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PubMed1990

Generation of potential structures for the G-domain of chloroplast EF-Tu using comparative molecular modeling.

Comparative molecular modeling has been used to generate several possible structures for the G-domain of chloroplast elongation factor Tu (EF-Tu(chl)) based on the crystallographic data of the homologous E. coli protein. EF-Tu(chl) contains a 10 amino acid insertion not present in the E. coli protein and this region has been modeled based on its predicted secondary structure. The insertion appears to lie on the surface of the protein. Its orientation could not be determined unequivocally but several likely structures for the nucleotide binding domain of EF-Tu(chl) have been developed. The effects of the presence of water in the Mg2+ coordination sphere and of the protonation state of the GDP ligand on the conformation of the guanine nucleotide binding site have been examined. Relative binding constants of several guanine nucleotide analogs for EF-Tu(chl) have been obtained. The interactions between EF-Tu(chl) and GDP predicted to be important by the models that have been developed are discussed in relation to the nucleotide binding properties of this factor and to the interactions proposed to be important in the binding of guanine nucleotides to related proteins.

Chloroplasts↗
PubMed2003

Selective agonist binding of (S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid (AMPA) and 2S-(2alpha,3beta,4beta)-2-carboxy-4-(1-methylethenyl)-3-pyrrolidineacetic acid (kainate) receptors: a molecular modeling study.

Molecular models were constructed, using the published X-ray structure of rat glutamate receptor 2 (GluR2), for the ligand-binding domains of the human (S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid (AMPA)- and kainate-selective ionotropic glutamate receptors (iGluRs): GluR1-7 and KA1-2. Based on the analysis of the known X-ray structures of GluR2 in complex with glutamate, kainate, and AMPA, we have constructed binding motifs (relative positioning of a ligand in the binding site and the physico-chemical interactions that take place) for selected agonist ligands and found explanations for ligand-binding selectivity to homomeric receptors among the different iGluRs. Even a single sequence difference can explain significant differences in ligand-binding affinities between two receptors. In total, there are seven residues surrounding the binding cavity that affect agonist selectivity: in GluR2, these residues are Pro478, Thr480, Leu650, Ser654, Thr686, Tyr702, and Met708. Each of these seven positions has been shown, or is predicted, to influence the presence of one or more water molecules that, when present, may form bridging hydrogen bonds between particular ligands and receptors. By using this knowledge it should be possible to design new selective agonist ligands with high affinity for any AMPA/kainate receptor.

Amino Acid Sequence↗
PubMed1998

Investigation of I1-imidazoline receptors using microphysiometry and molecular modelling.

The molecular identity and structure of imidazoline receptors is still poorly understood. For example the I1-imidazoline binding site (I1-site) is localised to the plasma membrane, but it is not clear if this represents a conventional receptor. The I1-site reportedly has both high and low affinity binding states. Again it is not clear if these sites represent different states of the same receptor, or distinct molecular entities. The signal transduction mechanisms of I1-imidazoline receptors are beginning to be unravelled. There is clear evidence that ligands with high affinity for I1-sites stimulate phosphatidylcholine-selective phospholipase C in the rat adrenal medullary tumour cell line PC-12, but this may not be the case in all cell types. We investigated the possible role of this novel pathway in bovine adrenal medullary cells. Radioligand binding studies with [3H]clonidine confirmed the presence of I1-sites in membranes from these cells. Using microphysiometry, a recently developed technique for determining cellular activation, the extracellular acidification rates of cultured bovine adrenal medullary cells were unaffected by a number of imidazolines considered to be agonists at the I1-site. This suggests that there is no I1-site mediated stimulation of phosphatidylcholine specific phospholipase C in these cells. However, nicotine-stimulated increases in extracellular acidification were blocked by 100 microM clonidine. Ion channels have been suggested as another possible I1-imidazoline 'receptor' family, and may represent the low affinity I1-site detected in binding studies. I1-Site ligands can be shown to bind to, or block, several members of the ligand-gated ion channel superfamily, including the 5HT3, K+ATP, NMDA and nicotinic acetylcholine receptors. The I1-site ligands appear to be binding to, and acting at, the previously described phencyclidine binding site in these channels. Furthermore, molecular modelling suggests that I1-site selective ligands share a common three-dimensional structure with phencyclidine, and that I2-site selective ligands do not have this structure. This suggests that a phencyclidine-binding site motif may represent a novel site of action for I1-site ligands, and a search for receptors based on this motif may reveal novel imidazoline 'receptors'.

Adrenal Medulla↗
PubMed2001

Probing site specificity of DNA binding metallointercalators by NMR spectroscopy and molecular modeling.

The molecular recognition of oligonucleotides by chiral ruthenium complexes has been probed by NMR spectroscopy using the template Delta-cis-alpha- and Delta-cis-beta-[Ru(RR-picchxnMe(2)) (bidentate)](2+), where the bidentate ligand is one of phen (1,10-phenanthroline), dpq (dipyrido[3,2-f:2',3'-h]quinoxaline), or phi (9,10-phenanthrenequinone diimine) and picchxnMe(2)() is N,N'-dimethyl-N,N'-di(2-picolyl)-1,2-diaminocyclohexane. By varying only the bidentate ligand in a series of complexes, it was shown that the bidentate alone can alter binding modes. DNA binding studies of the Delta-cis-alpha-[Ru(RR-picchxnMe(2))(phen)](2+) complex indicate fast exchange kinetics on the chemical shift time scale and a "partial intercalation" mode of binding. This complex binds to [d(CGCGATCGCG)](2) and [d(ATATCGATAT)](2) at AT, TA, and GA sites from the minor groove, as well as to the ends of the oligonucleotide at low temperature. Studies of the Delta-cis-beta-[Ru(RR-picchxnMe(2))(phen)](2+) complex with [d(CGCGATCGCG)](2) showed that the complex binds only weakly to the ends of the oligonucleotide. The interaction of Delta-cis-alpha-[Ru(RR-picchxnMe(2))(dpq)](2+) with [d(CGCGATCGCG)](2) showed intermediate exchange kinetics and evidence of minor groove intercalation at the GA base step. In contrast to the phen and dpq complexes, Delta-cis-alpha- and Delta-cis-beta-[Ru(RR-picchxnMe(2))(phi)](2+) showed evidence of major groove binding independent of the metal ion configuration. DNA stabilization induced by complex binding to [d(CGCGATCGCG)](2) (measured as DeltaT(m)) increases in the order phen < dpq and DNA affinity in the order phen < dpq < phi. The groove binding preferences exhibited by the different bidentate ligands is explained with the aid of molecular modeling experiments.

Binding Sites↗
PubMed1997

Design of thermolabile bacteriophage repressor mutants by comparative molecular modeling.

Comparative molecular modeling was performed with repressor protein Rro of the temperate Lactococcus lactis bacteriophage r1t using the known 3D-structures of related repressors in order to obtain thermolabile derivatives of Rro. Rro residues presumed to stabilize a nonhomologous but structurally conserved hydrophobic pocket, which was shown to be important for thermostability of the Escherichia coli bacteriophage lambda repressor CI, were randomized. Of the derivatives that exhibited various temperature-sensitive phenotypes, one was shown to hold promise for both fundamental and industrial applications that require the controlled production of (heterologous) proteins in L. lactis.

Amino Acid Sequence↗
PubMed1999

A hypothesis for what conformation of the major adduct of (+)-anti-B[a]PDE (N2-dG) causes G-->T versus G-->A mutations based upon a correlation between mutagenesis and molecular modeling results.

Molecular modeling (simulated annealing) was used to study the conformations in dsDNA of [+ta]-B[a]P-N2-dG (R.E. Kozack and E.L.Loechler, accompanying paper), which is the major benzo[a]pyrene (B[a]P) adduct. Sixteen classes of conformations were identified, and are analyzed herein vis-a-vis the two most prominent B[a]P mutations, G-->T and G-->A base substitutions. Eight conformations seem more relevant to frameshift mutagenesis, so they are excluded, leaving eight conformations as follows. Two conformations (BPmi5 and BPmi3) retain Watson-Crick G:C base pairing having the B[a]P moiety of the adduct in the minor groove. Two conformations (BPma5 and BPma3) have the Hoogsteen orientation with B[a]P in the major groove. Four conformations are base displaced and have B[a]P stacked in the helix with the dG moiety of the adduct displaced into either the major groove (Gma5 and Gma3) or the minor groove (Gmi5 and Gmi3). Three of these eight conformations (BPma5, BPma3 and Gma3) are universally high in energy. The two conformations that retain G:C base pairing potential (BPmi5 and BPmi3) are likely to be non-mutagenic. Of the three remaining conformations, Gmi5 can be relatively low in energy, but is distorted. A correlation exists between the calculated energies for the remaining two base displaced conformations and mutagenesis for [+ta]-B[a]P-N2-dG, leading to the hypothesis that Gma5 is responsible for G-->T mutations and Gmi3 is responsible for G-->A mutations. Gma5 and Gmi3 resemble each other, except that dG is in the major and minor grooves, respectively. An incipient rationale for this hypothesis is discussed: DNA polymerase might be triggered to follow a different mutagenic pathway depending upon whether a non-informational lesion has bulk protruding into the major or minor groove. A pathway for interconversion between these eight conformations is also proposed and its implications are discussed; e.g. four steps are required to interconvert between Gma5 and Gmi3.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed1995

Modelling molecular stability in gamma B crystallin.

Molecular modelling and dynamics simulations of gamma B crystallin and a number of its adducts were used to simulate effects of post-translational modifications. N-terminal modifications which disrupted the surface charge network of gamma-crystallin did not produce significant unfolding in any part of the gamma-crystallin molecule (P > 0.05) consistent with the results of in vitro aggregation studies. There were no significant changes to the molecular volume of the protein, suggesting that adduct formation did not result in molten globule formation. Adduct formation did however increase the vulnerability of particular gamma-crystallin cysteine residues to sulphydryl bond formation and so increased the possibility of mixed disulphide formation with glutathione. Modelling of such secondary modification products (containing both N-terminal modifications and glutathione adducts) demonstrated significant (P < 0.05) structural changes. This suggests that a post-translational modification pathway leading to crystallin cross-linking and cataractogenesis proceeds via a number of co-operative steps involving both modification at the N-terminus and mixed glutathione formation.

Computer Simulation↗
PubMed1995

Interaction between a Fab fragment against gp41 of human immunodeficiency virus 1 and its peptide epitope: characterization using a peptide epitope library and molecular modeling.

The molecular interaction of the Fab fragment of the human monoclonal antibody 3D6, directed against the transmembrane protein gp41 of human immunodeficiency virus (HIV) 1, with its peptide epitope is characterized by a panel of overlapping peptides, a peptide epitope library and molecular modeling techniques. The sequence CSGKLICTTAVPW, corresponding to amino acids 605-617 of gp41, was identified as the best binding peptide (KD = 1 x 10(-8) mol/l). This peptide served as a starting point to prepare a cellulose-bound peptide epitope library in which each residue of the epitope is substituted by all L- and D-amino acids, resulting in 494 epitope peptide variants which were subsequently analyzed for binding 3D6. The library was synthesized to identify residues critical for binding and to obtain information about the molecular environment of the epitope peptide bound to 3D6. Both cysteine residues, as well as isoleucine 6, threonine 8 and proline 12, of the epitope were highly sensitive to substitution. Using the data obtained from the epitope characterization, as well as a low-resolution electron density map of a 3D6 Fab-peptide complex, a 3-D model of the Fab-peptide complex was generated by molecular modeling. The modeling experiments predict binding of the peptide, which is cyclized via the two cysteine residues, to a pocket formed dominantly by the hypervariable loops complementarity determining regions CDR3L, CDR2H and CDR3H.

Amino Acid Sequence↗
PubMed1992

The three binding domain model of adenosine receptors: molecular modeling aspects.

Using molecular modeling, adenosine receptor ligands were fitted together to maximize correlations between the three most important factors controlling binding to the receptor, namely steric, hydrophobic, and electrostatic complimentarily. Structure-activity relationships can be explained by three binding domains on the receptors. These are hydrophobic, aromatic, and ribose binding domains. We propose that the N6, C2, and C8 hydrophobic binding domains are not discreet but occupy the same region of the receptor.

Adenosine↗
PubMed2002

Designing selective COX-2 inhibitors: molecular modeling approaches.

Molecular modeling approaches have been successfully used to gain insight into the molecular mechanism of selective cyclooxygenase-2 (COX-2) inhibition. These approaches are based on X-ray structure data and results from structure-activity relationships and site-directed mutagenesis experiments. The recognition process of substrates and inhibitors by COX isoenzymes can be visualized by applying algorithms to describe local properties on the enzyme surface, thus allowing key differences in structure to be studied that may confer differential sensitivity to inhibitors. The virtual screening techniques for COX isoenzymes are rapidly improving, and the search for new selective COX-2 inhibitors has been stimulated by the tremendous success of meloxicam, celecoxib and rofecoxib in the pharmaceutical market and their potential use in new indications.

Animals↗
PubMed2000

Nontrivial extension of the two-dimensional ising model: the d-dimensional "molecular" model

A recently proposed molecular model is discussed as a nontrivial extension of the Ising model. For d=2 the two models are shown to be equivalent, while for d>2 the molecular model describes a peculiar second order transition from an isotropic high-temperature phase to a low-dimensional anisotropic low-temperature state. The general mean-field analysis is compared with the results achieved by a variational Migdal-Kadanoff real space renormalization group method and by standard Monte Carlo sampling for d=3. By finite size scaling the critical exponent has been found to be nu=0.44+/-0.02, thus establishing that the molecular model does not belong to the universality class of the Ising model for d>2.

Journal Article↗
PubMed2002

Molecular modeling of four stereoisomers of the major B[a]PDE adduct (at N(2)-dG) in five cases where the structure is known from NMR studies: molecular modeling is consistent with NMR results.

The potent mutagen/carcinogen benzo[a]pyrene (B[a]P) is metabolically activated to (+)-anti-B[a]PDE, which is known to induce a variety of mutations (e.g., GC --> TA, GC --> AT, etc.). One hypothesis for this complexity is that different mutations are induced by different conformations of its major adduct [+ta]-B[a]P-N(2)-dG when bypassed during DNA replication (perhaps by different DNA polymerases). Our previous molecular modeling studies have suggested that conformational complexity might be extensive in that B[a]P-N(2)-dG adducts appeared capable of adopting at least sixteen potential conformational classes in ds-DNA [e.g., Kozack and Loechler (1999) Carcinogenesis 21, 1953], although only eight seemed likely to be relevant to base substitution mutagenesis. Such molecular modeling studies are only likely to be valuable for the interpretation of mutagenesis results if global minimum energy conformations for adducts are found and if the differences in the energies of these different conformations can be computed reasonably accurately. One approach to assessing the reliability of our molecular modeling techniques is considered herein. Using a five-step molecular modeling protocol, which importantly included a molecular dynamics version of simulated annealing, eight conformations are studied in each of five cases. (The five cases are listed below, and were chosen because in each case the preferred solution conformation is known from a NMR study.) Of the eight conformations studied, the one computed to be lowest in energy is the same conformation as the one observed by NMR in four of the five cases: 5'-CGC sequence with [+ta]-, [-ta]-, and [+ca]-B[a]P-N(2)-dG, and 5'-TGC sequence with [+ta]-B[a]P-N(2)-dG. In the fifth case (5'-CGC sequence with [-ca]-B[a]P-N(2)-dG), the known NMR conformation is computed to be second lowest in energy, but it is within approximately 1.7 kcal of the computed lowest energy conformation. These results suggest that molecular modeling is surprisingly accurate in computing lowest energy conformations and that it should be useful in assessing the relative energies of different conformations. This is especially important given that currently molecular modeling is the only means available to study the energetics of minor conformations of DNA adducts.

Benzo(a)pyrene↗
PubMed2002

A study of the interaction of Cr(III) complexes and their selective binding with B-DNA: a molecular modeling approach.

Molecular modeling and energy minimisation calculations have been used to investigate the interaction of chromium(III) complexes in different ligand environments with various sequences of B-DNA. The complexes are [Cr(salen)(H(2)O)(2)](+); salen denotes 1, 2 bis-salicylideneaminoethane, [Cr(salprn)(H(2)O)(2)](+); salprn denotes 1, 3 bis- salicylideneaminopropane, [Cr(phen)(3)](3+); phen denotes 1, 10 phenanthroline and [Cr(en)(3)](3+); en denotes ethylenediamine. All the chromium(III) complexes are interacted with the minor groove and major groove of d(AT)(12), d(CGCGAATTCGCG)(2) and d(GC)(12) sequences of DNA. The binding energy and hydrogen bond parameters of DNA-Cr complex adduct in both the groove have been determined using molecular mechanics approach. The binding energy and formation of hydrogen bonds between chromium(III) complex and DNA has shown that all complexes of chromium(III) prefer minor groove interaction as the favourable binding mode.

Binding Sites↗
PubMed2006

The role of molecular modeling in bionanotechnology.

Molecular modeling is advocated here as a key methodology for research and development in bionanotechnology. Molecular modeling provides nanoscale images at atomic and even electronic resolution, predicts the nanoscale interaction of unfamiliar combinations of biological and inorganic materials, and evaluates strategies for redesigning biopolymers for nanotechnological uses. The methodology is illustrated in this paper through reviewing three case studies. The first one involves the use of single-walled carbon nanotubes as biomedical sensors where a computationally efficient, yet accurate, description of the influence of biomolecules on nanotube electronic properties through nanotube-biomolecule interactions was developed; this development furnishes the ability to test nanotube electronic properties in realistic biological environments. The second case study involves the use of nanopores manufactured into electronic nanodevices based on silicon compounds for single molecule electrical recording, in particular, for DNA sequencing. Here, modeling combining classical molecular dynamics, material science and device physics, described the interaction of biopolymers, e.g., DNA, with silicon nitrate and silicon oxide pores, furnished accurate dynamic images of pore translocation processes, and predicted signals. The third case study involves the development of nanoscale lipid bilayers for the study of embedded membrane proteins and cholesterol. Molecular modeling tested scaffold proteins, redesigned apolipoproteins found in mammalian plasma that hold the discoidal membranes in the proper shape, and predicted the assembly as well as final structure of the nanodiscs. In entirely new technological areas such as bionanotechnology, qualitative concepts, pictures and suggestions are sorely needed; these three case studies document that molecular modeling can serve a critical role in this respect, even though it may still fall short on quantitative precision.

Biosensing Techniques↗
PubMed1995

Seven-helix bundles: molecular modeling via restrained molecular dynamics.

Simulated annealing via restrained molecular dynamics (SA/MD) has been used to model compact bundles of seven approximately (anti)parallel alpha-helices. Seven such helix bundles occur, e.g., in bacteriorhodopsin, in rhodopsin, and in the channel-forming N-terminal domain of Bacillus thuringiensis delta-endotoxin. Two classes of model are considered: (a) those consisting of seven Ala20 peptide chains; and (b) those containing a single polypeptide chain, made up of seven Ala20 helices linked by GlyN interhelix loops (where N = 5 or 10). Three different starting C alpha templates for SA/MD are used, in which the seven helices are arranged (a) on a left-handed circular template, (b) on a bacteriorhodopsin-like template, or (c) on a zig-zag template. The ensembles of models generated by SA/MD are analyzed in terms of their geometry and energetics, and the most stable structures from each ensemble are examined in greater detail. Structures resembling bacteriorhodopsin and structures resembling delta-endotoxin are both represented among the most stable structures. delta-Endotoxin-like structures arise from both circular and bacteriorhodopsin-like C alpha templates. A third helix-packing mode occurs several times among the stable structures, regardless of the C alpha template and of the presence or absence of interhelix loops. It is characterized by a "4 + 1" core, in which four helices form a distorted left-handed supercoil around a central, buried helix. The remaining two helices pack onto the outside of the core. This packing mode is comparable with that proposed for rhodopsin on the basis of two-dimensional electron crystallographic and sequence analysis studies.

Amino Acid Sequence↗
PubMed2004

Evaluation of deuterium isotope effects in normal-phase LC-MS-MS separations using a molecular modeling approach.

Molecular modeling of stationary phases presents a unique challenge because there is little available experimentally derived structural information. Verified interaction mechanisms at a molecular level with analytes are also rare. Molecular mechanics calculations using the Tripos force field were carried out to qualitatively and quantitatively assess stationary phase interactions. Binding energy values of -15.40, 15.28, -12.53, and -12.34 kcal/mol, respectively, are obtained for olanzapine (OLZ), OLZ-D3, des-methyl olanzapine (DES), and DES-D8 that corresponded to the retention behavior of the four compounds observed using liquid chromatography-mass spectrometry (MS)-MS. The model explains, semiquantitatively, the deuterium isotope effect in the normal-phase chromatographic separation of these compounds.

Journal Article↗
PubMed1985

Transposition in plants: a molecular model.

A molecular model for transposition of plant transposable elements is described. This process may occur via excision and re-integration of the element. Excision generates DNA sequence diversity which suggests the participation of DNA repair enzymes in the healing of the donor molecule.

DNA Transposable Elements↗
PubMed1978

Phleomycin and bleomycin: molecular model building studies.

Molecular model building studies were conducted to simulate phleomycin-bleomycin (PB) antibiotics and thus assess a hypothetical polyphleomycin-DNA complex proposed earlier. While the latter model was not conclusively proved it was found to be quite consistent with the structure of PB compounds.

Anti-Bacterial Agents↗