Modeling the Mechanical Response of Microtubule Lattices to Pressure.

Microtubules, the largest and stiffest filaments of the cytoskeleton, have to be well adapted to the high levels of crowdedness in cells to perform their multitude of functions. Furthermore, fundamental processes that involve microtubules, such as the maintenance of the cellular shape and cellular motion, are known to be highly dependent on external pressure. In light of the importance of pressure for the functioning of microtubules, numerous studies interrogated the response of these cytoskeletal filaments to osmotic pressure, resulting from crowding by osmolytes, such as poly(ethylene glycol)/poly(ethylene oxide) (PEG/PEO) molecules, or to direct applied pressure.

Proof of Principle that Molecular Modeling Followed by a Biophysical Experiment Can Develop Small Molecules that Restore Function to the Cardiac Thin Filament in the Presence of Cardiomyopathic Mutations.

This article reports a coupled computational experimental approach to design small molecules aimed at targeting genetic cardiomyopathies. We begin with a fully atomistic model of the cardiac thin filament. To this we dock molecules using accepted computational drug binding methodologies.

Mechanics of the Microtubule Seam Interface Probed by Molecular Simulations and in Vitro Severing Experiments.

Microtubules (MTs) are structural components essential for cell morphology and organization. It has recently been shown that defects in the filament's lattice structure can be healed to create stronger filaments in a local area and ultimately cause global changes in MT organization and cell mobility. The ability to break, causing a defect, and heal appears to be a physiologically relevant and important feature of the MT structure.

Measurement and Prediction of Chlorine Kinetic Isotope Effects in Enzymatic Systems.

Approaches to determine chlorine kinetic isotope effects (Cl-KIEs) on enzymatic dehalogenations are discussed and illustrated by representative examples. Three aspects are considered. First methodology for experimental measurement of Cl-KIEs, with stress being on FAB-IRMS technique developed in our laboratory, is described.

Molybdenum Trihydride Complexes: Computational Model of Oxidatively Induced Reductive Elimination of Dihydrogen.

Recent experimental work shows that the 18-electron molybdenum complexes (1,2,4-CHtBu)Mo(PMe)H (CpMoH) and (CHiPr)Mo(PMe)H (CpMoH) undergo oxidatively induced reductive elimination of dihydrogen (H), slowly forming the 15-electron monohydride species in tetrahydrofuran and acetonitrile. The 17-electron [CpMoH] derivative was stable enough to be characterized by X-ray diffraction, while [CpMoH] was not. Density functional theory calculations of the H elimination pathways for both complexes in the gas phase and in a continuum solvent model indicate that H elimination from [CpMoH] has a lower barrier than that from [CpMoH].

Molybdenum Trihydride Complexes: Computational Determinations of Hydrogen Positions and Rearrangement Mechanisms.

In crystal structures of the molybdenum complexes [(1,2,4-C5H2(t)Bu3)Mo(PMe3)2H3] (Cp(t)Bu3) and [(C5H(i)Pr4)Mo(PMe3)2H3] (Cp(i)Pr4), the Mo-bound hydrogen positions were resolved for Cp(t)Bu3, but not for Cp(i)Pr4. NMR experiments revealed the existence of an unknown mechanism for hydrogen atom exchange in these molecules, which can be "frozen out" for Cp(t)Bu3 but not for Cp(i)Pr4. Density functional theory calculations of the most stable conformations for both complexes in the gas phase and in a continuum solvent model indicate that the H's of the Cp(i)Pr4 complex are unresloved because of their disorder, which does not occur for Cp(t)Bu3.

A computational study on enzymatically driven oxidative coupling of chlorophenols: an indirect dehalogenation reaction.

Density functional theory calculations have been used to describe the mechanism of the dimerization reaction catalyzed by peroxidases and predict whether it could be accompanied by chlorine isotopic fractionation when various chlorophenols are used as their substrates. Since free radicals formed during the catalytic cycle of peroxidases can undergo coupling reactions (either radical-radical or radical-molecule) that can lead to dimers and also polymers formation four different pathways have been considered: radical-anion, radical-cation, radical-radical (singlet state) and radical-radical (triplet state). The following substrates have been investigated: 2-chlorophenol, 4-chlorophenol, 2,4,6-trichlorophenol and 4-chloro-2,6-dimethylphenol.

Oxidative dechlorination of halogenated phenols catalyzed by two distinct enzymes: Horseradish peroxidase and dehaloperoxidase.

The mechanism of the dehalogenation step catalyzed by dehaloperoxidase (DHP) from Amphitrite ornata, an unusual heme-containing protein with a globin fold and peroxidase activity, has remarkable similarity with that of the classical heme peroxidase, horseradish peroxidase (HRP). Based on quantum mechanical/molecular mechanical (QM/MM) modeling and experimentally determined chlorine kinetic isotope effects, we have concluded that two sequential one electron oxidations of the halogenated phenol substrate leads to a cationic intermediate that strongly resembles a Meisenheimer intermediate - a commonly formed reactive complex during nucleophilic aromatic substitution reactions especially in the case of arenes carrying electron withdrawing groups.

Kinetic isotope effects on dehalogenations at an aromatic carbon.

In order to interpret the observed isotopic fractionation it is necessaryto understand its relationship with the isotope effect(s) on steps that occur during the conversion of the initial reactant to the final product. We examine this relationship from the biochemical point of view and elaborate on the consequences of the assumptions that it is based on. We illustrate the discrepancies between theoretical and experimental interpretation of kinetic isotope effects on examples of dehalogenation reactions that occur at an aromatic carbon atom.

Mechanism of the reaction catalyzed by DL-2-haloacid dehalogenase as determined from kinetic isotope effects.

dl-2-Haloacid dehalogenase from Pseudomonas sp. 113 is a unique enzyme because it acts on the chiral carbons of both enantiomers, although its amino acid sequence is similar only to that of d-2-haloacid dehalogenase from Pseudomonas putida AJ1 that specifically acts on (R)-(+)-2-haloalkanoic acids. Furthermore, the catalyzed dehalogenation proceeds without formation of an ester intermediate; instead, a water molecule directly attacks the alpha-carbon of the 2-haloalkanoic acid.