Protein side-chain dynamics and residual conformational entropy.
Changes in residual conformational entropy of proteins can be significant components of the thermodynamics of folding and binding. Nuclear magnetic resonance (NMR) spin relaxation is the only experimental technique capable of probing local protein entropy, by inference from local internal conformational dynamics. To assess the validity of this approach, the picosecond-to-nanosecond dynamics of the arginine side-chain N(epsilon)-H(epsilon) bond vectors of Escherichia coli ribonuclease H (RNase H) were determined by NMR spin relaxation and compared to the mechanistic detail provided by molecular dynamics (MD) simulations. The results indicate that arginine N(epsilon) spin relaxation primarily reflects persistence of guanidinium salt bridges and correlates well with simulated side-chain conformational entropy. In particular cases, the simulations show that the aliphatic part of the arginine side chain can retain substantial disorder while the guanidinium group maintains its salt bridges; thus, the N(epsilon)-H(epsilon) bond-vector orientation is conserved and side-chain flexibility is concealed from N(epsilon) spin relaxation. The MD simulations and an analysis of a rotamer library suggest that dynamic decoupling of the terminal moiety from the remainder of the side chain occurs for all five amino acids with more than two side-chain dihedral angles (R, K, E, Q, and M). Dynamic decoupling thus may represent a general biophysical strategy for minimizing the entropic penalties of folding and binding.
Trbovic
Nikola
N
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.
Cho
Jae-Hyun
JH
Abel
Robert
R
Friesner
Richard A
RA
Rance
Mark
M
Palmer
Arthur G
AG
D001120:Arginine / Q000737:chemistry*; D003198:Computer Simulation; D019277:Entropy; D029968:Escherichia coli Proteins / Q000737:chemistry; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D016914:Ribonuclease H / Q000737:chemistry*
D029968:Escherichia coli Proteins; D001120:Arginine; D016914:Ribonuclease H