1. Arsenic and Microbes: Looking for clues to battle against mass arsenic poisoning.
Arsenic is one of the most hazardous substances present in our environment. Every day millions of people across the world and in India are exposed to arsenic poisoning through contaminated drinking water. Crops like rice, wheat and corn cultivated in arsenic contaminated farms have been shown up take arsenic in their composition, adding to the arsenic woes.
It has been of interest to observe that many microbes flourish in regions of high arsenic contamination. All such species have evolved arsenic resistance and detoxification mechanisms to survive under arsenic rich environments. My group is involved in making X-ray crystallographic studies on proteins responsible for arsenic resistance in microbial species. We complement our crystallographic studies with biochemical and computational tools to understand the structural basis of arsenic resistance in microbes. We identify the arsenic regulatory genes in microbes through bioinformatics studies, express their target proteins through contemporary recombinant techniques and characterize those molecular machines through biochemical, crystallographic and computational studies.
2. Redox sensing protein Rex: A possible target for antibiotics.
Microbial pathogens inhabit different environments in their life cycle which may be classified into aerobic, anaerobic or microaerobic environments. Under microaerobic or anaerobic conditions, microbes switch to anaerobic respiration pathways like lactate dyhydrogenation, nitrate reduction etc. Microbial species continually monitor the level of oxygen in their environment through a few direct or indirect methods. Sensing the ratio of concentrations of NAD+ and NADH is one of the indirect ways of measuring the aerobicity of the environment. Under aerobic conditions, NAD+ is reduced to NADH in the citric acid cycle and subsequently re-oxidized to NAD+ in the electron transport chain. In the absence of sufficient molecular oxygen, electron transport chain will be inhibited leading to an accumulation of NADH inside the cells. Rex is a redox sensing protein present in several species including pathogens like Strepotoccus, Staphylococcus etc., that senses the oxidative state of the environment by monitoring [NAD+]/[NADH] ratio. Several crystal structures of Rex from several species indicate that regulatory mechanism of Rex is allosteric. We have been undertaking computational studies to decipher the allostery behind Rex regulation using molecular modelling, docking and dynamics simulations studies.
3. Molecular modelling of enzymes associated with Lysosomal storage disease.
Lysosomal storage diseases (LSD) are single gene disorders caused by malfunctioning of specific enzymes in the lysosome. Mucopolysaccharidosis (MPS) are a sub group of LSD caused by mutations in any one of the genes that encodes enzymes which catabolise a certain class of carbohydrate polymers called glycosaminoglycans like Heparin sulfate, Chondroitin sulfate etc. Deficient activity of any of these enzymes results in accumulation of the unmetabolised substrates in the lysosome. This leads to a series of symptoms like developmental delay, mental retardation, abnormal skeletal development and problems in locomotion. These disorders manifest in early childhood, and many patients seldom live beyond their teens. Understanding how mutations affect the structure and function of these enzymes will help in devising appropriate treatments. Eleven enzymes have been identified as being associated with MPS of which only for a few crystal structures are known. Our group is attempting to construct the molecular models of the enzymes in collaboration with Dr. Sudha Srinivasan at the Centre for Human Genetics, Bangalore. Further, mutations observed in patients are mapped onto the models in order to determine how they affect protein structure and hence its function, through computational studies.
- Kang, Y., Brame, K., Jetter, J., Bothner, B., Wang, G., Thiyagarajan, S. and McDermott, T. (2016)
Regulatory Activities of Four ArsR Proteins in Agrobacterium tumefaciens 5A
Appl Environ Microbiol. 82(12):3471-80
- Padmanabhan, B., Ramu, M., Mathur, S., Unni, S. and Thiyagarajan, S. (2016)
Identification of New Inhibitors for Human SIRT1: An in-silico Approach
Med Chem. 12(4):347-61.
- 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.
- Gupta, C.M., Thiyagarajan, S. and Sahasrabuddhe, A.A. (2015)
Unconventional actins and actin-binding proteins in human protozoan parasites.
Int. J. Parasitol., 45(7), 435-47.
- 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.
- 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.
- 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)
- Bhattacharjee, H., Mukhopadhyay, R., Thiyagarajan, S. and Rosen, B.P. (2008) “Aquaglyceroporins: ancient channels for metalloids” J. Biol. 7:33.
- Bharanidharan, D., Thiyagarajan, S. and Gautham, N. (2007) Hexammine-ruthenium (III) ion interactions with Z-DNA” Acta Crystallogr. F63, 1008 – 1013.
- 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.
- Thiyagarajan, S. and Gautham, N. (2005) “Sequence dependent structural effects in left handed DNA” Crystallography Reviews 11, 337 – 355.
- 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.
- 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.
- 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.
- 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.
- 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.