Improved treatment of the protein backbone in empirical force fields.
Empirical force field-based calculations of proteins, including protein-folding studies, have improved our understanding of the relationship of their structure to their biological function. However, limitations in the accuracy of empirical force fields in the treatment of the peptide backbone exist. Presented is a grid correction approach to improve the treatment of the peptide backbone phi/psi conformational energies. Inclusion of this correction with the CHARMM22 all-atom protein force field is shown to lead to significant improvement in the treatment of the conformational energies of both the peptide model compound, the alanine dipeptide, and of proteins in their crystal environment. The developed approach is suggested to lead to significant improvements in the accuracy of empirical force fields to treat peptides and proteins.
MacKerell
Alexander D
AD
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA. amackere@rx.umaryland.edu
Feig
Michael
M
Brooks
Charles L
CL
D004151:Dipeptides / Q000737:chemistry*; D005998:Glycine / Q000737:chemistry; D008956:Models, Chemical; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity; D013329:Structure-Activity Relationship; D013499:Surface Properties; D013816:Thermodynamics
D004151:Dipeptides; D011506:Proteins; C002956:alanylalanine; D005998:Glycine