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Ruthenium-based CO releasing molecules (CO-RMs), CORM-2 and CORM-3, have been widely used as surrogates of CO for studying its biological effects in vitro and in vivo with much success. However, several previous solution-phase and in-vitro studies have revealed the ability for such CO-RMs to chemically modify proteins and reduce aromatic nitro groups due to their intrinsic chemical reactivity under certain conditions. In our own work of studying the cytoprotective effects of CO donors, we were in need of assessing chemical factors that could impact the interpretation of results from CO donors including CORM-2,3 in various in-vitro assays. For this, we examined the effects of CORM-2,3 toward representative reagents commonly used in various bioassays including resazurin, tetrazolium salts, nitrites and azide-based H(2)S probes. We have also examined the effect of CORM-2,3 on glutathione disulfide (GSSG), which is a very important redox regulator. Our studies show the ability for these CO-RMs to induce a number of chemical and/or spectroscopic changes for several commonly used biological reagents under near physiological conditions. These reactions/spectroscopic changes cannot be duplicated with CO-deleted CO-RMs (iCORMs), which are often used as negative controls. Further, both CORM-2 and -3 are capable of consuming and reducing GSSG in solution. We hope the results described will help future design of control experiments in using Ru-based CO-RMs in similar experiments.

Despite decades of research, the location and molecular identity of the proton release group together with the subsequent proton release pathway remain controversial even for the simplest light-driven proton pump, bacteriorhodopsin, according to the most recent experiments and simulations. Yet despite this nagging lack of knowledge for the generic case, even more complex pumps are currently under investigation. The proton release group disclosed by our large-scale simulations satisfies available experimental results, especially the broad Zundel continuum absorption subject to a striking anisotropy observed only recently. Moreover, our simulations delineate the seamless pathway by which the excess proton (being stored in an ultrastrong centered H-bond involving two glutamates) is finally translocated into the extracellular medium.

Understanding the molecular details of antibiotic resistance by the bacterial enzymes β-lactamases is vital for the development of novel antibiotics and inhibitors. In this spirit, the detailed mechanism of deacylation of the acyl-enzyme complex formed by cephalothin and class C β-lactamase is investigated here using hybrid quantum-mechanical/molecular-mechanical molecular dynamics methods. The roles of various active-site residues and substrate in the deacylation reaction are elucidated. We identify the base that activates the hydrolyzing water molecule and the residue that protonates the catalytic serine (Ser64). Conformational changes in the active sites and proton transfers that potentiate the efficiency of the deacylation reaction are presented. We have also characterized the oxyanion holes and other H-bonding interactions that stabilize the reaction intermediates. Together with the kinetic and mechanistic details of the acylation reaction, we analyze the complete mechanism and the overall kinetics of the drug hydrolysis. Finally, the apparent rate-determining step in the drug hydrolysis is scrutinized.

The catalytic power of enzymes is usually ascribed to a few catalytically competent residues as revealed by site-directed mutagenesis studies in conjunction with biochemical, thermodynamic and structural analyses. Surprisingly, the mutations of such pivotal residues in a GTPase that can hydrolyse GTP even to GMP, namely hGBP1, have been reported to result only in marginal changes of the catalytic rate compared to the wild type. Our large-scale ab initio quantum-mechanical/molecular-mechanical (QM/MM) metadynamics simulations disclose that the replacement of catalytically competent residues by the inert amino acid alanine, S73A and E99A, opens a plethora of molecularly different reaction pathways featuring very similar energy barriers and thus rates. These hitherto unknown reaction channels are established by mechanistically involving far-distant residues using “floating” water molecules, which connect them via hydrogen-bonding bridges to the nucleophilic water molecule, thus allowing for efficient long-distance proton transfer via the Grotthuss mechanism. Given the generic nature of the disclosed detour mechanisms that provide the molecular underpinning of catalytic versatility and thus mutational robustness of hGBP1, it is expected that the same concept is operational for GTPases in a broad sense.

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 β 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.\ud \ud