Protein NMR structures refined without NOE data

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Ryu, Hyojung ^a,b   Kim, Tae Rae ^c   Ahn, SeonJoo ^a   Ji, Sunyoung ^a,b   Lee, Jinhyuk ^a,b  

^a Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^b University of Science and Technology (UST)   (South Korea)

^c Seoul National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DATA ANALYSIS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PROTEIN DATA BANK; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SIMULATION; STRUCTURE ANALYSIS; X RAY; CHEMICAL STRUCTURE; CHEMISTRY; PROCEDURES; PROTEIN CONFORMATION; PROTEIN DATABASE; X RAY CRYSTALLOGRAPHY;

PROTEIN;

CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS;

EID: 84953343055     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0108888     Document Type: Article

References (47)

1. Zhang Y (2009) Protein structure prediction: when is it useful? Curr Opin Struct Biol 19: 145-155.
2. Chopra G, Summa CM, Levitt M (2008) Solvent dramatically affects protein structure refinement. Proc Natl Acad Sci U S A 105: 20239-20244.
3. Qian B, Raman S, Das R, Bradley P, McCoy AJ, et al. (2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450: 259-264.
4. Baker D, Sali A (2001) Protein structure prediction and structural genomics. Science 294: 93-96.
5. Jagielska A, Wroblewska L, Skolnick J (2008) Protein model refinement using an optimized physics-based all-atom force field. Proc Natl Acad Sci U S A 105: 8268-8273.
6. Nugent T, Cozzetto D, Jones DT (2013) Evaluation of predictions in the CASP10 model refinement category. Proteins.
7. Kim TR, Yang JS, Shin S, Lee J (2013) Statistical torsion angle potential energy functions for protein structure modeling: A bicubic interpolation approach. Proteins 81: 1156-1165.
8. Chopra G, Kalisman N, Levitt M (2010) Consistent refinement of submitted models at CASP using a knowledge-based potential. Proteins 78: 2668-2678.
9. Lu H, Skolnick J (2003) Application of statistical potentials to protein structure refinement from low resolution ab initio models. Biopolymers 70: 575-584.
10. Zhu J, Fan H, Periole X, Honig B, Mark AE (2008) Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins 72: 1171-1188.
11. Summa CM, Levitt M (2007) Near-native structure refinement using in vacuo energy minimization. Proc Natl Acad Sci U S A 104: 3177-3182.
12. Lin MS, Head-Gordon T (2011) Reliable protein structure refinement using a physical energy function. J Comput Chem 32: 709-717.
13. Chen J, Im W, Brooks CL 3rd (2004) Refinement of NMR structures using implicit solvent and advanced sampling techniques. J Am Chem Soc 126: 16038-16047.
14. Chen J, Won HS, Im W, Dyson HJ, Brooks CL 3rd (2005) Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. J Biomol NMR 31: 59-64.
15. Chen J, Brooks CL 3rd (2007) Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins 67: 922-930.
16. Chen J, Brooks CL 3rd, Khandogin J (2008) Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol 18: 140-148.
17. Linge JP, Williams MA, Spronk CA, Bonvin AM, Nilges M (2003) Refinement of protein structures in explicit solvent. Proteins 50: 496-506.
18. Lee MR, Tsai J, Baker D, Kollman PA (2001) Molecular dynamics in the endgame of protein structure prediction. J Mol Biol 313: 417-430.
19. Schlitter J, Engels M, Kruger P (1994) Targeted molecular dynamics: a new approach for searching pathways of conformational transitions. J Mol Graph 12: 84-89.
20. Isralewitz B, Baudry J, Gullingsrud J, Kosztin D, Schulten K (2001) Steered molecular dynamics investigations of protein function. J Mol Graph Model 19: 13-25.
21. Hamelberg D, Mongan J, McCammon JA (2004) Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys 120: 11919-11929.
22. Melnik BS, Garbuzynskiy SO, Lobanov MY, Galzitskaya OV (2005) The difference between protein structures obtained by x-ray analysis and nuclear magnetic resonance. Molecular Biology.
23. Clore GM, Gronenborn AM (1998) New methods of structure refinement for macromolecular structure determination by NMR. Proc Natl Acad Sci U S A 95: 5891-5898.
24. Nabuurs SB, Nederveen AJ, Vranken W, Doreleijers JF, Bonvin AM, et al. (2004) DRESS: a database of REfined solution NMR structures. Proteins 55: 483-486.
25. Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CA, et al. (2005) RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins 59: 662-672.
26. Yang JS, Kim JH, Oh S, Han G, Lee S, et al. (2012) STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures. Nucleic Acids Res 40: D525-530.
27. Mao B, Tejero R, Baker D, Montelione GT (2014) Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures. J Am Chem Soc 136: 1893-1906.
28. Nilges M (1997) Ambiguous distance data in the calculation of NMR structures. Fold Des 2: S53-57.
29. Clore GM, Nilges M, Sukumaran DK, Brunger AT, Karplus M, et al. (1986) The three-dimensional structure of alpha1-purothionin in solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics. EMBO J 5: 2729-2735.
30. MacKerell AD Jr, Bashford B, Dunbrack RL, Evanseck JD, Field MJ, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B.
31. Lazaridis T, Karplus M (1999) Effective energy function for proteins in solution. Proteins 35: 133-152.
32. Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, et al. (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30: 1545-1614.
33. Zhang Y, Skolnick J (2004) Scoring function for automated assessment of protein structure template quality. Proteins 57: 702-710.
34. Doreleijers JF, Raves ML, Rullmann T, Kaptein R (1999) Completeness of NOEs in protein structure: a statistical analysis of NMR. J Biomol NMR 14: 123-132.
35. Chen H, Kihara D (2008) Estimating quality of template-based protein models by alignment stability. Proteins 71: 1255-1274.
36. Yang Y, Zhou Y (2008) Specific interactions for ab initio folding of protein terminal regions with secondary structures. Proteins 72: 793-803.
37. Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, et al. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35: W375-383.
38. Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8: 477-486.
39. Hooft RW, Vriend G, Sander C, Abola EE (1996) Errors in protein structures. Nature 381: 272.
40. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, et al. (2008) BioMagResBank. Nucleic Acids Res 36: D402-408.
41. Kim TR, Oh S, Yang JS, Lee S, Shin S, et al. (2012) A simplified homology-model builder toward highly protein-like structures: an inspection of restraining potentials. J Comput Chem 33: 1927-1935.
42. Ramelot TA, Raman S, Kuzin AP, Xiao R, Ma LC, et al. (2009) Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. Proteins 75: 147-167.
43. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
44. Bruünger AT (1992) X-PLOR, Version 3.1: a system for X-ray crystallography and NMR. New Haven: Yale University Press. xvii, 382 p.
45. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, et al. (2005) The Amber biomolecular simulation programs. J Comput Chem 26: 1668-1688.
46. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54: 905-921.
47. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612.