Prof. Y. U. Sasidhar

 Room No. 308 (Protein Dynamics Lab)

 Department of Chemistry, IIT Bombay, Powai,  

 Mumbai 400076, INDIA.

 Tel: +91-22-2576 7179 (O), +91-22-2576 4176 (Lab)                    
 Fax: +91-22-2572 3480       

 Email: sasidhar@iitb.ac.in 

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We are looking for bright, motivated and research oriented MSc students to join as PhD students. A prospective student will have a good background in physical chemistry/ biophysical chemistry at MSc level and in mathematics ( calculus and vectors ). Knowledge of programming principles is an advantage.

Applicants for Post Doctoral position may contact.



Academic Background

 

     1978- 1980  : M. Sc in Physics, Indian Institute of Technology, Madras.

 

     1980- 1986  : Ph. D in Physics, Indian Institute of Technology, Madras.

 

Research Areas 

 

General: Biophysical Chemistry   Specific: Protein Folding and  Dynamics

 

The major area of research in our group is  Protein Folding and Dynamics. The mechanism by which an unfolded protein folds to its native and functional structure is called  protein folding and deciphering the fundamental principles that underlie the process is the objective of our investigations. We study early folding events by considering peptide as well as protein models. We are also investigating the nature of the unfolded state under physiological conditions using peptide models. To achieve our objectives we use molecular dynamics technique.

 The atomic level detailed structural information that we seek can not  be obtained from experimental studies alone.

 We are also looking at the role played by protein dynamics in its function. Further we are interested in exploiting protein dynamics in the design of agonists and antagonists.

Publications


Apoorva Badaya; Yellamraju U. Sasidhar, 2022, The role of temperature in the binding of the disordered epitope region of human thrombopoietin to antibody: A molecular dynamics simulations study,, Journal of Molecular Graphics and Modelling, 111, 2022, 108098, https://doi.org/10.1016/j.jmgm.2021.108098.

Gupta, Shubhangi; Sasidhar, Y.U, 2019, Conformational dynamics of Ribonuclease Sa and its S48Pmutant: Implications for the stability of the mutant protein, J. Mol. Graph. Model. 2019, 88, 71-80.

Sunita Patel, Sasidhar, Y.U. and Kandala V. R. Chary (2017),Mechanism of Initiation, Association, and Formation of Amyloid Fibrils Modeled with the N-Terminal Peptide Fragment, IKYLEFIS, of Myoglobin G-Helix. J. Phys. Chem. B, 2017, 121 (32), pp 7536 - 7549.

Gupta, S.; Sasidhar, Y. U. (2017), Impact of Turn Propensity on the Folding Rates of Z34C Protein: Implications for the Folding of Helix-Turn-Helix Motif. *The Journal of Physical Chemistry B., 2017, 121,(6), 1268-1283.

Shukla, R. T., Sasidhar,Y.U. (2015) . Conformational dynamics of a short antigenic peptide in its free and antibody-bound forms gives insight into the role of ßturns in peptide immunogenicity. ( Accepted in Proteins: Structure, Function and Bioinformatics )

Kaur, H., & Sasidhar, Y. U. (2015). Environmental polarity induces conformational transitions in a helical peptide sequence from bacteriophage T4 lysozyme and its tandem duplicate: A molecular dynamics simulation study. Journal of Molecular Modeling, 21(4)

Shukla, R.T. , Sasidhar, Y.U. (2013) Energetics of β-turn formation in a mutant peptide YPGDV from influenza hemagglutinin: An MD simulation study, Phys. Chem. Chem. Phys 15, 18571-18583.


Shukla, R. T., Kumar, N., Sasidhar,Y.U. (2013) Molecular dynamics simulations of certain mutant peptide models from Staphylococcal nuclease reveal that initial hydrophobic collapse associated with turn propensity drives β-hairpin folding. J. Peptide Sci., 19, 516-527


Kaur, H., and Sasidhar Y.U. (2013). Molecular Dynamics Study of an Insertion/Duplication Mutant of Bacteriophage T4 Lysozyme Reveals the Nature of a-ßransition in Full Protein Context. Phys. Chem. Chem. Phys. DOI

 

Shukla, R. T., Baliga, C., and Sasidhar Y.U. (2013). The role of loop closure propensity in the refolding of rop protein probed by molecular dynamics simulations. Journal of Molecular Graphics and Modelling. 40, 10-21.

 

Kaur, H., and Sasidhar Y.U. (2012). For the sequence YKGQ, the turn and extended conformational forms are separated by small barriers and the turn propensity persists even at high temperatures: Implications for protein folding. Journal of Physical Chemistry B. 116(12), 3850-3860.

 

Upadhyay, S. K., and Sasidhar Y.U. (2012). Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: Implication for transcriptional activation of GAL genes. Journal of Computer-Aided Molecular Design. 26(7), 847-864. (Retrieved from www.scopus.com).

 

Patel, S. and Sasidhar Y.U. (2008) A shorter peptide model from staphylococcal nuclease for the folding-unfolding equilibrium of a β-hairpin shows that unfolded state has significant contribution from compact conformational states . J Struct Biol. 2008 Oct;164(1):60-74.

 

Patel, S., Balaji, P.V., Sasidhar, Y.U. (2007) The sequence TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase displays structural ambivalence and interconverts between alpha-helical and beta-hairpin conformations mediated by collapsed conformational states. J. Pept. Sci., 13:314-26.

 

Patel, S., Taimni R.,  Sasidhar, Y.U. (2007) A small tripeptide AFA undergoes two state cooperative conformational transitions: Implications for conformational biases in unfolded states. Protein Pept Lett. 14:581-9.

 

Patel, S., Sasidhar, Y.U. (2007) Loop Propensity of the Sequence YKGQP from Staphylococcal Nuclease: Implications for the Folding of Nuclease. J. Pept. Sci.13:679-692.

 

Sujatha, M.S., Sasidhar,Y.U.  and Balaji, P.V., (2007) MP2/6-311++G(d,p) study on galactose-aromatic residue analog complexes in different position-orientations of the saccharide relative to aromatic residues. J. Mol. Struct. (Theochem),.814, 11-24.

 

Patel, S., Sista, P., Balaji, P.V., Sasidhar, Y.U. (2006) Beta-hairpins with native-like and non-native hydrogen bonding patterns could form during the refolding of staphylococcal nuclease. J. Mol. Graph. Model., 25:103-15.

 

M.S.Sujatha, Sasidhar,Y.U. and Balaji, P.V. (2005) Insights into the role of aromatic residue in galactose-binding sites: MP2/6-311G++** study on galactose- and glucose-aromatic residue analog complexes. Biochemistry, 44, 8554-8562. 

 

M.S.Sujatha, Sasidhar,Y.U. and Balaji, P.V. (2004) Energetics of galactose- and glucose-aromatic amino acid interactions: implications for binding in galactose-specific proteins. Protein Sci., 13, 2502-2514.

 

Sasidhar, Y. U.  and Ratna Prabha, C. (2000) Conformational features of reduced and disulfide intact forms  of hen egg white lysozyme   in   aqueous   solution   in    the    presence    of 3-chloro-1,2-propanediol and  dioxane  :  Implications  for protein folding intermediates. Indian J. Biochem. Biophys., 37, 97-106.
 
Sasidhar, Y. U. and Ramakrishna, V. (2000) Conformational features of a hexapeptide model Ac-TGAAKA-NH2 corresponding to a hydrated a helical segment from Glyceraldehyde 3-Phosphate  Dehydrogenase : Implications for the role of turns in helix folding. Indian J. Biochem. Biophys., 37, 34-44.

Sasidhar, Y. U., Ratna Prabha, C. and Gidwani, A. (1999) Conformational features of certain peptides from lysozyme and their possible role in the folding of lysozyme. Journal of Biosciences, 24, Supplement 1, 64.

Ratnaprabha, C. and Sasidhar, Y. U. (1998) Conformational features of disulfide intact and reduced forms of hen egg white lysozyme in aqueous solution in the presence of  trifluoroethanol (TFE): Implications for protein folding intermediates. J. Chem. Soc., Faraday Trans., 94, 3631-3637.

Ramakrishna, V. and Sasidhar, Y. U. (1998 ) Conformational features of a peptide model Ac-DTVKLMYKGQPMTFR-NH2, corresponding to  an early folding b hairpin region of Staphylococcal  nuclease. Indian J. Biochem. Biophys., 35, 333- 338. 

Ramakrishna, V.  and Sasidhar, Y. U. (1997) A Pentapeptide Model for an Early Folding Step in the Refolding of Staphylococcal Nuclease : The Role of its Turn Propensity. Biopolymers, 41, 181-191.