Protein flexibility prediction by an all-atom mean-field statistical theory.
We extended a mean-field model to proteins with all atomic detail. The all-atom mean-field model was used to calculate the dynamic and thermodynamic properties of a three-helix bundle fragment of Staphylococcal protein A (Protein Data Bank [PDB] ID 1BDD) and alpha-spectrin SH3 domain protein (PDB ID 1SHG). We show that a model with all-atomic detail provides a significantly more accurate prediction of flexibility of residues in proteins than does a coarse-grained residue-level model. The accuracy of flexibility prediction is further confirmed by application of the method to 18 additional proteins with the largest size of 224 residues.
Howard Hughes Medical Institute Center for Single Molecule Biophysics and Department of Physiology and Biophysics, State University of New York at Buffalo, 14214, USA.
B P
BP
Pandey
Chi
C
Zhang
Xianzhang
X
Yuan
Jian
J
Zi
Yaoqi
Y
Zhou
D008433:Mathematics; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013049:Spectrin / Q000737:chemistry* / Q000378:metabolism; D013205:Staphylococcal Protein A / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics; D018909:src Homology Domains
D013205:Staphylococcal Protein A; D013049:Spectrin