Prof. S Thiyagarajan

Prof. S Thiyagarajan

Associate Professor, Structural Biology and Informatics


Vidwan-ID : 562948

Research Focus Key Words

Structural biology and bioinformatics, microbial stress response, lysosomal storage disease, monogenic disorders, computer aided drug design

Background

Prof. S Thiyagarajan received his PhD in physics, crystallography and biophysics from the University of Madras in 2006. Subsequently he did two post docs, one at the Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, and the other at the department of Cell and Organism Biology, Lund University, Sweden. He joined Madurai Kamaraj University as an Assistant Professor in computational biology in 2010. He moved to IBAB in May, 2013.

Education

Ph.D:  University of Madras, Chennai, TN, India

Postdoctoral Research:

  1. Wayne State University, Detroit, MI, USA
  2. Lund University, Sweden

Professional experience

Assistant Professor in Computational Biology, Madurai Kamaraj University, Madurai, TN, India

Research Interest Profile

Our group is interested in X-ray crystallography, protein biochemistry and computational biology studies of DNA and metal binding proteins, from the perspective of microbial stress response, especially arsenic toxicity and redox stress. We also undertake structural and computational studies of the lysosomal storage diseases and a few monogenic disorders. We undertake computer aided drug design using small molecule and phytochems on known potential target for metabolic diseases.

Lab members

  1. Gopinatha Krishnappa
  2. Hemant Kumar Sistla
  3. Aman Viswakarma
  4. Priya Bhatia
  5. Samta 

Collaborators

  1. Dr. Barry P Rosen: Florida International University, Miami, FL,  USA
  2. Dr. Sudha Srinivasan: Centre for Human Genetics, Bengaluru, India
  3. Dr. P. Saravanan: Indian Veterinary Research Institute, Bengaluru, India

Research Publications

  1. Gopinatha K, Harshitha N, Harshavardini B S, Mitali M, Sivaraman P, Veenakumari H B, S Thiyagarajan, Balasundaram P
    Structural Basis for the Essential Role of Ca2+ in the Lytic Activity of Staphylococcus aureus PlyGRCS Endolysin Targeting Methicillin-Resistant Staphylococcus aureus
    Proteins, doi: 10.1002/prot.26777 (2024)
  2. Vishwakarma A, Padmashali N, and Thiyagarajan S
    AnnoDUF: A Web-Based Tool for Annotating Functions of Proteins Having Domains of Unknown Function
    J. Proteome Res., https://doi.org/10.1021/acs.jproteome.4c00251 (2024)
  3. Madhavan A, Paramasivam S, V V Dhanesh, Deepak P R S, Gopinath S, Adwitiya D, Hosamani M, B P Sreenivasa, R P T Selvan, Aniket S, Samta G,S Thiyagarajan, Pallab C
    Diagnostic and prophylactic potential of a stabilized foot-and-mouth disease serotype Asia1 virus like particles designed through a structure guided approach
    International Journal of Biological Macromolecules, doi: 10.1016/j.ijbiomac.2024.134366 (2024)
  4. Samuel, J,  Ghosh S and Thiyagarajan S
    Identification and characterization of domain-specific inhibitors of DENV NS3 and NS5 proteins by in silico screening methods
    J. Biomol. Struct. Dyn. doi: 10.1080/07391102.2024.2313161 (2024)
  5. Aparna Madhavan, Dhanesh VV, DPR Selvaraj, Shreya Gopinath, Sreenivasa BP, Tamil Selvan RP, Aniket Sanyal, Thiyagarajan S and Saravanan P (2021)
    An optimized protocol for purification of virus-like particles of foot-and-mouth disease virus produced in the baculovirus expression system.
    The Pharma Innovation Journal, SP-10(10): 33-37 (2021)
  6. Thierry Franza, Annika Rogstam, S. Thiyagarajan, Matthew J. Sullivan, Aurelie Derré-Bobillot, Mikael C. Bauer, Kelvin G. K. Goh, Violette Da Cunha, Philippe Glaser, Derek T. Logan, Glen C. Ulett, Claes von Wachenfeldt, Philippe Gaudu (2021)
    NAD+ pool depletion as a signal for the Rex regulon involved in Streptococcus agalactiae virulence
    Plos Pathogens, Aug 9;17(8):e1009791 https://doi.org/10.1371/journal.ppat.1009791 (2021)
  7. Kottapalli Srividya, Snober S. Mir, Thiyagarajan S and Aamir Nazir (2021)
    Dietary Factors and SARS-CoV-2 Contagion: in silico studies on Modulation of Viral and Host Proteins by Spice Actives
    J. Biomol. Struct. Dyn, Jul 13;1-12 (2021)
  8. Mondal P, Natesha J, Abdul Salam A A, Thiyagarajan S and Meeran S M (2020)
    Traditional Medicinal Plants against Replication, Maturation and Transmission Targets of SARS-CoV-2: Computational Investigation
    J. Biomol. Struct. Dyn. Nov 5;1-18 (2020)
  9. Sruthi U, Snehal A, Thiyagarajan S and Padmanabhan B (2020)
    Identification of a repurposed drug as an inhibitor of Spike protein of human coronavirus SARS-CoV-2 by computational methods
    J. BioSci, 45:130 (2020)
  10. Viswanathan V,  Thiyagarajan  S, Erbe V, Raghunathan S, Rajendran V, Siddaramappa S (2020)
    Characterization of Heumann’s pigmented and non-pigmented strains of [Pseudomonas] Sphingomonas echinoides
    Biologia 75;1445-1453 (2020)
  11. Sruthi Unni, S. Thiyagarajan, M. M. Srinivas Bharath, and B. Padmanabhan (2019)
    Tryptophan Oxidation in the UQCRC1 Subunit of Mitochondrial Complex III (Ubiquinol-Cytochrome C Reductase) in a Mouse Model of Myodegeneration Causes Large Structural Changes in the Complex: A Molecular Dynamics Simulation Study.
    Sci. Rep., 9:10694.
  12. Prabaharan C, Kandavelu P, Packianathan C, Rosen BP4, and Thiyagarajan S (2019)
    Structures of two ArsR As(III)-responsive transcriptional repressors: Implications for the mechanism of derepression.
    J. Struct. Biol., 207(2):209-217.
  13. Siddaramappa S, Viswanathan V, Thiyagarajan S, Narjala A. (2018)
    Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales.MicrobGenom. 4(4):e000172.
  14. Yoon-Suk Kang, Keenan Brame, Jonathan Jetter, Brian Bothner, Gejiao Wang and S. Thiyagarajan and Timothy McDermott (2016)
    RegulatoryActivities of Four ArsR Proteins in Agrobacterium tumefaciens 5A. Applied and Environmental Microbiology 82(12):3471-80
  15. Balasundaram Padmanabhan, Manjula Ramu, Sruti Mathur, Sruthi Unni and Saravanamuthu Thiyagarajan. (2016)
    Identification of New Inhibitors for Human SIRT1: An in-silico ApproachMedicinal Chemistry 12(4):347-61.
  16. Mathew, J. Jagadeesh, S.M., Bhat, M. Udhaya Kumar, S., Thiyagarajan, S. and Srinivasan, S. (2015) 
    Mutations in ARSB in MPS VI patients in India.Mol. Genet. Metab. Reports, 4, 53-61
  17. Gupta, C.M., Thiyagarajan, S. and Sahasrabuddhe, A. (2015)
    “Unconventional actins and actin-binding proteins in human protozoan parasites” ,Int. J. Parasitol.45(7), 435-447
  18. Santha, S., Eswari, P.J.P., Rosen, B.P. and Thiyagarajan, S. (2011)
    “Purification, crystallization and preliminary X-ray diffraction studies of an arsenic repressor ArsR from Corynebacterium glutamicum”, Acta Crystallogr.F67, 1616-1618.
  19. Kandegedara, A., Thiyagarajan, S., Kondapalli, K.C.,  Stemmler, T.L. and Rosen, B.P. (2009)
    “Role of bound Zn(II) in the CadC Cd(II)/Pb(II)/Zn(II) responsive repressor” J. Biol. Chem.284, 14958 – 14965.
  20. Ordóñez, E.*, Thiyagarajan, S. *, Cook, J.D, Stemmler, T.L., Gil J.A., Mateos, L.M. and Rosen, B.P  (2008)
    “Evolution of metal(loid) binding sites in transcriptional regulators” J. Biol. Chem. 283, 25706 – 25714. (*Both authors contributed equally to this work)
  21. Bhattacharjee, H., Mukhopadhyay, R., Thiyagarajan, S. and Rosen, B.P. (2008)
    “Aquaglyceroporins: ancient channels for metalloids” J. Biol. 7:33.
  22. Bharanidharan, D., Thiyagarajan, S. and Gautham, N. (2007)
    Hexammine-ruthenium (III) ion interactions with Z-DNA” Acta Crystallogr. F63, 1008 – 1013.
  23. Thiyagarajan, S.,Rajan, S.S. and Gautham, N. (2006)
    “Effect of DNA structural flexibility on promoter strength—molecular dynamics studies of E. coli promoter sequences” Biochem.Biophys. Res.Commun.341, 557 – 566.
  24. Thiyagarajan, S. and Gautham, N. (2005)
    “Sequence dependent structural effects in left handed DNA” Crystallography Reviews11, 337 – 355.
  25. Thiyagarajan, S.,Rajan, S.S. and Gautham, N. (2005)
    “Structure of d(CGCGCA). d(TGCGCG) in two crystal forms: effects of sequence and crystal packing in Z-DNA” Acta Crystallogr.D61, 1125 – 1131.
  26. Thiyagarajan, S.,Rajan, S.S. and Gautham, N. (2004)
    “Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA). d(TGCGCG) in two crystal forms” Nucleic Acids Res.32, 5945 – 5953.
  27. Thiyagarajan, S., Satheesh Kumar, P., Rajan, S.S. and Gautham, N. (2002)
    “Structure of d(TGCGCA)2 at 293K: comparison of the effects of sequence and of temperature” Acta Crystallogr.D58, 1381 – 1384.
  28. Chandra Mohan, K., Ravikumar, K., Shetty, M.M., Thiyagarajan, S. and Rajan S.S. (2003)
    “Crystal amd molecular structures of 1,4-dihydro-6-methyl-5-N,N-diethyl carbamoyl-4-phenyl-2(3H)-pyrimidinethione (1) and 1,4-dihydro-6-methyl-5-N-methyl carbamoyl-4-(2’-nitrophenyl)-2(3H)-pyrimidinethione hemihydrate” J Chem Crystallogr. 33, 113 – 121.
  29. Thiyagarajan S.,Karthe P., Rajan S.S., Gautham N., Kumar A. and Katti S.B. (2001) 
    “Crystal and Molecular structure of 3′ deoxy guanosine N2 isobutryl dehydrate” Crystal Research and Technology, 36 , 485 – 492.

Address

Institute of Bioinformatics and Applied Biotechnology
Biotech Park, Electronic City Phase I,
Bengaluru 560100,
India

Phone

080-2852-8900, extension 124

Email

sthiyaga@ibab.ac.in