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)
, 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
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.
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).
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.
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.
Sasidhar, Y.U. (2007) Loop Propensity of the Sequence YKGQP from
Staphylococcal Nuclease: Implications for the Folding of Nuclease. J. Pept.
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.
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.
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.
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,
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,