Mechanism and Kinetics of Aztreonam Hydrolysis Catalyzed by Class-C β-Lactamase: A Temperature-Accelerated Sliced Sampling Study.

Enhanced sampling of large number of collective variables (CVs) is inevitable in molecular dynamics (MD) simulations of complex chemical processes such as enzymatic reactions. Because of the computational overhead of hybrid quantum mechanical/molecular mechanical (QM/MM)-based MD simulations, especially together with density functional theory, predictions of reaction mechanism, and estimation of free-energy barriers have to be carried out within few tens of picoseconds. We show here that the recently developed temperature-accelerated sliced sampling method allows one to sample large number of CVs, thereby enabling us to obtain rapid convergence in free-energy estimates in QM/MM MD simulation of enzymatic reactions.

Mechanism of Mg-Accompanied Product Release in Sugar Nucleotidyltransferases.

The nucleotidyl transfer reaction, catalyzed by sugar nucleotidyltransferases (SNTs), is assisted by two active site Mg ions. While studying this reaction using X-ray crystallography, we captured snapshots of the pyrophosphate (product) as it exits along a pocket. Surprisingly, one of the active site Mg ions remains coordinated to the exiting pyrophosphate.

Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics.

Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling is based on filling the free energy basins by biasing potentials and thus for cases with flat, broad, and unbound free energy wells, the computational time to sample them becomes very large. To alleviate this problem, we combine the standard Umbrella Sampling (US) technique with MTD to sample orthogonal collective variables (CVs) in a simultaneous way.

Prevalence and genotypes of HPV in female renal transplant recipients in North India.

Estimation of the prevalence of high-risk human papillomavirus (HPV) genotypes in female renal transplant recipients is important for formulating strategies for prevention and screening of cervical cancer in the susceptible group. Data from developing countries are very limited. The study was prospective, cross-sectional, and hospital-based.