Protein Side-Chain Dynamics and Residual Conformational Entropy

Abstract

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 Nε-Hε bond vectors of E. 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 Nε 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 Nε-Hε bond-vector orientation is conserved and side-chain flexibility is concealed from Nε 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.

Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations

“…S8), consistent with other studies (40). Conformational heterogeneity appears in the SC of a highly buried Arg while still maintaining ordered contacts (41). These and other examples illustrate that upon folding, surface and core residues lose an amount of entropy that depends on context.…”

Will molecular dynamics simulations of proteins ever reach equilibrium?

“…16,17,19,20 Therefore, MD simulations are often used to supplement the NMR measurements to provide the total conformational entropy of the protein. 16,21,22,23,24,25,26,27,28,29 Protein conformational entropies are the main topic of this study, but it should be remembered that there are other important contributions to the total entropy as well, e.g. from the solvent.…”

“…The conformational entropy of the simulated proteins has been calculated with four different methods. In the first, which we will denote dihedral-distribution histogramming (DDH), 24,55 the protein Cartesian coordinates were converted to internal (bond, angle, and torsion) coordinates. Previous calculations have shown that entropy contributions from the bond and angle fluctuations are negligible.…”

Characterizing Active Site Conformational Heterogeneity along the Trajectory of an Enzymatic Phosphoryl Transfer Reaction

“…The 15 N ϵ ‐ 1 H ϵ order parameter is not sensitive to all arginine side‐chain motions, since there exist multiple conformations of the side‐chain that have a similar orientation of the H ϵ −N ϵ bond vector 16. However, although a strict relationship between the order parameter and conformational entropy is not available, important information about conformational entropy can be obtained from the order parameters.…”

“…[17] Shown are 80 000 randomly selected data points out of the totally 8×10 6 obtained. Included as black points are the correlations obtained previously from MD simulations of RNaseH16 (see Supporting Information). b) Histogram showing the distribution of conformational entropies for an order parameter of 0.46< S 2 <0.48. c) Histogram showing the distribution of conformational entropies for an order parameter of 0.89< S 2 <0.91.…”