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M Vijayan

Publications and source records attributed to M Vijayan.

16 recordsLinked to original sources
PubMed1992

Additional binding sites in lysozyme. X-ray analysis of lysozyme complexes with bromophenol red and bromophenol blue.

The binding sites in hen egg-white lysozyme for neutral bromophenol red (BPR) and ionized bromophenol blue (BPB) have been characterized at 2 A resolution. In either case, the dye-bound enzyme is active against the polysaccharide, but not against the cell wall. Both binding sites are outside, but close to, the hexasaccharide binding cleft in the enzyme. The binding site of BPR made up of Arg5, Lys33, Phe34, Asn37, Phe38, Ala122, Trp123 and possibly Arg125, is close to subsite F while that of BPB made up of Tyr20, Arg21, Asn93, Lys96, Lys97 and Ser100, is close to subsites A and B. The binding sites of the neutral dye and the ionized dye are thus spatially far apart. The peptide component of the bacterial cell wall probably interacts with these cells during enzyme action. Such interactions are perhaps necessary for appropriately positioning the enzyme molecule on the bacterial cell wall.

Binding Sites↗
PubMed1991

X-ray studies on crystalline complexes involving amino acids and peptides. XXIII. Variability in ionization state, conformation and molecular aggregation in the complexes of succinic acid with DL- and L-lysine.

Crystalline complexes of succinic acid with DL- and L-lysine have been prepared and analysed by X-ray diffraction. DL-Lysine complex: C6H15N2O2+.-1/2C4H4O4(2-).1/2C4H6O4, Mr = 264.2, P1, a = 5.506 (4), b = 8.070 (2), c = 14.089 (2) A, alpha = 92.02 (1), beta = 100.69 (3), gamma = 95.85 (3) degrees, Z = 2, Dx = 1.44 g cm-3, R = 0.059 for 2546 observed reflections. Form I of the L-lysine complex: C6H15N2O2+.C4H5O4-, Mr = 264.2, P1, a = 5.125 (2), b = 8.087 (1), c = 8.689 (1) A, alpha = 112.06 (1), beta = 99.08 (2), gamma = 93.77 (2) degrees, Z = 1, Dm = 1.34 (3), Dx = 1.34 g cm-3, R = 0.033 for 1475 observed reflections. Form II of the L-lysine complex: C6H15N2O2+.1/4C4H4O4(2-).-1/4C4H6O4.1/4(C4H5O4.. .H...C4H4O4)2-, Mr = 264.2, P1, a = 10.143 (4), b = 10.256 (2), c = 12.916 (3) A, alpha = 105.00 (2), beta = 99.09 (3), gamma = 92.78 (3) degrees, Z = 4, Dm = 1.37 (4), Dx = 1.38 g cm-3, R = 0.067 for 2809 observed reflections. The succinic acid molecules in the structures exhibit a variety of ionization states. Two of the lysine conformations found in the complexes have been observed for the first time in crystals containing lysine. Form II of the L-lysine complex is highly pseudosymmetric. In all the complexes, unlike molecules aggregate into separate alternating layers. The basic element of aggregation in the lysine layer in the complexes is an S2-type head-to-tail sequence.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acids↗
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↗
PubMed1990

Crystal structure of low humidity tetragonal lysozyme at 2.1-A resolution. Variability in hydration shell and its structural consequences.

Tetragonal crystals of hen egg white lysozyme undergo a reversible transformation, accompanied by loss of water, when the relative humidity of the environment is reduced to about 90%. The structure of the low humidity form has been analyzed, using x-ray data collected at 88% relative humidity, in order to explore the variability in protein hydration caused by a change in the amount of water surrounding the protein molecule and the consequent conformational perturbations in the molecule. The structure has been refined by the restrained least-squares method to an R value of 0.162 for 6269 observed reflections in the 10-2.1-A resolution shell. The refined structure provides interesting examples for the variability in helical parameters, the role of interactions involving side chains and water in the stabilization of secondary structural features, and favorable specific hydration sites. The protein molecule as a whole moves slightly in the low humidity form from its position in the native crystals. The hydration shell tends to move along with the protein. Significant changes, however, occur in the hydration shell. These changes cause structural perturbations in the enzyme molecule, which are most pronounced in regions involved in substrate binding.

Animals↗
PubMed1990

X-ray studies on crystalline complexes involving amino acids and peptides. XIX. Effects of change in chirality in the complexes of succinic acid with DL- and L-arginine.

Crystals of DL-arginine hemisuccinate dihydrate (I)(monoclinic; P2(1)/c; a = 5.292, b = 16.296. c = 15.203 A; beta = 92.89 degrees; Z = 4) and L-arginine hemisuccinate hemisuccinic acid monohydrate (II) (triclinic; P1; a = 5.099; b = 10.222, c = 14.626 A; alpha = 77.31, beta = 89.46, gamma = 78.42 degrees; Z = 2) were grown under identical conditions from aqueous solutions of the components in molar proportions. The structures were solved by direct methods and refined to R = 0.068 for 2585 observed reflections in the case of (I) and R = 0.036 for 2154 observed reflections in the case of (II). Two of the three crystallographically independent arginine molecules in the complexes have conformations different from those observed so far in the crystal structures containing arginine. The succinic acid molecules and the succinate ions in the structures are centrosymmetric and planar. The crystal structure of (II) is highly pseudosymmetric. Arginine-succinate interactions in both the complexes involve specific guanidyl-carboxylate interactions. The basic elements of aggregation in both the structures are ribbons made up of alternating arginine dimers and succinate ions. However, the ribbons pack in different ways in the two structures. (II) presents an interesting case in which two ionisation states of the same molecule coexist in a crystal. The two complexes provide a good example of the effect of change in chirality on stoichiometry, conformation, aggregation, and ionisation state in the solid state.

Amino Acids↗
PubMed1989

X-ray studies on crystalline complexes involving amino acids and peptides. Part XX. Crystal structures of DL-arginine acetate monohydrate and DL-lysine acetate and a comparison with the corresponding L-amino acid complexes.

Crystals of DL-arginine acetate monohydrate, C6H15N4O2+C2H3O2-.H2O, are monoclinic, P2(1)/c, with a = 13.552(2), b = 5.048(2), c = 18.837(3) A, beta = 101.34(2) degrees and Z = 4, and those of DL-lysine acetate, C6H15N2O2+.C2H3O2- are triclinic, P1, with a = 5.471(2), b = 7.656(2), c = 12.841(2) A, alpha = 94.48(1), beta = 94.59(2), gamma = 98.83(2) degrees and Z = 2. The structures have been solved by direct methods and refined to R = 0.058 and 0.077 for 1522 and 1259 observed reflections respectively. The difference in the number and the nature of proton donors leads to a difference in hydrogen bond density in the two structures. The basic elements of aggregation in both the structures are pairs of amino acid molecules, each pair stabilized by two centrosymmetrically related hydrogen bonds involving alpha-amino and alpha-carboxylate groups, stacked along the shortest dimension to form columns. The pairs are held together in each column by head-to-tail sequences. The columns stack along a crystallographic axis to form layers. Adjacent layers are bridged by acetate ions. The amino acid-acetate interactions are primarily through side chains and involve specific interactions and characteristic interaction patterns. The gross features of molecular aggregation are nearly the same in DL-arginine acetate monohydrate and L-arginine acetate whereas they are substantially different in the lysine complexes. In both cases, one of the two head-to-tail sequences in the L complex is replaced by a hydrogen bonded loop involving alpha-amino and alpha-carboxylate groups, in the DL complex. This may have implications for prebiotic condensation during chemical evolution.

Acetates↗
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↗
PubMed1988

X-ray studies on crystalline complexes involving amino acids and peptides. XV. Crystal structures of L-lysine D-glutamate and L-lysine D-aspartate monohydrate and the effect of chirality on molecular aggregation.

L-Lysine D-glutamate crystallizes in the monoclinic space group P2(1) with a = 4.902, b = 30.719, c = 9.679 A, beta = 90 degrees and Z = 4. The crystals of L-lysine D-aspartate monohydrate belong to the orthorhombic space group P2(1)2(1)2(1) with a = 5.458, b = 7.152, c = 36.022 A and Z = 4. The structures were solved by the direct methods and refined to R values of 0.125 and 0.040 respectively for 1412 and 1503 observed reflections. The glutamate complex is highly pseudosymmetric. The lysine molecules in it assume a conformation with the side chain staggered between the alpha-amino and the alpha-carboxylate groups. The interactions of the side chain amino groups of lysine in the two complexes are such that they form infinite sequences containing alternating amino and carboxylate groups. The molecular aggregation in the glutamate complex is very similar to that observed in L-arginine D-aspartate and L-arginine D-glutamate trihydrate, with the formation of double layers consisting of both types of molecules. In contrast to the situation in the other three LD complexes, the unlike molecules in L-lysine D-aspartate monohydrate aggregate into alternating layers as in the case of most LL complexes. The arrangement of molecules in the lysine layer is nearly the same as in L-lysine L-aspartate, with head-to-tail sequences as the central feature. The arrangement of aspartate ions in the layers containing them is, however, somewhat unusual. Thus the comparison between the LL and the LD complexes analyzed so far indicates that the reversal of chirality of one of the components in a complex leads to profound changes in molecular aggregation, but these changes could be of more than one type.

Aspartic Acid↗
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↗
PubMed1985

Arrangement of subunits in peanut lectin. Rotation function and chemical cross-linking studies.

X-ray intensity data from the native orthorhombic crystals of peanut lectin have been collected using oscillation photography. Rotation function studies using data up to a resolution of 4.5 A indicate that the four subunits in the molecule, which constitute the asymmetric unit in the crystals, are related to one another by three mutually perpendicular noncrystallographic 2-fold axes. Chemical cross-linking experiments in solution followed by sodium dodecyl sulfate gel electrophoresis, carried out in parallel, suggest that there is more than one type of intersubunit approach in the molecule. Rotation function and cross-linking studies thus show that the tetrameric molecule of peanut lectin is a dimer of a dimer. The two monomers in a dimer are related by a 2-fold axis. The two dimers are in turn related by another 2-fold axis perpendicular to the one that relates the two monomers in the dimer, endowing the molecule with 222 (D2) symmetry.

Cross-Linking Reagents↗
PubMed1985

X-ray characterisation of an additional binding site in lysozyme.

Bromophenol red (BPR) binds to lysozyme and inhibits its activity against bacterial cell walls, but not against the polysaccharide component of peptidoglycan. The binding site of BPR in the enzyme has been characterised by X-ray analysis of the complex at 5.5A resolution. The new binding site, which is outside the cleft close to subsite F, is presumably involved in interactions with the peptide component of peptidoglycan, in the action of lysozyme against bacterial cell walls.

Animals↗
PubMed1979

An analysis of side-chain conformation in proteins.

The crystal structures of a number of globular proteins are currently available. An analysis of the distribution of side-chains among different allowed conformations in these proteins has been carried out. The observed conformations of individual residues are discussed on the basis of well-known stereochemical criteria. The population distribution of side-chains in different allowed regions in conformational space can be explained largely on the basis of simple steric considerations. In addition to examining the conformational behaviour of individual residues, some population distributions of conformational angles of general interest involving groups of residues have also been analyzed.

Amino Acids↗