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.
Pandey
B P
BP
Howard Hughes Medical Institute Center for Single Molecule Biophysics and Department of Physiology and Biophysics, State University of New York at Buffalo, 14214, USA.
Zhang
Chi
C
Yuan
Xianzhang
X
Zi
Jian
J
Zhou
Yaoqi
Y
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