Computational study of ketosteroid isomerase: insights from molecular dynamics simulation of enzyme bound substrate and intermediate

Delta(5)-3-Ketosteroid Isomerase (KSI) catalyzes the isomerization of 5,6-unsaturated ketosteroids to their 4,5-unsaturated isomers at a rate approaching the diffusion limit. The isomerization reaction follows a two-step general acid-base mechanism starting with Asp38-CO(2)(-) mediated proton abstraction from a sp(3)-hybridized carbon atom, alpha to carbonyl group, providing a dienolate intermediate. In the second step, Asp38-CO(2)H protonates the C6 of the intermediate providing a 4,5-unsaturated ketosteroid. The details of the mechanism have been highly controversial despite several experimental and computational studies of this enzyme. The general acid-base catalysis has been proposed to involve either a catalytic diad or a cooperative hydrogen bond mechanism. In this paper, we report our results from the 1.5 nanosecond molecular dynamics (MD) simulation of enzyme bound natural substrate (E.S) and enzyme bound intermediate (E.In) solvated in a TIP3P water box. The final coordinates from our MD simulation strongly support the cooperative hydrogen bond mechanism. The MD simulation of E.S and E.In shows that both Tyr14 and Asp99 are hydrogen bonded to the O3 of the substrate or intermediate. The average hydrogen bonding distance between Tyr14-OH and O3 becomes shorter and exhibits less fluctuation on E.S --> E.In. We also observe dynamic motions of water moving in and out of the active site in the E.S structures. This free movement of water disappears in the E.In structures. The active site is shielded by hydrophobic residues, which come together and squeeze out the waters from the active site in the E.In complex.     

A facile and novel route to unprecedented manganese C4 cumulenic complexes

The theoretically characterized (DFT) C4 cumulenic species Mn(C5H4R)(dmpe) [=C=C=C=C(SnPh3)2] was obtained by photolysis of the C(sp2)-Sn bond in the vinylidene complex Mn(C5H4R)(dmpe)[=C=C(SnPh3)-C[triple bond]CSnPh3], which in turn was prepared by a thermal reaction from MnC5H4R(dmpe)(C7H8) and Ph3Sn-C4-SnPh3.     

Efficient formation of novel and versatile building blocks from mucohalic acids: new substitute for tetronic acid and γ-alkylidenebutenolide

Novel and useful building blocks were synthesized efficiently by DABCO mediated highly selective dehalogenation of Knoevenagel aldol adducts of mucochloric acid and mucobromic acid. These new compounds were found to undergo palladium catalyzed C-C bond forming reactions (Suzuki and Sonogashira cross-coupling) in high yields.     

Computer simulations of trypanosomal nucleoside hydrolase: determination of the protonation state of the bound transition-state analogue

Inosine-uridine nucleoside hydrolase (IU-NH) catalyzes the hydrolysis of nucleosides into base and ribose moieties via a ribooxocarbenium ion transition state, which has been characterized using kinetic isotope effects. Protozoan parasites lack de novo purine and pyrimidine biosynthesis and depend on the purine salvage from the host. Vern Schramm and co-workers characterized p-aminophenyliminoribitol (pAPIR) to be a potent inhibitor of IU-NH from Crithidia fasciculata with K(d) of 30 nM. The cyclic amine function of the iminoribitol ring can be either protonated (pAPIRH(+)) or unprotonated (pAPIR). pAPIRH(+) resembles the charge and geometry of the ribooxocarbenium ion transition state and can be looked upon as a transition-state analogue inhibitor; however, it is known that the pAPIR species is initially bound to the enzyme. We have characterized the pAPIRH(+) species as resident of the active site using ab initio calculations and molecular dynamics simulations. This is a novel use of molecular dynamics to investigate the protonation state of the bound ligand to the active site. Nanosecond molecular dynamics simulations reveal a short hydrogen-bonding network between pAPIRH(+)-O2'-Asp14-His241 triad, which is not seen in the crystal structure. Other features discussed are: hydrogen bonding between pAPIRH(+) and Asn168, unusual geometry of the iminoribitol ring, and hydrophobic interactions.     

Bleaching-resistant,Near-continuous Single-molecule Fluorescence and FRET Based on Fluorogenic and Transient DNA Binding

Photobleaching of fluorescent probes limits the observation span of typical single-molecule fluorescence measurements and hinders observation of dynamics at long timescales. Here, we present a general strategy to circumvent photobleaching by replenishing fluorescent probes via transient binding of fluorogenic DNAs to complementary DNA strands attached to a target molecule. Our strategy allows observation of near-continuous single-molecule fluorescence for more than an hour, a timescale two orders of magnitude longer than the typical photobleaching time of single fluorophores under our conditions. Using two orthogonal sequences, we show that our method is adaptable to Förster Resonance Energy Transfer (FRET) and that can be used to study the conformational dynamics of dynamic structures, such as DNA Holliday junctions, for extended periods. By adjusting the temporal resolution and observation span, our approach enables capturing the conformational dynamics of proteins and nucleic acids over a wide range of timescales.     

Beryllium bonding with noble gas atoms

Quantum chemical calculations were carried out to investigate the nature of the bonding between a neutral Be₃ ring and noble gas atom. Electronic structure calculation for these complexes was carried out at different computational levels in association with natural bond orbital, quantum theory of atoms in molecules, electron localization function, symmetry adapted perturbation theory, and molecular electrostatic potential surface analysis of Be₃ complexes. The Be atoms in the Be₃ moiety are chemically bonded to one another, with the Be Be bond dissociation energy being ~125 kJ mol⁻¹. The Be₃ ring interacts with the noble gases through non-covalent interactions. The binding energies of the noble gas atoms with the Be₃ ring increases with increase in their atomic number. The non-covalent interaction index, density overlap region indicator and independent gradient model analyses reveal the presence of non-covalent inter-fragment interactions in the complexes. Energy decomposition analysis reveals that dispersion plays the major role towards stabilizing these systems.     

Synthesis of a new family of hexakisferrocenyl hexagons and their electrochemical behavior

The design and synthesis of two new hexakisferrocenyl hexagons has been achieved via coordination-driven self-assembly wherein the size and relative distribution of six ferrocene moieties has been precisely controlled. Insight into the structure and electronic properties of these supramolecules was obtained through electrochemical studies.     

The Mechanisms of Rectification in Au|Molecule|Au Devices Based on Langmuir–Blodgett Monolayers of Iron(III) and Copper(II) Surfactants

Langmuir–Blodgett films of metallosurfactants were used in Au|molecule|Au devices to investigate the mechanisms of current rectification.     

Synthesis,characterization and fluorescence properties of hexanuclear zinc(II) complexes

Two hexanuclear zinc(II) complexes, [Zn₆(L¹)₂(μ₂-OH)₂(μ₂-CH₃COO)₈] · CH₃CN (1 · CH₃CN) and [Zn₆(L²)₂(μ₂-OH)₂(μ₂-CH₃COO)₈] · 4CH₃CN (2 · 4CH₃CN), where HL¹ = 4-methyl-2,6-bis(cyclohexylmethyliminomethyl)-phenol and HL² = 4-methyl-2,6-bis(1-naphthalylmethyliminomethyl)-phenol, have been synthesized and characterized by elemental analysis, FT-IR and fluorescence spectroscopic methods, and by X-ray diffraction analysis. In the asymmetric unit of complex 1, two of the three zinc atoms have pentacoordinate geometries and the other is tetrahedrally coordinated, whereas the three distinct Zn atoms in complex 2 adopt three different coordination environments, namely distorted octahedral, trigonal bipyramidal and tetrahedral. The fluorescence properties of the ligands and complexes have been investigated.