[Show abstract][Hide abstract] ABSTRACT: Protein function often requires large-scale domain motion. An exciting new development in the experimental characterization of domain motions in proteins is the application of neutron spin-echo spectroscopy (NSE). NSE directly probes coherent (i.e., pair correlated) scattering on the ~1-100 ns timescale. Here, we report on all-atom molecular-dynamics (MD) simulation of a protein, phosphoglycerate kinase, from which we calculate small-angle neutron scattering (SANS) and NSE scattering properties. The simulation-derived and experimental-solution SANS results are in excellent agreement. The contributions of translational and rotational whole-molecule diffusion to the simulation-derived NSE and potential problems in their estimation are examined. Principal component analysis identifies types of domain motion that dominate the internal motion's contribution to the NSE signal, with the largest being classic hinge bending. The associated free-energy profiles are quasiharmonic and the frictional properties correspond to highly overdamped motion. The amplitudes of the motions derived by MD are smaller than those derived from the experimental analysis, and possible reasons for this difference are discussed. The MD results confirm that a significant component of the NSE arises from internal dynamics. They also demonstrate that the combination of NSE with MD is potentially useful for determining the forms, potentials of mean force, and time dependence of functional domain motions in proteins.
[Show abstract][Hide abstract] ABSTRACT: Nucleosome repositioning is a fundamental process in gene function. DNA elasticity is a key element of loop-mediated nucleosome repositioning. Two analytical models for DNA elasticity have been proposed: the linear sub-elastic chain (SEC), which allows DNA kinking, and the worm-like chain (WLC), with a harmonic bending potential. In vitro studies have shown that nucleosomes reposition in a discontiguous manner on a segment of DNA and this has also been found in ground-state calculations with the WLC analytical model. Here we study using Monte Carlo simulation the dynamics of DNA loop-mediated nucleosome repositioning at physiological temperatures using the SEC and WLC potentials. At thermal energies both models predict nearest-neighbor repositioning of nucleosomes on DNA, in contrast to the repositioning in jumps observed in experiments. This suggests a crucial role of DNA sequence in nucleosome repositioning.
[Show abstract][Hide abstract] ABSTRACT: The bacterial organomercurial lyase, MerB, catalyzes the protonolysis of organomercurial compounds. MerB cleaves Hg-C bonds of various substrates ranging from the methylmercury cation (MeHg) to merbromin. Upon Hg-C bond cleavage, Hg2+ and an organic molecule are produced. For example, methane is the product resulting from the protonolysis of MeHg. The release pathway and mechanism of the organic product are unclear. Here, we have applied molecular dynamics and free energy simulations to study the dissociation of a series of organic molecules. The x-ray crystallographic structure of MerB with a bound Hg2+ cation was used as the starting model, and the organic products were manually placed in the active site. The umbrella sampling method was used to obtain free energy profiles for the dissociation pathways. Several hydrophobic sidechains of MerB were found to interact with the organic molecules and may have important roles in the dissociation processes. The relatively low free energy barriers of dissociation suggest that organic product dissociation is not rate limiting.