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. Within this scheme, we construct the equilibrium distribution of CVs from biased distributions obtained from independent MTD simulations with umbrella potentials. Reweighting is carried out by a procedure that combines US reweighting and Tiwary-Parrinello MTD reweighting within the Weighted Histogram Analysis Method (WHAM). The approach is ideal for a controlled sampling of a CV in a MTD simulation, making it computationally efficient in sampling flat, broad, and unbound free energy surfaces. This technique also allows for a distributed sampling of a high-dimensional free energy surface, further increasing the computational efficiency in sampling. We demonstrate the application of this technique in sampling high-dimensional surface for various chemical reactions using ab initio and QM/MM hybrid molecular dynamics simulations. Further, to carry out MTD bias reweighting for computing forward reaction barriers in ab initio or QM/MM simulations, we propose a computationally affordable approach that does not require recrossing trajectories. © 2016 Wiley Periodicals, Inc.

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. Female renal transplant recipients, who had received the graft at least 6 mo earlier, were enrolled. Women who visited the outpatient unit for varied complaints and who underwent a normal cervical examination were recruited as controls. A pap smear was obtained in all women. HPV genotyping array kit was utilized for identifying 21 HPV genotypes. Forty renal transplant recipient women and 80 controls were enrolled. The median age of cases and controls was 40 yr (range, 24-69 yr) and 38 yr (range, 23-72 yr), respectively. The mean duration since transplant was 53±42.6 mo (range, 6-168 mo). There was no evidence of cervical dysplasia in any pap smear. High-risk HPV was detected in 32.5% (13/40) and 17.5% (14/80) of cases and controls, respectively (P=0.18). Of the 21 genotypes screened, 7 subtypes were detected. HPV 16 and 31 were the most common (5/13; 38.5%) subtypes observed in the cases, followed by HPV 18 (30.7%). HPV 16 was the most common subtype in controls (10/14; 71.4%). Five (38.5%) renal transplant recipients harbored multiple HPV genotypes, as compared with 4 (28.6%) controls (P=1.0). The prevalence of high-risk HPV in female renal transplant recipients was 1.9 times that observed among controls, although there was no evidence of cervical dysplasia.

Mechanism and Kinetics of Aztreonam Hydrolysis Catalyzed by Class-C ß-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. Moreover, the method is shown to be efficient in exploring flat and broad free-energy basins that commonly occur in enzymatic reactions. We demonstrate this by studying deacylation and reverse acylation reactions of aztreonam drug catalyzed by a class-C ß lactamase (CBL) bacterial enzyme. Mechanistic details and nature of kinetics of aztreonam hydrolysis by CBL are elaborated here. The results of this study point to characteristics of the aztreonam drug that are responsible for its slow hydrolysis.

Mechanism of Mg2+-Accompanied Product Release in Sugar Nucleotidyltransferases.

The nucleotidyl transfer reaction, catalyzed by sugar nucleotidyltransferases (SNTs), is assisted by two active site Mg2+ 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 Mg2+ ions remains coordinated to the exiting pyrophosphate. This hints at the participation of Mg2+ in the process of product release, besides its role in catalyzing nucleotidyl transfer. These observations are further supported by enhanced sampling molecular dynamics simulations. Free energy computations suggest that the product release is likely to be rate limiting in SNTs, and the origin of the high free energy barrier for product release could be traced back to the "slow" conformational change of an Arg residue at the exit end of the pocket. These results establish a dual role for Mg2+, and propose a general mechanism of product release during the nucleotidyl transfer by SNTs.