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V Dhanaraj

Publications and source records attributed to V Dhanaraj.

28 records · Page 2Linked to original sources
PubMed1995

Comparisons of the three-dimensional structures, specificities and glycosylation of renins, yeast proteinase A and cathepsin D.

The crystal structures of complexes of the aspartic proteinases, human and mouse renins, yeast proteinase A and cathepsin D, with peptide analogue inhibitors are compared. Differences occur in the relative positions of the domain comprising residues 190-302 (pepsin numbering) compared to the remaining structure and in the nature and position of the irregular regions joining the beta-strands and alpha-helices. The first three of the five residues of the oligosaccharide structures attached to Asn 67 of yeast proteinase and cathepsin D cover the same region of the protein surface. All enzymes have an unusual, proline-rich region (292-297) which acts as a second flap (in addition to that involving residues 72-81). This covers the active site cleft, but can be very close to the substrate/inhibitor at P3' and P4' only in the renins.

Amino Acid Sequence↗
PubMed1994

Crystal structure of peanut lectin, a protein with an unusual quaternary structure.

The x-ray crystal structure of the tetrameric T-antigen-binding lectin from peanut, M(r) 110,000, has been determined by using the multiple isomorphous replacement method and refined to an R value of 0.218 for 22,155 reflections within the 10- to 2.95-A resolution range. Each subunit has essentially the same characteristic tertiary fold that is found in other legume lectins. The structure, however, exhibits an unusual quaternary arrangement of subunits. Unlike other well-characterized tetrameric proteins with identical subunits, peanut lectin has neither 222 (D2) nor fourfold (C4) symmetry. A noncrystallographic twofold axis relates two halves of the molecule. The two monomers in each half are related by a local twofold axis. The mutual disposition of the axes is such that they do not lead to a closed point group. Furthermore, the structure of peanut lectin demonstrates that differences in subunit arrangement in legume lectins could be due to factors intrinsic to the protein molecule and, contrary to earlier suggestions, are not necessarily caused by interactions involving covalently linked sugar. The structure provides a useful framework for exploring the structural basis and the functional implications of the variability in the subunit arrangement in legume lectins despite all of them having nearly the same subunit structure, and also for investigating the general problem of "open" quaternary assembly in oligomeric proteins.

Arachis↗
PubMed1992

X-ray analyses of peptide-inhibitor complexes define the structural basis of specificity for human and mouse renins.

X-ray analyses have defined the three-dimensional structures of crystals of mouse and human renins complexed with peptide inhibitors at resolutions of 1.9 and 2.8 A, respectively. The exquisite specificity of renin arises partly from ordered loop regions at the periphery of the binding cleft. Although the pattern of main-chain hydrogen bonding in other aspartic proteinase inhibitor complexes is conserved in renins, differences in the positions of secondary structure elements (particularly helices) also lead to improved specificity in renins for angiotensinogen substrates.

Amino Acid Sequence↗
PubMed1992

Crystallization and preliminary X-ray analysis of complexes of peptide inhibitors with human recombinant and mouse submandibular renins.

Inhibitor-complexed crystals of mouse and human renins suitable for X-ray analysis have been prepared. The mouse renin is complexed with a non-hydrolysable decapeptide analogue of rat angiotensinogen containing a hydroxyethylene isostere in place of the scissile bond. The crystals are monoclinic, space group P2(1) with cell dimensions a = 78.3 A, b = 117.8 A, c = 85.9 A, beta = 101.18 degrees containing four molecules per asymmetric unit. The human renin is fully glycosylated and complexed with a tetrapeptide containing norstatine. The complex crystallises in the cubic space group P2(1)3 with a = 143.1 A and has two molecules in the asymmetric unit. The rotation function of the mouse renin complex indicates pseudo 222 symmetry while that of human renin indicates a pseudo 2-fold axis. Full structural analyses of the two complexes are underway.

Amino Acid Sequence↗
PubMed1992

Multidisciplinary cycles for protein engineering: site-directed mutagenesis and X-ray structural studies of aspartic proteinases.

The specificity and pH profile of aspartic proteinases have evolved to include not only pepsin with a broad specificity and an optimal activity in acid media, but also renin, with high specificity for angiotensinogen and activity close to neutral pH. Comparisons of the structures and catalytic activities of aspartic proteinases provide helpful clues for engineering new activity profiles. We illustrate an approach that involves recombinant DNA techniques, biochemistry, structure determination and biocomputing. We use the 3-D structures of inhibitor complexes of several aspartic proteinases to define likely intermediates and specificity sub-sites. The multidisciplinary research is organised as cycles, in which each cycle tests a design hypothesis proposed in the previous cycle. We use one member of the aspartic proteinase family, chymosin, to illustrate these ideas in engineering enzymes with altered pH optima and specificities.

Amino Acid Sequence↗
PubMed1991

Preparation and X-ray characterization of four new crystal forms of jacalin, a lectin from Artocarpus integrifolia.

Four new crystal forms of the anti-T lectin from jackfruit (Artocarpus integrifolia) have been prepared and characterized. Three of them, two monoclinic (P21, a = 59.4 A, b = 83.3 A, c = 63.5 A, beta = 107.7 degrees; C2, a = 106.1 A, b = 53.9 A, c = 128.0 A, beta = 95.0 A) and one orthorhombic (C222(1), a = 98.1 A, b = 67.3 A, c = 95.1 A) were grown with 2-methylpentan-2,4-diol (MPD) as the precipitant while the fourth, an hexagonal form (P6(1)22, a = b = 129.6 A, c = 157.9 A), was obtained in the presence of methyl-alpha-D-galactopyranoside with polyethylene glycol 4000 as the precipitant. The reported relative molecular mass (Mr) of the lectin was found to be inconsistent with the solvent content of the crystals estimated using measured densities. The Mr was redetermined using size-exclusion chromatography in the presence of methyl-alpha-D-galactopyranoside and Ferguson-plot analysis of mobilities in polyacrylamide gel electrophoresis. The redetermined Mr (66,000) is consistent with the measured crystal densities. The orthorhombic and the hexagonal forms, which have one half molecule and one molecule, respectively, in the asymmetric unit, are suitable for high-resolution X-ray analysis.

Lectins↗
PubMed1988

Structural studies of analgesics and their interactions. XII. Structure and interactions of anti-inflammatory fenamates. A concerted crystallographic and theoretical conformational study.

A theoretical conformational analysis of fenamates, which are N-arylated derivatives of anthranilic acid or 2-aminonicotinic acid with different substituents on the aryl (phenyl) group, is reported. The analysis of these analgesics, which are believed to act through the inhibition of prostaglandin biosynthesis, was carried out using semi-empirical potential functions. The results and available crystallographic observations have been critically examined in terms of their relevance to drug action. Crystallographic studies of these drugs and their complexes have revealed that the fenamate molecules share a striking invariant feature, namely, the six-membered ring bearing the carboxyl group is coplanar with the carboxyl group and the bridging imino group, the coplanarity being stabilized by resonance interactions and an internal hydrogen bond between the imino and carboxyl groups. The results of the theoretical analysis provide a conformational rationale for the observed invariant coplanarity. The second six-membered ring, which provides hydrophobicity in a substantial part of the molecule, has limited conformational flexibility in meclofenamic, mefenamic and flufenamic acids. Comparison of the conformational energy maps of these acids shows that they could all assume the same conformation when bound to the relevant enzyme. The present study provides a structural explanation for the difference in the activity of niflumic acid, which can assume a conformation in which the whole molecule is nearly planar. The main role of the carboxyl group appears to be to provide a site for intermolecular interactions in addition to helping in stabilizing the invariant coplanar feature and providing hydrophilicity at one end of the molecule. The fenamates thus provide a good example of conformation-dependent molecular asymmetry.

Analgesics↗
PubMed1987

Crystal structures of 1 : 1 complexes of meclofenamic acid with choline and ethanolamine.

The hydrated 1:1 complex of meclofenamic acid with choline crystallizes in the orthorhombic space group Pna2(1) with a = 9.637(1), b = 12.962(5), c = 33.099(4) A and Z = 8. Crystals of the corresponding anhydrous complex with ethanolamine are triclinic, space group P1, with a = 9.232(3), b = 12.287(5), c = 17.033(3) A, alpha = 70.21(2), beta = 76.72(2), gamma = 68.21(3) degrees and Z = 4. The structures have been solved by direct methods and refined to R values of 0.062 and 0.079, respectively for 1942 and 2852 observed reflections. The four crystallographically independent meclofenamate anions in the complexes have nearly the same molecular geometry which in turn is very similar to that found in the crystal structure of free meclofenamic acid. The choline and ethanolamine molecules assume a gauche conformation with respect to the central C-C bond. The invariant structural features observed in the crystals of the free fenamates are retained by the meclofenamate ions in the complexes. These features are the rigid coplanar geometry of the six-membered ring carrying the carboxyl group, the carboxyl group and the imino nitrogen atom, and the internal hydrogen bond connecting the imino and the carboxyl groups. The crystal structures are stabilised by ionic interactions between the carboxylate groups of meclofenamate ions and choline or ethanolamine cations, and hydrogen bonds. The choline complex exhibits pseudosymmetry and the distribution of molecules in it is nearly centrosymmetric although the space group is noncentrosymmetric. The packing of molecules in the crystals is such that the polar columns are surrounded by non-polar regions. The core of each column in the choline complex is made up of water molecules connected by hydrogen bonds involving disordered protons. The results of the X-ray structure analysis of fenamates and their crystalline complexes provide some insights into structure-function relationships in this family of drugs.

Choline↗
PubMedDate not supplied

Protein-protein interactions in receptor activation and intracellular signalling.

We review here signalling complexes that we have defined using X-ray analysis in our laboratory. They include growth factors and their receptors: nerve growth factor (NGF) and its hetero-hexameric 7S NGF storage complex, hepatocyte growth factor/scatter factor (HGF/SF) NK1 dimers and fibroblast growth factor (FGF1) in complex with its receptor (FGFR2) ectodomain and heparin. We also review our recent structural studies on intracellular signalling complexes, focusing on phosducin transducin GPry, CK2 protein kinase and its complexes, and the cyclin D-dependent kinase, Cdk6, bound to the cell cycle inhibitor p19INK4d. Comparing the structures of these complexes with others we show that the surface area buried in signalling interactions does not always give a good indication of the strength of the interactions. We show that conformational changes are often important in complexes with intermediate buried surface areas of 1500 to 2000 A2, such as Cdk6INK4 interactions. Some interactions involve recognition of continuous epitopes, where there is no necessity for a tertiary structure and very often the binding conformation is induced during the process of interaction, for example phosducin binding to the betagamma subunits (Gtbetagamma) of the heterotrimeric G protein transducin.

Animals↗