How main-chains of proteins explore the free-energy landscape in native states.
Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an alpha/beta protein (crambin) and a beta-sheet polypeptide (BS2) in their "native" states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive C(alpha) atoms, increases as a power law of time, t(alpha), with an exponent alpha between 0.08 and 0.39 (alpha = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles.
Senet
Patrick
P
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
Maisuradze
Gia G
GG
Foulie
Colette
C
Delarue
Patrice
P
Scheraga
Harold A
HA
D000595:Amino Acid Sequence; D019277:Entropy; D008956:Models, Chemical; D010455:Peptides / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary
D010455:Peptides; D010940:Plant Proteins; C024934:crambin protein, Crambe abyssinica