Prediction of methyl-side chain dynamics in proteins.
A simple analytical model is presented for the prediction of methyl-side chain dynamics in comparison with S(2) order parameters obtained by NMR relaxation spectroscopy. The model, which is an extension of the local contact model for backbone order parameter prediction, uses a static 3D protein structure as input. It expresses the methyl-group S(2) order parameters as a function of local contacts of the methyl carbon with respect to the neighboring atoms in combination with the number of consecutive mobile dihedral angles between the methyl group and the protein backbone. For six out of seven proteins the prediction results are good when compared with experimentally determined methyl-group S(2) values with an average correlation coefficient r = 0.65+/-0.14. For the unusually rigid cytochrome c(2) no significant correlation between prediction and experiment is found. The presented model provides independent support for the reliability of current side-chain relaxation methods along with their interpretation by the model-free formalism.
Ming
Dengming
D
Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA 01610, USA.
Brüschweiler
Rafael
R
D002244:Carbon / Q000737:chemistry; D018360:Crystallography, X-Ray; D045362:Cytochromes c2 / Q000737:chemistry*; D004583:Electrons; D005418:Flavodoxin / Q000737:chemistry; D016333:HIV Protease / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D015233:Models, Statistical; D008962:Models, Theoretical; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D025801:Ubiquitin / Q000737:chemistry
D005418:Flavodoxin; D011506:Proteins; D025801:Ubiquitin; D002244:Carbon; D045362:Cytochromes c2; D016333:HIV Protease