Vivek S. Bharadwaj

Insights into the Glycyl Radical Enzyme Active Site of Benzylsuccinate Synthase: A Computational Study

The fumarate addition reaction, catalyzed by the enzyme benzylsuccinate synthase (BSS), is considered to be one of the most intriguing and energetically challenging reactions in biology. BSS belongs to the glycyl radical enzyme family and catalyzes the fumarate addition reaction, which enables microorganisms to utilize hydrocarbons as an energy source under anaerobic conditions. Unfortunately, the extreme sensitivity of the glycyl radical to oxygen has hampered the structural and kinetic characterization of BSS, thereby limiting our knowledge on this enzyme. To enhance our molecular-level understanding of BSS, a computational approach involving homology modeling, docking studies, and molecular dynamics (MD) simulations has been used to deduce the structure of BSSs catalytic subunit (BSSα) and illuminate the molecular basis for the fumarate addition reaction. We have identified two conserved and distinct binding pockets at the BSSα active site: a hydrophobic pocket for toluene binding and a polar pocket for fumaric acid binding. Subsequent dynamical and energetic evaluations have identified Glu509, Ser827, Leu390, and Phe384 as active site residues critical for substrate binding. The orientation of substrates at the active site observed in MD simulations is consistent with experimental observations of the syn addition of toluene to fumaric acid. It is also found that substrate binding tightens the active site and restricts the conformational flexibility of the thiyl radical, leading to hydrogen transfer distances conducive to the proposed reaction mechanism. The stability of substrates at the active site and the occurrence of feasible radical transfer distances between the thiyl radical, substrates, and the active site glycine indicate a substrate-assisted radical transfer pathway governing fumarate addition.

Impact of water dilution and cation tail length on ionic liquid characteristics: Interplay between polar and non-polar interactions

The recalcitrance of lignocellulosic biomass poses a major challenge that hinders the economical utilization of biomass for the production of biofuel, plastics, and chemicals. Ionic liquids have become a promising solvent that addresses many issues in both the pretreatment process and the hydrolysis of the glycosidic bond for the deconstruction of cellulosic materials. However, to make the use of ionic liquids economically viable, either the cost of ionic liquids must be reduced, or a less expensive solvent (e.g., water) may be added to reduce the overall amount of ionic liquid used in addition to reducing the viscosity of the binary liquid mixture. In this work, we employ atomistic molecular dynamics simulations to investigate the impact of water dilution on the overall liquid structure and properties of three imidazolium based ionic liquids. It is found that ionic liquid-water mixtures exhibit characteristics that can be grouped into two distinct regions, which are a function of the ionic liquid concent...

Acetylcholine promotes binding of α-conotoxin MII at α3 β2 nicotinic acetylcholine receptors.

α‐Conotoxin MII (α‐CTxMII) is a 16‐residue peptide with the sequence GCCSNPVCHLEHSNLC, containing Cys2–Cys8 and Cys3–Cys16 disulfide bonds. This peptide, isolated from the venom of the marine cone snail Conus magus, is a potent and selective antagonist of neuronal nicotinic acetylcholine receptors (nAChRs). To evaluate the impact of channel–ligand interactions on ligand‐binding affinity, homology models of the heteropentameric α3β2‐nAChR were constructed. The models were created in MODELLER with the aid of experimentally characterized structures of the Torpedo marmorata‐nAChR (Tm‐nAChR, PDB ID: 2BG9) and the Aplysia californica‐acetylcholine binding protein (Ac‐AChBP, PDB ID: 2BR8) as templates for the α3‐ and β2‐subunit isoforms derived from rat neuronal nAChR primary amino acid sequences. Molecular docking calculations were performed with AutoDock to evaluate interactions of the heteropentameric nAChR homology models with the ligands acetylcholine (ACh) and α‐CTxMII. The nAChR homology models described here bind ACh with binding energies commensurate with those of previously reported systems, and identify critical interactions that facilitate both ACh and α‐CTxMII ligand binding. The docking calculations revealed an increased binding affinity of the α3β2‐nAChR for α‐CTxMII with ACh bound to the receptor, and this was confirmed through two‐electrode voltage clamp experiments on oocytes from Xenopus laevis. These findings provide insights into the inhibition and mechanism of electrostatically driven antagonist properties of the α‐CTxMIIs on nAChRs.

Impact of Water-Dilution on the Solvation Properties of the Ionic Liquid 1-Methyltriethoxy-3-ethylimidazolium Acetate for Model Biomass Molecules.

Many studies have suggested that the processing of lignocellulosic biomass could provide a renewable feedstock to supplant much of the current demand on petroleum sources. Currently, alkyl imidazolium-based ionic liquids (ILs) have shown considerable promise in the pretreatment, solvation, and hydrolysis of lignocellulosic materials although their high cost and unfavorable viscosity has limited their widespread use. Functionalizing these ILs with an oligo(ethoxy) tail has previously been shown through experiment to decrease the ILs viscosity resulting in enhanced mass transport characteristics, in addition to other favorable traits including decreased inhibition of some enzymes. Additionally, the use of cosolvents to mitigate the cost and unfavorable traits of ILs is an area of growing interest with particular attention on water as the presence of water in biomass processes is inevitable. Through the use of biased and unbiased molecular dynamics (MD) simulations, this study provides a molecular-level perspective of the various solvent-solvent and solvent-solute interactions in binary mixtures of water and 1-methyltriethoxy-3-ethylimidazolium acetate ([Me-(OEt)3-Et-IM+] [OAc-]) in the presence of model cellulose compounds (i.e., glucose and cellobiose). It is observed that at ∼75% w/w IL and water a transition in the nanostructure of the solvent occurs between water-like and IL-like solvation characteristics. It is shown that H-bonding interactions between the anion and water are a major driving force that significantly impacts the solvent properties of the IL as well as conformational preferences of the cellulosic model compound. In addition, it is found that the oligo(ethoxy) cation tail is responsible for the reduction in the propensity for tail aggregation as compared to alkyl tails of similar length, which, combined with increased ionic shielding, results in increased diffusion and enhanced water-like solvation characteristics.

Molecular Simulations of Fatty‐Acid Methyl Esters and Representative Biodiesel Mixtures

Despite the importance of fatty-acid methyl esters (FAMEs) as key components of various green solvents, detergents, plasticizers, and biodiesels, our understanding of these systems at the molecular level is limited. An enhanced molecular-level perspective of FAMEs will enable a detailed analysis of the polymorph and crystallization phenomena that adversely impact flow properties at low temperatures. Presented here, is the parameterization and validation of a charge-modified generalized amber force field (GAFF) for eight common FAMEs and two representative biodiesel mixtures. Our simulations accurately reproduce available experimental data (e.g. densities and self-diffusivity coefficients) and their trends, with respect to temperature and degree of unsaturation. Structural analyses from our simulations provide a more detailed picture of liquid-phase molecular ordering in FAMEs and confirm recent experimental hypotheses. This study provides a firm foundation to initiate further studies into the mechanisms that drive crystallization phenomena at the molecular level.