information and Modeling

Volumn 56, Issue 7, 2016, Pages 1304-1312

  Feig, Michael ^a,b  

^a Michigan State University   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; PROTEINS;

ASSESSMENT CRITERIA; COMPUTATIONAL MODEL; HIGH RESOLUTION; LOCAL PROTEIN STRUCTURES; LOCAL REFINEMENT; MOLECULAR DYNAMICS SIMULATIONS; PROTEIN STRUCTURES; TORSION ANGLE;

MOLECULAR DYNAMICS;

PROTEIN;

CHEMISTRY; INTERNET; MOLECULAR DYNAMICS; PROTEIN CONFORMATION;

INTERNET; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEINS;

EID: 84979502166     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.6b00222     Document Type: Article

References (37)

1. Drenth, J. Principles of Protein X-ray Crystallography; Springer: New York, 2007.
2. Wuthrich, K. Protein Structure Determination in Solution by NMR-Spectroscopy J. Biol. Chem. 1990, 265, 22059-22062
3. Kühlbrandt, W. Cryo-EM Enters a New Era eLife 2014, 3, e03678 10.7554/eLife.03678
4. Westbrook, J.; Feng, Z. K.; Chen, L.; Yang, H. W.; Berman, H. M. The Protein Data Bank and Structural Genomics Nucleic Acids Res. 2003, 31, 489-491 10.1093/nar/gkg068
5. Baker, D.; Sali, A. Protein Structure Prediction and Structural Genomics Science 2001, 294, 93-96 10.1126/science.1065659
6. Sali, A.; Blundell, T. L. Comparative Protein Modelling by Satisfaction of Spatial Restraints J. Mol. Biol. 1993, 234, 779-815 10.1006/jmbi.1993.1626
7. Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Shaw, D. E. How Fast-Folding Proteins Fold Science 2011, 334, 517-520 10.1126/science.1208351
8. Osguthorpe, D. J. Ab initio Protein Folding Curr. Opin. Struct. Biol. 2000, 10, 146-152 10.1016/S0959-440X(00)00067-1
9. Kryshtafovych, A.; Fidelis, K.; Moult, J. CASP10 Results Compared to Those of Previous CASP Experiments Proteins: Struct., Funct., Genet. 2014, 82, 164-174 10.1002/prot.24448
10. Eisenberg, D.; Luthy, R.; Bowie, J. U. VERIFY3D: Assessment of Protein Models with Three-Dimensional Profiles Methods Enzymol. 1997, 277, 396-404 10.1016/S0076-6879(97)77022-8
11. Wiederstein, M.; Sippl, M. J. ProSA-web: Interactive Web Service for the Recognition of Errors in Three-Dimensional Structures of Proteins Nucleic Acids Res. 2007, 35, W407-W410 10.1093/nar/gkm290
12. Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. PROCHECK: A Program to Check the Stereochemical Quality of Protein Structures J. Appl. Crystallogr. 1993, 26, 283-291 10.1107/S0021889892009944
13. Chen, V. B.; Arendall, W. B.; Headd, J. J.; Keedy, D. A.; Immormino, R. M.; Kapral, G. J.; Murray, L. W.; Richardson, J. S.; Richardson, D. C. MolProbity: All-Atom Structure Validation for Macromolecular Crystallography Acta Crystallogr., Sect. D: Biol. Crystallogr. 2010, 66, 12-21 10.1107/S0907444909042073
14. CASP11 Web Site. http://www.predictioncenter.org/casp11/index.cgi (accessed May 27, 2016),.
15. Zemla, A.; Venclovas, C.; Moult, J.; Fidelis, K. Processing and Analysis of CASP3 Protein Structure Predictions Proteins: Struct., Funct., Genet. 1999, 37, 22-29 10.1002/(SICI)1097-0134(1999)37:3+<22::AID-PROT5>3.0.CO;2-W
16. Mirjalili, V.; Feig, M. Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles J. Chem. Theory Comput. 2013, 9, 1294-1303 10.1021/ct300962x
17. Mirjalili, V.; Noyes, K.; Feig, M. Physics-Based Protein Structure Refinement through Multiple Molecular Dynamics Trajectories and Structure Averaging Proteins: Struct., Funct., Genet. 2014, 82, 196-207 10.1002/prot.24336
18. Headd, J. J.; Immormino, R. M.; Keedy, D. A.; Emsley, P.; Richardson, D. C.; Richardson, J. S. Autofix for Backward-Fit Sidechains: Using MolProbity and Real-Space Refinement to Put Misfits in Their Place J. Struct. Funct. Genomics 2009, 10, 83-93 10.1007/s10969-008-9045-8
19. Heo, L.; Park, H.; Seok, C. GalaxyRefine: Protein Structure Refinement Driven by Side-Chain Repacking Nucleic Acids Res. 2013, 41, W384-W388 10.1093/nar/gkt458
20. Ryu, H.; Kim, T.-R.; Ahn, S.; Ji, S.; Lee, J. Protein NMR Structures Refined wtihout NOE Data PLoS One 2014, 9, e108888 10.1371/journal.pone.0108888
21. Feig, M.; Mirjalili, V. Protein Structure Refinement via Molecular-Dynamics Simulations: What Works and What Does Not? Proteins: Struct., Funct., Genet. 2015, 10.1002/prot.24871
22. Feig, M.; Karanicolas, J.; Brooks, C. L., III MMTSB Tool Set: Enhanced Sampling and Multiscale Modeling Methods for Applications in Structural Biology J. Mol. Graphics Modell. 2004, 22, 377-395 10.1016/j.jmgm.2003.12.005
23. Feig, M.; Rotkiewicz, P.; Kolinski, A.; Skolnick, J.; Brooks, C. L. I. Accurate Reconstruction of All-Atom Protein Representations From Side-Chain-Based Low-Resolution Models Proteins: Struct., Funct., Genet. 2000, 41, 86-97 10.1002/1097-0134(20001001)41:1<86::AID-PROT110>3.3.CO;2-P
24. Bower, M. J.; Cohen, F. E.; Dunbrack, R. L. Prediction of Protein Side-chain Rotamers from a Backbone-dependent Rotamer Library: A New Homology Modeling Tool J. Mol. Biol. 1997, 267, 1268-1282 10.1006/jmbi.1997.0926
25. Krivov, G. G.; Shapovalov, M. V.; Dunbrack, R. L. Improved Prediction of Protein Side-Chain Conformations with SCWRL4 Proteins: Struct., Funct., Genet. 2009, 77, 778-795 10.1002/prot.22488
26. Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: The Biomolecular Simulation Program J. Comput. Chem. 2009, 30, 1545-1614 10.1002/jcc.21287
27. Jabs, A.; Weiss, M. S.; Hilgenfeld, R. Non-Proline cis Peptide Bonds in Proteins J. Mol. Biol. 1999, 286, 291-304 10.1006/jmbi.1998.2459
28. Feig, M.; Harada, R.; Mori, T.; Yu, I.; Takahashi, K.; Sugita, Y. Complete Atomistic Model of a Bacterial Cytoplasm Integrates Physics, Biochemistry, and Systems Biology J. Mol. Graphics Modell. 2015, 58, 1-9 10.1016/j.jmgm.2015.02.004
29. Best, R. B.; Zhu, X.; Shim, J.; Lopes, P.; Mittal, J.; Feig, M.; MacKerell, A. D., Jr Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone , and Side-Chain 1 and 2 Dihedral Angles J. Chem. Theory Comput. 2012, 8, 3257-3273 10.1021/ct300400x
30. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical-Integration of Cartesian Equations of Motion of a System with Constraints-Molecular-Dynamics of N-Alkanes J. Comput. Phys. 1977, 23, 327-341 10.1016/0021-9991(77)90098-5
31. locPREFMD Web Service. http://feig.bch.msu.edu/web/services/locprefmd/ (accessed May 27, 2016).
32. Zhang, Y.; Skolnick, J. Scoring Function for Automated Assessment of Protein Structure Template Quality Proteins: Struct., Funct., Genet. 2007, 68, 1020-1020 10.1002/prot.21643
33. Zhang, Y.; Skolnick, J. Scoring Function for Automated Assessment of Protein Structure Template Quality Proteins: Struct., Funct., Genet. 2004, 57, 702-710 10.1002/prot.20264
34. Engh, R. A.; Huber, R. Accurate Bond and Angle Parameters for X-Ray Protein-Structure Refinement Acta Crystallogr., Sect. A: Found. Crystallogr. 1991, 47, 392-400 10.1107/S0108767391001071
35. Feig, M.; MacKerell, A. D., Jr.; Brooks, C. L., III Force Field Influence on the Observation of -Helical Protein Structures in Molecular Dynamics Simulations J. Phys. Chem. B 2003, 107, 2831-2836 10.1021/jp027293y
36. MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III Improved Treatment of the Protein Backbone in Empirical Force Fields J. Am. Chem. Soc. 2004, 126, 698-699 10.1021/ja036959e
37. MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III Extending the Treatment of Backbone Energetics in Protein Force Fields: Limitations of Gas-Phase Quantum Mechanics in Reproducing Protein Conformational Distributions in Molecular Dynamics Simulations J. Comput. Chem. 2004, 25, 1400-1415 10.1002/jcc.20065