Structural determinants of ligand binding in the ternary complex of human ileal bile acid binding protein with glycocholate and glycochenodeoxycholate obtained from solution NMR.

Unlabelled: Besides aiding digestion, bile salts are important signal molecules exhibiting a regulatory role in metabolic processes. Human ileal bile acid binding protein (I-BABP) is an intracellular carrier of bile salts in the epithelial cells of the distal small intestine and has a key role in the enterohepatic circulation of bile salts. Positive binding cooperativity combined with site selectivity of glycocholate and glycochenodeoxycholate, the two most abundant bile salts in the human body, make human I-BABP a unique member of the family of intracellular lipid binding proteins.

Sodium-assisted formation of binding and traverse conformations of the substrate in a neurotransmitter sodium symporter model.

Therapeutics designed to increase synaptic neurotransmitter levels by inhibiting neurotransmitter sodium symporters (NSSs) classify a strategic approach to treat brain disorders such as depression or epilepsy, however, the critical elementary steps that couple downhill flux of sodium to uphill transport of neurotransmitter are not distinguished as yet. Here we present modelling of NSS member neuronal GAT1 with the substrate γ-aminobutyric acid (GABA), the major inhibitory neurotransmitter. GABA binding is simulated with the occluded conformation of GAT1 homodimer in an explicit lipid/water environment.

Hydrogen bond network topology in liquid water and methanol: a graph theory approach.

Networks are increasingly recognized as important building blocks of various systems in nature and society. Water is known to possess an extended hydrogen bond network, in which the individual bonds are broken in the sub-picosecond range and still the network structure remains intact. We investigated and compared the topological properties of liquid water and methanol at various temperatures using concepts derived within the framework of graph and network theory (neighbour number and cycle size distribution, the distribution of local cyclic and local bonding coefficients, Laplacian spectra of the network, inverse participation ratio distribution of the eigenvalues and average localization distribution of a node) and compared them to small world and Erdős-Rényi random networks.

Modeling the electron-impact dissociation of methane.

The product yield of the electron-impact dissociation of methane has been studied with a combination of three theoretical methods: R-matrix theory to determine the electronically inelastic collisional excitation cross sections, high-level electronic structure methods to determine excited states energies and derivative couplings, and trajectory surface hopping (TSH) calculations to determine branching in the dissociation of the methane excited states to give CH(3), CH(2), and CH. The calculations involve the lowest 24 excited-state potential surfaces of methane, up to the ionization energy. According to the R-matrix calculations, electron impact preferentially produces triplet excited states, especially for electron kinetic energies close to the dissociation threshold.

Bimolecular reactions of vibrationally excited molecules. Roaming atom mechanism at low kinetic energies.

Quasiclassical trajectory calculations have been performed for the H + H'X(v) → X + HH' abstraction and H + H'X(v) → XH + H' (X = Cl, F) exchange reactions of the vibrationally excited diatomic reactant at a wide collision energy range extending to ultracold temperatures. Vibrational excitation of the reactant increases the abstraction cross sections significantly. If the vibrational excitation is larger than the height of the potential barrier for reaction, the reactive cross sections diverge at very low collision energies, similarly to capture reactions.

Characterization of binding mode of imatinib to human α1-acid glycoprotein.

Imatinib (IMT) is a selective tyrosine kinase inhibitor, used in the treatment of chronic myeloid leukemia and gastrointestinal stromal tumors. Its strong plasma protein binding was found to belong to the F1*S genetic variant of α(1)-acid glycoprotein (AGP). In this work, comparative AGP binding studies were performed with IMT fragment molecules to reveal which parts of the molecule are important in the high-affinity interaction provoking specific spectral changes.

Assessing structure, function and druggability of major inhibitory neurotransmitter gamma-aminobutyrate symporter subtypes.

Ambient level of gamma -aminobutyric acid (GABA), the major inhibitory neurotransmitter of the brain is mediated by neuronal and glial GABA transporters (GATs), members of the sodium and chloride ion-dependent solute carrier family. The neuronal GABA transporter subtype (GAT-1) has already been proven to be the target for the antiepileptic drug Tiagabine. However, druggability of glial GAT-2 and GAT-3 is yet to be established.

Substrate-Na+ complex formation: coupling mechanism for gamma-aminobutyrate symporters.

Crystal structures of transmembrane transport proteins belonging to the important families of neurotransmitter-sodium symporters reveal how they transport neurotransmitters across membranes. Substrate-induced structural conformations of gated neurotransmitter-sodium symporters have been in the focus of research, however, a key question concerning the mechanism of Na(+) ion coupling remained unanswered. Homology models of human glial transporter subtypes of the major inhibitory neurotransmitter gamma-aminobutyric acid were built.

Emerging the role of the structure of brain membrane targets recognizing glutamate.

Ligand-bound and free structures of brain membrane targets for L-glutamate (Glu) suggest the view, that quaternary rearrangements are associated with ligand binding. Rearrangement of the machinery of the signaling apparatus, such as molecular switches, recognition sites and the target structures for ligand binding of Glu-operated ion channel and heptahelical G-protein-coupled family receptors have been quantified and compared with the use of the root mean square (RMS) values. In addition to conformational rearrangement of the Glu receptor structures in complex with a series of ligands, conformations of Glu in various target structures became available.

Major human gamma-aminobutyrate transporter: in silico prediction of substrate efficacy.

The inhibitory gamma-aminobutyric acid transporter subtype 1 (GAT1) maintains low resting synaptic GABA level, and is a potential target for antiepileptic drugs. Here we report a high scored binding mode that associates GABA with gating in a homology model of the human GAT1. Docking and molecular dynamics calculations recognize the amino function of GABA in the H-bonding state favoring TM1 and TM8 helix residues Y60 and S396, respectively.

F1F0-ATP synthase functions as a co-chaperone of Hsp90-substrate protein complexes.

Inhibition of heat shock protein 90 (Hsp90) has emerged as a novel intervention for the treatment of solid tumors and leukemias. Here, we report that F(1)F(0)-ATP synthase, the enzyme responsible for the mitochondrial production of ATP, is a co-chaperone of Hsp90. F(1)F(0)-ATP synthase co-immunoprecipitates with Hsp90 and Hsp90-client proteins in cell lysates of MCF-7, T47D, MDA-MB-453, and HT-29 cancer cells.

Molecular dynamics study of active-site interactions with tetracoordinate transients in acetylcholinesterase and its mutants.

The role of active-site residues in the dealkylation reaction in the P(S)C(S) diastereomer of 2-(3,3-dimethylbutyl)methylphosphonofluoridate (soman)-inhibited Torpedo californica acetylcholinesterase (AChE) was investigated by full-scale molecular dynamics simulations using CHARMM: >400 ps equilibration was followed by 150-200 ps production runs with the fully solvated tetracoordinate phosphonate adduct of the wild-type, Trp84Ala and Gly199Gln mutants of AChE. Parallel simulations were carried out with the tetrahedral intermediate formed between serine-200 Ogamma of AChE and acetylcholine. We found that the NepsilonH in histidine H(+)-440 is positioned to protonate the oxygen in choline and thus promote its departure.

Origins and diversity of the aging reaction in phosphonate adducts of serine hydrolase enzymes: what characteristics of the active site do they probe?

Molecular mechanics and dynamics combined with semiempirical calculations were carried out for purposes of comparison of the active site characteristics of AChE, trypsin, and chymotrypsin as probed by their diastereomeric adducts with 2-(3,3-dimethylbutyl) methylphosphonofluoridate (soman), methylphosphonate monoester anions, and tetravalent carbonyl intermediates of the reactions of the natural substrates in each case. Glu199 is a key residue in the electrostatic catalytic mechanism of AChE, in removal of the leaving group, and possibly by acting as an alternate general base catalyst. "Pushing" of an alkoxy ligand by Glu199 and the numerous small van der Waals interactions promote dealkylation in phosphonate adducts of AChE much more effectively than any other enzyme.

Efficient product clearance through exit channels in substrate hydrolysis by acetylcholinesterase.

The channels connecting the active site of acetylcholinesterase (AChE) to the protein exterior were mapped by computational techniques in order to find potential exit routes for charged reaction products. 3.9% of the total volume of the AChE monomer is hollow space and over 50% of the void is located in the center; it is partitioned into three chambers, a deep entry channel, below it a wide channel located in a slightly positive region of AChE and ideally suitable for the exit of negatively charged fragments and a small chamber above Trp84 and Met83.

Enantioselective and reversible inhibition of trypsin and alpha-chymotrypsin by phosphonate esters.

Trypsin is inactivated by the levorotatory enantiomers (most likely PS) of 4-nitrophenyl 4-H-, 4-CH3-,4-OCH3-, and 4-Cl-phenacyl methylphosphonates (PMNs) with second-order rate constants between 231 and 884 M-1 s-1. 4-NO2-PMN hydrolyzes before inhibiting the enzyme. The second-order rate constants for the inactivation of alpha-chymotrypsin by the levorotatory enantiomers of the five PMNs are between 37,000 and 770,000 M-1 s-1, and those for the dextrorotatory enantiomers are between 400 and 640 M-1 s-1; the enantioselectivity is 90-1880.