Mechanistic complexities of sulfite oxidase: An enzyme with multiple domains, subunits, and cofactors.

Sulfite oxidase (SO) deficiency, an inherited disease that causes severe neonatal neurological problems and early death, arises from defects in the biosynthesis of the molybdenum cofactor (Moco) (general sulfite oxidase deficiency) or from inborn errors in the SUOX gene for SO (isolated sulfite oxidase deficiency, ISOD). The X-ray structure of the highly homologous homonuclear dimeric chicken sulfite oxidase (cSO) provides a template for locating ISOD mutation sites in human sulfite oxidase (hSO). Catalysis occurs within an individual subunit of hSO, but mutations that disrupt the hSO dimer are pathological.

Static polarizabilities within the generalized Kohn-Sham semicanonical projected random phase approximation (GKS-spRPA).

An analytical implementation of static dipole polarizabilities within the generalized Kohn-Sham semicanonical projected random phase approximation (GKS-spRPA) method for spin-restricted closed-shell and spin-unrestricted open-shell references is presented. General second-order analytical derivatives of the GKS-spRPA energy functional are derived using a Lagrangian approach. By resolution-of-the-identity and complex frequency integration methods, an asymptotic O(N⁡log(N)) scaling of operation count and O(N) scaling of storage is realized, i.

Method for Identifying Common Features in Reactive Trajectories of a Transition Path Sampling Ensemble.

Simulation methods like transition path sampling (TPS) generate an abundance of information buried in the collection of reactive trajectories that they generate. However, only limited use has been made of this information, mainly for the identification of the reaction coordinate. The standard TPS tools have been designed for monitoring the progress of the system from reactants to products.

Ligand-Centered Triplet Diradical Supported by a Binuclear Palladium(II) Dipyrrindione.

Oligopyrroles form a versatile class of redox-active ligands and electron reservoirs. Although the stabilization of radicals within oligopyrrolic π systems is more common for macrocyclic ligands, bidentate dipyrrindiones are emerging as compact platforms for one-electron redox chemistry in transition-metal complexes. We report the synthesis of a bis(aqua) palladium(II) dipyrrindione complex and its deprotonation-driven dimerization to form a hydroxo-bridged binuclear complex in the presence of water or triethylamine.

Role of Protein Motions in Catalysis by Formate Dehydrogenase.

We have analyzed the reaction catalyzed by formate dehydrogenase using transition path sampling. This system has recently received experimental attention using infrared spectroscopy and heavy-enzyme studies. Some of the experimental results point to the possible importance of protein motions that are coupled to the chemical step.

A Classical Molecular Dynamics Simulation Study of Interfacial and Bulk Solution Aggregation Properties of Dirhamnolipids.

The rhamnolipids are a unique class of biosurfactants produced by the bacteria . These molecules display a high level of surface activity as well as biodegradability. In this study nonionic dirhamnolipid was investigated by utilizing molecular dynamics simulation at the air-water interface as well as in bulk water.

Macromolecular Engineering of the Outer Coordination Sphere of [2Fe-2S] Metallopolymers to Enhance Catalytic Activity for H Production.

Small-molecule catalysts inspired by the active sites of [FeFe]-hydrogenase enzymes have long struggled to achieve fast rates of hydrogen evolution, long-term stability, water solubility, and oxygen compatibility. We profoundly improved on these deficiencies by grafting polymers from a metalloinitiator containing a [2Fe-2S] moiety to form water-soluble poly(2-dimethylamino)ethyl methacrylate metallopolymers () using atom transfer radical polymerization (ATRP). This study illustrates the critical role of the polymer composition in enhancing hydrogen evolution and aerobic stability by comparing the catalytic activity of with a nonionic water-soluble metallopolymer based on poly(oligo(ethylene glycol) methacrylate) prepared via ATRP () with the same [2Fe-2S] metalloinitiator.

Molecular Dynamics Simulation of the Oil Sequestration Properties of a Nonionic Rhamnolipid.

A detailed molecular dynamics simulation study is presented on the behavior of aggregates composed of the nonionic monorhamnolipid α-rhamnopyranosyl-β-hydroxydecanoyl-β-hydroxydecanoate (Rha-C10-C10) and decane in bulk water. A graph theoretical approach was utilized to characterize the size and composition of the many aggregates generated in our simulations. Overall, we observe that the formation of oil in Rha-C10-C10 aggregates is a favorable process.

In Vivo Ambient Serotonin Measurements at Carbon-Fiber Microelectrodes.

The mechanisms that control extracellular serotonin levels in vivo are not well-defined. This shortcoming makes it very challenging to diagnose and treat the many psychiatric disorders in which serotonin is implicated. Fast-scan cyclic voltammetry (FSCV) can measure rapid serotonin release and reuptake events but cannot report critically important ambient serotonin levels.

Diamagnetic Imaging Agents with a Modular Chemical Design for Quantitative Detection of β-Galactosidase and β-Glucuronidase Activities with CatalyCEST MRI.

Imaging agents for the noninvasive in vivo detection of enzyme activity in preclinical and clinical settings could have fundamental implications in the field of drug discovery. Furthermore, a new class of targeted prodrug treatments takes advantage of high enzyme activity to tailor therapy and improve treatment outcomes. Herein, we report the design and synthesis of new magnetic resonance imaging (MRI) agents that quantitatively detect β-galactosidase and β-glucuronidase activities by measuring changes in chemical exchange saturation transfer (CEST).

Targeting a Rate-Promoting Vibration with an Allosteric Mediator in Lactate Dehydrogenase.

We present a new type of allosteric modulation in which a molecule bound outside the active site modifies the chemistry of an enzymatic reaction through rapid protein dynamics. As a test case for this type of allostery, we chose an enzyme with a well-characterized rate-promoting vibration, lactate dehydrogenase; identified a suitable small molecule for binding; and used transition path sampling to obtain ensembles of reactive trajectories. We found that the small molecule significantly affected the reaction by changing the position of the transition state and, through applying committor distribution analysis, showed that it removed the protein component from the reaction coordinate.

Modulating Enzyme Catalysis through Mutations Designed to Alter Rapid Protein Dynamics.

The relevance of sub-picosecond protein motions to the catalytic event remains a topic of debate. Heavy enzymes (isotopically substituted) provide an experimental tool for bond-vibrational links to enzyme catalysis. A recent transition path sampling study with heavy purine nucleoside phosphorylase (PNP) characterized the experimentally observed mass-dependent slowing of barrier crossing (Antoniou, D.

The enzymatic reaction catalyzed by lactate dehydrogenase exhibits one dominant reaction path.

Enzymes are the most efficient chemical catalysts known, but the exact nature of chemical barrier crossing in enzymes is not fully understood. Application of transition state theory to enzymatic reactions indicates that the rates of all possible reaction paths, weighted by their relative probabilities, must be considered in order to achieve an accurate calculation of the overall rate. Previous studies in our group have shown a single mechanism for enzymatic barrier passage in human heart lactate dehydrogenase (LDH).

Stable mixed-valent radicals from platinum(II) complexes of a bis(dioxolene) ligand.

Three diplatinum(II) complexes [{PtL}2(μ-thea)] (H4thea = 2,3,6,7-tetrahydroxy-9,10-dimethyl-9,10-dihydro-9,10-ethanoanthracene) have been prepared, with diphosphine or bipyridyl "L" co-ligands. One-electron oxidation of these complexes gave radical cations containing a mixed-valent [thea·](3-) ligand with discrete catecholate and semiquinonate centers separated by quaternary methylene spacers. The electronic character of these radicals is near the Robin-Day class II/III border determined by UV/Vis/NIR and EPR spectroscopies.

Z-Selective ring opening of vinyl oxetanes with dialkyl dithiophosphate nucleophiles.

Dialkyl dithiophosphates selectively ring open vinyl oxetanes in excellent yields under mild reaction conditions to form useful allylic thiophosphate products with high Z-selectivity.

Protein dynamics and the enzymatic reaction coordinate.

This chapter discusses progress over the past 15 years in understanding the role of protein dynamics in enzymatically catalyzed chemical reactions. Research has shown that protein motion on all timescales from femtoseconds to milliseconds can contribute to function, and in particular in some enzymes there are sub-picosecond motions, on the same timescale as barrier passage, the couple directly to chemical transformation, and are thus part of the reaction coordinate. Approaches such as transition path sampling and committor analysis have greatly enhanced our understanding of these processes.

Changes in protein architecture and subpicosecond protein dynamics impact the reaction catalyzed by lactate dehydrogenase.

We have previously established the importance of a promoting vibration, a subpicosecond protein motion that propagates through a specific axis of residues, in the reaction coordinate of lactate dehydrogenase (LDH). To test the effect that perturbation of this motion would have on the enzymatic reaction, we employ transition path sampling to obtain transition path ensembles for four independent LDH enzymatic systems: the wild type enzyme, a version of the enzyme expressing heavy isotopic substitution, and two enzymes with mutations in the promoting vibration axis. We show that even slight changes in the promoting vibration of LDH result in dramatic changes in enzymatic chemistry.

New directions in targeting protein kinases: focusing upon true allosteric and bivalent inhibitors.

Over the past decade, therapeutics that target subsets of the 518 human protein kinases have played a vital role in the fight against cancer. Protein kinases are typically targeted at the adenosine triphosphate (ATP) binding cleft by type I and II inhibitors, however, the high sequence and structural homology shared by protein kinases, especially at the ATP binding site, inherently leads to polypharmacology. In order to discover or design truly selective protein kinase inhibitors as both pharmacological reagents and safer therapeutic leads, new efforts are needed to target kinases outside the ATP cleft.

Split-protein systems: beyond binary protein-protein interactions.

It has been estimated that 650,000 protein-protein interactions exist in the human interactome (Stumpf et al., 2008), a subset of all possible macromolecular partnerships that dictate life. Thus there is a continued need for the development of sensitive and user-friendly methods for cataloguing biomacromolecules in complex environments and for detecting their interactions, modifications, and cellular location.

Profiling small molecule inhibitors against helix-receptor interactions: the Bcl-2 family inhibitor BH3I-1 potently inhibits p53/hDM2.

We validate a practical methodology for the rapid profiling of small molecule inhibitors of protein-protein interactions. We find that a well known BH3 family inhibitor can potently inhibit the p53/hDM2 interaction.

A turn-on split-luciferase sensor for the direct detection of poly(ADP-ribose) as a marker for DNA repair and cell death.

Designed sensors comprising split-firefly luciferase conjugated to tandem poly(ADP-ribose) binding domains allow for the direct solution phase detection of picogram quantities of PAR and for monitoring temporal changes in poly(ADP-ribosyl)ation events in mammalian cells.

Glycopeptides related to beta-endorphin adopt helical amphipathic conformations in the presence of lipid bilayers.

A series of glycosylated endorphin analogues designed to penetrate the blood-brain barrier (BBB) have been studied by circular dichroism and by 2D-NMR in the presence of water; TFE/water; SDS micelles; and in the presence of both neutral and anionic bicelles. In water, the glycopeptides showed only nascent helix behavior and random coil conformations. Chemical shift indices and nuclear Overhauser effects (NOE) confirmed helices in the presence of membrane mimics.

Quantitative Correlation of Raman Spectral Indicators in Determining Conformational Order in Alkyl Chains.

The correlation of Raman spectral indicators for the determination of alkyl chain interactions and conformational order is presented. These investigations probe the conformational order of bulk octadecane and low molecular weight polyethylene as they undergo solid/liquid phase transitions. Spectral indicators are quantitatively correlated to the [ν(CH)]/[ν(CH)], as this is the primary indicator of rotational and conformational order obtained empirically from Raman spectra.