The role of temperature in the binding of the disordered epitope region of human thrombopoietin to antibody: A molecular dynamics simulations study,
Apoorva Badaya, Yellamraju U. Sasidhar,
Journal of Molecular Graphics and Modelling, 111, 2022, 108098, https://doi.org/10.1016/j.jmgm.2021.108098
Inhibition of the activity of HIV-1 protease through antibody binding and mutations probed by molecular dynamics simulations
Badaya, Apoorva; Sasidhar, Yellamraju U.
Sci. Reports, 2020, 10, 5501.
Conformational dynamics of Ribonuclease Sa and its S48Pmutant: Implications for the stability of the mutant protein
Gupta, Shubhangi; Sasidhar, Yellamraju U.
J. Mol. Graph. Model, 2019, 88, 71-80.
Conformational and dynamical basis for cross-reactivity observed between anti HIV-1 protease antibody with protease and an epitope peptide from it
Badaya Apoorva, Sasidhar Yellamraju U.
Int J Biol Macromol., 2018, 118(Pt B), 1696-1707
Impact of Turn Propensity on the Folding Rates of Z34C Protein: Implications for the Folding of Helix-Turn-Helix Motif.
Gupta, Shubhangi; Sasidhar, Yellamraju U.
J. Phys. Chem. B, 2017, 121, 1268-1283
Mechanism of Initiation, Association, and Formation of Amyloid Fibrils Modeled with the N-Terminal Peptide Fragment, IKYLEFIS, of Myoglobin G-Helix.
Patel, Sunita; Sasidhar, Yellamraju U.; Chary, Kandala V. R.
J. Phys. Chem. B, 2017, 121, 7536-7549
Conformational dynamics of a short antigenic peptide in its free and antibody bound forms gives insight into the role of β-turns in peptide immunogenicity.
Shukla, Rashmi Tambe; Sasidhar, Yellamraju U.
Proteins: Struct., Funct., Bioinf., 2015, 83, 1352-1367
Environmental polarity induces conformational transitions in a helical peptide sequence from bacteriophage T4 lysozyme and its tandem duplicate: a molecular dynamics simulation study.
Kaur, Harpreet; Sasidhar, Yellamraju U.
J. Mol. Model., 2015, 21, 41640
Energetics of β-turn formation in a mutant peptide YPGDV from influenza hemagglutinin: an MD simulation study.
Shukla, Rashmi Tambe; Sasidhar, Yellamraju U.
Phys. Chem. Chem. Phys., 2013, 15, 18571-18583
Molecular dynamics simulations of certain mutant peptide models from staphylococcal nuclease reveal that initial hydrophobic collapse associated with turn propensity drives β-hairpin folding.
Shukla, Rashmi Tambe; Kumar, Naveen; Sasidhar, Yellamraju U.
J. Pept. Sci., 2013, 19, 516-527
Molecular dynamics study of an insertion/duplication mutant of bacteriophage T4 lysozyme reveals the nature of α β transition in full protein context.
Kaur, Harpreet; Sasidhar, Yellamraju U.
Phys. Chem. Chem. Phys., 2013, 15, 7819-7830
The role of loop closure propensity in the refolding of Rop protein probed by molecular dynamics simulations.
Shukla, Rashmi Tambe; Baliga, Chetana; Sasidhar, Yellamraju U.
J. Mol. Graphics Modell., 2013, 40, 44470
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.
Kaur, Harpreet; Sasidhar, Yellamraju U.
J. Phys. Chem. B, 2012, 116, 3850-3860
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.
Upadhyay, Sanjay K.; Sasidhar, Yellamraju U.
J. Comput.-Aided Mol. Des., 2012, 26, 847-864
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.
Patel, Sunita; Sasidhar, Yellamraju U.
J. Struct. Biol., 2008, 164, 60-74
A small tripeptide AFA undergoes two state cooperative conformational transitions: implications for conformational biases in unfolded states.
Patel, Sunita; Taimni, Richa; Sasidhar, Yellamraju U.
Protein Pept. Lett., 2007, 14, 581-589
Loop propensity of the sequence YKGQP from staphylococcal nuclease: implications for the folding of nuclease.
Patel, Sunita; Sasidhar, Yellamraju U.
J. Pept. Sci., 2007, 13, 679-692
MP2/6-311++G(d,p) study on galactose-aromatic residue analog complexes in different position-orientations of the saccharide relative to aromatic residue.
Sujatha, Mannargudi S.; Sasidhar, Yellamraju U.; Balaji, Petety V.
J. Mol. Struct.: THEOCHEM, 2007, 814, 45597
The sequence TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase displays structural ambivalence and interconverts between α-helical and β-hairpin conformations mediated by collapsed conformational states.
Patel, Sunita; Balaji, Petety V.; Sasidhar, Yellamraju U.
J. Pept. Sci., 2007, 13, 314-326
β-Hairpins with native-like and non-native hydrogen bonding patterns could form during the refolding of staphylococcal nuclease.
Patel, Sunita; Sista, Prakash; Balaji, Petety V.; Sasidhar, Yellamraju U.
J. Mol. Graphics Modell., 2006, 25, 103-115
Insights into the Role of the Aromatic Residue in Galactose-Binding Sites: MP2/6-311G++** Study on Galactose- and Glucose-Aromatic Residue Analogue Complexes.
Sujatha, Mannargudi S.; Sasidhar, Yellamraju U.; Balaji, Petety V.
Biochemistry, 2005, 44, 8554-8562
Energetics of galactose- and glucose-aromatic amino acid interactions: Implications for binding in galactose-specific proteins.
Sujatha, Mannargudi S.; Sasidhar, Yellamraju U.; Balaji, Petety V.
Protein Sci., 2004, 13, 2502-2514
Conformational features of a hexapeptide model Ac-TGAAKA-NH2 corresponding to a hydrated α helical segment from glyceraldehyde 3-phosphate dehydrogenase: Implications for the role of turns in helix folding.
Sasidhar, Y. U.; Ramakrishna, V.
Indian J. Biochem. Biophys., 2000, 37, 33-44
Conformational features of reduced and disulfide intact forms of hen egg white lysozyme in aqueous solution in presence of 3-chloro-1,2-propanediol and dioxane: implications for protein folding intermediates.
Sasidhar, Y. U.; Prabha, C. Ratna.
Indian J. Biochem. Biophys., 2000, 37, 97-106
Conformational features of a peptide model Ac-DTVKLMYKGQPMTFR-NH2, corresponding to an early folding β hairpin region of Staphylococcal nuclease.
Ramakrishna, V.; Sasidhar, Y. U.
Indian J. Biochem. Biophys., 1998, 35, 333-338
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.
Ratnaprabha, C.; Sasidhar, Y. U.
J. Chem. Soc., Faraday Trans., 1998, 94, 3631-3637
Harnessing D-amino acids for peptide motif designs. Synthesis and solution conformation of Boc-D-Glu-Ala-Gly-Lys-NHMe and Boc-L-Glu-Ala-Gly-Lys-NHMe.
Bobde, Vivek; Sasidhar, Y. U.; Durani, Susheel.
Int. J. Pept. Protein Res., 1994, 43, 209-18
Conformation of bioactive peptides: synthetic enkephalins.
Saran, Anil; Dhingra, M. M.; Sasidhar, Y. U.
J. Mol. Struct.: THEOCHEM, 1991, 79, 315-34
Conformational preference of Leu side chain in melanostatin in DMSO.
Sasidhar, Y. U.; Dhingra, M. M.; Saran, Anil.
Indian J. Biochem. Biophys., 1990, 27, 69-75
Proton and deuteron magnetic resonance study of cadmium bromate dihydrate [Cd(BrO3)2·2H2O and Cd(BrO3)2·2D2O].
Sasidhar, Y. Uma; Rao, K. V. S. Rama.
J. Mol. Struct., 1986, 147, 113-26
Proton and deuteron magnetic resonance study of strontium bromate monohydrate and strontium bromate monohydrate-d2.
Sasidhar, Y. Uma; Rao, K. V. S. Rama.
J. Phys. C: Solid State Phys., 1986, 19, 6241-52
Proton magnetic resonance of zinc bromate hexahydrate.
Sasidhar, Y. Uma; Rao, K. V. S. Rama.
Cryst. Lattice Defects Amorphous Mater., 1986, 13, 125-8