18 results on '"Chandra, N R"'
Search Results
2. An Effort of Furniture Design Development through the Utilization of Rice Straw Gogo Red Rice Slegreng Variety.
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Sumarno, Dharsono, and Ardi Chandra, N. R.
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RICE straw ,FURNITURE design ,RED rice ,FURNITURE ,RICE ,HANDICRAFT ,DATA modeling - Abstract
Rice is a staple food source and therefore widely planted by farmers. Straw is a residual waste of rice harvests which has not been utilized optimally. This residual waste can be used in semi-finished products and finished products, especially crafts and furniture for the export market. This study considers the use of waste straw for the needs of the handicraft industry and mining. The second objective is furniture and craft design innovation using a straw. Experiments were carried out by twisting straw so that it becomes a certain diameter and length. The upland variety of slegereng red rice straw was the research object owing to its greater length and hgher strength than other types. Data was derived from literature and informants, and evaluated using interactive analysis models, including data reduction, data display and data verification. The study demonstrates that waste straw can be used in furniture and craft product design innovations. The application is on chairs, tables, stools, tissue boxes, table lamps, frames and so on. [ABSTRACT FROM AUTHOR]
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- 2020
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3. Computational analysis of multivalency in lectins: structures of garlic lectin-oligosaccharide complexes and their aggregates
- Author
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Ramachandraiah, G., primary, Chandra, N. R., additional, Surolia, A., additional, and Vijayan, M., additional
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- 2003
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4. X-ray Studies on Crystalline Complexes Involving Amino Acids and Peptides. XXXIII. Crystal Structures of L- and DL-Arginine Complexed with Oxalic Acid and a Comparative Study of Amino Acid–Oxalic Acid Complexes
- Author
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Chandra, N. R., primary, Prabu, M. M., additional, Venkatraman, J., additional, Suresh, S., additional, and Vijayan, M., additional
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- 1998
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5. Crystallization and preliminary crystallographic studies on the mannose-specific lectin from garlic
- Author
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Chandra, N. R., primary, Dam, T. K., additional, Surolia, A., additional, and Vijayan, M., additional
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- 1997
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6. Water-dependent domain motion and flexibility in ribonuclease A and the invariant features in its hydration shell. An X-ray study of two low-humidity crystal forms of the enzyme.
- Author
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Kishan, R. V. R., Chandra, N. R., Sudarsanakumar, C., Suguna, K., and Vijayan, M.
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- 1995
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7. Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation.
- Author
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Datta, S, Prabu, M M, Vaze, M B, Ganesh, N, Chandra, N R, Muniyappa, K, and Vijayan, M
- Abstract
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.
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- 2000
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8. BioSuite: A comprehensive bioinformatics software package (A unique industry-academia collaboration)
- Author
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Acharya, M. S., Alaguraj, V., Anandhi, R., Anwaruddin, M., Arun, S. K., Arundhoti, B., Bag, S., Balaji, P. V., Balakrishnan, N., Balasubramaniam, C., Banerjee, A., Bansal, M., Basu, A., Bhadra, Bharanidharan, D., Bharatam, P. V., Bhattacharyya, D., Biswas, P., Brahmachari, S. K., Chaitanya, K. S., Chakrabarti, A., Chakrabarti, P. P., Chakraborty, P., Chandra, N. R., Chaudhuri, P., Das, S., Dash, D., Desiraju, G. R., Dixit, A., Eswari, P. J., Gautham, M., Ghosh, A., Gopalkrishnan, B., Gyanrajkumar, Hansia, P., Hariharan, M., Hariharaputran, S., Hasnain, S. E., Iqbal, P., Irshad, A., Issaac, R., Jain, V., Jayaram, B., Jeyakani, J., Jignesh, S., Karandikar, R. L., Karthikeyan, R., Kashaw, S. K., Kathiravan, T., Krishnan, N., Sankaran Krishnaswamy, Kumar, D., Kumar, J. J., Mandal, C., Mande, S., Marikkannu, R., Mastanarao, K., Mathur, R., Mohan Katta, A. V. S. K., Mona, T., Murali, T., Murthy, M. R. N., Nagarajaram, A., Nageswara Rao, P., Narayanan, P. J., Narendranath, S., Nirnimesh, Nishant, G., Pandey, R. K., Paramsivam, N., Patel, R. Y., Prasad Reddy, S. P. V., Prasad, P. A., Prathipati, P., Priya, S., Priya, V., Raghava, G. P. S., Raja Rao, V. V., Rajgopal, S., Ramakumar, S., Ranjan, A., Ranjan, S., Ravikumar, M., Reddi, B. R., Rohini, S., Sandhu, K. S., Sankha, S., Saxena, A. K., Scaria, V., Sekar, K., Seshadri, J., Shaikh, S. A., Shankar, R., Sravan Kumar, P., Srinivas, S. T. P. T., Srinivasan, N., Srividhya, K. V., Subrahmanyam, C., Suguna, K., Suman, D., Swaminathan, S., Swamy, C. S., Uma Maheswara Rao, C., Umadevi, P., Vasanthakumar, B., Vidyasagar, M., Vijaykrishnan, S., Vindal, V., Vishveshwara, S., and Yashodeep, H.
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Molecular-Dynamics ,Genetic Algorithm ,Identification ,Program ,Bioinformatics ,Search ,Proteins ,Dna ,Industry-Academia Collaboration ,Sequence ,Biosuite ,Prediction ,Software ,Alignment
9. BioSuite: A comprehensive bioinformatics software package (A unique industry-academia collaboration)
- Author
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Vidyasagar, M., Mande, S., Rajgopal, S., Gopalkrishnan, B., Srinivas, S. T. P. T., Uma Maheswara Rao, C., Kathiravan, T., Mastanarao, K., Narendranath, S., Rohini, S., Irshad, A., Murali, T., Subrahmanyam, C., Mona, T., Sankha, S., Priya, V., Suman, D., Raja Rao, V. V., Nageswara Rao, P., Issaac, R., Yashodeep, H., Arundhoti, B., Nishant, G., Jignesh, S., Chaitanya, K. S., Prasad Reddy, S. P. V., Chakraborty, P., Hasnain, S. E., Nagarajaram, A., Ranjan, A., Acharya, M. S., Anwaruddin, M., Arun, S. K., Gyanrajkumar, Kumar, D., Priya, S., Ranjan, S., Reddi, B. R., Seshadri, J., Sravan Kumar, P., Swaminathan, S., Umadevi, P., Vindal, V., Vijaykrishnan, S., Saxena, A. K., Dixit, A., Prathipati, P., Kashaw, S. K., Mandal, C., Bag, S., Balakrishnan, N., Bansal, M., Chandra, N. R., Murthy, M. R. N., Ramakumar, S., Sekar, K., Srinivasan, N., Suguna, K., Vishveshwara, S., Anandhi, R., Bhadra, Das, S., Hansia, P., Hariharaputran, S., Jeyakani, J., Karthikeyan, R., Pandey, R. K., Swamy, C. S., Vasanthakumar, B., Balaji, P. V., Patel, R. Y., Jayaram, B., Shaikh, S. A., Chakrabarti, P. P., Banerjee, A., Chakrabarti, A., Karandikar, R. L., Chaudhuri, P., Raghava, G. P. S., Ghosh, A., Paramsivam, N., Brahmachari, S. K., Dash, D., Balasubramaniam, C., Basu, A., Biswas, P., Hariharan, M., Mathur, R., Sandhu, K. S., Vinod Scaria, Shankar, R., Narayanan, P. J., Jain, V., Nirnimesh, Krishnaswamy, S., Alaguraj, V., Marikkannu, R., Mohan Katta, A. V. S. K., Krishnan, N., Srividhya, K. V., Eswari, P. J., Bharatam, P. V., Iqbal, P., Bhattacharyya, D., Desiraju, G. R., Kumar, J. J., Ravikumar, M., Gautham, M., Prasad, P. A., and Bharanidharan, D.
10. Computational analysis of proteome of H5N1 avian influenza virus to define T cell epitopes with vaccine potential.
- Author
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Parida R, Shaila MS, Mukherjee S, Chandra NR, and Nayak R
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- Animals, Epitopes, B-Lymphocyte immunology, Epitopes, B-Lymphocyte metabolism, Epitopes, T-Lymphocyte chemistry, Epitopes, T-Lymphocyte metabolism, Histocompatibility Antigens Class I metabolism, Histocompatibility Antigens Class II metabolism, Humans, Influenza A Virus, H5N1 Subtype metabolism, Models, Molecular, Peptides immunology, Peptides metabolism, Protein Binding, Proteome analysis, Proteome immunology, Epitopes, T-Lymphocyte immunology, Influenza A Virus, H5N1 Subtype immunology, Influenza Vaccines immunology
- Abstract
The existing vaccines against influenza are based on the generation of neutralizing antibody primarily directed against surface proteins - hemagglutinin and neuraminidase. In this work, we have computationally defined conserved T cell epitopes of proteins of influenza virus H5N1 to help in the design of a vaccine with haplotype specificity for a target population. The peptides from the proteome of H5N1 virus which are predicted to bind to different HLAs, do not show similarity with peptides of human proteome and are also identified to be generated by proteolytic cleavage. These peptides could be made use of in the design of either a DNA vaccine or a subunit vaccine against influenza.
- Published
- 2007
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11. Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: crystallographic and comparative analysis of 11 structures of Mycobacterium smegmatis RecA.
- Author
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Krishna R, Prabu JR, Manjunath GP, Datta S, Chandra NR, Muniyappa K, and Vijayan M
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- Binding Sites, Crystallography, X-Ray, DNA-Binding Proteins chemistry, Glycine chemistry, Models, Molecular, Protein Conformation, Protein Folding, Protein Structure, Tertiary, Rec A Recombinases classification, Mycobacterium smegmatis enzymology, Rec A Recombinases chemistry
- Abstract
Mycobacterium smegmatis RecA and its nucleotide complexes crystallize in three different, but closely related, forms characterized by specific ranges of unit cell dimensions. The six crystals reported here and five reported earlier, all grown under the same or very similar conditions, belong to these three forms, all in space group P6(1). They include one obtained by reducing relative humidity around the crystal. In all crystals, RecA monomers form filaments around a 6(1) screw axis. Thus, the c-dimension of the crystal corresponds to the pitch of the RecA filament. As reported for Escherichia coli RecA, the variation in the pitch among the three forms correlates well with the motion of the C-terminal domain of the RecA monomers with respect to the main domain. The domain motion is compatible with formation of inactive as well as active RecA filaments involving monomers with a fully ordered C domain. It does not appear to influence the movement upon nucleotide-binding of the switch residue, which is believed to provide the trigger for transmitting the effect of nucleotide binding to the DNA-binding region. Interestingly, partial dehydration of the crystal results in the movement of the residue similar to that caused by nucleotide binding. The ordering of the DNA-binding loops, which present ensembles of conformations, is also unaffected by domain motion. The conformation of loop L2 appears to depend upon nucleotide binding, presumably on account of the movement of the switch residue that forms part of the loop. The conformations of loops L1 and L2 are correlated and have implications for intermolecular communications within the RecA filament. The structures resulting from different orientations of the C domain and different conformations of the DNA-binding loops appear to represent snapshots of the RecA at different phases of activity, and provide insights into the mechanism of action of RecA.
- Published
- 2007
- Full Text
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12. A combined immuno-informatics and structure-based modeling approach for prediction of T cell epitopes of secretory proteins of Mycobacterium tuberculosis.
- Author
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Vani J, Shaila MS, Chandra NR, and Nayak R
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- Amino Acid Sequence, Antigens, Bacterial immunology, Antigens, Bacterial metabolism, Computer Simulation, Mycobacterium tuberculosis metabolism, Protein Binding, Protein Conformation, Antigens, Bacterial chemistry, Computational Biology, Epitopes, T-Lymphocyte chemistry, Epitopes, T-Lymphocyte immunology, Models, Molecular, Mycobacterium tuberculosis chemistry, Mycobacterium tuberculosis immunology
- Abstract
The role of secretory proteins of Mycobacterium tuberculosis in pathogenesis and stimulation of specific host responses is well documented. They are also shown to activate different cell types, which subsequently present mycobacterial antigens to T cells. Therefore identification of T cell epitopes from this set of proteins may serve to define candidate antigens with vaccine potential. Fifty-two secretory proteins of M. tuberculosis H37Rv were analyzed computationally for the presence of HLA class I binding nonameric peptides. All possible overlapping nonameric peptide sequences from 52 secretory proteins were generated in silico and analyzed for their ability to bind to 33 alleles belonging to A, B and C loci of HLA class I. Fifteen percent of generated peptides are predicted to bind to HLA with halftime of dissociation T(1/2) >or=100 min and 73% of the peptides predicted to bind are mono-allelic in their binding. The structural basis for recognition of no-namers by different HLA molecules was studied employing structural modeling of HLA class I-peptide complexes and there exists a good correlation between structural analysis and binding prediction. Pathogen peptides that could behave as self- or partially self-peptides in the host were eliminated using a comparative study with the human proteome, thus reducing the number of peptides for analysis. The implications of the finding for vaccine development are discussed vis-à-vis the limitations of the use of subunit vaccine and DNA vaccine.
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- 2006
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13. Structural similarity and functional diversity in proteins containing the legume lectin fold.
- Author
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Chandra NR, Prabu MM, Suguna K, and Vijayan M
- Subjects
- Carbohydrates chemistry, Models, Molecular, Plant Lectins, Protein Folding, Protein Structure, Quaternary, Protein Structure, Secondary, Fabaceae chemistry, Lectins chemistry
- Abstract
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.
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- 2001
- Full Text
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14. Sequence and structural determinants of mannose recognition.
- Author
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Ramachandraiah G and Chandra NR
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- Amino Acid Motifs, Amino Acid Sequence, Animals, Lectins metabolism, Molecular Sequence Data, Proteins metabolism, Lectins chemistry, Mannose metabolism
- Abstract
Mannose, an abundant cell surface monosaccharide binds to a diverse set of receptors, which are involved in a variety of important cellular processes. Structural analysis has been carried out on all the proteins containing non-covalently bound mannose as a monosaccharide in the Protein Data Bank, to identify common recognition principles. Proteins, highly specific to mannose, belonging to the super family of bulb lectins, are found to contain a consensus sequence motif QXDXNXVXY, which has been identified to be essential for mannose binding. Analysis of this motif in the crystal structures of bulb lectins has led to the understanding of the contribution of individual residues in mannose recognition. Comparison with other mannose binding proteins, reveals common hydrogen bonding patterns in all of them, despite differences in sequence, overall fold and the substructures at the binding sites of individual proteins. A database analysis also suggests that although the topology of the backbone, as at the binding site in bulb lectins, can generate mannose binding capability in a few other proteins, sequence and disposition of not only the residues in the motif, but also the residues in the neighborhood play a crucial role in allowing that property to be retained.
- Published
- 2000
15. Crystal structure of a dimeric mannose-specific agglutinin from garlic: quaternary association and carbohydrate specificity.
- Author
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Chandra NR, Ramachandraiah G, Bachhawat K, Dam TK, Surolia A, and Vijayan M
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- Amino Acid Sequence, Binding Sites, Carbohydrate Metabolism, Crystallography, X-Ray, Dimerization, Mannose chemistry, Mannose-Binding Lectins, Models, Molecular, Molecular Sequence Data, Plant Lectins, Plant Proteins chemistry, Protein Structure, Secondary, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Agglutinins chemistry, Garlic metabolism, Lectins chemistry, Plants, Medicinal, Protein Conformation
- Abstract
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., (Copyright 1998 Academic Press.)
- Published
- 1999
- Full Text
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16. X-ray studies on crystalline complexes involving amino acids and peptides XXXIV. Novel mode of aggregation, interaction patterns and chiral effects in the maleic acid complexes of DL- and L- arginine.
- Author
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Ravishankar R, Chandra NR, and Vijayan M
- Subjects
- Amino Acids, Arginine metabolism, Crystallography, X-Ray, Maleates metabolism, Peptides, Water, Arginine chemistry, Maleates chemistry, Models, Molecular
- Abstract
Amino acid - carboxylic acid complexes provide useful information in relation to molecular interactions in present day biological systems and to prebiotic self-organisation. The crystal structures of the complexes of maleic acid with DL- arginine (orthorhombic; Pca2(1); a=15.9829, b=5.4127, c=16.1885; R=0.0522 for 956 reflections) and L- arginine (triclinic; P1; a=5.2641, b=8.0388, c=9.7860, alpha=106.197, beta=97.275, gamma=101.64; R=0.039 for 1749 reflections) have been determined. The complexes are made up of positively charged zwitterionic arginine molecules and negatively charged semi-maleate ions which contain an intramolecular symmetric O-H-O hydrogen bond. In both the structures, the amino acid molecules aggregate into layers. In each layer, S2 head-to-tail sequences are interconnected through specific intermolecular interactions between alpha-carboxylate and guanidyl groups, an arrangement observed for the first time in crystal structures involving arginine. The carboxylate-guanidyl interactions are of different types in the two complexes and consequently aggregation patterns in them exhibit substantial differences. Interactions between the amino acid layers involve the semi-maleate ions in both the complexes. In addition, water-bridges also exist in the L complex. The full potential of the guanidyl group for specific interactions is realized in both the structures. The L complex contains an array of water-mediated salt bridges. The structures demonstrate that the effect of chirality on molecular aggregation can span a wide range.
- Published
- 1998
- Full Text
- View/download PDF
17. A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme.
- Author
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Chandra NR, Muirhead H, Holbrook JJ, Bernstein BE, Hol WG, and Sessions RB
- Subjects
- Animals, Crystallography, X-Ray, Geobacillus stearothermophilus, Trypanosoma brucei brucei, Models, Molecular, Phosphoglycerate Kinase chemistry, Protein Conformation
- Abstract
The occurrence of large domain motions associated with the mechanism of action of many proteins is well established. We present a general method of predicting domain closure applicable to proteins containing domains separated by an apparent hinge. The method attempts to allow for natural directional bias within the closing protein by repeatedly applying a weak pulling force over a short distance between pairs of atoms chosen at random in the two domains in question. Appropriate parameters governing the pulling function were determined empirically. The method was applied to the bi-lobal protein PGK and a closed-form activated ternary complex generated for Bacillus stearothermophilus PGK. This model was compared with the recently determined crystal structure of closed-form Trypanosoma brucei PGK. The model predicts the correct hinge regions, although the magnitude of movement at one hinge point was overestimated, and provides a reasonable representation of the closed-form ternary complex.
- Published
- 1998
18. Functional characterization of the precursor and spliced forms of RecA protein of Mycobacterium tuberculosis.
- Author
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Kumar RA, Vaze MB, Chandra NR, Vijayan M, and Muniyappa K
- Subjects
- Adenosine Triphosphate metabolism, Amino Acid Sequence, Base Sequence, DNA, Bacterial genetics, DNA, Bacterial metabolism, DNA, Single-Stranded genetics, DNA, Single-Stranded metabolism, Escherichia coli genetics, Genetic Complementation Test, Models, Molecular, Molecular Sequence Data, Molecular Structure, Molecular Weight, Mycobacterium tuberculosis genetics, Mycobacterium tuberculosis pathogenicity, Protein Conformation, Protein Precursors genetics, RNA Splicing, Rec A Recombinases genetics, Recombination, Genetic, Virulence, Mycobacterium tuberculosis metabolism, Protein Precursors chemistry, Protein Precursors metabolism, Rec A Recombinases chemistry, Rec A Recombinases metabolism
- Abstract
The recA locus of pathogenic mycobacteria differs from that of nonpathogenic species because it contains large intervening sequences nested in the RecA homology region that are excised by an unusual protein-splicing reaction. In vivo assays indicated that Mycobacterium tuberculosis recA partially complemented Escherichia coli recA mutants for recombination and mutagenesis. Further, splicing of the 85 kDa precursor to 38 kDa MtRecA protein was necessary for the display of its activity, in vivo. To gain insights into the molecular basis for partial and lack of complementation by MtRecA and 85 kDa proteins, respectively, we purified both of them to homogeneity. MtRecA protein, but not the 85 kDa form, bound stoichiometrically to single-stranded DNA in the presence of ATP. MtRecA protein was cross-linked to 8-azidoadenosine 5'-triphosphate with reduced efficiency, and kinetic analysis of ATPase activity suggested that it is due to decreased affinity for ATP. In contrast, the 85 kDa form was unable to bind ATP, in the presence or absence of ssDNA and, consequently, was entirely devoid of ATPase activity. Molecular modeling studies suggested that the decreased affinity of MtRecA protein for ATP and the reduced efficiency of its hydrolysis might be due to the widening of the cleft which alters the hydrogen bonds and the contact area between the enzyme and the substrate and changes in the disposition of the amino acid residues around the magnesium ion and the gamma-phosphate. The formation of joint molecules promoted by MtRecA protein was stimulated by SSB when the former was added first. The probability of an association between the lack and partial levels of biological activity of RecA protein(s) to that of illegitimate recombination in pathogenic mycobacteria is considered.
- Published
- 1996
- Full Text
- View/download PDF
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