A Catalyst pharmacophore model has been developed for the benzodiazepine site within the GABAA receptor complex. The model is based on a pharmacophore model originally proposed by Cook and co-workers (Drug Des. Discovery 1995, 12, 193–248) and further developed by Kahnberg et al. (J. Med. Chem. 2002, 45, 4188–4201). The Catalyst pharmacophore model has been validated by using a series of flavonoids with varying affinities for the benzodiazepine receptor and has then been used as a search query in database searching with the aim of finding novel structures which have the possibility to be modified into novel lead compounds. Five of the hits from the database searching were purchased and their affinities for the benzodiazepine site of the GABAA receptor were determined. Two of the compounds displayed Ki values below 10μM. The substance showing highest potency in-vitro displayed an affinity of 121nM making it an interesting compound for optimization. The false positive compounds (Ki values >10μM affinities) have been analysed in terms of conformational energy penalties and possibilities for hydrogen bond interactions. The analysis clearly demonstrates the need for post processing of Catalyst hits.
Homologues of the selenoprotein glutathione peroxidase (GPx) have been previously identified in poxviruses and in RNA viruses including HIV-1 and hepatitis C virus (HCV). Sequence analysis of the NS4 region of Japanese encephalitis virus (JEV) suggests it may encode a structurally related but functionally distinct selenoprotein gene, more closely related to the iron-binding protein ferredoxin than to GPx, with three highly conserved UGA codons that align with essential Cys residues of ferredoxin. Comparison of the probe JEV sequence to an aligned family of ferredoxin sequences gave an overall 30.3% identity and 45.8% similarity, and was statistically significant at 4.9 S.D. (P < 10−6) above the average score computed for randomly shuffled sequences. A 3-dimensional model of the hypothetical JEV protein (JEV model) was constructed by homology modeling using SYBYL, based upon a high resolution X-ray structure of ferredoxin (PDB code: 1awd). The JEV model and the model from 1awd were subsequently subjected to molecular dynamics simulations in aqueous medium using AMBER 6. The solution structure of the JEV model indicates that it could fold into a tertiary structure globally similar to ferredoxin 1awd, with RMSD between the averaged structures of 1.8 Å for the aligned regions. The modeling and MD simulations data also indicate that this structure for the JEV protein is energetically favorable, and that it could be quite stable at room temperature. This protein might play a role in JEV infection and replication via TNF and other cellular stimuli mediated via redox mechanisms.
In this paper, all-atom molecular dynamics simulations in explicit solvent are used to investigate the structural and dynamical determinants of the alpha-helical to beta-hairpin conformational transition of the 12-28 fragment from the full length Abeta Alzheimer's peptide. The transition from alpha-helical to beta-structure requires the peptide to populate intermediate beta-bend geometries in which several mainly hydrophobic interactions are partially formed. This is followed by the sudden collapse to ordered beta-hairpin structures and the simultaneous disruption of the hydrophobic side-chain interactions with a consequent increase in solvent exposure. The solvent exposure of hydrophobic side-chains belonging to a sequence of five consecutive residues in the beta-hairpin defines a possible starting point for the onset of the aggregation mechanisms. Several different conformations of model oligomeric (dimeric and tetrameric) aggregates are then investigated. These simulations show that while hydrophobic contacts are important to bring together different monomers with a beta-hairpin like conformation, more specific interactions such as hydrogen-bonding and coulombic interactions, should be considered necessary to provide further stabilization and ordering to the nascent fibrillar aggregates.
In a strong magnetic field, covalently bonded hydrogen nuclei located over the plane of an anisotropic π bond-containing functional group experience magnetic shielding (or deshielding) that results from the combined effect of the magnetic anisotropy of the functional group and other nearby covalent bonds plus other intramolecular shielding effects. These effects can now be calculated with reasonable accuracy using ab initio methods. We have investigated several computational probes of the magnetic shielding surface near anisotropic functional groups and compared the results to previous reports of experimental observations in example structures. GIAO-HF in Gaussian 03 was employed to calculate isotropic shielding values and to predict the net NMR shielding increment for several computational probes: methane, diatomic hydrogen, a hydrogen atom, a helium atom, or a ghost atom, each held in various positions over simple test molecules (ethene, ethyne, benzene and HCN) that contain the functional groups studied. Also, the effect of performing single point calculations versus constrained geometry-optimized calculations was examined. In addition, the effect of the angle of the orientation of the probe molecule (in the case of CH4 and H2) relative to the π bond in the test molecule was studied. Finally, the atomic charges in the molecular probes (CH4 and H2) were computed to investigate the nature of the interaction of the probe with the test molecule. The optimal, most economical computational results were obtained using single point calculations of a diatomic hydrogen probe oriented perpendicular to the surface (or axis) of the test molecule.
Analyses of the primary sequence of hemoglobin-binding protein HgbA from Actinobacillus pleuropneumoniae by comparative modelling and by a Hidden Markov Model identified its topological similarities to bacterial outer membrane receptors BtuB, FepA, FhuA, and FecA of Escherichia coli. The HgbA model has a globular N-terminal cork domain contained within a 22-stranded β barrel domain, its folds being similar to the structures of outer membrane receptors that have been solved by X-ray crystallography. The barrel domain of the HgbA model superimposes onto the barrel domains of the four outer membrane receptors with rmsd values less than 1.0Å. This feature is consistent with a phylogenetic tree which indicated clustering of polypeptide sequences for three barrel domains. Furthermore, the HgbA model shares the highest structural similarity to BtuB, with the modelled HgbA barrel having approximately the same elliptical cross-section and height as that of BtuB. Extracellular loop regions of HgbA are predicted to be more extended than those of the E. coli outer membrane receptors, potentially facilitating a protein–protein interface with hemoglobin. Fold recognition modelling of the HgbA loop regions showed that 10 out of 11 predicted loops are highly homologous to known structures of protein loops that contribute to heme/iron or protein–protein interactions. Strikingly, HgbA loop 2 has structural homology to a loop in bovine endothelial nitric acid oxidase that is proximal to a heme-binding site; and HgbA loop 7 contains a histidine residue conserved in a motif that is involved in heme/hemoglobin interactions. These findings implicate HgbA loops 2 and 7 in recognition and binding of hemoglobin or the heme ligand.
A diverse set of 53 cyclooxygenase-2 (COX-2) inhibitors which were aligned in two different ways were subjected to CoMFA analysis. The first method of alignment of the molecules was based on the binding information sourced from the crystallographic study, from which CoMFA Model 1 was derived. The second mode of alignment was generated by docking the inhibitors in the binding pocket using the DOCK and AFFINITY suite of programs; this gave a second model. The CoMFA Model 2 was slightly better than Model 1 in terms of the statistical parameters r(2) and q(2). The two models could predict very well the activity of a test set of diverse molecules, with a predictive r(2) of 0.593 and 0.768, respectively. Besides the QSAR results, the docking studies give a deep insight into the H-bonding interactions between the inhibitors and residues in the active site of the enzyme, which can be exploited in designing better inhibitors. Useful ideas on activity improvement could be gleaned from these models.
In a previous work, a theoretical approach, suitable to describe systems having a large number of fermions, was proposed, and results for ferromagnetic surface clusters of medium size (100-1000 atoms) were presented. The aim of the present contribution is to complete this previous work. Several significant theoretical and technical details, omitted previously, are provided here. The obtained spin orbitals are analyzed, by studying their symmetry, energy, and d contribution properties.
Protein and DNA structures are represented at varying levels of details using ellipsoidal RGBA textured splats. The splat texture at each level is generated by rendering its children in a hierarchical model, from a distribution of viewing directions, and averaging the result. For rendering, the ellipsoids to be used are chosen adaptively, depending on the distance to the viewpoint. This technique is applied to visualize DNA coiling around nucleosomes in chromosomes.
Although it is well established that benzimidazole (BZMs) compounds exert their therapeutic effects through binding to helminth β-tubulin and thus disrupting microtubule-based processes in the parasites, the precise location of the benzimidazole-binding site on the β-tubulin molecule has yet to be determined. In the present study, we have used previous experimental data as cues to help identify this site. Firstly, benzimidazole resistance has been correlated with a phenylalanine-to-tyrosine substitution at position 200 of Haemonchus contortus β-tubulin isotype-I. Secondly, site-directed mutagenesis studies, using fungi, have shown that other residues in this region of the protein can influence the interaction of benzimidazoles with β-tubulin. However, the atomic structure of the αβ-tubulin dimer shows that residue 200 and the other implicated residues are buried within the protein. This poses the question: how might benzimidazoles interact with these apparently inaccessible residues? In the present study, we present a mechanism by which those residues generally believed to interact with benzimidazoles may become accessible to the drugs. Furthermore, by docking albendazole-sulphoxide into a modelled H. contortus β-tubulin molecule we offer a structural explanation for how the mutation conferring benzimidazole resistance in nematodes may act, as well as a possible explanation for the species-specificity of benzimidazole anthelmintics.
A three-dimensional (3-D) model of both subunits of interleukin 12 (IL-12) has been created through molecular modeling. Initial assignment of coordinates in the model of the p40 subunit was based on established amino acid sequence homology between the second and third domains of p40 and the human growth hormone receptor (GHR) and new observations of similarity between the first domain of p40 and the N-terminal domain of CD4. Human growth hormone (GH) served as the reference protein for the p35 chain. Furthermore, thorough analysis of the amino acid sequence of IL-12 revealed two distinct regions of the p40 subunit that display homology with other proteins. The first region (in domain two) contains the sequence RGD, which is found in adhesion proteins (such as fibronectin), and the nearby sequence VTCG, which occurs in a diverse set of molecules, Including thrombospondin, properdin, and circumsporozoite proteins of Plasmodium. The second region of homology spans the third domain of p40 and shows marked similarity with the gastrointestinal peptides, such as secretin and glucagon and their preprohormones. We conclude (1) that the regions of homology define functionally important segments of p40 that are fully exposed at the protein surface, and (2) that the third domain of p40 (and its equivalent in the cytokine receptor family) is derived from the same ancestral genes as the gastrointestinal peptides.
AM1 quantum mechanical reaction coordinate (RC) calculations were run to simulate the rate-limiting deacylation (hydrolysis) reaction for a series of para-X-PhC(O)NHCH2-C(Y)-S-papain intermediates, where X = OCH3, CH3, H, Cl, NO2 and Y = O (thioester) or S (dithioester), for which a large body of structural kinetic, and spectroscopic data is available. Several reaction zones, in particular the so-designated Large Zone and Small Zone, were extracted for these RC simulations from the fully solvated and energy-minimized X-ray crystal structure of papain (pdb9pap) bound to the appropriate substrate moiety. The major structural difference between these two zones was rite absence of the oxyanion hole in the latter. For both the thioester and dithioester cases, the calculated E(alpha) value associated with the parent (X = H) acyl-enzyme intermediate was lower by ca. 10 kcal/mol for the Large Zone than for the Small Zone. The magnitude of this difference suggests that the oxidation hole plays a functional if not essential role in stabilizing the anionic tetrahedral intermediate with the cystein proteases. The calculated E(alpha) value was lower by ca. 10 kcal/mol for the thioester [-C(O)-S-] than for the corresponding dithioester [-C(S)-S-], in qualitative agreement with kinetic data for this series of substrates which reveal that the specific rate constant for deacylation k(3) is ca. 60 times larger for the former. This difference is also consistent with both AM1 and 6-31G* calculations on model intermediates, which indicate that the weaker polarity of the dithioester compared with the thioester [i.e., -C(<--S)-S- versus -C(-->O)-S-] renders the former a much poorer site for nucleophilic attack. The anionic tetrahedral intermediate is energetically more stable for the dithioester than for the corresponding thioester, a finding that is discussed in terms of its kinetic and mechanistic implications. The mode of attack by the H2O nucleophile is ''concerted'' rather than ''sequential'' in terms of the order of proton proton abstraction by His-159 and nucleophilic attack on the acyl-enzyme intermediate. While the presumably key S-thiol ... N nonbonded contact remained almost constant (ca. 2.90 Angstrom) up to formation of the [TS] structure, the substrate torsion angles phi and psi rotated significantly as the hybridization around the reaction sire transforms from sp(2) to sp(3) during formation of the tertahedral intermediate. The AM1-calculated frontier molecular orbitals for model thioester and dithioester acyl-enzyme intermediates generally associate the HOMOs with the reaction site and the LUMOs with the benzamide moiety. Computer graphics images corroborate our view that, in relation ro the S-thiol ... N interaction, the HOMOS and LUMOs should be identified, respectively, with S-thiol and N rather than the reverse, as suggested by other workers.
A three-dimensional model of the carbohydrate recognition domain of a rat macrophage C-type lectin has been constructed by comparative modeling and assessed by inverse folding analysis. Comparative modeling in the presence of low sequence similarity was based on information provided by comparison of X-ray structures and sequence-structure alignments. The sequence-structure compatibility of the model was sound. Its binding site was analyzed in comparison to the X-ray structure of a galactose-specific mutant of the mannose-binding protein. The specificity of the macrophage lectin was discussed in light of mutagenesis data on asialoglycoprotein receptors.
Similarities in the molecular structure and surface properties of the allosteric modulators of muscarinic receptors, alcuronium, gallamine, tubocurarine, and the hexamethonium compound W84, a well-known pharmacological tool, are explored. The analysis of the molecular electrostatic potential (MEP) as well as of the shape of the molecular surface is performed by self-organizing neural networks. A distorted sandwich conformation of W84 is suggested to be the active form. The importance of the MEP for binding of these compounds could be established.
VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
The ras oncogene product p21 functions as a molecular switch in the early section of the signal transduction pathway that is involved in cell growth and differentiation. When the protein is in its GTP-complexed form it is active in signal transduction, whereas it is inactive in its GDP-complexed form. The transforming activity of p21(ras) is neutralized by the mouse monoclonal antibody Y13-259, possibly by preventing GDP-GTP exchange. A molecular model of the variable fragment of Y13-259 has been derived using a knowledge-based prediction approach and computer-assisted modeling techniques. An analysis of this model while complexed with p21(ras)/(GDP) indicated that the two molecular switch regions are constrained by complex formation. Antibody binding inhibits GDP-GTP exchange through a mechanism of steric hindrance. Having identified necessary bound sites for inhibition, and explored their electrostatic properties, it should be possible to proceed with the design of antibody mimics as therapeutic agents in cancer control.
STATIS, a data analysis method used when data can be expressed as matrices, seems particularly well suited to characterize the internal molecular motions and conformational states extracted from MD trajectories. We first outline this method and the "adapted STATIS" method. Applications are presented for 18-crown-6 (simulated for 2 nsec in acetonitrile solution) and for the (L30)2Cu+ catenate (stimulated for 150 psec in chloroform). STATIS should be valuable for the classification of molecular conformations and simplified visualization of MD trajectories.
Molecular dynamics simulations of the reactions between gaseous fluorine atoms and (SiFx)n adsorbates on the Si{100} — (2 × 1) surface are performed using the SW potential and compared to simulations with the WWC reparameterization of the SW potential. Theoretical and experimental work has demonstrated that the reactive fluorosilyl layer during siliconfluorine etching is composed of tower-like adspecies of SiF, SiF2, and SiF3 groups. The objective of the simulations is to determine how the chemical composition, mechanism of formation, and energy distribution of the etched gas-phase products depend on the identity of the reacting adsorbate, the incident kinetic energy, and the parameterization of the potential energy function. Three reactions are simulated: F(g) + SiF3(a), F(g) + SiF2SiF3(a), and F(g) + SiF2SiF2SiF3(a). SiF4 is the major product and Si2F6 and Si3F8 are minor products. In Si2F6 and Si3F8, the silicon-fluorine bond that is formed is stronger than the silicon-silicon bond in the molecule and, therefore, the majority of these products have enough energy to dissociate and will fragment before reaching the detector. An SN2-like mechanism is the primary mechanism responsible for the formation of SiF4, Si2F6, and Si3F8. In addition, at higher energies, the simulations have discovered a previously unknown mechanism for the formation of SiF4, which involves an insertion between a silicon-silicon bond. The results of the simulations with the two potentials differ quite substantially in their prediction of the reactivity of the adsorbates. The SW potential predicts a 2- to 3-eV lower energy threshold for reaction and a much higher reaction cross-section, especially for the SiF4 product. These results are explained in terms of the differences in the potential energy functions used to describe the silicon-fluorine interactions. In addition, the results are compared to experimental data on silicon-fluorine etching.
The tensor fields of pressure strain imposed on protein molecules have been visualized by computer graphics and computational geometry. The pressure-induced deformations of lysozyme and myoglobin were analyzed by the present method, which regards each molecule as a patchwork of microscopic continuous bodies of Delaunay tetrahedra. The strain tensor describes the deformation of each tetrahedron. The illustrated deformations turned out to be complex and inhomogeneous ones in which local expansions and contractions concomitantly occurred. Not only the pressure deformation but also any other type of moderate deformation can be analyzed by this method.
While docking methodologies are now frequently being developed, a careful examination of the molecular surface representation, which necessarily is employed by them, is largely overlooked. There are two important aspects here that need to be addressed: how the surface representation quantifies surface complementarity, and whether a minimal representation is employed. Although complementarity is an accepted concept regarding molecular recognition, its quantification for computation is not trivial, and requires verification. A minimal representation is important because docking searches a conformational space whose extent and/or dimensionality grows quickly with the size of surface representation, making it especially costly with big molecules, imperfect interfaces, and changes of conformation that occur in binding. It is essential for a docking methodology to establish that it employs an accurate, concise molecular surface representation.Here we employ the face center representation of molecular surface, developed by Lin et al.,(1) to investigate the complementarity of molecular interface. We study a wide variety of complexes: protein/small ligand, oligomeric chain-chain interfaces, proteinase/protein inhibitors, antibody/antigen, NMR structures, and complexes built from unbound, separately solved structures. The complementarity is examined at different levels of reduction, and hence roughness, of the surface representation, from one that describes subatomic details to a very sparse one that captures only the prominent features on the surface. Our simulation of molecular recognition indicates that in all cases, quality interface complementarity is obtained. We show that the representation is powerful in monitoring the complementarity either in its entirety, or in selected subsets that maintain a fraction of the face centers, and is capable of supporting molecular docking at high fidelity and efficiency. Furthermore, we also demonstrate that the presence of explicit hydrogens in molecular structures may not benefit docking, and that the different classes of protein complexes may hold slightly different degrees of interface complementarity.
DL_POLY_2.0 is a general-purpose parallel molecular dynamics simulation package developed at Daresbury Laboratory under the auspices of the Council for the Central Laboratory of the Research Councils. Written to support academic research, it has a wide range of applications and is designed to run on a wide range of computers: from single processor workstations to parallel supercomputers. Its structure, functionality, performance, and availability are described.
