Barstar Has a Highly Dynamic Hydrophobic Core:  Evidence from Molecular Dynamics Simulations and Nuclear Magnetic Resonance Relaxation Data

Abstract

The dynamic behavior of the ribonuclease inhibitor barstar has been investigated by molecular dynamics (MD) simulations in explicit water. Two 2.5 ns MD simulations were performed, and an ensemble of 25 000 structures was generated. This ensemble reproduces the solution structures and is consistent with the experimental structural restraints from NMR spectroscopy. Reorientation of the backbone NH bond vectors and side chain methyl groups was monitored by calculation of autocorrelation functions and the generalized S2 order parameters. Order parameters derived for motion in the approximately 100 ps time scale were compared with those obtained from NMR relaxation measurements. Consistent with experiment, the backbone NH bond vectors were relatively rigid. In contrast, the side chain methyl groups exhibited a wide dynamic range, from restricted motion comparable to that of the backbone to rapid unrestricted motion. The order parameters for the methyl groups correlate well with their spatial separation from the backbone and are residue-type dependent. Smaller S2axis values were observed for leucine methyl groups, in part due to side chain hopping between two predominant rotamers (g+t and tg-). Motions such as the flipping of aromatic rings and the hopping of leucine side chains were prevalent within the hydrophobic core, suggesting that the core is fluid-like with low energy barriers between native conformational substates. Thus, our studies suggest that the entropy of the native state can be significant and should not be discounted in thermodynamic considerations of protein folding. On the basis of our results, the side chain motion represents the primary source of the residual entropy of the native state and entropic considerations based solely on backbone dynamics would be incomplete.

Solution structure and dynamics of a de novo designed three-helix bundle protein

“…W4 was partially buried ( em ϭ 342 nm) and appeared to adopt two distinct, well populated orientations ( 1 ϭ Ϫ60.0°and 180°). Similar behavior has been observed for a natural three-helix bundle containing protein (44). Similarly, an IgG-binding domain shows two distinct rotamers for an interfacial phenylalanine residue (45).…”

Molecular Dynamics Characterization of the C2 Domain of Protein Kinase Cβ

“…Because proteins are systems where long-range electrostatics are expected to play an important role in determining molecular conformational energies and structures, the choice of the cut-off for non-bonded interactions is significantly important for the quality of the simulation. The value of 10 Å adopted here was shown (28,32,33,(37)(38)(39) to be a good compromise between the requirement for accurate treatment of long-range electrostatics and the requirement for a reasonable calculation time, of which the evaluation of non-bonded interactions is by far the determinant part. The solvent molecules were equilibrated initially by energy minimization and subsequently by performing 15 ps of MD.…”

Role of methyl groups in dynamics and evolution of biomolecules

“…Molecular dynamics simulations and NMR data reveal [11,[17][18][19]] that among the methyl groups the methionine methyl is the most dynamic (i.e., has the lowest energy barrier for rotation), followed by leucine and then the delta methyl group on isoleucine. Of course, their individual energy barriers depend on the position of the residue in the protein 3-D structure.…”