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At least 307 records · Page 17Linked to original sources
PubMed1994

Molecular modelling of the Dolichos biflorus seed lectin and its specific interactions with carbohydrates: alpha-D-N-acetyl-galactosamine, Forssman disaccharide and blood group A trisaccharide.

The three-dimensional structure of Dolichos biflorus seed lectin has been constructed using five legume lectins for which high resolution crystal structures were available. The validity of the resulting model has been thoroughly investigated. Final structure optimization was conducted for the lectin complexed with alpha GalNAc, providing thereby the first three-dimensional structure of lectin/GalNAc complex. The role of the N-acetyl group was clearly evidenced by the occurrence of a strong hydrogen bond between the protein and the carbonyl oxygen of the carbohydrate and by hydrophobic interaction between the methyl group and aromatic amino acids. Since the lectin specificity is maximum for the Forssman disaccharide alpha GalNAc(1-3) beta GalNAc-O-Me and the blood group A trisaccharide alpha GalNAc(1-3)[alpha Fuc(1-2)] beta Gal-O-Me, the complexes with these oligosaccharides have been also modelled.

ABO Blood-Group System↗
PubMed1989

GEOM: a new tool for molecular modelling based on distance geometry calculations with NMR data.

GEOM is a new graphics tool which allows the use of distance geometry to compute linear and cyclic structures typically arising in drug design situations. Modified amino acids or monomeric organic entities can be easily constructed in an interactive way and deposited in the library of the distance geometry program together with geometric information required for structure calculation in dihedral angle space. In addition, GEOM is able to produce all files needed to calculate a structure based on NMR data (NOE and J-coupling constraints) and it permits the graphic analysis and comparison of computed structures. The application of GEOM is demonstrated in three examples: modelling of cyclosporin A structures with and without a limited set of H-bond constraints and modelling of a cyclic hexapeptide with a full NMR data set.

Computer Graphics↗
PubMed1996

Particle sizes of purified kappa-casein: metal effect and correspondence with predicted three-dimensional molecular models.

kappa-Casein as purified from bovine milk exhibits a rather unique disulfide bonding pattern as revealed by SDS-PAGE. The disulfide-bonded caseins present range from dimer to octamer and above and preparations contain about 10% monomer. All of these heterogenous polymers, however, self-associated into nearly spherical uniform particles with an average radius of 8.9 nm as revealed by negatively stained transmission electron micrographs. Evidence is presented that multivalent cations play a role in the stabilization of these spherical particles. Treatment with EDTA causes disruption of the kappa-casein particles and leads to a broder size distribution as judged by electron microscopy and dynamic light scattering. The size and shape of the particles are in accord with earlier proposed 3D models for kappa-casein that actually predicted participation of divalent cations in the structure.

Amino Acids↗
PubMed2001

Substrate binding and catalytic mechanism of class B beta-lactamases: a molecular modelling study.

Increased resistance to beta-lactam antibiotics is mainly due to beta-lactamases whose production by pathogenic bacteria makes their broad activity spectrum especially frightening. X-ray structures of several zinc beta-lactamases have revealed the coordination of the two metal ions, but their mode of action remains unclear. Geometry optimisation of stable complexes along the reaction pathway of benzylpenicillin hydrolysis highlighted a proton shuttle occurring from D120 of the Bacillus cereus beta-lactamase to the beta-lactam nitrogen via Zn2 which is central to the network. First, the Zn1 ion has a structural role maintaining Zn-bound waters, WAT1 and WAT2, either directly or through the Zn1 tetrahedrally coordinated histidine ligands. The Zn2 ion has a more catalytic role, stabilising the tetrahedral intermediate, accepting the beta-lactam nitrogen atom as a ligand. The role of Zn2 and the flexibility in the coordination geometry of both Zn ions is of crucial importance for catalysis.

Bacillus cereus↗
PubMed1997

Factor VIII gene mutations found by a comparative study of SSCP, DGGE and CMC and their analysis on a molecular model of factor VIII protein.

Screening of the factor VIII (FVIII) gene which spans 186 kb and codes for 26 exons, was originally hampered by its size but is now feasible because rapid DNA scanning methodologies have been developed. The present study for the first time directly compares the three most widely applied screening methods, denaturing gradient gel electrophoresis (DGGE), single-stranded conformational polymorphism (SSCP) and chemical mismatch cleavage (CMC) for their sensitivity of mutation detection in a selected group of ten haemophilia A patients. Nine of these patients are known to be cross-reacting material positive and eight exhibited a mild to moderate phenotype. Of the ten patients screened, we identified mutations in nine by all three screening methods. Of the mutations characterised, two are previously unpublished. T to C (S373P) and G to A (D525N). In one mildly affected haemophiliac, we identified a second T to C sequence change in the 5' untranslated region at -601 bp, probably having no effect on FVIII gene expression. Modelling studies were performed on those mutations lying within the A domains of FVIII (D525N, R527W, I566T) to study the possible effect of these mutations on structure and/or function. When the three methods are performing optimally and have been standardised, our experience is that CMC and DGGE are equally efficient at sequence variation detection while SSCP is slightly less sensitive.

Computer Simulation↗
PubMed2001

Steric control of stereoselective interactions between the platinum(II) complex [PtCl2(1,4-diazacycloheptane)] and DNA: comparison with cis-[PtCl2(NH3)2] and [PtCl2(ethane-1,2-diamine)] using DNA binding and molecular modeling studies.

The rate and extent of binding of [PtCl2(hpip)] (hpip=homopiperazine-1,4-diazacycloheptane) and cis-[PtCl2(NH3)2] to calf thymus DNA was measured using atomic absorption spectroscopy and it was found that [PtCl2(hpip)] bound both more rapidly and to a greater extent than did cis-[PtCl2(NH3)2]. The binding of [PtCl2(hpip)] and [PtCl2(en)] (en=ethane-1,2-diamine) to salmon sperm DNA and to synthetic, self-complementary 10-base-pair and 52-base-pair oligonucleotides was studied using enzymatic digestion and HPLC analysis of the products. [PtCl2(hpip)] forms approximately two-fold fewer GpG and ApG intrastrand adducts and concomitantly more monofunctional adducts than does [PtCl2(en)]. In the case of [PtCl2(hpip)], two GpG adducts, corresponding to the different orientations of the hpip ligand with respect to the DNA, were observed in a 1:3.3 ratio. The minor product corresponds to the orientation in which the bulkier propylene chain of the hpip ligand is adjacent to, and makes close contacts with, the floor of the major groove. When the reaction was repeated with a synthetic oligonucleotide decamer duplex, the ratio of the two forms was approximately 1:1.9 and with the 52-mer duplex it was 1:2.4, revealing an apparent systematic dependence of stereoselectivity on nucleotide size. Computer modeling of the two adducts formed by [PtCl2(hpip)] and those formed by [PtCl2(en)] and cis-[PtCl2(NH3)2] revealed that non-bonded interactions between the hpip ligand and the DNA were probably responsible for both the decreased proportion of GpG adducts formed by [PtCl2(hpip)] and the stereoselectivity exhibited in the formation of these adducts. This is the first case in which the stereoselectivity can be ascribed to steric factors alone.

Base Sequence↗
PubMed2003

Molecular modeling of the rabbit colonic (HKalpha2a) H+, K+ ATPase.

A model of the HKalpha2a subunit of the rabbit colonic H+, K+ ATPase has been generated using the crystal structure of the Ca(+2) ATPase as a template. A pairwise sequence alignment of the deduced primary sequences of the two proteins demonstrated that they share 29% amino acid sequence identity and 47% similarity. Using O (version 7) the model of HKalpha2a was constructed by interactively mutating, deleting, and inserting the amino acids that differed between the pairwise sequence alignment of the Ca(+2) ATPase and HKalpha2a. Insertions and deletions in the HKalpha2a sequence occur in apparent extra-membraneous loop regions. The HKalpha2a model was energy minimized and globally refined to a level comparable to that of the Ca(+2) ATPase structure using CNS. The charge distribution over the surface of HKalpha2a was evaluated in GRASP and possible secondary structure elements of HKalpha2a were visualized in BOBSCRIPT. Conservation and placement of residues that may be involved in ouabain binding by the H+, K+ ATPase were considered and a putative location for the beta subunit was postulated within the structure.

Amino Acid Sequence↗
PubMed2004

Hydrogen bonding interactions in E- or Z-2-phenyl-3-( X'-pyridyl)propenoic acid ( X=2, 3 or 4) assemblies--a molecular modeling study.

The agglomeration properties of stereoisomeric 2-phenyl-3-(X'-pyridyl)propenoic acids (X=2, 3 or 4) were studied by the PM3 semiempirical quantum chemical method. Calculations revealed that dimers kept together by the intermolecular hydrogen bonding interactions of the carboxylic groups could be built from both stereoisomers irrespective of the position of the nitrogen heteroatom. The dimers of the Z-isomers could also be built through (aromatic)C-H...N hydrogen bonds between the dimer units. The longest agglomerate was the pentamer of the dimers when the nitrogen was in the 2' position. Longer hydrogen-bonded agglomerates than dimers could only be constructed from the E-isomer with the nitrogen in position 4'. Here, the trimer of the dimers proved to be the longest hydrogen-bonded entity and similarly to the Z-isomers, the dimer units are kept together by (aromatic)C-H...N intermolecular hydrogen bonds.

Acrylates↗
PubMed2004

Molecular modeling of dipeptide and its analogous systems with water.

Intermolecular hydrogen-bond interactions in the monohydrated complexes of formamide, N-methylacetamide and glycylglycine have been studied using ab initio and DFT methods. The geometries were optimized using second-order Møller-Plesset perturbation theory and the B3LYP DFT functional with the 6-311++G** basis set. It is observed that hydrogen-bond interactions at the carbonyl group of the peptide moiety are stronger than those at the amino group of the formamide and N-methylacetamide molecules. Because of the presence of cyclic hydrogen-bonding interactions in glycylglycine, the interaction at the amino group is higher than at the carbonyl. The 13C and 15N NMR shielding values were calculated for the non-hydrated and monohydrated complexes. Condensed Fukui functions have also been calculated for non-hydrated formamide, N-methylacetamide and glycylglycine molecules at the B3LYP/6-311++G** level of theory, and the results are discussed.

Acetamides↗
PubMed2004

Molecular modeling of the interleukin-19 receptor complex. Novel aspects of receptor recognition in the interleukin-10 cytokine family.

The interleukin-10 (IL-10) cytokine family consists of several viral and human homologs that exhibit distinct receptor binding specificities. In the present study, the complex between interleukin-19 (IL-19) and its physiological receptor-the interleukin-20 receptor alpha-chain (IL-20R1)-was modeled. The most prominent feature of this complex is an extended binding interface formed by a long loop of IL-20R1 and a bulge region of IL-19. The two regions exhibit complementary charges and have no structural counterparts in the IL-10/IL-10R1 complex but show some resemblance to the complex between interferon-gamma (IFN-gamma) and its receptor. Sequence comparison of the three cytokines (IL-19, IL-20, IL-24) that bind the IL-20R1 reveals a considerable conservation of the length of the interacting loops. One residue suggested to play a key role in receptor binding specificity is a conserved glutamate. The binding interface of IL-20R1 is rich in aromatic residues while the interfaces of its cytokine ligands are mainly formed by more flexible aliphatic amino acids. This structural feature might play an important role for the specific recognition of a single receptor chain by three different cytokines. [Figure: see text]. Comparison of the ligand/receptor interfaces in theA IL-10/IL-10R1,B IL-19/IL-20R1 andC IFN-gamma/receptor complexes. The translucent Connolly surfaces of the receptor and the ligand are shown in yellow and white, respectively. The backbone of the receptor and ligand are highlighted by a red and blue/green tube, respectively. For clarity, only one domain of the intertwined dimes is shown for IL-10 and IFN-gamma. Arrows denote the location of helix B and the corresponding structural elements in IL-19 and IFN-gamma as well as the location of receptor loop L2. As evident fromB andC an extended interaction surface is created in the IL-19/IL-20R1 and IFN-gamma/receptor complexes by the interaction of this structural element with a long loop of the respective receptor.

Amino Acid Sequence↗
PubMed2005

Molecular models of protein kinase 6 from Plasmodium falciparum.

Cyclin-dependent kinases (CDKs) have been identified as potential targets for development of drugs, mainly against cancer. These studies generated a vast library of chemical inhibitors of CDKs, and some of these molecules can also inhibit kinases identified in the Plasmodium falciparum genome. Here we describe structural models for Protein Kinase 6 from P. falciparum (PfPK6) complexed with Roscovitine and Olomoucine. These models show clear structural evidence for differences observed in the inhibition, and may help designing inhibitors for PfPK6 generating new potential drugs against malaria.

Amino Acid Sequence↗
PubMed2005

Three-dimensional structure of the catalytic domain of the yeast beta-(1,3)-glucan transferase Gas1: a molecular modeling investigation.

The three-dimensional (3D) structure of the catalytic domain of Gas1p, a protein belonging to the only family of beta-(1,3)-glucan transferases so far identified in yeasts and some pathogenic fungi (family GH-72), has been predicted by combining results derived from threading methods, multiple sequence alignments and secondary-structure predictions. The 3D model has allowed the identification of several residues that are predicted to play a crucial role in structural integrity, substrate recognition and catalysis. In particular, the model of the catalytic domain can be useful for designing site-directed mutagenesis experiments and for developing inhibitors of Gas1p enzymatic activity.

Binding Sites↗
PubMed2007

Molecular model for host–guest interaction of tetraamino-tert-butylthiacalix[4]arene and tetraamino-tert-butylcalix[4]arene receptors with carboxylate and dicarboxylate guests: an ONIOM study.

Geometry optimizations of tetraamino-tert-butylthiacalix[4]arene (tatbtc4a) and tetraamino-tert-butylcalix[4]arene (tatbc4a) complexes with acetate, oxalate,malonate, succinate, glutarate, adipate, and pimelate were carried out using the integrated MO:MO method. Thermodynamic quantities, preorganization energies and complexation energies of these complexes were obtained at the ONIOM(B3LYP/6-31G(d):AM1) level of theory. The relative stabilities of the tatbtc4a and tatbc4a complexes with carboxylate guests are reported. The complexes tatbtc4a/malonate and tatbc4a/oxalate were found to be the most stable species. The selectivity of the tatbtc4a receptor toward to malonate with respect to oxalate, in terms of selectivity coefficient, K(oxalatemalonate) is 9.90×10(2).

Calixarenes↗
PubMed2006

Investigation of the structure of 6-amino-4-methylamino-5-nitrosopyrimidine by X-ray diffraction, NMR and molecular modeling.

The structure of 6-amino-4-methylamino-5-nitrosopyrimidine in the solid state and dimethylsulfoxide solution was investigated using single crystal X-ray diffraction and (1)H, (13)C NMR spectroscopy methods. Hartree-Fock (HF) and density functional (DFT) levels of theory were used to interpret the experimental data obtained by X-ray and NMR methods.

Computer Simulation↗