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M Vijayan

Publications and source records attributed to M Vijayan.

At least 55 records · Page 3Linked to original sources
PubMed2002

Re-refinement using reprocessed data to improve the quality of the structure: a case study involving garlic lectin.

The structure of dimeric garlic lectin was previously determined to an effective resolution of 2.8A using X-ray intensity data processed by the XDS package and refined using X-PLOR [Chandra et al. (1999), J. Mol. Biol. 285, 1157--1168]. Repeated attempts to grow better crystals with a view to improving the definition of the structure did not succeed. The available raw data were then reprocessed using DENZO. The structure was re-refined with both X-PLOR and CNS separately using the reprocessed data, which extended to a resolution of 2.2A. These two sets of refinements and the two sets using the XDS-processed data afforded an opportunity to compare the performance of different data-processing and refinement packages when dealing with data from weakly diffracting crystals. The best results were obtained when CNS was employed for refinement using data processed by DENZO. The quality and the resolution of the map and the definition of the structure improved substantially. In particular, the amino-acid residues at the variable locations in the sequence, and hence the isolectins, could be identified with a high degree of confidence. It could be established that the crystal asymmetric unit contains two identical heterodimers. The new refined structure also provided a better definition of other finer structural details.

Amino Acid Sequence↗
PubMed2002

Crystallization and preliminary X-ray studies of the single-stranded DNA-binding protein from Mycobacterium tuberculosis.

Single-stranded DNA-binding proteins play an important role in DNA replication, repair and recombination. The protein from Mycobacterium tuberculosis (MtSSB) is a tetramer with 164 amino-acid residues in each subunit. The protein readily crystallizes in space group P3(1)21 (or P3(2)21) at pH 7.4 under appropriate conditions. Under different conditions, but at the same pH, orthorhombic crystals belonging to space group I222 or I2(1)2(1)2(1) were obtained after several months. Similar orthorhombic crystals were obtained when protein samples stored for several months were used for crystallization. The orthorhombic crystals obtained in different experiments, though similar to one another, exhibited variations in unit-cell parameters, presumably on account of different extents of proteolytic cleavage of the C-terminal region. Molecular-replacement calculations using different search models did not yield the structure. As part of attempts to solve the structure using isomorphous replacement, a good mercury derivative of the trigonal crystal has been prepared.

Crystallization↗
PubMed2001

X-ray studies on crystalline complexes involving amino acids and peptides. XXXVIII. Crystal structures of the complexes of L-arginine and L-histidine with glutaric acid and a comparative study of amino acid-glutaric acid complexes.

The complexes of glutaric acid with L-arginine and L-histidine (two crystal forms) exhibit different stoichiometries and ionization states. The aggregation patterns in two of the crystals are remarkably similar to those observed earlier in similar structures, while the pattern in the remaining one has not been seen earlier. The variability in the ionization state and stoichiometry observed in amino acid-dicarboxylic acid complexes appears to represent subtle differences in the response of a molecule to the presence in its neighbourhood of another type of molecule. The glutaric acid molecules (or glutarate or semiglutarate ions) in their complexes and in other crystals favour a fully extended conformation, albeit with frequent departures from it. The change in the chirality of the component molecules in the complex could lead to drastic changes in the aggregation pattern; alternatively, the effects of the change are accommodated through small adjustments in essentially the same pattern.

Amino Acids↗
PubMed2001

The combination of molecular dynamics with crystallography for elucidating protein-ligand interactions: a case study involving peanut lectin complexes with T-antigen and lactose.

Peanut lectin binds T-antigen [Galbeta(1-3)GalNAc] with an order of magnitude higher affinity than it binds the disaccharide lactose. The crystal structures of the two complexes indicate that the higher affinity for T-antigen is generated by two water bridges involving the acetamido group. Fresh calorimetric measurements on the two complexes have been carried out in the temperature range 280-313 K. Four sets of nanosecond molecular-dynamics (MD) simulations, two at 293 K and the other two at 313 K, were performed on each of the two complexes. At each temperature, two somewhat different protocols were used to hydrate the complex in the two runs. Two MD runs under slightly different conditions for each complex served to assess the reliability of the approach for exploring protein-ligand interactions. Enthalpies based on static calculations and on MD simulations favour complexation involving T-antigen. The simulations also brought to light ensembles of direct and water-mediated protein-sugar interactions in both the cases. These ensembles provide a qualitative explanation for the temperature dependence of the thermodynamic parameters of peanut lectin-T-antigen interaction and for the results of one of the two mutational studies on the lectin. They also support the earlier conclusion that the increased affinity of peanut lectin for T-antigen compared with that for lactose is primarily caused by additional water bridges involving the acetamido group. The calculations provide a rationale for the observed sugar-binding affinity of one of the two available mutants. Detailed examination of the calculations point to the need for exercising caution in interpreting results of MD simulations: while long simulations are not possible owing to computational reasons, it is desirable to carry out several short simulations with somewhat different initial conditions.

Anti-Bacterial Agents↗
PubMed2001

The effect of stabilizing additives on the structure and hydration of proteins: a study involving tetragonal lysozyme.

In order to elucidate the effect of stabilizing additives on the structure of proteins and the associated ordered water molecules in the hydration shell, the crystal structures of tetragonal lysozyme grown in the presence of sucrose, sorbitol and trehalose have been refined. Also refined are the structures of orthorhombic and monoclinic lysozyme grown under the conditions in which tetragonal lysozyme is normally grown. A comparison of the two sets of structures with the structure of native tetragonal lysozyme shows that the effect of the additives on the structure of the protein molecule is less than that of the normal minor changes associated with differences in molecular packing. Surprisingly, the same is true of the effect on the hydration shell, represented by the ordered water molecules attached to the protein. Thus, it appears that the cause of the stabilizing effect of the additives needs to be sought outside the immediate neighbourhood of the protein molecule. Sorbitol and trehalose do not coherently interact with the protein. One sucrose molecule binds at the active-site cleft of the enzyme.

Animals↗
PubMed2001

Mutational analysis at Asn-41 in peanut agglutinin. A residue critical for the binding of the tumor-associated Thomsen-Friedenreich antigen.

Peanut agglutinin is a clinically important lectin due to its application in the screening of mature and immature thymocytes as well as in the detection of cancerous malignancies. The basis for these applications is the remarkably strong affinity of the lectin for the tumor-associated Thomsen-Friedenreich antigen (T-antigen) and more so due to its ability to distinguish T-antigen from its cryptic forms. The crystal structure of the complex of peanut agglutinin with T-antigen reveals the basis of this specificity. Among the contacts involved in providing this specificity toward T-antigen is the water-mediated interaction between the side chain of Asn-41 and the carbonyl oxygen of the acetamido group of the second hexopyranose ring of the sugar molecule. Site-directed mutational changes were introduced at this residue with the objective of probing the role of this residue in T-antigen binding and possibly engineering an altered species with increased specificity for T-antigen. Of the three mutants tested, i.e. N41A, N41D, and N41Q, the last one shows improved potency for recognition of T-antigen. The affinities of the mutants can be readily explained on the basis of the crystal structure of the complex and simple modeling. In particular, the change of asparagine to glutamine could lead to a direct interaction of the side chain with the sugar while at the same time retaining the water bridge. This study strengthens the theory that in lectins the nonprimary contacts generally made through water bridges are involved in imparting exquisite specificity.

Antigens, Tumor-Associated, Carbohydrate↗
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

Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal packing directed by interactions at the combining site.

The crystal structures of a monoclinic and a triclinic form of the peanut lectin-lactose complex, grown at pH 4.6, have been determined. They contain two and one crystallographically independent tetramers, respectively. The unusual "open" quaternary structure of the lectin, observed in the orthorhombic complex grown in neutral pH, is retained at the acidic pH. The sugar molecule is bound to three of the eight subunits in the monoclinic crystals, whereas the combining sites in four are empty. The lectin-sugar interactions are almost the same at neutral and acidic pH. A comparison of the sugar-bound and free subunits indicates that the geometry of the combining site is relatively unaffected by ligand binding. The combining site of the eighth subunit in the monoclinic crystals is bound to a peptide stretch in a loop from a neighboring molecule. The same interaction exists in two subunits of the triclinic crystals, whereas density corresponding to sugar exists in the combining sites of the other two subunits. Solution studies show that oligopeptides with sequences corresponding to that in the loop bind to the lectin at acidic pH, but only with reduced affinity at neutral pH. The reverse is the case with the binding of lactose to the lectin. A comparison of the neutral and acidic pH crystal structures indicates that the molecular packing in the latter is directed to a substantial extent by the increased affinity of the peptide loop to the combining site at acidic pH.

Carbohydrates↗
PubMed2001

Structural similarity and functional diversity in proteins containing the legume lectin fold.

Knowledge of structural relationships in proteins is increasingly proving very useful for in silico characterizations and is also being exploited as a prelude to almost every investigation in functional and structural genomics. A thorough understanding of the crucial features of a fold becomes necessary to realize the full potential of such relationships. To illustrate this, structures containing the legume lectin-like fold were chosen for a detailed analysis since they exhibit a total lack of sequence similarity among themselves and also belong to diverse functional families. A comparative analysis of 15 different families containing this fold was therefore carried out, which led to the determination of the minimal structural principles or the determining region of the fold. A critical evaluation of the structural features, such as the curvature of the front sheet, the presence of the hydrophobic cores and the binding site loops, suggests that none of them are crucial for either the formation or the stability of the fold, but are required to generate diversity and specificity to particular carbohydrates. In contrast, the presence of the three sheets in a particular geometry and also their topological connectivities seem to be important. The fold has been shown to tolerate different types of protein-protein associations, most of them exhibiting different types of quaternary associations and some even existing as complexes with other folds. The function of every family in this study is discussed with respect to its fold, leading to the suggestion that this fold can be linked to carbohydrate recognition in general.

Carbohydrates↗
PubMed2000

Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation.

Sequencing of the complete genome of Mycobacterium tuberculosis, combined with the rapidly increasing need to improve tuberculosis management through better drugs and vaccines, has initiated extensive research on several key proteins from the pathogen. RecA, a ubiquitous multifunctional protein, is a key component of the processes of homologous genetic recombination and DNA repair. Structural knowledge of MtRecA is imperative for a full understanding of both these activities and any ensuing application. The crystal structure of MtRecA, presented here, has six molecules in the unit cell forming a 6(1) helical filament with a deep groove capable of binding DNA. The observed weakening in the higher order aggregation of filaments into bundles may have implications for recombination in mycobacteria. The structure of the complex reveals the atomic interactions of ADP-AlF(4), an ATP analogue, with the P-loop-containing binding pocket. The structures explain reduced levels of interactions of MtRecA with ATP, despite sharing the same fold, topology and high sequence similarity with EcRecA. The formation of a helical filament with a deep groove appears to be an inherent property of MtRecA. The histidine in loop L1 appears to be positioned appropriately for DNA interaction.

Adenosine Diphosphate↗
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↗
PubMed2000

X-ray studies on crystalline complexes involving amino acids and peptides. XXXV. Invariance and variability in amino acid aggregation in the complexes of maleic acid with L-histidine and L-lysine.

The crystal structures of complexes of maleic acid with L-histidine and L-lysine have been determined. The two crystallographically independent amino acid molecules in the L-histidine complex have different closed conformations, while the lysine molecule in its complex has the most favourable conformation sterically with an all-trans sidechain trans to the alpha-carboxylate group. The maleic acid molecules exist as semi-maleate ions of similar conformation and contain a symmetric O...H...O hydrogen bond. Amino acid cations and semi-maleate anions aggregate into alternate layers in both the structures. The arrangement of molecules in the histidine layer in L-histidine semi-maleate is closer to that in the crystals of the free amino acid than in other L-histidine complexes. On the other hand, the arrangement of lysine molecules in its semi-maleate complex is different from any observed so far. However, the well established characteristic interaction patterns involving amino and carboxylate groups still play a major role in holding the molecules together in the crystal of the complex.

Amino Acids↗
PubMed2000

Hydration, mobility and accessibility of lysozyme: structures of a pH 6.5 orthorhombic form and its low-humidity variant and a comparative study involving 20 crystallographically independent molecules.

The structure analyses of orthorhombic lysozyme grown at pH 6.5 and its low-humidity variant are reported. The structures of the same form grown at pH 9.5 and 4.5 and that of the low-humidity variant of the pH 9.5 form are available. A comparison between them shows that the changes in molecular geometry and hydration caused by changes in the amount of solvent surrounding protein molecules are more pronounced than those caused by variation in pH. In particular, the conformation and the mutual orientation of the catalytic residues Glu35 and Asp52 remain unaffected by change in pH. A comparative study involving 20 crystallographically independent lysozyme molecules, including five in the orthorhombic form, leads to the delineation of the relatively rigid, moderately flexible and highly flexible regions of the molecule. Half the binding cleft (subsites D, E and F) belong to the rigid region but the other half (subsites A, B and C) belong to a flexible region. There is no marked correlation between relative rigidity and conservation of side-chain conformation except at the binding site. The study permits the identification of seven invariant water molecules associated with the protein. Most of them are involved in important tertiary interactions, while one occurs in the active-site cleft. The study demonstrates a weak correlation between non-accessibility and rigidity. On average, the level of hydration of polar atoms increases rapidly with accessible atomic surface area, but levels off at about 15 A(2) at a little over one ordered water molecule per polar protein atom. Only 15 N and O atoms are hydrated in all 20 molecules. 13 of these are hydrated by the seven invariant water molecules. Of the seven, only one water molecule is totally buried within the protein.

Animals↗
PubMed1999

Variability in quaternary association of proteins with the same tertiary fold: a case study and rationalization involving legume lectins.

Legume lectins constitute a family of proteins in which small alterations arising from sequence variations in essentially the same tertiary structure lead to large changes in quaternary association. All of them are dimers or tetramers made up of dimers. Dimerization involves side-by-side or back-to-back association of the flat six-membered beta-sheets in the protomers. Variations within these modes of dimerization can be satisfactorily described in terms of angles defining the mutual disposition of the two subunits. In all tetrameric lectins, except peanut lectin, oligomerization involves the back-to-back association of side-by-side dimers. An attempt has been made to rationalize the observed modes of oligomerization in terms of hydrophobic surface area buried on association, interaction energy and shape complementarity, by constructing energy minimised models in each of which the subunit of one legume lectin is fitted in the quaternary structure of another. The results indicate that all the three indices favor and, thus, provide a rationale for the observed arrangements. However, the discrimination provided by buried hydrophobic surface area is marginal in a few instances. The same is true, to a lesser extent, about that provided by shape complementarity. The relative values of interaction energy turns out to be a still better discriminator than the other two indices. Variability in the quaternary association of homologous proteins is a widely observed phenomenon and the present study is relevant to the general problem of protein folding.

Biopolymers↗
PubMed1999

Crystal structure of a dimeric mannose-specific agglutinin from garlic: quaternary association and carbohydrate specificity.

A mannose-specific agglutinin, isolated from garlic bulbs, has been crystallized in the presence of a large excess of alpha-d-mannose, in space group C2 and cell dimensions, a=203.24, b=43.78, c=79.27 A, beta=112.4 degrees, with two dimers in the asymmetric unit. X-ray diffraction data were collected up to a nominal resolution of 2.4 A and the structure was solved by molecular replacement. The structure, refined to an R-factor of 22.6 % and an Rfree of 27.8 % reveals a beta-prism II fold, similar to that in the snowdrop lectin, comprising three antiparallel four-stranded beta-sheets arranged as a 12-stranded beta-barrel, with an approximate internal 3-fold symmetry. This agglutinin is, however, a dimer unlike snowdrop lectin which exists as a tetramer, despite a high degree of sequence similarity between them. A comparison of the two structures reveals a few substitutions in the garlic lectin which stabilise it into a dimer and prevent tetramer formation. Three mannose molecules have been identified on each subunit. In addition, electron density is observed for another possible mannose molecule per dimer resulting in a total of seven mannose molecules in each dimer. Although the mannose binding sites and the overall structure are similar in the subunits of snowdrop and garlic lectin, their specificities to glycoproteins such as GP120 vary considerably. These differences appear, in part, to be a direct consequence of the differences in oligomerisation, implying that variation in quaternary association may be a mode of achieving oligosaccharide specificity in bulb lectins.

Agglutinins↗