Refinement of protein structures in explicit solvent

Proteins: Structure, Function and Genetics

Volumn 50, Issue 3, 2003, Pages 496-506

  Linge, Jens P ^a   Williams, Mark A ^b   Spronk, Christian A E M ^c   Bonvin, Alexandre M J J ^d   Nilges, Michael ^a  

^a INSTITUT PASTEUR   (France)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^d UTRECHT UNIVERSITY   (Netherlands)

Author keywords

Dihedral angle; Force field; Molecular dynamics; NMR; Omega angle; Protein structure; Validation; Water refinement

Indexed keywords

CRAMBIN; DIMETHYL SULFOXIDE; INTERLEUKIN 4; PROTEIN; SOLVENT; UBIQUITIN; UNCLASSIFIED DRUG; WATER;

ARTICLE; CALCULATION; COMPUTER PROGRAM; COVALENT BOND; ENERGY; MOLECULAR DYNAMICS; MOLECULAR WEIGHT; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; VALIDATION PROCESS;

DIMETHYL SULFOXIDE; INTERLEUKIN-4; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PLANT PROTEINS; PROTEINS; SOLVENTS; UBIQUITIN; WATER;

EID: 0037441524     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10299     Document Type: Article

References (42)

1. Linge JP, Nilges M. Influence of non-bonded parameters on the quality of NMR structures: a new force-field for NMR structure calculation. J Biomol NMR 1999;13:51-59.
2. Spronk CA, Linge JP, Hilbers CW, Vuister GW. Improving the quality of protein structures derived by NMR spectroscopy. J Biomol NMR 2002;22:281-289.
3. Xia B, Tsui V, Case DA, Dyson HJ, Wright PE. Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water. J Biomol NMR 2002;22:317-331.
4. Engh RA, Huber R. Accurate bond and angle parameters for X-ray structure refinement. Acta Crystallogr A 1991;47:392-400.
5. Jorgensen WI, Tirado-Rives J. The OPLS potential function for proteins. Energy minimization for crystals of cyclic peptides and crambin. J Am Chem Soc 1988;110:1657-1666.
6. Hooft RW, Vriend G, Sander C, Abola EE. Errors in protein structures. Nature 1996;381:272.
7. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PRO-CHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993;26:283-291.
8. Oldfield TJ. SQUID: a program for the analysis and display of data from crystallography and molecular dynamics. J Mol Graph 1992;10:247-252.
9. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, 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, Reiber WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watan-abe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998;102:3586-3616.
10. Powers R, Garrett DS, March CJ, Frieden EA, Gronenborn AM, Clore GM. Three-dimensional solution structure of human interleukin-4 determined by multidimensional heteronuclear magnetic resonance spectroscopy. Science 1992;19:1673-1677.
11. Linge JP, Habeck H, Rieping W, Nilges M. ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics 2003. In Press.
12. Walter MR, Cook WJ, Zhao BG, Cameron RP, Ealick SE, Walter RL, Reichert P, Nagabhushan TL, Trotta PP, Bugg CE. Crystal structure of recombinant human interleukin-4. J Biol Chem 1992;267:20371-20376.
13. Wlodawer A, Pavlovsky A, Gustchina A. Crystal structure of human recombinant human interleukin-4 at 2.25 Å resolution. FEBS Lett 1992;309:59-64.
14. Cornilescu G, Marquardt JL, Ottiger M, Bax A. Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc 1998;120:6836-6837.
15. Vijay-Kumar S, Bugg CE, Cook WJ. Structure of ubiquitin refined at 1.8 Å resolution. J Mol Biol 1987;194:531-544.
16. Jelsch C, Teeter MM, Lamzin V, Pichon-Pesme V, Blessing RH, Lecomte C. Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin. Proc Natl Acad Sci USA 2000;97:3171-3176.
17. Hendrickson WA. Stereochemically restrained refinement of macromolecular structures. Meth Enzymol 1985;115:252-270.
18. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
19. Liu H, Müller-Plathe F, van Gunsteren WF. A molecular dynamics simulation study with a combined quantum mechanical and molecular mechanical potential energy function: solvent effects on the conformational equilibrium of dimethoxyethane. J Chem Phys 1995;102:1722-1730.
20. Doreleijers JF, Rullmann JA, Kaptein R. Quality assessment of NMR structures: a statistical survey. J Mol Biol 1998;281:149-164.
21. Allen FHS, Brice MD, Cartwright BA, Doubleday A, Higgs H, Hummelink T, Hummelink-Peters BG, Kennard O, Mother-well WDS, Rodgers JR, Watson DG. The Cambridge Crystallographic Data Centre: computer-based search, retrieval analysis and display of information. Acta Crystallogr B 1979;35:2331-2339.
22. Smith LJ, Bolin KA, Schwalbe H, MacArthur MW, Thornton JM, Dobson CM. Analysis of main chain torsion angles in proteins: prediction of coupling constants for native and random coil conformations. J Mol Biol 1996;255:494-506.
23. MacArthur MW, Thornton JM. Conformational analysis of protein structures derived from NMR data. Proteins 1993;17:232-251.
24. Rice LM, Briinger AT. Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins 1994;19:277-290.
25. Stein EG, Rice LM, Brünger AT. Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. J Magn Reson 1997;124:154-164.
26. Nilges M, O'Donoghue SI. Ambiguous NOEs and automated NOESY assignment. Prog NMR Spectrosc 1998;32:107-139.
27. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
28. Folmer RH, Hilbers CW, Konings RN, Nilges M. Floating stereospecific assignment revisited: application to an 18 kDa protein and comparison with J-coupling data. J Biomol NMR 1997;9:245-258.
29. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187-217.
30. Bruccoleri RE, Karplus M. Spatially constrained minimization of macromolecules. J Comput Chem 1986;7:165-175.
31. Hooft RW, Sander C, Vriend G. Objectively judging the quality of a protein structure from a Ramachandran plot. Comput Appl Biosci 1997;13:425-430.
32. Ramachandran GN, Ramakrishnan C, Sasisekharan V. Stereochemistry of polypeptide chain configurations. J Mol Biol 1963;7:95-99.
33. Sippl MJ. Recognition of errors in three-dimensional structures of proteins. Proteins 1993;17:355-362.
34. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang J-S, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography and NMR system (CNS): a new software suite for macromolecular structure determination. Acta Crystallogr D 1998;54:905-921.
35. Zweckstetter M, Bax AJ. Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR. J Am Chem Soc 2000;122:3791-3792.
36. Ryckaert JP, Ciocotti G, Berendsen HJC. Numerical integration of Cartesian equations of motion of a system with constraints - Molecular dynamics of N-alkanes. J Comput Phys 1977;23:327-341.
37. MacArthur MW, Thornton JM. Deviations from planarity of the peptide bond in peptides and proteins. J Mol Biol 1996;264:1180-1195.
38. Kuszewski J, Gronenborn AM, Clore GM. Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases. Protein Sci 1996;5:1067-1080.
39. Kuszewski J, Gronenborn AM, Clore GM. Improvements and extentions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids. J Magn Reson 1997;125:171-177.
40. Beglov D, Roux B. Dominant solvation effects from the primary shell of hydration: approximation for molecular dynamics simulations. Biopolymers 1995;35:171-178.
41. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer D, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
42. Luginbiihl P, Giintert P, Billeter M, Wüthrich K. The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules. J Biomol NMR 1996;8:136-146.