Quantum Mechanics/Molecular mechanics calculations predict A1, not A2, is present in melanopsin (Opn4m) of red-eared slider turtles (Trachemys scripta elegans).

Melanopsin is a photopigment that plays a role in non-visual, light-driven, cellular processes such as modulation of circadian rhythms, retinal vascular development, and the pupillary light reflex (PLR). In this study, computational methods were used to understand which chromophore is harbored by melanopsin in red-eared slider turtles (Trachemys scripta elegans). In mammals, the vitamin A derivative 11-cis-retinal (A1) is the chromophore, which provides functionality for melanopsin.

Computational Insights into Prostaglandin E Ligand Binding and Activation of G-Protein-Coupled Receptors.

G-protein coupled receptors (GPCRs) are eukaryotic integral membrane proteins that regulate signal transduction cascade pathways implicated in a variety of human diseases and are consequently of interest as drug targets. For this reason, it is of interest to investigate the way in which specific ligands bind and trigger conformational changes in the receptor during activation and how this in turn modulates intracellular signaling. In the present study, we investigate the way in which the ligand Prostaglandin E2 interacts with three GPCRs in the E-prostanoid family: EP1, EP2, and EP3.

Eigenvector centrality for characterization of protein allosteric pathways.

Determining the principal energy-transfer pathways responsible for allosteric communication in biomolecules remains challenging, partially due to the intrinsic complexity of the systems and the lack of effective characterization methods. In this work, we introduce the eigenvector centrality metric based on mutual information to elucidate allosteric mechanisms that regulate enzymatic activity. Moreover, we propose a strategy to characterize the range of correlations that underlie the allosteric processes.

Electron Transfer Assisted by Vibronic Coupling from Multiple Modes.

Understanding the effect of vibronic coupling on electron transfer (ET) rates is a challenge common to a wide range of applications, from electrochemical synthesis and catalysis to biochemical reactions and solar energy conversion. The Marcus-Jortner-Levich (MJL) theory offers a model of ET rates based on a simple analytic expression with a few adjustable parameters. However, the MJL equation in conjunction with density functional theory (DFT) has yet to be established as a predictive first-principles methodology.

Probing the remarkable thermal kinetics of visual rhodopsin with E181Q and S186A mutants.

We recently reported a very unusual temperature dependence of the rate of thermal reaction of wild type bovine rhodopsin: the Arrhenius plot exhibits a sharp "elbow" at 47 °C and, in the upper temperature range, an unexpectedly large activation energy (114 ± 8 kcal/mol) and an enormous prefactor (10 s). In this report, we present new measurements and a theoretical model that establish convincingly that this behavior results from a collective, entropy-driven breakup of the rigid hydrogen bonding networks (HBNs) that hinder the reaction at lower temperatures. For E181Q and S186A, two rhodopsin mutants that disrupt the HBNs near the binding pocket of the 11-cis retinyl chromophore, we observe significant decreases in the activation energy (∼90 kcal/mol) and prefactor (∼10 s), consistent with the conclusion that the reaction rate is enhanced by breakup of the HBN.

Characterization of Protein Tyrosine Phosphatase 1B Inhibition by Chlorogenic Acid and Cichoric Acid.

Protein tyrosine phosphatase 1B (PTP1B) is a known regulator of the insulin and leptin signaling pathways and is an active target for the design of inhibitors for the treatment of type II diabetes and obesity. Recently, cichoric acid (CHA) and chlorogenic acid (CGA) were predicted by docking methods to be allosteric inhibitors that bind distal to the active site. However, using a combination of steady-state inhibition kinetics, solution nuclear magnetic resonance experiments, and molecular dynamics simulations, we show that CHA is a competitive inhibitor that binds in the active site of PTP1B.

Molecular structure, spectroscopy, and photoinduced kinetics in trinuclear cyanide bridged complex in solution: a first-principles perspective.

We investigate the molecular structure of the solvated complex, [(NC)6Fe-Pt(NH3)4-Fe(CN)6](4-), and related dinuclear and mononuclear model complexes using first-principles calculations. Mixed nuclear complexes in both solution and crystal phases were widely studied as models for charge transfer (CT) reactions using advanced spectroscopical and electrochemical tools. In contrast to earlier interpretations, we find that the most stable gas phase and solvated geometries are substantially different from the crystal phase geometry, mainly due to variance in the underlying oxidation numbers of the metal centers.