Prediction of NMR order parameters in proteins using weighted protein contact-number model

Theoretical Chemistry Accounts

Volumn 121, Issue 3-4, 2008, Pages 197-200

  Huang, Shao Wei ^a   Shih, Chien Hua ^a   Lin, Chih Peng ^a   Hwang, Jenn Kang ^a  

^a NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

Author keywords

NMR order parameter; Prediction; Protein dynamics; Weighted protein contact number

Indexed keywords

EID: 53549083216     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-008-0465-0     Document Type: Article

References (28)

1. LW Yang I Bahar 2005 Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes Structure 13 893 904
2. M Mukherjee K Dutta MA White D Cowburn RO Fox 2006 NMR solution structure and backbone dynamics of domain III of the E protein of tick-borne Langat flavivirus suggests a potential site for molecular recognition Protein Sci 15 1342 1355
3. A Warshel 2002 Molecular dynamics simulations of biological reactions Acc Chem Res 35 385 395
4. H Berman K Henrick H Nakamura JL Markley 2007 The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data Nucleic Acids Res 35 D301 303
5. M Levitt A Warshel 1975 Computer simulation of protein folding Nature 253 694 698
6. JA McCammon BR Gelin M Karplus 1977 Dynamics of folded proteins Nature 267 585 590
7. A Warshel 1976 Bicycle-pedal model for the first step in the vision process Nature 260 679 683
8. A Warshel WW Parson 2001 Dynamics of biochemical and biophysical reactions: insight from computer simulations Q Rev Biophys 34 563 679
9. M Karplus JA McCammon 2002 Molecular dynamics simulations of biomolecules Nat Struct Biol 9 646 652
10. SA Showalter R Bruschweiler 2007 Validation of molecular dynamics simulations of biomolecules using NMR spin relaxation as benchmarks: application to the AMBER99SB force field J Chem Theory Comput 3 961 975
11. M Rueda C Ferrer-Costa T Meyer A Perez J Camps A Hospital JL Gelpi M Orozco 2007 A consensus view of protein dynamics Proc Natl Acad Sci USA 104 796 801
12. F Zhang R Bruschweiler 2002 Contact model for the prediction of NMR N-H order parameters in globular proteins J Am Chem Soc 124 12654 12655
13. MM Tirion 1996 Large amplitude elastic motions in proteins from a single-parameter, atomic analysis Phys Rev Lett 77 1905 1908
14. I Bahar AR Atilgan B Erman 1997 Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential Fold Des 2 173 181
15. D Ming R Bruschweiler 2006 Reorientational contact-weighted elastic network model for the prediction of protein dynamics: comparison with NMR relaxation Biophys J 90 3382 3388
16. S Pfeiffer D Fushman D Cowburn 2001 Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the betaARK1 PH domain J Am Chem Soc 123 3021 3036
17. N Tjandra SE Feller RW Pastor A Bax 1995 Rotational diffusion anisotropy of human ubiquitin from 15N NMR relaxation J Am Chem Soc 117 12562 12566
18. M Buck J Boyd C Redfield DA MacKenzie DJ Jeenes DB Archer CM Dobson 1995 Structural determinants of protein dynamics: analysis of 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme Biochemistry 34 4041 4055
19. K Harata M Muraki 1997 X-ray structure of turkey-egg lysozyme complex with tri-N-acetylchitotriose. Lack of binding ability at subsite A Acta Crystallogr D Biol Crystallogr 53 650 657
20. M Akke NJ Skelton J Kordel AG Palmer 3rd WJ Chazin 1993 Effects of ion binding on the backbone dynamics of calbindin D9k determined by 15N NMR relaxation Biochemistry 32 9832 9844
21. LA Svensson E Thulin S Forsen 1992 Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography J Mol Biol 223 601 606
22. W Feng R Tejero DE Zimmerman M Inouye GT Montelione 1998 Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: evidence for conformational dynamics in the single-stranded RNA-binding site Biochemistry 37 10881 10896
23. Q Li C Khosla JD Puglisi CW Liu 2003 Solution structure and backbone dynamics of the holo form of the frenolicin acyl carrier protein Biochemistry 42 4648 4657
24. B Halle 2002 Flexibility and packing in proteins Proc Natl Acad Sci USA 99 1274 1279
25. SM Kristensen G Siegal A Sankar PC Driscoll 2000 Backbone dynamics of the C-terminal SH2 domain of the p85[alpha] subunit of phosphoinositide 3-kinase: effect of phosphotyrosine-peptide binding and characterization of slow conformational exchange processes J Mol Biol 299 771 788
26. S Yun DS Jang DH Kim KY Choi HC Lee 2001 15N NMR relaxation studies of backbone dynamics in free and steroid-bound Delta 5-3-ketosteroid isomerase from Pseudomonas testosteroni Biochemistry 40 3967 3973
27. JT Stivers C Abeygunawardana AS Mildvan 1996 15N NMR relaxation studies of free and inhibitor-bound 4-oxalocrotonate tautomerase: backbone dynamics and entropy changes of an enzyme upon inhibitor binding Biochemistry 35 16036 16047
28. C Redfield J Boyd LJ Smith RA Smith CM Dobson 1992 Loop mobility in a four-helix-bundle protein: 15N NMR relaxation measurements on human interleukin-4 Biochemistry 31 10431 10437