PubMed Health⌕ Search

Biomedical subjects

S A Islam

Publications and source records attributed to S A Islam.

27 records · Page 2Linked to original sources
PubMed1989

A predicted three-dimensional structure for the human immunodeficiency virus binding domains of CD4 antigen.

A predicted three-dimensional structure of the two N-terminal extracellular domains of human CD4 antigen, a cell surface glycoprotein, is reported. This region of CD4, particularly the first domain, has been identified as containing the binding region for the envelope gp120 protein of the human immunodeficiency virus. The model was predicted based on the sequence homology of each domain with the variable light chain of immunoglobulins. The framework beta-sheet regions were taken from the crystal coordinates of REI. For one region in the first domain of CD4 there was an ambiguity in the alignment with REI and two alternate models are presented. Loops connecting the framework were modelled from fragments selected from a database of main chain coordinates from all known protein structures. Residues identified as involved in binding gp120 have been located in several other studies within the first domain of CD4. Epitopes from eight monoclonal antibodies have been mapped onto residues in both domains. Competition of these antibodies with each other and with gp120 can be interpreted from the structural model.

Amino Acid Sequence↗
PubMed1987

Analysis of the relationship between side-chain conformation and secondary structure in globular proteins.

The relationship between the preferred side-chain dihedral angles and the secondary structure of a residue was examined. The structures of 61 proteins solved to a resolution of 2.0 A (1 A = 0.1 nm) or better were analysed using a relational database to store the information. The strongest feature observed was that the chi 1 distribution for most side-chains in an alpha-helix showed an absence of the g- conformation and a shift towards the t conformation when compared to the non-alpha/beta structures. The exceptions to this tendency were for short polar side-chains that form hydrogen bonds with the main-chain which prefer g+. Shifts in the chi 1 preferences for residues in the beta-sheet were observed. Other side-chain dihedral angles (chi 2, chi 3, chi 4) were found to be influenced by the main-chain. This paper presents more accurate distributions for the side-chain dihedral angles which were obtained from the increased number of proteins determined to high resolution. The means and standard deviations for chi 1 and chi 2 angles are presented for all residues according to the secondary structure of the main-chain. The means and standard deviations are given for the most popular conformations for side-chains in which chi 3 and chi 4 rotations affect the position of C atoms.

Amino Acid Sequence↗
PubMed1985

Comparative computer graphics and solution studies of the DNA interaction of substituted anthraquinones based on doxorubicin and mitoxantrone.

1-[[(Diethylamino)ethyl]amino]- and 1,4-, 1,5-, and 1,8-bis[[(diethylamino)ethyl]amino]anthraquinones are shown to intercalate into DNA. Computer graphics modelling of their intercalation into the self-complementary deoxydinucleoside d(CpG) showed differences in binding properties. While the 1-substituted compound can bind from either groove, the 1,8-disubstituted compound binds with both substituents in the major groove. In the low-energy state of the complex with the 1,5-disubstituted compound, this ligand "straddles" the site with a substituent in each groove--to do this, the compound must bind to a non-base-paired region, so inducing base pairing. The 1,4-compound binds from the major groove; "straddling" is also possible if full minimization of deoxydinucleoside geometry is performed. The differences in binding mode and interaction energies are reflected in the affinities of interaction (1,5- greater than 1,4- much greater than 1,8- greater than 1-); also the antiproliferative effects in vitro are in general agreement with this ranking.

Animals↗
PubMed1983

Experimental and computer graphics simulation analyses of the DNA interaction of 1,8-bis-(2-diethylaminoethylamino)-anthracene-9,10-dione, a compound modelled on doxorubicin.

The crystal structure of the anthraquinone derivative 1,8-bis-(2-diethylaminoethylamino)-anthracene-9,10-dione has been established. This compound was prepared as a potential DNA-intercalating agent based on the proven intercalators doxorubicin and mitoxantrone. Its DNA-binding properties have been examined experimentally by spectroscopic, thermal denaturation and ccc-DNA unwinding techniques: the results are consistent with an intercalative mode of binding to DNA. Computer graphics stimulation of the intercalative docking of this compound into the self-complementary dimer of d(CpG) has provided a minimum energy geometrical arrangement for the bound drug in the intercalation site comparable to that for proflavine when intercalated into the same d(CpG) model system. Entry of the compound into the site can only occur via the major groove.

Animals↗
PubMed1983

Computer modelling studies of the covalent interactions between DNA and the enantiomers of anti-7,8-diol,9,10-epoxy-benzo[a]pyrene.

The molecular structures of adducts between the + and - enantiomers of 7,8-diol 9,10-epoxy benzo[a]pyrene and a double-stranded model for DNA, have been examined by empirical energy calculations. Low-energy structures were only obtained for A form, and not B form DNA. Both + and - adducts are of approximately equal energy. Some structural differences in the orientation of the BP chromophore in the two adducts were found.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed1983

Molecular modelling studies on the non-covalent intercalative interactions between DNA and the enantiomers of anti-benzo[a]pyrene 7,8-diol-9,10-epoxide.

The non-covalent intercalative interactions between a deoxydinucleoside model for DNA and the enantiomers of anti-benzo[a]pyrene diol-epoxide, have been studied by molecular mechanics and computer graphics methods. Stereoselective differences between major and minor groove sites, and between the enantiomers have been found in terms of attractive close contacts.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed1981

Molecular structures of three hydroxyl derivatives of the hepatic carcinogen acetylaminofluorene. Evidence for preferred orientation of the acetylamino side-chain.

The molecular and crystal structures of three hydroxyl derivatives of 2-acetylaminofluorene (AAF), have been determined by X-ray crystallographic analysis. The structures of l-hydroxyl-AAF, N-hydroxyl-AAF and 3-hydroxyl-AAF have shown that in general their geometries are similar, both in respect bond distances and angles, and in respect of side-chain disposition. Possible reasons for the differences in biological activity between the three derivatives are discussed.

2-Acetylaminofluorene↗