Studies on gene expression using the operator-repressor system of bacteriophage lambda macromolecular interactions leading to high fidelity of protein synthesis
Returning to India in 1986, he joined Bose Institute, Kolkata as a senior lecturer in the department of biophysics.[4] He served the Institute till 2004 holding positions of reader and then professor of biophysics when he moved to the Indian Institute of Chemical Biology (IICB) as its director.[6] After completing 10 years as the director of IICB, he returned to Bose Institute in 2014 as a senior professor and dean of studies. While at IICB, he has served the nation in several different high-level capacities such as the founder-director-in-charge of the National Institute of Pharmaceutical Education and Research, Kolkata (NIPER) (2007–14), the cluster director of 11 Biological institutes of the Council of Scientific and Industrial Research (CSIR) (2009–14), member of the governing body of the CSIR and as a visiting professor at Osaka University (2012).[7] He has served as the president of the West Bengal Academy of Science and Technology. He is the founder-president of the Chemical Biology Society of India. He currently serves as a member of the board of directors of the International Chemical Biology Society. He also served as the director (officiating) of Bose Institute during the critical Centenary year.[8][citation needed] In addition, Roy played the very crucial role as an advisory committee member to successfully conduct the 'International Conference on Genome Biology 2019' hosted by the School of Biological Sciences (SBS), Madurai Kamaraj University.[9]
Research
Roy's researches during his stint in the US was on protein folding and nuclear magnetic resonance studies of DNA[4] and those researches identified the first hydropathy model which helped in predicting the exteriors and interiors of proteins by analyzing sequence information.[7] He is also reported to have performed the complete assignment of a nucleic acid imino proton spectra using Nuclear Overhauser effect, regio-specific isotope labeling of sugars in nucleic acids and working along with Ad Bax and R. H. Griffey, developed an indirect 2D-NMR detection method, all reported to be for the first time.[7] Later focusing his attention on bacteriophage lambda, he studied the gene expression of the bacterial virus using its operator-repressor system.[10] Through his collaborative work with Sankar Adhya in 1998, he elucidated the role of differential contact in the transcription regulation mechanism and demonstrated the theory in many genetic regulatory circuits.[4] His current work is focused on peptidetherapeutics[7] and he holds patents for some of his work.[11][12][13]
Roy has published his research work through a number of articles published in peer-reviewed journals[note 1] and ResearchGate, an online repository of scientific papers, has listed 155 of them.[14] He is the Co-author of "Chemical Biology of the Genome" published by Elsevier/AP. He is a joint editor of Subcellular Biochemistry, volume on Proteins: Structure, Function, and Engineering published by Plenum Press, New York, USA and Protein-Protein interaction Regulators published by Royal Society of Chemistry, UK. He has guided around 30 scholars in their doctoral studies.[4] When the Chemical Biology Society of India was formed in 2013, he became its founder president and holds the position.[15] He is a former president of the West Bengal Academy of Science and Technology and is its incumbent vice president.[16]
Gene Expression and its Regulation -- An Evolutionary Perspective by Siddhartha Roy. 2025. Published by Springer-Nature.
Chemical Biology of the Genome by Siddhartha Roy & Tapas Kundu. 2021. Published by Elsevier/AP.
Protein-Protein interaction Regulators, edited by Siddhartha Roy & Haian Fu. 2021. Published by Royal Society of Chemistry, UK
Subcellular Biochemistry, Volume 24 on Proteins: Structure, Function, and Engineering, edited by B B Biswas & Siddhartha Roy. 1995. Published by Plenum Press, New York, USA.
Selected bibliography
Gitashri Naiya, Paromita Raha, Manas Mondal, Uttam Pal, Rajesh Saha, Susobhan Choudhury, Subrata Batabyal, Samir Kumar Pal, Dhananjay Bhattacharyya, Nakul Chandra Maiti, Siddhartha Roy (June 2016). "Conformational Selection Underpins Recognition of Multiple DNA sequences by Proteins and Consequent Functional Actions". Physical Chemistry Chemical Physics. 18 (31): 21618–21628. Bibcode:2016PCCP...1821618N. doi:10.1039/C6CP03278H. PMID27426617.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Samir Kumar Pal, Susobhan Choudhury, Basusree Ghosh, Priya Singh, Raka Ghosh, Siddhartha Roy (June 2016). "Ultrafast Differential Flexibility of Cro-protein Binding Domains of Two Operator DNAs with Different Sequences". Physical Chemistry Chemical Physics. 18 (27): 17983–17990. Bibcode:2016PCCP...1817983C. doi:10.1039/C6CP02522F. PMID27326896.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Siddhartha Roy, Piya Ghosh, Neeladri Roy, Abhishek Mazumder, Koushik Roy, Asit Kumar Manna, Shampa Mallick, Israr Ahmed (May 2012). "Peptide based Molecules as Protein-Protein Interaction Inhibitors: Tools for Chemical Genetics and Therapy". Current Chemical Biology. 6 (2): 145–163. doi:10.2174/2212796811206020145.{{cite journal}}: CS1 maint: multiple names: authors list (link)
DNA-Bound p53-DNA-Binding Domain Interconverts between Multiple Conformations: Implications for Partner Protein Recognition. Bhattacharjee, S., Mukherjee, S., and Roy, S.* (2021) J Phys Chem B, 125, 5832-5837.https://doi.org/10.1021/acs.jpcb.1c03794
A peptide-based synthetic transcription factor selectively activates transcription in a mammalian cell. Roy, K., Mazumder, A., Ghosh, P., Naiya, G., Ghosh, B., & Roy, S.* (2018) Chem Commun. 54, 1611-1614.https://doi.org/10.1039/C7CC09279B
A Peptide-based Synthetic Transcription Factor Selectively Down-regulates the Proto-oncogene CFOS in Tumour Cells and Inhibits Proliferation. Chakraborty, M. and Roy, S.* (2016) Chem Commun, 53, 376-379.https://doi.org/10.1039/C6CC08086C
Specific Sequence of a Beta-turn in Human La Protein May Contribute to Species Specificity of Hepatitis C Virus. Kumar, A., Manna, AK., Ray, U., Mullick, R., Basu, G., Das, S., & Roy, S.* (2014) J Virol, 88, 4319-27. https://doi.org/10.1128/jvi.00049-14
A Synthetic Peptide Mimic of l-Cro shows Sequence-Specific Binding in vitro and in vivo. Mazumder, A., Maiti, A., Roy, K., & Roy, S.* (2012) ACS Chem Biol, 7, 1084-94. https://doi.org/10.1021/cb200523n
Peptide-protein interactions suggest that acetylation of lysines 381 and 382 of p53 is important for positive coactivator 4/p53 interaction. Debnath, S., Chatterjee, S., Arif, M., Kundu, TK., & Roy, S.* (2011) J Biol Chem, 286, 25076-87.https://doi.org/10.1074/jbc.M110.205328
Differential recognition of phosphorylated transactivation domains of p53 by different p300 domains. Polley, S., Guha, S., Roy, NS., Kar, S., Sakaguch,i K., Chuman, Y., Swaminathan, V., Kundu, T., & Roy, S.* (2008) J Mol Biol, 376, 8-12. https://doi.org/10.1016/j.jmb.2007.11.082
Switching DNA-binding specificity by unnatural amino acid substitution. Maiti, A., & Roy, S.* (2005) Nucleic Acids Res, 33, 5896-903. https://doi.org/10.1093/nar/gki899
Asynchronous basepair openings in transcription initiation: regulation by enhancing the rate limiting step. Roy, S., Lim, HM., & Adhya, S. (2004) EMBO J, 23, 869-75.https://doi.org/10.1038/sj.emboj.7600098
Glutamate counteracts the denaturing effect of urea through its effect on the denatured state. Mandal, AK., Samaddar, S., Banerjee, R., Lahiri, S., Bhattacharyya, A., & Roy, S.* (2003) J Biol Chem, 278, 36077-84. https://doi.org/10.1074/jbc.M211207200
Solvation Change and Ion release During Aminoacylation by Aminoacyl-tRNA synthetases. Bannerjee, R., Mandal, AK., Shah, R., Guha, S., Samaddar, S., Bhattacharyya, A., & Roy, S.* (2003) Nucleic Acids Res, 31, 6035-42. https://doi.org/10.1093/nar/gkg779
DnaK-sigma32 interaction is temperature dependent: Implication for the mechanism of heat-shock response. Chattopadhyay, R., & Roy, S.* (2002) J Biol Chem, 277, 33641-7. https://doi.org/10.1074/jbc.M203197200
Effect of phosphorylation on the structure and fold of transactivation domain of p53. Kar S., Sakaguchi, K., Shimohigashi, Y., Samaddar, S., Banerjee, R., Basu, G., Swaminathan, V., Kundu, TK., & Roy, S.* (2002) J Biol Chem, 277, 15579-85. https://doi.org/10.1074/jbc.M106915200
Effect of osmolytes and chaperone-like action of P-protein on folding of nucleocapsid protein of Chandipura virus. Majumder A, Basak S, Raha T, Chowdhury SP, Chattopadhyay D, Roy S.* (2001) J Biol Chem. 276, 30948-55.https://doi.org/10.1074/jbc.M011705200
A "master" in base unpairing during isomerization of a promoter upon RNA polymerase binding. Lim, HM., Lee, HJ., Roy, S., & Adhya, S. (2001) Proc Natl Acad Sci(U S A), 98, 14849-52. https://doi.org/10.1073/pnas.261517398
Damage-mediated phosphorylation of human p53 threonine 18 through a cascade mediated by a casein 1-like kinase. Effect on Mdm2 binding. Sakaguchi, K., Saito, S., Higashimoto, Y., Roy, S., Anderson, CW., & Appella, E. (2000) J Biol Chem, 275, 9278-83. https://doi.org/10.1074/jbc.275.13.9278
Interaction of Gal repressor with inducer and operator: induction of gal transcription from repressor-bound DNA. Chatterjee, S., Zhou, YN., Roy, S., & Adhya, S. (1997) Proc Natl Acad Sci (USA), 94 2957-2962. https://doi.org/10.1073/pnas.94.7.2957
A fluorescence anisotropy study of tetramer-dimer equilibrium of l-repressor and its implications for function. Banik, U., Mandal, N.C., Bhattacharyya, B., & Roy, S.* (1993) J Biol Chem, 268, 3938-3943. https://doi.org/10.1016/S0021-9258(18)53562-6
An operator induced conformational change of C-terminal domain of l-repressor. Saha, R., Banik, U., Mandal, N.C., Bhattacharyya, B., & Roy, S.* (1992) J Biol Chem, 267, 5862-5867. https://doi.org/10.1016/S0021-9258(18)42633-6
15N-guanosine-labeled oligonucleotide as probe for protein-nucleic acid interaction in the major groove. Massefski, W., Redfield, AG., Das Sarma, U., Bannerji, A., & Roy, S.* (1990) J Am Chem Soc, 112, 5350-5351. https://doi.org/10.1021/ja00169a052
Solid state deuterium NMR study of thymidine. Base rigidity and ribose ring flexibility in deoxynucleosides. Hiyama, Y., Roy, S., Cohen, JS. & Torchia, DA. (1989) J Am Chem Soc, 111, 8609-8613. https://doi.org/10.1021/ja00205a008
New enzymic synthesis of 2'-deoxynucleoside-2',2'-d2 and the determination of sugar ring flexibility by solid-state deuterium NMR. Roy, S.,* Hiyama, Y., Torchia, DA., & Cohen, JS. (1986) J Am Chem Soc, 108, 1675-1678. https://doi.org/10.1021/ja00267a043
NMR study of slowly exchanging protons in yeast tRNAasp. Figueroa, N., Keith, G., Leroy, J.L., Plateau, P., Roy, S., & Gueron, M. (1983) Proc Natl Acad Sci (USA), 80, 4330-4333. https://doi.org/10.1073/pnas.80.14.4330
Nuclear Overhauser effect study of yeast tRNAvalI:Evidence of uridine-Pseudouridine base pairing. Schejter, E., Roy, S., Sanchez, V., & Redfield, AG. (1982) Nucleic Acids Res, 10, 8297-8305. https://doi.org/10.1093/nar/10.24.8297
Procedure for C2 deuteration of nucleic acids and determination of AY 31 pseudouridine conformation by nuclear overhauser effect. Roy, S., Papastavros, M.Z., & Redfield, AG. (1982) Nucleic Acids Res, 10, 8341-8349. https://doi.org/10.1093/nar/10.24.8341
Roy, S., & Redfield, AG. Nuclear Overhauser effect study and assignment of D stem and reverse hoogsteen base pair proton of yeast tRNAasp. (1981) Nucleic Acids Res, 9, 7073-7083. https://doi.org/10.1093/nar/9.24.7073
Hydrophobic basis of packing in globular proteins. Rose, GD. & Roy, S. (1980) Proc Natl Acad Sci (USA), 77, 4643-4647. https://doi.org/10.1073/pnas.77.8.4643
1st Subhendu Bandyopadhyay, B. Ghosh, Parasuraman Jaisankar, Bikas C Pal, Siddhartha Roy, Nath Paul, Arjun Ram, U. Mabalirajan, Nahid Ali, Arun Bandyopadhyay, Aditya Konar, J. Bagchi Chakraborty, I. Choudhury Mukherjee, Jaydeep Chaudhuri, Sanjit Kumar Mahato, A. Manna, Roma Sinha, Pradyot Bhattacharya, J. Vinayagam, D. P. Jana, Sudeshna Chowdhury (April 2011). "Inhibitors of IL-4 and IL-5 for the treatment of bronchial asthma (Patent 1032DEL2011)". {{cite journal}}: Cite journal requires |journal= (help)CS1 maint: multiple names: authors list (link) CS1 maint: numeric names: authors list (link)
