Biomedical subjects

N Manoj

Publications and source records attributed to N Manoj.

8 recordsLinked to original sources

PubMed2006

Structure absorption spectra correlation in a series of 2,6-dimethyl-4-arylpyrylium salts.

A combined experimental and theoretical study of the absorption spectra of a group of closely related pyrylium perchlorates 1-11 are presented. Minor changes in the position of the substituents lead to drastic changes in the absorption spectra in this series of compounds. We have attempted to explain the observed changes using the x,y-band notation developed by Balaban and co-workers. Absorption spectra of all compounds are compared with results from time-dependent density functional theory (TDDFT) and Zerner's intermediate neglect of differential overlap (ZINDO/S) level calculations. Results of the calculations are in good agreement with experimental observations and an interesting correlation between Balaban's notations and the MO transitions are obtained for simple derivatives. It is suggested that for more complex systems such as alpha- and beta-naphthyl substituted systems, the empirical method is not appropriate.

Journal Article↗

PubMed2001

X-ray studies on crystalline complexes involving amino acids and peptides. XXXVII. Novel aggregation patterns and effect of chirality in the complexes of DL- and L-lysine with glutaric acid.

The complexes of glutaric acid with DL-lysine contain singly positively charged zwitterionic lysinium ions and singly negatively charged semi-glutarate ions. Both the ions exhibit different conformations in the two complexes. The structures contain head-to-tail sequences of amino acids. However, the aggregation patterns in the two complexes are entirely different, demonstrating the effect of chirality on molecular aggregation. These patterns also turn out to be different from those so far observed, in structures containing amino acids. The structures contain characteristic interaction patterns involving linear arrays of alternating amino and carboxylate groups.

Crystallography, X-Ray↗

PubMed2001

Crystallization and preliminary X-ray studies of snake gourd lectin: homology with type II ribosome-inactivating proteins.

The lectin from the seeds of snake gourd (Trichosanthes anguina) has been crystallized in two forms using the hanging-drop method. Both the forms are hexagonal, with the asymmetric unit containing one subunit consisting of two polypeptide chains linked through disulfide bridges. Intensity data from one of the forms were collected at room temperature as well as at low temperature to 3 A resolution. Molecular-replacement studies indicate that the lectin is homologous to type II ribosome-inactivating proteins. Partial refinement confirms this conclusion.

Crystallization↗

PubMed2001

Signature of quaternary structure in the sequences of legume lectins.

Legume lectins exhibit a wide variety of oligomerization and sugar specificity while retaining the characteristic jelly-roll tertiary fold. An attempt has been made here to find whether this diversity is reflected in their primary structures by constructing phylogenetic trees. Dendrograms based on sequence alignment showed clustering related to the oligomeric nature of legume lectins. Though the clustering primarily follows the oligomeric states, it also appears to correlate with different sugar specificities indicating an interdependence of these two properties. Analysis of the structure-based alignment and the alignment of the sequences of the carbohydrate-binding loops alone also revealed the same features. By a close examination of the interfaces of the various oligomers it was also possible, in some cases, to pinpoint a few key residues responsible for the stabilization of the interfaces.

Amino Acid Sequence↗

PubMed2000

Carbohydrate specificity and salt-bridge mediated conformational change in acidic winged bean agglutinin.

Structures of two crystal forms of the dimeric acidic winged bean agglutinin (WBAII) complexed with methyl-alpha-D-galactose have been determined at 3.0 A and 3.3 A resolution. The subunit structure and dimerisation of the lectin are similar to those of the basic lectin from winged bean (WBAI) and the lectin from Erythrina corallodendron (EcorL). The conformation of a loop and its orientation with respect to the rest of the molecule in WBAII are, however, different from those in all the other legume lectins of known structure. This difference appears to have been caused by the formation of two strategically placed salt bridges in the former. Modelling based on the crystal structures provides a rationale for the specificity of the lectin, which is very different from that of WBAI, for the H-antigenic determinant responsible for O blood group reactivity. It also leads to a qualitative explanation for the thermodynamic data on sugar-binding to the lectin, with special emphasis on the role of a tyrosyl residue in the variable loop in the sugar-binding region in generating the carbohydrate specificity of WBAII.

ABO Blood-Group System↗

PubMed2000

X-ray studies on crystalline complexes involving amino acids and peptides. XXXVI. Crystal structures of hydrated glycyl-L-histidine and L-histidyl-L-alanine complexes with oxalic acid.

The crystal structures of the complexes of oxalic acid with glycyl-L-histidine and L-histidyl-L-alanine were determined. The three crystallographically independent peptide molecules in the complexes have closed conformations. The terminal carboxyl group of the dipeptide and the oxalate ion in the Gly-His complex exhibit unusual ionization states and are connected by a symmetric O- - -O hydrogen bond. The peptide aggregation in the complex is almost identical to that in the corresponding semisuccinate complex and is similar to one of the predicted aggregation patterns for Ala-Ala, demonstrating that dipeptide aggregation is controlled primarily by main-chain interactions and is substantially unaffected by disturbing influences such as those arising from polar side chains, ions and water molecules. The peptide molecules in the highly pseudosymmetric crystals of the His-Ala complex, however, exhibit a hitherto unobserved aggregation pattern. Thus, in spite of the repeated occurrence of a few patterns, the possibility of the existence of new patterns needs to be taken into account.

Dipeptides↗

PubMed1999

Crystallization and preliminary crystallographic analysis of winged bean acidic lectin.

The acidic lectin (WBAII) from the winged bean (Psophocarpus tetragonolobus) binds to the H-antigenic determinant on human erythrocytes and to the T-antigenic disaccharide Gal-beta1,3-GalNAc. Two crystal forms of WBAII were obtained in the presence of methyl-alpha-D-galactose. Form I belongs to space group R3 with unit-cell dimensions a = b = 182.11, c = 44.99 A and has one dimer in the asymmetric unit. Form II belongs to space group C2 with unit-cell dimensions a = 135.36, b = 127.25, c = 139.98 A, beta = 95. 9 degrees and has four dimers in the asymmetric unit. Intensity data were collected to 3.0 A and to 3.5 A from crystals of form I and II, respectively. The structures were solved by the molecular-replacement method using the coordinates of the basic form of winged bean lectin.

Carbohydrate Metabolism↗

PubMed1999

Structure of basic winged-bean lectin and a comparison with its saccharide-bound form.

The crystal structure of the saccharide-free form of the basic form of winged-bean agglutinin (WBAI) has been solved by the molecular-replacement method and refined at 2.3 A resolution. The final R factor is 19.7% for all data in the resolution range 8.0-2.3 A. The asymmetric unit contains two half-dimers, each located on a crystallographic twofold axis. The structure of the saccharide-free form is compared with that of the complex of WBAI with methyl-alpha-D-galactoside. The complex is composed of two dimers in the asymmetric unit. The intersubunit interactions in the dimer are nearly identical in the two structures. The binding site of the saccharide-free structure contains three ordered water molecules at positions similar to those of the hydroxyl groups of the carbohydrate which are hydrogen bonded to the protein. Superposition of the saccharide-binding sites of the two structures shows that the major changes involve expulsion of these ordered water molecules and a shift of about 0.6 A of the main-chain atoms of the variable loop.

Binding Sites↗