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 Erdos-Rényi random networks. Various characteristic properties (e.g. the local cyclic and bonding coefficients) of the network in liquid water could be reproduced by small world and/or Erdos-Rényi networks, but the ring size distribution of water is unique and none of the studied graph models could describe it. Using the inverse participation ratio of the Laplacian eigenvectors we characterized the network inhomogeneities found in water and showed that similar phenomena can be observed in Erdos-Rényi and small world graphs. We demonstrated that the topological properties of the hydrogen bond network found in liquid water systematically change with the temperature and that increasing temperature leads to a broader ring size distribution. We applied the studied topological indices to the network of water molecules with four hydrogen bonds, and showed that at low temperature (250 K) these molecules form a percolated or nearly-percolated network, while at ambient or high temperatures only small clusters of four-hydrogen bonded water molecules exist.

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. The divergence is quenched by rotational excitation but returns if the reactant rotates fast. The thermal rate coefficients for vibrationally excited reactants are very large, approach or exceed the gas kinetic limit because of the capture-type divergence at low collision energies. The Arrhenius activation energies assume small negative values at and below room temperature, if the vibrational quantum number is larger than 1 for HCl and larger than 3 for HF. The exchange reaction also exhibits capture-type divergence, but the rate coefficients are larger. Comparisons are presented between classical and quantum mechanical results at low collision energies. At low collision energies the importance of the exchange reaction is enhanced by a roaming atom mechanism, namely, collisions leading to H atom exchange but bypassing the exchange barrier. Such collisions probably have a large role under ultracold conditions. The calculations indicate that for roaming to occur, long-range attractive interaction and small relative kinetic energy in the chemical reaction at the first encounter are necessary, which ensures that the partners can not leave the attractive well. Large orbital angular momentum of the primary products (equivalent to large rotational excitation in a unimolecular reaction) is favorable for roaming.

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. The potential surfaces of excited states are characterized by numerous avoided and real crossings such that the TSH calculations show rapid cascading down to the lowest excited singlet or triplet states, and then slower the dissociation of these lowest states. Product branching for electron-impact dissociation was therefore estimated by combining the electron-impact excitation cross sections with TSH product branching ratios that were obtained from the lowest singlet and triplet states, with the singlet dissociation giving a comparable formation of CH(2) and CH(3) while triplet dissociation gives CH(3) exclusively. The overall branching in electron-impact dissociation is dominated by CH(3) over CH(2). A small branching yield for CH is also predicted.

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. In accordance with selectivity data for subtype 2 vs. 3, docking and molecular dynamics calculations suggest similar orthosteric substrate (inhibitor) conformations and binding crevices but distinguishable allosteric Zn(2+) ion binding motifs. Considering the occluded conformational states of glial human gamma-aminobutyric acid transporter subtypes, we found major semi-extended and minor ring-like conformations of zwitterionic gamma-aminobutyric acid in complex with Na(+) ion. The existence of the minor ring-like conformation of gamma-aminobutyric acid in complex with Na(+) ion may be attributed to the strengthening of the intramolecular H-bond by the electrostatic effect of Na(+) ion. Coupling substrate uptake into cells with the thermodynamically favorable Na(+) ion movement through substrate-Na(+) ion complex formation may be a mechanistic principle featuring transmembrane neurotransmitter-sodium symporter proteins.

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. High resolution data revealed that the extended Glu conformation is conserved in the binding crevice of all ionotropic Glu receptors (iGluRs). Furthermore, the extended conformations of Glu that characterize iGluRs and mGluRs are distinguishable by distance and torsion angle parameters, such as deltaC1-C2 and Calpha-Cbeta-Cgamma-C2. By contrast, a bent Glu conformation is recognized in Glu transporters.

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. This ligand binding mode visibly ensures the passage of GABA and substrate inhibitors (R)-homo-beta-Pro, (R)-nipecotic acid, and guvacine. It might therefore represent the principle, sufficient for sorting out less-effective or non-GAT ligands such as beta-Pro, (S)-nipecotic acid, (R)-baclofen, Glu, and Leu.

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

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. Solution NMR structure of the ternary complex of human I-BABP with glycocholate and glycochenodeoxycholate reveals an extensive network of hydrogen bonds and hydrophobic interactions stabilizing the bound bile salts. Conformational changes accompanying bile salt binding affects four major regions in the protein including the C/D, E/F and G/H loops as well as the helical segment. Most of these protein regions coincide with a previously described network of millisecond time scale fluctuations in the apo protein, a motion absent in the bound state. Comparison of the heterotypic doubly ligated complex with the unligated form provides further evidence of a conformation selection mechanism of ligand entry. Structural and dynamic aspects of human I-BABP-bile salt interaction are discussed and compared with characteristics of ligand binding in other members of the intracellular lipid binding protein family. PROTEIN DATA BANK ACCESSION NUMBERS: The coordinates of the 10 lowest energy structures of the human I-BABP : GCDA : GCA complex as well as the distance restraints used to calculate the final ensemble have been deposited in the Brookhaven Protein Data Bank with accession number 2MM3.

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. Simulations performed in the 1-10 ns range of time elucidated persistent formation of halfextended minor and H-bridged major GABA conformations, referred to as binding and traverse conformations, respectively. The traverse GABA conformation was further stabilized by GAT1-bound Na(+)(1). We also observed Na(+)(1) translocation to GAT1-bound Cl(-) as well as the appearance of water molecules at GABA and GAT1-bound Na(+)(2), conjecturing causality. Scaling dynamics suggest that the traverse GABA conformation may be valid for developing substrate inhibitors with high efficacy. The potential for this finding is significant with impact not only in pharmacology but wherever understanding of the mechanism of neurotransmitter uptake is valuable.

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. Inhibition of F(1)F(0)-ATP synthase by efrapeptins results in the disruption of the Hsp90 complexing with its substrate proteins and, in most cases, in the degradation of the latter. Hsp90-client proteins affected by the inhibition of F(1)F(0)-ATP synthase included ERalpha, mutated p53 (m.p53), Hsp70, Hsp27, and caspase-3 but not Raf-1. This is the first report identifying caspase-3 as a substrate protein of Hsp90. Unlike typical Hsp90 inhibitors, efrapeptin treatment triggers Hsp70 downregulation in parallel with depletion of Hsp90. This suggests that suppression of Hsp90 chaperone function through inhibition of F(1)F(0)-ATP synthase does not result in activation of transcription factor HSF-1, a generally unfavorable consequence of anti-cancer treatments based on Hsp90 inhibition.