The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: Comparison with NMR parameters

Biochemistry and Cell Biology

Volumn 76, Issue 2-3, 1998, Pages 164-170

  Van Der Spoel, David ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Chemical shift; Dihedral probability distribution; J coupling; Molecular dynamics (MD); Nuclear magnetic resonance (NMR) spectroscopy

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; DATA ANALYSIS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PROBABILITY; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

EID: 0032454154     PISSN: 08298211     EISSN: None     Source Type: Journal    
DOI: 10.1139/o98-025     Document Type: Article

References (43)

1. 15N relaxation using inverse detected NMR spectroscopy: the central helix is flexible. Biochemistry, 31: 5269-5278.
2. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., and Hermans, J. 1981. Interaction models for water in relation to protein hydration. In Intermolecular forces. Edited by B. Pullman. D. Reidel Publishing Company, Dordrecht, the Netherlands. pp. 331-342.
3. Berendsen, H.J.C., Postma, J.P.M., DiNola, A., and Haak, J.R. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81: 3684-3690.
4. Berendsen, H.J.C., van der Spoel, D., and van Drunen, R. 1995. GROMACS: a message-passing parallel molecular dynamics implementation. Comp. Phys. Comm. 91: 43-56.
5. Brüschweiler, R., and Case, D.A. 1994. Adding harmonic motion to the karplus relation for spin-spin coupling. J. Am. Chem. Soc. 116: 11199-11200.
6. Brüschweiler, R., Roux, B., Blackledge, M., Griesinger, C., Karplus, M., and Ernst, R.R. 1992. Influence of rapid intramolecular motion on NMR cross-relaxation rates. a molecular dynamics study of antamanide in solution. J. Am. Chem. Soc. 114: 2289-2302.
7. Case, D.A., Dyson, H.J., and Wright, P.E. 1994. Use of chemical shifts and coupling constants in nuclear magnetic resonance structural studies on peptides and proteins. Methods Enyzmol. 239: 392-415.
8. 1H-NMR spectra of ferrichrome peptides. i. The non-amide proteins. Biopolymers, 17: 617-636.
9. 1 rotamer populations from NMR data by the CUPID method. J. Am. Chem. Soc. 114: 6200-6207.
10. Dzakula, Z., Westler, W.M., Edison, A.S., and Markley, J.L. 1992b. The CUPID method for calculating the continuous probability distribution of rotamers from NMR data. J. Am. Chem. Soc. 114: 6195-6199.
11. Dzakula, Z., Westler, W.M., and Markley, J.L. 1996. Continuous probability distribution (CUPID) analysis of potentials for internal rotations. J. Magn. Reson. Ser. B, 111: 109-126.
12. 15N NMR relaxation measurements with a molecular dynamics simulation: backbone dynamics of the glucocorticod receptor DNA-binding domain. Proteins Struct. Funct. Genet. 17: 375-390.
13. Ewald, P.P. 1921. Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann. Phys., 64: 253-287.
14. Hess, B., Bekker, H., Berendsen, H.J.C., and Fraaije, J.G.E.M. 1997. LINCS: a linear constraint solver for molecular simulations. J. Comp. Chem. 18: 1463-1472.
15. Jiménez, M.A., Blanco, F.J., Rico, M., Santoro, J., Herranz, J., and Nieto, J.L. 1992. Periodic properties of proton conformational shifts in isolated protein helices. Eur. J. Biochem. 207: 39-49.
16. Karplus, M. 1959. Contact electron-spin coupling of nuclear magnetic moments. J. Chem. Phys. 30: 11-15.
17. 1H-nuclear magnetic resonance spectroscopy in peptides related to the N terminus of bovine pancreatic trypsin inhibitor. J. Mol. Biol. 230: 312-322.
18. 15N NMR relaxation measurements. J. Am. Chem. Soc. 114: 4934-4936.
19. Laskowksi, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. 1993. PROCHECK: a program to check the stereochemical quality of a protein structure. J. Appl. Crystallogr. 26: 283-291.
20. Lipari, G., and Szabo, A. 1982. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104: 4546-4559.
21. Lipari, G., Szabo, A., and Levy, R.M. 1982. Protein dynamics and NMR relaxation: comparison of simulations with experiment. Nature (London), 300: 197-198.
22. Ludvigsen, S., Andersen, K.V., and Poulsen, F.M. 1991. Accurate measurements of coupling constants from two-dimensional nuclear magnetic resonance spectra of proteins and determination of φ-angles. J. Mol. Biol. 217: 731-736.
23. Merutka, G., Dyson, H.J., and Wright, P.E. 1995. "Random coil" 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG. J. Biomol. NMR, 5: 14-24.
24. Miyamoto, S., and Kollman, P.A. 1992. SETTLE: an analytical version of the SHAKE and RATTLE algorithms for rigid water models. J. Comp. Chem. 13: 952-962.
25. Palmer, A.G., III, and Case, D.A. 1992. Molecular dynamics analysis of NMR relaxation in a zinc-finger peptide. J. Am. Chem. Soc. 114: 9059-9067.
26. HNα, in a globular protein. J. Mol. Biol. 180: 741-751.
27. Plaxco, K.W., Morton, C.J., Grimshaw, S.B., Jones, J.A., Pitkeathly, M., Campbell, I.D., and Dobson, C.M. 1997. The effects of guanidine hydrochloride on the random coil conformations and NMR chemical shifts of the peptide series GGXGG. J. Biomol. NMR, 10: 221-230.
28. Serrano, L. 1995. Comparison between Φ distribution of the amino acids in the protein database and NMR data indicates that amino acids have various Φ propensities in the random coil conformation. J. Mol. Biol. 254: 322-333.
29. 1H NMR spin-spin coupling constants. Biochemistry, 30: 986-996.
30. Smith, P.E., van Schaik, R.C., Szyperski, T., Wüthrich, K., and van Gunsteren, W.F. 1995. Internal mobility of the basic pancreatic trypsin inhibitor in solution: a comparison of NMR spin relaxation measurements and molecular dynamics simulations. J. Mol. Biol. 246: 356-365.
31. Smith, L.J., Bolin, K.A., Schwalbe, H., MacArthur, M.W., Thornton, J.M., and Dobson, C.M. 1996. Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations. J. Mol. Biol. 255: 494-506.
32. Swindells, M.B., MacArthur, M.W., and Thornton, J.M. 1995. Intrinsic φ/ψ propensities of amino acids, derived from the coil region of known structures. Nat. Struct. Biol. 2: 596-603.
33. 13C chemical shifts of amino acids in aqueous solution containing organic solvents: application to the secondary structure characterization of peptides in aqueous trifluoroethanol solution. J. Biomol. NMR, 4: 47-59.
34. van der Spoel, D. 1996. Structure and dynamics of peptides: theoretical aspects of protein folding. Ph.D. thesis, University of Groningen, Groningen, the Netherlands.
35. van der Spoel, D., van Buuren, A.R., Tieleman, D.P., and Berendsen, H.J.C. 1996a. Molecular dynamics simulations of peptides from BPTI: a closer look at amide-aromatic interactions. J. Biomol. NMR, 8: 229-238.
36. van der Spoel, D., Feenstra, K.A., Hemminga, M.A., and Berendsen, H.J.C. 1996b. Molecular modelling of the RNA binding N-terminal part of CCMV coat protein in solution with phosphate ions. Biophys. J. 71: 2920-2932.
37. van der Spoel, D., van Buuren, A.R., Apol, E., Meulenhoff, P.J., Tieleman, D.P., Sijbers, A.L.T.M., van Drunen, R., and Berendsen, H.J.C. 1997. Gromacs user manual version 1.5. Available from Nijenborgh 4, 9747 AG Groningen, The Netherlands (http://rugmd0.chem.rug.nl/∼gmx).
38. van Gunsteren, W.F., and Berendsen, H.J.C. 1987. Gromos-87 manual. Available from Biomos BV, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
39. 15N-enriched proteins. J. Am. Chem. Soc. 115: 7772-7777.
40. Wagner, G. 1993. NMR relaxation and protein mobility. Curr. Biol. 3: 748-754.
41. Williamson, M.P., and Asakura, T. 1993. Empirical comparisons of models for chemical-shift calculation in proteins. J. Magn. Reson. Ser. B, 101: 63-71.
42. 15N random coil NMR chemical shifts of the common amino acids. I. Investigation of nearest-neighbor effects. J. Biomol. NMR, 5: 67-81.
43. Wishart, D.S., and Sykes, B.D. 1994. Chemical shifts as a tool for structure determination. Methods Enyzmol. 239: 363-391.