Publications
2023
Allosteric determinants in High Temperature Requirement A enzymes are conserved and regulate the population of active conformations. Gupta, A. K., Singh, K., Patidar, Y., Sharma, R., Sardesai, A. A., Reddy, G., Gopal, B. (2023). ACS Chemical Biology doi:10.1021/acschembio.2c00921.
Characterization of RNase J. Muralidharan, V., Singh, A. K., Gopal, B. (2023). Methods Enzymol doi: 10.1016/bs.mie.2023.03.020.
Kesharwani S., Raj, P., Paul, A., Roy, K., Mehta, A., Gopal, A., Bhanot, A., Varshney, U., Gopal, B., Sundriyal, S. (2023) Crystal structures of non-uracil ring fragments in complex with Mycobacterium tuberculosis uracil DNA glycosylase (MtUng) as a starting point for novel inhibitor design: A case study with a barbituric acid fragment. Euro J Med Chem doi:10.1016/j.ejmech.2023.115604
Mutational and structural analyses of UdgX: insights into the active site pocket architecture and its evolution. Aroli, S., Woo, E-J., Gopal, B.,Varshney, U. (2023). Nucleic Acids Research doi: 10.1093/nar/gkad486
The unique N-terminal region of Mycobacterium tuberculosis Sigma Factor A (σA) plays a dominant role in the essential function of this protein. Singha, B., Behera, D., Khan, M. Z., Singh, N. K., Sowpati, D. T., Gopal, B., Nandicoori, V. K. (2023). J Biol Chem 299(3):102933.2023
2022
Curation and cheminformatics analysis of a Ugi-reaction derived library (URDL) of synthetically tractable small molecules for virtual screening application. Tandi, M., Tripathi, N., Gaur, A., Gopal, B., Sundriyal, S. (2022). Mol Divers doi:10.1007/s11030-022-10588-1.
Identification of a new and diverse set of Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) inhibitors using structure-based virtual screening: Experimental validation and molecular dynamics studies. Raj, P., Selvam, K., Roy, K., Mani Tripathi, S., Kesharwani, S., Gopal, B., Varshney, U., Sundriyal, S. (2022). Bioorg Med Chem Lett. 76:129008.
Mycobacterium tuberculosis Transcription Factor EmbR Regulates the Expression of Key Virulence Factors That Aid in Ex Vivo and In Vivo Survival. Kumar, S., Khan, M. Z., Khandelwal, N., Chongtham, C., Singha, B., Dabla, A., Behera, D., Singh, A., Gopal, B., Arimbasseri, G. A., Kamat, S. S., Nandicoori, V. K. (2022). Mbio 13: e03836-21.
Particle uptake driven phagocytosis in macrophages and neutrophils enhances bacterial clearance Sharma, P., Vijaykumar, A., Raghavan, J. V., Rananaware, S. R., Alakesh, A., Bodele, J., Rehman, J. U., Shukla, S., Wagde, V., Nadig, S., Chakrabarti, S., Visweswariah, S. S., Nandi, D., Gopal, B., Jhunjhunwala, S. (2022). J Control Release 343:131-141.
Structural variability of Mycobacterium tuberculosis SSB and susceptibility to inhibition. Raja, S., Paul, A., Raghavan, S., Narayanan, S., Shee, S., Singh, A., Varshney, U., Gopal, B., Vijayan, M. (2022). Curr Sci 122:281-289.
2021
Mycobacterium tuberculosis SufR responds to nitric oxide via its 4Fe–4S cluster and regulates Fe–S cluster biogenesis for persistence in mice. Anand, K., Tripathi, A., Shukla, K., Malhotra, N., Jamithireddy, A. K., Jha, R. K., Chaudhury, S. N., Rajmani, R. S., Ramesh, A., Nagaraja, V., Gopal, B., Nagaraju, G., Narain Seshayee, A. S., Singh, A. (2021).Redox Biol 46:102062
Novel insights into ATP-stimulated cleavage of branched DNA and RNA substrates through structure-guided studies of the Holliday junction resolvase RuvX. Thakur, M., Mohan, D., Singh, A.K., Agarwal, A., Gopal, B., Muniyappa, K. (2021). J Mol Biol 433:167014.
Redox regulation of the quorum-sensing transcription factor AgrA by coenzyme A. Baković, J. Yu, B.Y.K., Silva, D., Baczynska, M., Peak-Chew, S.Y., Switzer, A., Burchell, L., Wigneshweraraj, S., Vandanashree, M., Gopal, B., Filonenko, V., Skehel, M., Gout, I. (2021). Antioxidants doi:10.3390/antiox10060841.
Draft genome sequence of the community associated Staphylococcus aureus sequence type 88strain LVP-7, isolated from an ocular infection. Nadig, S., Murthy, S., Murali, V., Subramanya, H. S., Gopal, B., Vembar, S. (2021). Resource Announcements 10: 00077-00021.
Use of a molecular beacon based fluorescent method to assay uracyl DNA glycosylase (UNG) activity and inhibitor screening. Mehta, A., Raj, P., Sundriyal, S., Gopal, B., Varshney, U. BB Reports doi: 10.1016/j.bbrep.2021.100954
2020
Structural and biochemical characteristics of two Staphylococcus epidermidis RNase J paralogues RNase J1 and RNase J2. Raj, R., Nadig, S., Patel, T., Gopal, B. (2020). J Biol Chem doi:10.1074/jbc.RA120.014876.
Structural insights into the catalytic mechanism of Bacillus subtilis BacF. Deshmukh, A., Gopal, B. (2020). Acta Cryst F76:145-151.
Evaluation of specificity determinants in Mycobacterium tuberculosis s /anti-s factor interactions. Jamithireddy, A. K., Runthala, A., Gopal, B. (2020). Biochem Biophys Res Comm 521:900-906.
2019
Destabiliation of Insulin hexamer in Water-Ethanol binary mixture. Mukherjee S, Deshmukh AA, Mondal S, Gopal B, Bagchi B. (2019). J Phys Chem B. 123:10365-10375.
Selectivity among anti-s factors by Mycobacterium tuberculosis ClpX influences intracellular levels of Extracytoplasmic function s factors . Joshi, A. C., Kaur, P., Nair, R. K., Lele, D. S., Nandicoori, V. K., Gopal, B. (2019). J. Bacteriol 25:pii e0048-18.
2018
The crystal structure of Mycobacterium tuberculosis high temperature requirement A protein reveals an autoregulatory mechanism. Gupta, A. K., Behera, D., Gopal, B. (2018). Acta Cryst F74:803-809.
What gives an insulin hexamer its unique shape and stability? Role of ten confined water molecules. Mukherjee, S., Mondal, S., Deshmukh, A. A., Gopal, B., Bagchi, B. (2018). J. Phys. Chem B. 122:1631-1637.
Characterization of the Staphylococcus epidermidis polynucleotide phosphorylase and its interactions with ribonucleases RNaseJ1 and RNaseJ2. Raj, R., Mitra, S., Gopal, B. (2018). Biochem Biophys Res Comm 495:2078-2084.
2017
The fused Snoal_2 domain of the Mycobacterium tuberculosis sigma factor σ J modulates promoter recognition. Gautam, K., Gupta, A. K. & Gopal, B. (2017).Nucleic Acids Res doi: 10.1093/nar/gkx609.
Determination of redox sensitivity in structurally similar biological redox sensors. Jamithireddy, A. K., Samajdar, R. N., Gopal, B. & Bhattacharyya, A. J. (2017). J. Phys. Chem B doi: 10.1021/acs.jpcb.7b02081.
Design, synthesis and experimental validation of peptide ligand targeting Mycobacterium tuberculosis σ factors. Vishwanath, S., Banerjee, S., Jamithireddy, A. K., Srinivasan, N., Gopal, B., & Chatterjee, J. (2017). Biochemistry 56:2209-2218.
Probing the influence of non-covalent interaction networks identified by charge density analysis on the oxidoreductase BacC. Kumar, P., Balaram, H., Guru Row, T. N., & Gopal, B. (2017). Protein Engg Des Select. 30:263-270.
2016
The topology of the L-arginine exporter ArgO conforms to an Nin-Cout configuration in Escherichia coli: Requirement of the cytoplasmic N-terminal domain, functional helical interactions and an aspartate pair for ArgO function. Pathania, A., Gupta, A. K., Dubey, S, Gopal, B., Sardesai, A. S. (2016). J. Bacteriology 198: 3186-3199.
A point mutation in AgrC determines cytotoxic or colonizing properties associated with phenotypic variants of ST22 MRSA strains. Shambat, S.M., Siemens, N., Monk, I. R., Disha Mohan B, Mukundan, S. Krishnan, K. C., Prabhakara, S., Snall, J., Kearns, A., Vandenesch, F., Svensson, M., Kotb, M., Gopal, B., Arakere, G., Norrby-Teglund, A. (2016). Sci Reports 6: 31360-31372.
Conformational features of the Staphylococcus aureus AgrA-promoter interactions rationalize quorum-sensing triggered gene expression. Kalagiri, R., Fasim, A., Gopal, B. (2016). Biochem Biophys Rep 6: 124-134.
Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues Shivastava, P., Navratna, V., Silla, Y., Dewangan, R. P., Pramanik, A., Chaudhary, S., Rayasam, G. V., Kumar, A., Ugarkar, B., Gopal, B., Ramachandran, S. (2016). Sci Reports 6:30827-30844.
2015
Crystallographic studies of the extracytoplasmic function sigma factor SigJ from Mycobacterium tuberculosis Goutam, K., Gupta, A. K., Gopal, B. (2015). Acta Cryst. F71:946-950.
Structural basis for the catalytic mechanism of homoserine dehydrogenase. Navratna, V., Reddy, G. Gopal, B. (2015). Acta Cryst. D71: 1216-1225.
2014
Influence of the AgrC-AgrA complex in the response time of Staphylococcus aureus quorum sensing. Srivastava, S. K., Rajasree, K., Fasim, A., Arakere, G., Gopal, B. (2014). J. Bacteriology 196: 2876-2888.
Structural basis for the redox sensitivity of the Mycobacterium tuberculosis SigK-RskA σ-anti-σ complex. Shukla, J.K., Gupta, R., Thakur, K.G., Gokhale, R. S., Gopal, B. (2014). Acta Cryst. D70: 1026-1036.
Titania nanotube-modified screen printed carbon electrodes enhance the sensitivity in the electrochemical detection of proteins. Mandal, S.S., Navratna, V., Sharma, P., Gopal, B., Bhattacharyya, A. J. (2014). Bioelectrochemistry 98: 46-52.
Bi-domain protein tyrosine Phosphatases reveal an evolutionary adaptation to optimize signal transduction. Ahuja, L. G., Gopal, B. (2014). Antioxidants & Redox Signalling 20: 2141-2159.
2013
Crystallization and preliminary X-Ray diffraction studies of Staphylococcus aureus homoserine dehydrogenase. Navratna, V, Gopal, B. (2013). Acta Cryst F69:1216-1219.
Mycobacterium tuberculosis RsdA provides a conformational rationale for selective regulation of σ factor activity by proteolysis. Jaiswal R K, Suryaprabha T, Manjeera G, Gopal B. (2013). Nucleic Acids Res 41:3414-3423.
The crystal structure of an amidohydrolase SACOL0085 from Methicillin Resistant Staphylococcus aureus COL. Girish T S, Vivek B, Colaco M, Misquith S, Gopal B. (2013). Acta Cryst F69:103-108.
Structural insights into the role of Bacillus subtilis YwfH (BacG) in tetrahydrotyrosine synthesis. Rajavel M, Perinbam K, Gopal B. (2013). Acta Cryst D69:324-332.
2012
Analysis of conformational variation in macromolecular structural models. Srivastava S K, Gayathri S, Manjasetty B A, Gopal B. (2012). PLoS One. 2012;7(7):e39993.
Inter-domain interactions influence the stability and catalytic activity of the bi-domain protein tyrosine phosphatase PTP99A. Madan L L, Goutam K, Gopal B. (2012). Biochem Biophys Acta. 2012 Aug;1824:983-90.
2011
Conformational basis for substrate recruitment in Protein Tyrosine Phosphatase 10D Madan L L, Gopal B. (2011). Biochemistry 50: 10114-10125.
Modulation of catalytic activity in multi-domain protein tyrosine phosphatases Madan L L, Veeranna S, Shameer K, Reddy C C S, Sowdhamini R, Gopal, B. (2011). Plos One 6(9): e24766.
Structure and nucleotide specificity of Staphylococcus aureus dihydrodipicolinate reductase (DapB). Girish T S, Navratna V, Gopal B. (2011). FEBS Letts. 585: 2561-2567.
Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase Srivastava S K, Rajasree K, Gopal B. (2011). Biochem Biophys Acta (Proteins and Proteomics) 1814: 1349-1357.
Structural Biology of Mycobacterium tuberculosis: The Indian Efforts Arora A, Chandra N R, Das A, Gopal B, Mande S C, Prakash B, Ramachandran R, Sankaranarayanan R, Sekar K, Suguna K, Tyagi A K, Vijayan M.(2011). Tuberculosis (Edinb) 91(5) : 456-468.
2010
PeptideMine A webserver for the design of peptides for protein peptide binding studies derived from protein-protein interactomes. Shameer K , Madan L L, Veeranna S, Gopal B, Sowdhamini R . (2010). BMC Bioinformatics 11 : 473.
The crystal structure of Staphylococcus aureus metallopeptidase (Sapep) reveals large domain motions between the manganese bound and apo states. Girish T S , Gopal B. (2010). J. Biol. Chem 285, 29406-29415.
Over-expression and purification strategies for recombinant multi-protein oligomers: A case study of Mycobacterium tuberculosis s/ anti-s factor protein complexes Thakur K G, Jaiswal R K, Shukla J K, Praveena T, Gopal B. (2010). Prot. Exp. Purif. 74(2) : 223-230.
Role of a PAS sensor domain in the Mycobacterium tuberculosis transcription regulator Rv1364c. Jaiswal R K, Manjeera G, Gopal, B. (2010). Biochem Biophys Res Comm 398, 342-349.
Structural and biochemical basis for the redox sensitivity of Mycobacterium tuberculosis RslA Thakur K G, Praveena T, Gopal B. (2010). J. Mol. Biol.397, 1199-1208.
Analysis of multiple crystal forms of Bacillus subtilis BacB suggests a role for a metal ion as a nucleant for crystallization. Rajavel M, Gopal B. (2010). Acta Cryst D. 66, 635-639.
Inhibition of a protein tyrosine phosphatase using mesoporous oxides. Kapoor S, Girish T S, Mandal S S, Gopal B, Bhattacharyya A J. (2010). J. Phys. Chem B. 114: 3117-3121.
X-ray crystallographic and NMR studies of pantothenate synthetase provide insights into the mechanism of homotropic inhibition by pantoate. Chakrabarty K, Thakur G, Gopal B, Sarma S. (2010). FEBS J. 277:697-712.
Molecular Basis for the role of Staphylococcus aureus Penicillin Binding Protein 4 in antimicrobial resistance. Navratna V, Nadig S, Sood V, Prasad K, Arakere G, Gopal B. (2010). J. Bacteriology 192: 134-144.
Mycobacterium tuberculosis Rv2704 is a member of YjgF/YER057c/UK114 family. Thakur K G, Praveena T, Gopal B. (2010). Proteins 78:773-778.
2009
Role of Bacillus subtilis BacB in the synthesis of the antibiotic bacilysin. Rajavel M, Mitra A, Gopal B. (2009). J. Biol. Chem 284:31882-31892.
Structure-based phylogeny as a diagnostic for functional characterization of proteins with cupin fold Agarwal G, Rajavel M, Gopal B, Srinivasan N. (2009). PLoS One 4(5): e5736.
2008
Correlation between the sucrose synthase protein subfamilies, structure and expression in stress-derived Expressed Sequence Tag datasets. Jayashree B, Pradeep R, Kumar A, Gopal B. J. (2008).Proteomics Bioinformatics 1, 408-423.
Refolding and simultaneous purification by three phase partitioning of recombinant proteins from inclusion bodies. Raghava S, Barua B, Singh P K, Das M, Madan L L, Bhattacharyya S, Bajaj K, Gopal B, Varadarajan R, Gupta M N. (2008).Protein Sci 17,:1987-1997.
Structural and functional characterization of Staphylococcus aureus dihydrodipicolinate synthase. Girish T S, Sharma E, Gopal B. (2008).FEBS Letts 582,2923-2930.
Conformational studies suggest that the double stranded b helix scaffold provides an optimal balance between protein stability and function. Rajavel M, Kulkarni N N, Gopal B. (2008). Prot. Pept. Letts 15, 244-249.
Addition of a polypeptide stretch at the N-terminus improves the expression, stability and solubility of recombinant protein tyrosine phosphatases from Drosophila melanogaster. Madan L L, Gopal B. (2008). Prot. Exp. Purif.57, 234-243.
Structural and biophysical studies on two promoter recognition domains of the extra-cytoplasmic function s factor sC from Mycobacterium tuberculosis. Thakur K G, Joshi A M, Gopal B. (2008). J. Biol. Chem 282, 4711-4718.
2007
The crystal structure of the catalytic domain of the chick retinal neurite inhibitor- Receptor Protein Tyrosine Phosphatase CRYP-2 / cPTPRO. Girish T S, Gopal B. (2007).Proteins 65,1011-1015.
2006
Crystallization and preliminary X-Ray diffraction studies on the bicupin YwfC from Bacillus subtilis Rajavel M, Gopal B. (2006).Acta Cryst F62, 1259-1262.
Old fold in a new X-Ray diffraction dataset? Low-resolution molecular replacement using representative structural templates can provide phase information. Rajavel M, Warrier T, Gopal B. (2006).Proteins 64, 223-230.
2005
Crystallization and preliminary X-Ray diffraction studies on the N- and C- terminal domains of the extra-cytoplasmic sigma factor SigC from Mycobacterium tuberculosis. Thakur K G, Gopal B. (2005). Acta Cryst F61, 779-781.
Crystallization and Preliminary X-Ray diffraction studies on the catalytic domain of the of the chick neurite inhibitory factor CRYP-2. Girish T S, Gopal B. (2005). Acta Cryst F61, 381-383.
The mechanism of upstream activation in the rrnB operon of Mycobacterium smegmatis is different from the Escherichia coli paradigm. Arnvig K B, Gopal B, Papavinasasundaram K G, Cox R A, Colston M J. (2005). Microbiology 151, 467-473.
Crystal structure of a quercetin 2,3 dioxygenase from Bacillus subtilis suggests modulation of enzyme activity by a change in the metal ion at the active site(s) Gopal B, Madan L L, Betz S F, Kossiakoff A A. (2005). Biochemistry 44, 193-201.
2004
A high affinity interaction between NusA and the rrn nut site in Mycobacterium tuberculosis. Arnvig K B, Pennel S, Gopal B, Colston M J. (2004). Proc. Natl. Acad. Sci (USA) 101, 8325-8330.
2001
Crystal Structure of the transcription elongation / antitermination factor NusA from Mycobacterium tuberculosis. Gopal B, Haire L F, Gamblin S J, Dodson E J, Lane A N, Papavinasasundaram K G P, Colston M J, Dodson G. (2001). J. Mol. Biol. 314, 1087-1095.
Crystallization and preliminary X ray diffraction studies on the N-utilizing substance A (NusA) from Mycobacterium tuberculosis. Gopal B, Papavinasasundaram K G P, Colston M J, Dodson G, Haire L F. (2001). Acta Cryst D57, 1187-1188.
Spectroscopic and thermodynamic characterization of the transcription antitermination factor NusE and its interaction with NusB from Mycobacterium tuberculosis. Gopal B, Papavinasasundaram K G P, Colston M J, Dodson G, Major S, Lane A N. (2001). Biochemistry 40,Jan 30 920-928.
Tackling both the player and the ball: Lessons from crystallographic studies on the N-utilizing substance B (NusB) from Mycobacterium tuberculosis. Haire L F, Gopal B.(2001). J. Crystal Growth 232, 361-367.
Variability of calcium binding to EF-hand motifs probed by Electrospray Ionization Mass Spectrometry. Moorthy A K, Singh S K, Gopal B, Surolia A, Murthy M R N.(2001). J. Am. Soc. Mass. Spectrom. 12, 1296-1301.
2000
Crystal structure of NusB from Mycobacterium tuberculosis. Gopal B, Haire L F, Lane A N, Major S, Brannigan J A, Cox R A, Colston M J, Smerdon S J, Dodson G. (2000). Nature Struct Biol 7, 475-478.
Crystallization and preliminary X-ray diffraction studies on the N-utilizing substance B (NusB) from Mycobacterium tuberculosis. Gopal B, Cox R A, Colston M J, Dodson G G, Smerdon S J, Haire L F. (2000). Acta Cryst D56, 64-66.
1999
Structural and thermodynamic studies on protein stability. Gopal B. (1999). J. Ind Inst of Sci., 79, 551-553.
Thermodynamics of target peptide recognition by Calmodulin and a Calmodulin analogue : Implications for the role of the Central Linker. Moorthy A K, Gopal B, Satish P R, Bhattacharya S, Bhattacharya A, Murthy M R N, Surolia A. (1999). FEBS Letts 461, 19-24.
Temperature dependent cell transformation in a Calcium binding Protein from Entamoeba histolytica. Moorthy A K, Gopal B, Gopimohan C, Murthy M R N. (1999). Current Science 76, No. 7, 855-856.
Disulfide Engineering at the Dimer Interface of Lactobacillus casei Thymidylate Synthase : Crystal Structure of the T155C /E188C / C244T mutant. Velanker S S, Gokhale R S, Ray S S Gopal B, Parthasarathy S, Santi D V, Balaram P, Murthy M R N. (1999).Protein Science 8, 930-933.
Cavity Creating Mutation at the Dimer Interface in Plasmodium falciparum Triosephosphate isomerase : Restoring Protein Stability by Disulfide Crosslinking of Subunits. Gopal B, Ray S S, Gokhale R S, Balaram H, Murthy M R N, Balaram P. Biochemistry 38, 478-486.
Effect of amino acid substitutions at the subunit interface on the stability and aggregation properties of a dimeric protein: role of Arg 178 and Arg 218 at the Dimer interface of thymidylate synthase. Prasanna V, Gopal B, Murthy M R N, Santi D V, Balaram P. (1999).Proteins 34: 356-368.
1998
Induction of a spectrascopically defined .transition by Guanidium hydrochloride on a recombinant calcium binding protein from Entamoeba histolytica. Gopal B, Krishna Rao J V, Thomas C J, Bhattacharya A, Bhattacharya S, Murthy M R N, Surolia A. (1998). FEBS Letts 441, 71-76.
Crystals of a Thymidylate Synthase mutant offer insights into crystal packing and protein plasticity. Gopal B., Prasanna V., Parthasarathy S., Santi D. V., Balaram P & Murthy M. R. N. (1998). Current Science 75: 299-304.
Crystallization and preliminary X-ray studies of a recombinant calcium binding protein from Entamoeba histolytica. Gopal B., Suma R., Murthy M. R. N., Bhattacharya A & Bhattacharya S. (1998). Acta Cryst.D54: 1442-1445.
1997
Thermodynamics of metal ion binding and denaturation of a Calcium Binding Protein from Entamoeba histolytica. Gopal B., Swaminathan C. P., Bhattacharya S., Bhattacharya A., Murthy M. R. N. & Surolia A. (1997). Biochemistry 36: 10910-10917.
Allosteric determinants in High Temperature Requirement A enzymes are conserved and regulate the population of active conformations. Gupta, A. K., Singh, K., Patidar, Y., Sharma, R., Sardesai, A. A., Reddy, G., Gopal, B. (2023). ACS Chemical Biology doi:10.1021/acschembio.2c00921.
Characterization of RNase J. Muralidharan, V., Singh, A. K., Gopal, B. (2023). Methods Enzymol doi: 10.1016/bs.mie.2023.03.020.
Kesharwani S., Raj, P., Paul, A., Roy, K., Mehta, A., Gopal, A., Bhanot, A., Varshney, U., Gopal, B., Sundriyal, S. (2023) Crystal structures of non-uracil ring fragments in complex with Mycobacterium tuberculosis uracil DNA glycosylase (MtUng) as a starting point for novel inhibitor design: A case study with a barbituric acid fragment. Euro J Med Chem doi:10.1016/j.ejmech.2023.115604
Mutational and structural analyses of UdgX: insights into the active site pocket architecture and its evolution. Aroli, S., Woo, E-J., Gopal, B.,Varshney, U. (2023). Nucleic Acids Research doi: 10.1093/nar/gkad486
The unique N-terminal region of Mycobacterium tuberculosis Sigma Factor A (σA) plays a dominant role in the essential function of this protein. Singha, B., Behera, D., Khan, M. Z., Singh, N. K., Sowpati, D. T., Gopal, B., Nandicoori, V. K. (2023). J Biol Chem 299(3):102933.2023
2022
Curation and cheminformatics analysis of a Ugi-reaction derived library (URDL) of synthetically tractable small molecules for virtual screening application. Tandi, M., Tripathi, N., Gaur, A., Gopal, B., Sundriyal, S. (2022). Mol Divers doi:10.1007/s11030-022-10588-1.
Identification of a new and diverse set of Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) inhibitors using structure-based virtual screening: Experimental validation and molecular dynamics studies. Raj, P., Selvam, K., Roy, K., Mani Tripathi, S., Kesharwani, S., Gopal, B., Varshney, U., Sundriyal, S. (2022). Bioorg Med Chem Lett. 76:129008.
Mycobacterium tuberculosis Transcription Factor EmbR Regulates the Expression of Key Virulence Factors That Aid in Ex Vivo and In Vivo Survival. Kumar, S., Khan, M. Z., Khandelwal, N., Chongtham, C., Singha, B., Dabla, A., Behera, D., Singh, A., Gopal, B., Arimbasseri, G. A., Kamat, S. S., Nandicoori, V. K. (2022). Mbio 13: e03836-21.
Particle uptake driven phagocytosis in macrophages and neutrophils enhances bacterial clearance Sharma, P., Vijaykumar, A., Raghavan, J. V., Rananaware, S. R., Alakesh, A., Bodele, J., Rehman, J. U., Shukla, S., Wagde, V., Nadig, S., Chakrabarti, S., Visweswariah, S. S., Nandi, D., Gopal, B., Jhunjhunwala, S. (2022). J Control Release 343:131-141.
Structural variability of Mycobacterium tuberculosis SSB and susceptibility to inhibition. Raja, S., Paul, A., Raghavan, S., Narayanan, S., Shee, S., Singh, A., Varshney, U., Gopal, B., Vijayan, M. (2022). Curr Sci 122:281-289.
2021
Mycobacterium tuberculosis SufR responds to nitric oxide via its 4Fe–4S cluster and regulates Fe–S cluster biogenesis for persistence in mice. Anand, K., Tripathi, A., Shukla, K., Malhotra, N., Jamithireddy, A. K., Jha, R. K., Chaudhury, S. N., Rajmani, R. S., Ramesh, A., Nagaraja, V., Gopal, B., Nagaraju, G., Narain Seshayee, A. S., Singh, A. (2021).Redox Biol 46:102062
Novel insights into ATP-stimulated cleavage of branched DNA and RNA substrates through structure-guided studies of the Holliday junction resolvase RuvX. Thakur, M., Mohan, D., Singh, A.K., Agarwal, A., Gopal, B., Muniyappa, K. (2021). J Mol Biol 433:167014.
Redox regulation of the quorum-sensing transcription factor AgrA by coenzyme A. Baković, J. Yu, B.Y.K., Silva, D., Baczynska, M., Peak-Chew, S.Y., Switzer, A., Burchell, L., Wigneshweraraj, S., Vandanashree, M., Gopal, B., Filonenko, V., Skehel, M., Gout, I. (2021). Antioxidants doi:10.3390/antiox10060841.
Draft genome sequence of the community associated Staphylococcus aureus sequence type 88strain LVP-7, isolated from an ocular infection. Nadig, S., Murthy, S., Murali, V., Subramanya, H. S., Gopal, B., Vembar, S. (2021). Resource Announcements 10: 00077-00021.
Use of a molecular beacon based fluorescent method to assay uracyl DNA glycosylase (UNG) activity and inhibitor screening. Mehta, A., Raj, P., Sundriyal, S., Gopal, B., Varshney, U. BB Reports doi: 10.1016/j.bbrep.2021.100954
2020
Structural and biochemical characteristics of two Staphylococcus epidermidis RNase J paralogues RNase J1 and RNase J2. Raj, R., Nadig, S., Patel, T., Gopal, B. (2020). J Biol Chem doi:10.1074/jbc.RA120.014876.
Structural insights into the catalytic mechanism of Bacillus subtilis BacF. Deshmukh, A., Gopal, B. (2020). Acta Cryst F76:145-151.
Evaluation of specificity determinants in Mycobacterium tuberculosis s /anti-s factor interactions. Jamithireddy, A. K., Runthala, A., Gopal, B. (2020). Biochem Biophys Res Comm 521:900-906.
2019
Destabiliation of Insulin hexamer in Water-Ethanol binary mixture. Mukherjee S, Deshmukh AA, Mondal S, Gopal B, Bagchi B. (2019). J Phys Chem B. 123:10365-10375.
Selectivity among anti-s factors by Mycobacterium tuberculosis ClpX influences intracellular levels of Extracytoplasmic function s factors . Joshi, A. C., Kaur, P., Nair, R. K., Lele, D. S., Nandicoori, V. K., Gopal, B. (2019). J. Bacteriol 25:pii e0048-18.
2018
The crystal structure of Mycobacterium tuberculosis high temperature requirement A protein reveals an autoregulatory mechanism. Gupta, A. K., Behera, D., Gopal, B. (2018). Acta Cryst F74:803-809.
What gives an insulin hexamer its unique shape and stability? Role of ten confined water molecules. Mukherjee, S., Mondal, S., Deshmukh, A. A., Gopal, B., Bagchi, B. (2018). J. Phys. Chem B. 122:1631-1637.
Characterization of the Staphylococcus epidermidis polynucleotide phosphorylase and its interactions with ribonucleases RNaseJ1 and RNaseJ2. Raj, R., Mitra, S., Gopal, B. (2018). Biochem Biophys Res Comm 495:2078-2084.
2017
The fused Snoal_2 domain of the Mycobacterium tuberculosis sigma factor σ J modulates promoter recognition. Gautam, K., Gupta, A. K. & Gopal, B. (2017).Nucleic Acids Res doi: 10.1093/nar/gkx609.
Determination of redox sensitivity in structurally similar biological redox sensors. Jamithireddy, A. K., Samajdar, R. N., Gopal, B. & Bhattacharyya, A. J. (2017). J. Phys. Chem B doi: 10.1021/acs.jpcb.7b02081.
Design, synthesis and experimental validation of peptide ligand targeting Mycobacterium tuberculosis σ factors. Vishwanath, S., Banerjee, S., Jamithireddy, A. K., Srinivasan, N., Gopal, B., & Chatterjee, J. (2017). Biochemistry 56:2209-2218.
Probing the influence of non-covalent interaction networks identified by charge density analysis on the oxidoreductase BacC. Kumar, P., Balaram, H., Guru Row, T. N., & Gopal, B. (2017). Protein Engg Des Select. 30:263-270.
2016
The topology of the L-arginine exporter ArgO conforms to an Nin-Cout configuration in Escherichia coli: Requirement of the cytoplasmic N-terminal domain, functional helical interactions and an aspartate pair for ArgO function. Pathania, A., Gupta, A. K., Dubey, S, Gopal, B., Sardesai, A. S. (2016). J. Bacteriology 198: 3186-3199.
A point mutation in AgrC determines cytotoxic or colonizing properties associated with phenotypic variants of ST22 MRSA strains. Shambat, S.M., Siemens, N., Monk, I. R., Disha Mohan B, Mukundan, S. Krishnan, K. C., Prabhakara, S., Snall, J., Kearns, A., Vandenesch, F., Svensson, M., Kotb, M., Gopal, B., Arakere, G., Norrby-Teglund, A. (2016). Sci Reports 6: 31360-31372.
Conformational features of the Staphylococcus aureus AgrA-promoter interactions rationalize quorum-sensing triggered gene expression. Kalagiri, R., Fasim, A., Gopal, B. (2016). Biochem Biophys Rep 6: 124-134.
Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues Shivastava, P., Navratna, V., Silla, Y., Dewangan, R. P., Pramanik, A., Chaudhary, S., Rayasam, G. V., Kumar, A., Ugarkar, B., Gopal, B., Ramachandran, S. (2016). Sci Reports 6:30827-30844.
2015
Crystallographic studies of the extracytoplasmic function sigma factor SigJ from Mycobacterium tuberculosis Goutam, K., Gupta, A. K., Gopal, B. (2015). Acta Cryst. F71:946-950.
Structural basis for the catalytic mechanism of homoserine dehydrogenase. Navratna, V., Reddy, G. Gopal, B. (2015). Acta Cryst. D71: 1216-1225.
2014
Influence of the AgrC-AgrA complex in the response time of Staphylococcus aureus quorum sensing. Srivastava, S. K., Rajasree, K., Fasim, A., Arakere, G., Gopal, B. (2014). J. Bacteriology 196: 2876-2888.
Structural basis for the redox sensitivity of the Mycobacterium tuberculosis SigK-RskA σ-anti-σ complex. Shukla, J.K., Gupta, R., Thakur, K.G., Gokhale, R. S., Gopal, B. (2014). Acta Cryst. D70: 1026-1036.
Titania nanotube-modified screen printed carbon electrodes enhance the sensitivity in the electrochemical detection of proteins. Mandal, S.S., Navratna, V., Sharma, P., Gopal, B., Bhattacharyya, A. J. (2014). Bioelectrochemistry 98: 46-52.
Bi-domain protein tyrosine Phosphatases reveal an evolutionary adaptation to optimize signal transduction. Ahuja, L. G., Gopal, B. (2014). Antioxidants & Redox Signalling 20: 2141-2159.
2013
Crystallization and preliminary X-Ray diffraction studies of Staphylococcus aureus homoserine dehydrogenase. Navratna, V, Gopal, B. (2013). Acta Cryst F69:1216-1219.
Mycobacterium tuberculosis RsdA provides a conformational rationale for selective regulation of σ factor activity by proteolysis. Jaiswal R K, Suryaprabha T, Manjeera G, Gopal B. (2013). Nucleic Acids Res 41:3414-3423.
The crystal structure of an amidohydrolase SACOL0085 from Methicillin Resistant Staphylococcus aureus COL. Girish T S, Vivek B, Colaco M, Misquith S, Gopal B. (2013). Acta Cryst F69:103-108.
Structural insights into the role of Bacillus subtilis YwfH (BacG) in tetrahydrotyrosine synthesis. Rajavel M, Perinbam K, Gopal B. (2013). Acta Cryst D69:324-332.
2012
Analysis of conformational variation in macromolecular structural models. Srivastava S K, Gayathri S, Manjasetty B A, Gopal B. (2012). PLoS One. 2012;7(7):e39993.
Inter-domain interactions influence the stability and catalytic activity of the bi-domain protein tyrosine phosphatase PTP99A. Madan L L, Goutam K, Gopal B. (2012). Biochem Biophys Acta. 2012 Aug;1824:983-90.
2011
Conformational basis for substrate recruitment in Protein Tyrosine Phosphatase 10D Madan L L, Gopal B. (2011). Biochemistry 50: 10114-10125.
Modulation of catalytic activity in multi-domain protein tyrosine phosphatases Madan L L, Veeranna S, Shameer K, Reddy C C S, Sowdhamini R, Gopal, B. (2011). Plos One 6(9): e24766.
Structure and nucleotide specificity of Staphylococcus aureus dihydrodipicolinate reductase (DapB). Girish T S, Navratna V, Gopal B. (2011). FEBS Letts. 585: 2561-2567.
Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase Srivastava S K, Rajasree K, Gopal B. (2011). Biochem Biophys Acta (Proteins and Proteomics) 1814: 1349-1357.
Structural Biology of Mycobacterium tuberculosis: The Indian Efforts Arora A, Chandra N R, Das A, Gopal B, Mande S C, Prakash B, Ramachandran R, Sankaranarayanan R, Sekar K, Suguna K, Tyagi A K, Vijayan M.(2011). Tuberculosis (Edinb) 91(5) : 456-468.
2010
PeptideMine A webserver for the design of peptides for protein peptide binding studies derived from protein-protein interactomes. Shameer K , Madan L L, Veeranna S, Gopal B, Sowdhamini R . (2010). BMC Bioinformatics 11 : 473.
The crystal structure of Staphylococcus aureus metallopeptidase (Sapep) reveals large domain motions between the manganese bound and apo states. Girish T S , Gopal B. (2010). J. Biol. Chem 285, 29406-29415.
Over-expression and purification strategies for recombinant multi-protein oligomers: A case study of Mycobacterium tuberculosis s/ anti-s factor protein complexes Thakur K G, Jaiswal R K, Shukla J K, Praveena T, Gopal B. (2010). Prot. Exp. Purif. 74(2) : 223-230.
Role of a PAS sensor domain in the Mycobacterium tuberculosis transcription regulator Rv1364c. Jaiswal R K, Manjeera G, Gopal, B. (2010). Biochem Biophys Res Comm 398, 342-349.
Structural and biochemical basis for the redox sensitivity of Mycobacterium tuberculosis RslA Thakur K G, Praveena T, Gopal B. (2010). J. Mol. Biol.397, 1199-1208.
Analysis of multiple crystal forms of Bacillus subtilis BacB suggests a role for a metal ion as a nucleant for crystallization. Rajavel M, Gopal B. (2010). Acta Cryst D. 66, 635-639.
Inhibition of a protein tyrosine phosphatase using mesoporous oxides. Kapoor S, Girish T S, Mandal S S, Gopal B, Bhattacharyya A J. (2010). J. Phys. Chem B. 114: 3117-3121.
X-ray crystallographic and NMR studies of pantothenate synthetase provide insights into the mechanism of homotropic inhibition by pantoate. Chakrabarty K, Thakur G, Gopal B, Sarma S. (2010). FEBS J. 277:697-712.
Molecular Basis for the role of Staphylococcus aureus Penicillin Binding Protein 4 in antimicrobial resistance. Navratna V, Nadig S, Sood V, Prasad K, Arakere G, Gopal B. (2010). J. Bacteriology 192: 134-144.
Mycobacterium tuberculosis Rv2704 is a member of YjgF/YER057c/UK114 family. Thakur K G, Praveena T, Gopal B. (2010). Proteins 78:773-778.
2009
Role of Bacillus subtilis BacB in the synthesis of the antibiotic bacilysin. Rajavel M, Mitra A, Gopal B. (2009). J. Biol. Chem 284:31882-31892.
Structure-based phylogeny as a diagnostic for functional characterization of proteins with cupin fold Agarwal G, Rajavel M, Gopal B, Srinivasan N. (2009). PLoS One 4(5): e5736.
2008
Correlation between the sucrose synthase protein subfamilies, structure and expression in stress-derived Expressed Sequence Tag datasets. Jayashree B, Pradeep R, Kumar A, Gopal B. J. (2008).Proteomics Bioinformatics 1, 408-423.
Refolding and simultaneous purification by three phase partitioning of recombinant proteins from inclusion bodies. Raghava S, Barua B, Singh P K, Das M, Madan L L, Bhattacharyya S, Bajaj K, Gopal B, Varadarajan R, Gupta M N. (2008).Protein Sci 17,:1987-1997.
Structural and functional characterization of Staphylococcus aureus dihydrodipicolinate synthase. Girish T S, Sharma E, Gopal B. (2008).FEBS Letts 582,2923-2930.
Conformational studies suggest that the double stranded b helix scaffold provides an optimal balance between protein stability and function. Rajavel M, Kulkarni N N, Gopal B. (2008). Prot. Pept. Letts 15, 244-249.
Addition of a polypeptide stretch at the N-terminus improves the expression, stability and solubility of recombinant protein tyrosine phosphatases from Drosophila melanogaster. Madan L L, Gopal B. (2008). Prot. Exp. Purif.57, 234-243.
Structural and biophysical studies on two promoter recognition domains of the extra-cytoplasmic function s factor sC from Mycobacterium tuberculosis. Thakur K G, Joshi A M, Gopal B. (2008). J. Biol. Chem 282, 4711-4718.
2007
The crystal structure of the catalytic domain of the chick retinal neurite inhibitor- Receptor Protein Tyrosine Phosphatase CRYP-2 / cPTPRO. Girish T S, Gopal B. (2007).Proteins 65,1011-1015.
2006
Crystallization and preliminary X-Ray diffraction studies on the bicupin YwfC from Bacillus subtilis Rajavel M, Gopal B. (2006).Acta Cryst F62, 1259-1262.
Old fold in a new X-Ray diffraction dataset? Low-resolution molecular replacement using representative structural templates can provide phase information. Rajavel M, Warrier T, Gopal B. (2006).Proteins 64, 223-230.
2005
Crystallization and preliminary X-Ray diffraction studies on the N- and C- terminal domains of the extra-cytoplasmic sigma factor SigC from Mycobacterium tuberculosis. Thakur K G, Gopal B. (2005). Acta Cryst F61, 779-781.
Crystallization and Preliminary X-Ray diffraction studies on the catalytic domain of the of the chick neurite inhibitory factor CRYP-2. Girish T S, Gopal B. (2005). Acta Cryst F61, 381-383.
The mechanism of upstream activation in the rrnB operon of Mycobacterium smegmatis is different from the Escherichia coli paradigm. Arnvig K B, Gopal B, Papavinasasundaram K G, Cox R A, Colston M J. (2005). Microbiology 151, 467-473.
Crystal structure of a quercetin 2,3 dioxygenase from Bacillus subtilis suggests modulation of enzyme activity by a change in the metal ion at the active site(s) Gopal B, Madan L L, Betz S F, Kossiakoff A A. (2005). Biochemistry 44, 193-201.
2004
A high affinity interaction between NusA and the rrn nut site in Mycobacterium tuberculosis. Arnvig K B, Pennel S, Gopal B, Colston M J. (2004). Proc. Natl. Acad. Sci (USA) 101, 8325-8330.
2001
Crystal Structure of the transcription elongation / antitermination factor NusA from Mycobacterium tuberculosis. Gopal B, Haire L F, Gamblin S J, Dodson E J, Lane A N, Papavinasasundaram K G P, Colston M J, Dodson G. (2001). J. Mol. Biol. 314, 1087-1095.
Crystallization and preliminary X ray diffraction studies on the N-utilizing substance A (NusA) from Mycobacterium tuberculosis. Gopal B, Papavinasasundaram K G P, Colston M J, Dodson G, Haire L F. (2001). Acta Cryst D57, 1187-1188.
Spectroscopic and thermodynamic characterization of the transcription antitermination factor NusE and its interaction with NusB from Mycobacterium tuberculosis. Gopal B, Papavinasasundaram K G P, Colston M J, Dodson G, Major S, Lane A N. (2001). Biochemistry 40,Jan 30 920-928.
Tackling both the player and the ball: Lessons from crystallographic studies on the N-utilizing substance B (NusB) from Mycobacterium tuberculosis. Haire L F, Gopal B.(2001). J. Crystal Growth 232, 361-367.
Variability of calcium binding to EF-hand motifs probed by Electrospray Ionization Mass Spectrometry. Moorthy A K, Singh S K, Gopal B, Surolia A, Murthy M R N.(2001). J. Am. Soc. Mass. Spectrom. 12, 1296-1301.
2000
Crystal structure of NusB from Mycobacterium tuberculosis. Gopal B, Haire L F, Lane A N, Major S, Brannigan J A, Cox R A, Colston M J, Smerdon S J, Dodson G. (2000). Nature Struct Biol 7, 475-478.
Crystallization and preliminary X-ray diffraction studies on the N-utilizing substance B (NusB) from Mycobacterium tuberculosis. Gopal B, Cox R A, Colston M J, Dodson G G, Smerdon S J, Haire L F. (2000). Acta Cryst D56, 64-66.
1999
Structural and thermodynamic studies on protein stability. Gopal B. (1999). J. Ind Inst of Sci., 79, 551-553.
Thermodynamics of target peptide recognition by Calmodulin and a Calmodulin analogue : Implications for the role of the Central Linker. Moorthy A K, Gopal B, Satish P R, Bhattacharya S, Bhattacharya A, Murthy M R N, Surolia A. (1999). FEBS Letts 461, 19-24.
Temperature dependent cell transformation in a Calcium binding Protein from Entamoeba histolytica. Moorthy A K, Gopal B, Gopimohan C, Murthy M R N. (1999). Current Science 76, No. 7, 855-856.
Disulfide Engineering at the Dimer Interface of Lactobacillus casei Thymidylate Synthase : Crystal Structure of the T155C /E188C / C244T mutant. Velanker S S, Gokhale R S, Ray S S Gopal B, Parthasarathy S, Santi D V, Balaram P, Murthy M R N. (1999).Protein Science 8, 930-933.
Cavity Creating Mutation at the Dimer Interface in Plasmodium falciparum Triosephosphate isomerase : Restoring Protein Stability by Disulfide Crosslinking of Subunits. Gopal B, Ray S S, Gokhale R S, Balaram H, Murthy M R N, Balaram P. Biochemistry 38, 478-486.
Effect of amino acid substitutions at the subunit interface on the stability and aggregation properties of a dimeric protein: role of Arg 178 and Arg 218 at the Dimer interface of thymidylate synthase. Prasanna V, Gopal B, Murthy M R N, Santi D V, Balaram P. (1999).Proteins 34: 356-368.
1998
Induction of a spectrascopically defined .transition by Guanidium hydrochloride on a recombinant calcium binding protein from Entamoeba histolytica. Gopal B, Krishna Rao J V, Thomas C J, Bhattacharya A, Bhattacharya S, Murthy M R N, Surolia A. (1998). FEBS Letts 441, 71-76.
Crystals of a Thymidylate Synthase mutant offer insights into crystal packing and protein plasticity. Gopal B., Prasanna V., Parthasarathy S., Santi D. V., Balaram P & Murthy M. R. N. (1998). Current Science 75: 299-304.
Crystallization and preliminary X-ray studies of a recombinant calcium binding protein from Entamoeba histolytica. Gopal B., Suma R., Murthy M. R. N., Bhattacharya A & Bhattacharya S. (1998). Acta Cryst.D54: 1442-1445.
1997
Thermodynamics of metal ion binding and denaturation of a Calcium Binding Protein from Entamoeba histolytica. Gopal B., Swaminathan C. P., Bhattacharya S., Bhattacharya A., Murthy M. R. N. & Surolia A. (1997). Biochemistry 36: 10910-10917.