Chemical rescue of enzymes: proton transfer in mutants of human carbonic anhydrase II

In human carbonic anhydrase II (HCA II), the mutation of position 64 from histidine to alanine (H64A) disrupts the rate limiting proton transfer (PT) event, resulting in a reduction of the catalytic activity of the enzyme as compared to the wild-type. Potential of mean force (PMF) calculations utilizing the multistate empirical valence bond (MS-EVB) methodology for H64A HCA II yields a PT free energy barrier significantly higher than that found in the wild-type enzyme. This high barrier, determined in the absence of exogenous buffer and assuming no additional ionizable residues in the PT pathway, indicates the likelihood of alternate enzyme pathways that utilize either ionizable enzyme residues (self-rescue) and/or exogenous buffers (chemical rescue). It has been shown experimentally that the catalytic activity of H64A HCA II can be chemically rescued to near wild-type levels by the addition of the exogenous buffer 4-methylimidazole (4MI). Crystallographic studies have identified two 4MI binding sites, yet site-specific mutations intended to disrupt 4MI binding have demonstrated these sites to be nonproductive. In the present work, MS-EVB simulations show that binding of 4MI near Thr199 in the H64A HCA II mutant, a binding site determined by NMR spectroscopy, results in a viable chemical rescue pathway. Additional viable rescue pathways are also identified where 4MI acts as a proton transport intermediary from the active site to ionizable residues on the rim of the active site, revealing a probable mode of action for the chemical rescue pathway.     

Dielectric friction and solvation dynamics: Novel results on relaxation in dipolar liquids

In this article we present a new, general but simple, microscopic expression for time-dependent solvation energy of an ion. This expression is surprisingly similar to the expression for the time-dependent dielectric friction on a moving ion. We show that both the Chandra-Bagchi and the Fried-Mukamel formulations of solvation dynamics can be easily derived from this expression. This expression leads to an almost perfect agreement of the theory with all the available computer simulation results. Second, we show here for the first time that the mobility of a light solute ion can significantly accelerate its own solvation, specially in the underdamped limit. The latter result is also in excellent agreement with the computer simulations.     

Modulated Binary–Ternary Dual Semiconductor Heterostructures

A generic modular synthetic strategy for the fabrication of a series of binary‐ternary group II‐VI and group I‐III‐VI coupled semiconductor nano‐heterostructures is reported. Using Ag₂Se nanocrystals first as a catalyst and then as sacrificial seeds, four dual semiconductor heterostructures were designed with similar shapes: CdSe‐AgInSe₂, CdSe‐AgGaSe₂, ZnSe‐AgInSe₂, and ZnSe‐AgGaSe₂. Among these, dispersive type‐II heterostructures are further explored for photocatalytic hydrogen evolution from water and these are observed to be superior catalysts than the binary or ternary semi‐conductors. Details of the chemistry of this modular synthesis have been studied and the photophysical processes involved in catalysis are investigated.     

Effects of Hall current and slip condition on unsteady flow of a viscous fluid due to non-coaxial rotation of a porous disk and a fluid at infinity

The unsteady hydromagnetic flow due to non-coaxial rotations of a porous disk with slip condition and a fluid at infinity has been studied on taking Hall currents into account. An exact solution of the governing equation has been obtained by the Laplace transform technique. Asymptotic solution is obtained for large time. It is found that for large time there exists a thin boundary layer near the disk. The thickness of this layer decreases with increase in either suction or magnetic parameter.     

Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450cam

Proton-transfer reactions form an integral part of bioenergetics and enzymatic catalysis. The identification of proton-conducting pathways inside a protein is a key to understanding the mechanisms of biomolecular proton transfer. Proton pathways are modeled here as hydrogen bonded networks of proton-conducting groups, including proton-exchanging groups of amino acid side chains and bound water molecules. We focus on the identification of potential proton-conducting pathways inside a protein of known structure. However, consideration of the static structure alone is often not sufficient to detect suitable proton-transfer paths, leading, for example, from the protein surface to the active site buried inside the protein. We include dynamic fluctuations of amino acid side chains and water molecules into our analysis. To illustrate the method, proton transfer into the active site of cytochrome P450cam is studied. The cooperative rotation of amino acids and motion of water molecules are found to connect the protein surface to the molecular oxygen. Our observations emphasize the intrinsic dynamical nature of proton pathways where critical connections in the network may be transiently provided by mobile groups.     

Green synthesis of silver nanoparticle by <Emphasis Type="Italic">Penicillium purpurogenum</Emphasis> NPMF: the process and optimization

An eco-friendly microbial method for synthesis of silver colloid solution with antimicrobial activity is developed using a fungal strain of Penicillium purpurogenum NPMF. It is observed that increase in concentration of AgNO₃ increases the formation of silver nanoparticle. At 5 mM concentration highly populated polydispersed nanoparticles form. Furthermore, change in pH of the reaction mixture leads to change in shape and size of silver nanoparticles. At lower pH two peaks are observed in the absorption spectra showing polydispersity of nanoparticles. However, highly monodispersed spherical nanoparticles of 8–10 nm size form with 1 mM AgNO₃ concentration at pH 8. Antimicrobial activity of nanoparticles is demonstrated against pathogenic gram negative bacteria like Escherichia coli and Pseudomonas aeruginosa, and gram positive bacteria like Staphylococcus aureus. The antimicrobial activity of silver nanoparticles obtained at different initial pH show strong dependence on the surface area and shape of the nanoparticles.     

Unsteady Couette flow in a rotating system

The unsteady Couette flow between two infinite horizontal plates induced by the non-torsional oscillations of one of the plates in a rotating system under the boundary layer approximations is investigated. An exact solution of the governing equations has been obtained by using Laplace transform technique. It is shown that when the oscillating plate situated at an infinite distance from stationary plate then the problem reduces to the unsteady boundary layer problem in a rotating system with non-torsional oscillations of the free-stream velocity.     

Ionic and dipolar solvation dynamics in liquid water

The solvation time correlation function for solvation in liquid water was measured recently. The solvation was found to be very fast, with a time constant equal to 55 fs. In this article we present theoretical studies on solvation dynamics of ionic and dipolar solutes in liquid water, based on the molecular hydrodynamic approach developed earlier. The molecular hydrodynamic theory can successfully predict the ultrafast dynamics of solvation in liquid water as observed from recent experiments. The present study also reveals some interesting aspects of dipolar solvation dynamics, which differs significantly from that of ionic solvation. Dedicated to Prof. C N R Rao on his 60th birthday     

A theoretical study on the detection of proton transfer pathways in some mutants of human carbonic anhydrase II

Structural and kinetic studies of mutants can give much insight into the function of an enzyme. We report the detection of possible proton transfer pathways into the active site of a number of mutants of the enzyme human carbonic anhydrase II (HCA II). Using a recently developed method of path search in the protein conformational space, we identify hydrogen-bonded networks (or proton paths) that can dynamically connect the protein surface to the active site through fluctuations in protein structure and hydration. The feasibility of establishing such dynamical connectivities is assessed by computing the change in free energy of conformational fluctuations and compared to those identified earlier in the wild type enzyme. It is found that the point mutation facilitates or suppresses one or more of the alternative pathways. Our results allow the use of a generic set of pathways to correlate qualitatively the residual activity in the mutants to the molecular mechanism of proton transfer in the absence of His at position 64. We also demonstrate how the detected pathways may be used to compare the efficiencies of the mutants His-64-Ala/Asn-62-His and His-64-Ala/Asn-67-His using the empirical valence bond theory.