BOOK
Rao, V.S.R., Qasba, P.K., Balaji, P.V., and
Chandrasekaran, R. (1998)
Conformation of Carbohydrates.
Harwood Academic Publishers, The Netherlands.
OBITUARY
Sundararajan, P.R., Balaji, P.V. and Yathindra, N. (2013) Professor Vallurupalli Sita Raghavendra Rao. Curr. Sci., 105, 1303-1304.
ARTICLES IN PEER-REVIEWED JOURNALS
Srivastava, J. and Balaji, P.V. (2022) Clues to reaction specificity in PLP-dependent fold type I aminotransferases of monosacchride biosynthesis. Proteins: Structure, Function, and Bioinformatics, 90, 1247-1258. doi.org/10.1002/prot.26305
Srivastava, J., Sunthar, P. and Balaji, P.V. (2022) Monosacchraide biosynthesis pathways database. Glycobiology, 31, 1636-1644. doi.org/10.1093/glycob/cwab030
Anu Prabha and Balaji, P.V. (2021) Characterization of left-handed beta helix-domains, and identification and functional annotation of proteins containing such domains. Proteins: structure, function and bioinformatics, 89, 6-20.
PubMed id 32748987
doi.org/10.1002/prot.259990
Srivastava, J., Sunthar, P. and Balaji, P.V. (2020) The glycan alphabet is not universal: a hypothesis. Microbial Genomics, 6, mgen000452.
PubMed id 33048043.
doi.org/10.1099/mgen.0.000452.
Kaundinya, C.R., Savithri, H.S., Rao, K.K. and Balaji, P.V. (2018) EpsM from Bacillus subtilis 168 has UDP-2,4,6-trideoxy 2-acetamido 4-amino glucose acetyltransferase activity in vitro. Biochem. Biophys. Res. Comm., 505, 1057-1062.
PubMed id 30314705
Kaundinya, C.R., Savithri, H.S., Rao, K.K. and Balaji, P.V. (2018) In vitro characterization of N-terminal truncated EpsC from Bacillus subtilis 168, a UDP-N-acetyl 4,6-dehydratase. Arch. Biochem. Biophys., 657, 78-88.
PubMed id 30222950
Kaundinya, C.R., Savithri, H.S., Rao, K.K. and Balaji, P.V. (2018) EpsN from Bacillus subtilis 168 has UDP 2,6-dideoxy 2-acetamido 4-keto aminotransferase activity in vitro. Glycobiology, 28, 802-812.
PubMed id 29982582
Pardeshi, P., Rao, K.K. and Balaji, P.V. (2017) Rv3634c from Mycobacterium tuberculosis H37Rv encodes an enzyme with UDP-Gal/Glc and UDP-GalNAc 4-epimerase activities. PLoS ONE, 12, e0175193.
PubMed id 28403215
Prabhakar, P.K., Srivastava, A., Rao, K.K. and Balaji, P.V. (2016) Monomerization alters the dynamics of the lid region in Campylobacter jejuni CstII: an MD simulation study. J. Biomolec. Struct. Dyn., 34, 778-791.
PubMed id 26208676
Srivastava, A. and Balaji, P.V. (2015) Molecular events during the early stages of aggregation of GNNQQNY: an all atom MD simulation study of randomly dispersed peptides. J. Struct. Biol., 192, 376-391. With cover page illustration.
PubMed id 26433030
Prabhakar, P.K., Rao, K.K. and Balaji, P.V. (2014) The Cys78-Asn88 loop region of the Campylobacter jejuni CstII is essential for a2,3-sialyltransferase activity: analysis of the His85 mutants. J. Biochem., 156, 229-238.
PubMed id 24817703
Srivastava, A. and Balaji, P.V. (2014) Interplay of sequence, topology, and termini charge in determining the stability of the aggregates of GNNQQNY mutants: a molecular dynamics study. PLoS ONE, 9, e96660.
PubMed id 24817093
Kumar, M. and Balaji, P.V. (2014) CH...pi interactions in proteins: prevalence, pattern of occurrence, residue propensities, location and contribution to protein stability. J. Mol. Model., 20, 2136(1-14).
PubMed id 24526385
Kumari, M., Balaji, P.V. and Sunoj, R.B. (2012) Exploration of CH...pi mediated stacking interactions in saccharide : aromatic residue complexes through conformational sampling. Carbohydr. Res., 361, 133-140.
PubMed id 23017780
Srivastava, A. and Balaji, P.V. (2012) Size, orientation and organization of oligomers that nucleate amyloid fibrils: clues from MD simulations of pre-formed aggregates. Biochim. Biophys. Acta (Proteins and Proteomics), 1824, 963-973.
PubMed id 22609417
Kumari, M., Balaji, P.V. and Sunoj, R.B. (2012) Conformational mapping and energetics of saccharide-aromatic residue interactions: implications for the discrimination of anomers and epimers and in protein engineering. Org. Biomol. Chem., 10, 4186-4200.
PubMed id 22527756
Balaji, P.V. (2011) Contribution of C-H...pi interactions to the affinity and specificity of carbohydrate binding sites. Mini Rev. Org. Chem., 8, 222-228.
DOI: 10.2174/157019311796197355
Patel, R.Y. and Balaji, P.V. (2011) Structure and dynamics of glycosphingolipids in lipid bilayers: insights from molecular dynamics simulations. Int. J. Carbohydr. Chem., Vol. 2011, Article ID 950256.
DOI: 10.1155/2011/950256.
Kumar, M. and Balaji, P.V. (2011) Comparative genomics analysis of completely sequenced microbial genomes reveals the ubiquity of N-linked glycosylation in prokaryotes. Mol. Biosyst., 7, 1629-1645. Placed in the top 2% of published articles in Biology and Medicine by a member of the Faculty of 1000 (F1000).
Kumari, M., Balaji, P.V. and Sunoj, R.B. (2011) Quantification of binding affinities of essential sugars with tryptophan analogue and the ubiquitous role of C-H...pi interactions. Phys. Chem. Chem. Phys., 13, 6517-6530.
Jaiswal, R., Patel, .Y., Asthana, J., Jindal, B., Balaji, P.V. and Dulal Panda (2010)
E93R substitution of Escherichia coli FtsZ induces bundling of protofilaments, reduces GTPase activity and impairs bacterial cytokinesis.
J. Biol. Chem., 285, 31796-31805.
Rathinasamy, K., Jindal, B., Asthana, J., Singh, P., Balaji, P.V. and Panda, D. (2010) Griseofulvin stabilizes microtubule dynamics, activates p53 and inhibits the proliferation of MCF-7 cells synergistically with vinblastine. BMC Cancer, 10, 213.
Patel, R.Y. and Balaji, P.V. (2008)
Characterization of symmetric and asymmetric lipid bilayers composed of varying concentrations of ganglioside GM1 and DPPC.
J. Phys. Chem B, 112, 3346-3356.
Patel, R.Y. and Balaji, P.V. (2007)
Length and composition analysis of the cytoplasmic, transmembrane and stem regions of
human Golgi glycosyltransferases.
Protein Pept. Lett., 14, 601-609.
Patel, R.Y. and Balaji, P.V. (2007)
Fold recognition and comparative modeling of human beta3GalT I, II, IV, V and VI and beta3GalNAcT I: prediction of residues conferring acceptor substrate specificity.
J. Mol. Graph. Model., 26, 255-268.
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, R.Y. and Balaji, P.V. (2007)
Characterization of the conformational and orientational dynamics of ganglioside
GM1 in a dipalmitoylphosphatidylcholine bilayer by molecular dynamics simulations.
Biochim. Biophys. Acta (Biomembranes), 1768, 1628-1640.
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, 314-326.
Idicula-Thomas, S. and Balaji, P.V. (2007)
Correlation between the structural stability and aggregation propensity of proteins.
In Silico Biol., 7, 0023.
Article
Idicula-Thomas, S. and Balaji, P.V. (2007)
Protein aggregation: a perspective from amyloid and inclusion body formation.
Curr. Sci., 92, 758-767.
PDF
The NMITLI-BioSuite Team (2007)
BioSuite: a comprehensive bioinformatics software package (a unique industry-academia collaboration).
Curr. Sci., 92, 29-38.
PDF
Sujatha, M. S., and Balaji, P.V. (2006)
Fold recognition and comparative modeling of human alpha2,3-sialyltransferases reveal their
sequence and structural similarities to CstII from Campylobacter jejuni.
BMC Struct. Biol., 6, 9.
PDF
Coordinates of top models
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, 103-115.
Idicula-Thomas, S., Kulkarni, A.J., Kulkarni, B.D., Jayaraman, V.K. and Balaji, P.V. (2006)
A support vector machine-based method for predicting the propensity of a protein to be soluble or to form
inclusion body on over-expression in Escherichia coli.
Bioinformatics, 22, 278-284.
Patel, R.Y. and Balaji, P.V. (2006)
Identification of linkage-specific sequence motifs in sialyltransferases.
Glycobiology, 16, 108-116.
Patel, R.Y. and Balaji, P.V. (2005)
Effect of the choice of pressure coupling method on the spontaneous aggregation of DPPC molecules.
J. Phys. Chem. B, 109, 14667-14674.
Sujatha, M.S., 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.
Idicula-Thomas, S. and Balaji, P.V. (2005)
Understanding the relationhip between the primary structure of proteins
and their amyloidogenic propensity: clues from inclusion body formation.
Prot. Eng. Des. Sel., 18, 175-180.
Idicula-Thomas, S. and Balaji, P.V. (2005)
Understanding the relationship between the primary structure of proteins
and their propensity to be soluble on overexpression in Escherichia coli.
Prot. Sci., 14, 582-592.
Sujatha, M.S., Sasidhar,Y.U. and Balaji, P.V. (2004)
Energetics of galactose- and glucose-aromatic amino acid interactions:
implications for binding in galactose-specific proteins.
Prot. Sci., 13, 2502-2514.
Sujatha, M.S. and Balaji, P.V. (2004)
Identification of common structural features of binding sites in galactose-specific proteins.
Proteins. Struct. Funct. Bioinformatics., 55, 44-65.
Vasudevan, S.V. and Balaji, P.V. (2002)
Comparative analysis of ganglioside conformations by MD simulations:
implications for specific recognition by proteins.
J. Mol. Struct. (Theochem), 583, 215-232.
Vasudevan, S.V. and Balaji, P.V. (2002)
Conformation, orientation and dynamics of dodecylphosphocholine in micellar
aggregate: a 3.2 ns molecular dynamics simulation study.
Ind. J. Biochem. Biophys., 39, 87-92.
Vasudevan, S.V. and Balaji, P.V. (2002)
Molecular dynamics simulation of alpha2-8-linked disialoside: conformational
flexibility and implications for binding to proteins.
Biopolymers, 63, 168-180.
Vasudevan, S.V. and Balaji, P.V. (2001)
Dynamics of ganglioside headgroup in lipid environment: molecular dynamics
simulations of GM1 embedded in dodecylphosphocholine micelle.
J. Phys. Chem. B, 105, 7033-7041.
Ramakrishnan, B., Balaji, P.V. and Qasba, P.K. (2002)
Crystal structure of beta1,4-galactosyltransferase complex with UDP-Gal reveals an oligosaccharide acceptor binding site.
J. Mol. Biol., 318, 491-502.
Qasba, P.K., Balaji, P.V. and Rao, V.S.R. (1997)
Conformational analysis of Asn-linked oligosaccharides:
implications in biological processes.
J. Mol. Struct. (Theochem)., 395-396, 333-360.
PDF
Balaji, P.V., Rao, V.S.R. and Qasba, P.K. (1996)
Molecular dynamics simulations of hybrid and complex type oligosaccharides.
Int. J. Biol. Macromol., 18, 101-114.
PDF
Boeggeman, E.E., Balaji, P.V. and Qasba, P.K. (1995)
Functional domains of bovine beta1->4-galactosyltransferase.
Glycoconj. J., 12, 865-878.
PDF
Rao, V.S.R., Balaji, P.V. and Qasba, P.K. (1995)
Controversial iduronate ring conformation.
Glycobiology, 5, 273-276.
PDF
Qasba, P.K., Balaji, P.V. and Rao, V.S.R. (1994)
Molecular dynamics simulations of oligosaccharides and their conformation in the crystal structure of lectin-carbohydrate complex: importance of the torsion angle psi for the orientation of alpha1->6-arm.
Glycobiology, 4, 805-815. [PMID: 7734844;
Medline]
Balaji, P.V., Qasba, P.K. and Rao, V.S.R. (1994)
Molecular dynamics simulations of high mannose oligosaccharides.
Glycobiology, 4, 497-515. [PMID: 7827412;
Medline]
Balaji, P.V., Qasba, P.K. and Rao, V.S.R. (1993)
Molecular dynamics study of asialoglycoprotein receptor ligands.
Biochemistry, 32, 12599-12611. [PMID: 8251478;
Medline]
Boeggeman, E.E., Balaji, P.V., Sethi, N., Masibay, A.S. and
Qasba, P.K. (1993)
Expression of deletion constructs of bovine beta1->4-galactosyltransferase in Escherichia coli: importance of Cys134 for its activity.
Prot. Eng., 6, 779-785. [PMID: 8248102;
Medline]
Masibay, A.S., Balaji, P.V., Boeggeman, E.E. and Qasba, P.K. (1993)
Mutational analysis of the Golgi retention signal of bovine beta1->4 galactosyltransferase.
J. Biol. Chem., 268, 9908-9916.
PDF
Seshadri, K., Balaji, P.V., Rao, V.S.R. and
Vishveshwara, S. (1993)
Computer modeling studies of ribonuclease A - pyrimidine nucleotide complexes.
J. Biomol. Struct. Dyn., 11, 395-415. [PMID: 8286064;
Medline]
Balaji, P.V., Saenger, W. and Rao, V.S.R. (1993)
Computer modelling studies on the binding of 2',5'-linked dinucleotides to RNase T1 - Influence of subsite interactions on substrate binding.
J. Biomol. Struct. Dyn., 10, 891-903. [PMID: 8391269;
Medline]
Balaji, P.V. and Rao, V.S.R. (1992)
Computer modeling studies on the subsite interactions of ribonuclease T1.
J. Biomol. Struct. Dyn., 9, 971-989. [PMID: 1326282;
Medline]
Balaji, P.V., Saenger, W. and Rao, V.S.R. (1992)
Modes of binding of 2'-AMP to RNase T1 - A computer modeling study.
J. Biomol. Struct. Dyn., 9, 959-969. [PMID: 1524709;
Medline]
Balaji, P.V. and Rao, V.S.R. (1991)
Computer modelling studies of ribonuclease T1-2'-deoxy-2'-fluoroguanylyl-(3',5')-cytidine complex.
Ind. J. Biochem. Biophys., 28, 358-362. [PMID: 1812067;
Medline]
Balaji, P.V., Saenger, W. and Rao, V.S.R. (1991)
Modes of binding of guanosine monophosphates to ribonuclease T1 - A computer-modelling study.
Curr. Sci., 60, 363-373.
PDF
Balaji, P.V., Saenger, W. and Rao, V.S.R. (1991)
Computer modeling studies on the mechanism of action of ribonuclease T1.
J. Biomol. Struct. Dyn., 9, 215-231. [PMID: 1741959;
Medline]
Balaji, P.V., Saenger, W. and Rao, V.S.R. (1990)
Computer modeling studies of ribonuclease T1-guanosine monophosphate complexes.
Biopolymers, 30, 257-272. [PMID: 2177661;
Medline]
Rao, V.S.R., Biswas, M., Mukhopadhyay, C. and Balaji, P.V. (1989)
Computer simulation of protein-carbohydrate complexes: application to arabinose-binding protein and pea lectin.
J. Mol. Struct., 194, 203-214.
PDF
ARTICLES IN CONFERENCE PROCEEDINGS
Patel, R.Y. and Balaji, P.V. (2006)
Molecular dynamics simulations of spontaneous aggregation of dipalmitoyl-phosphatidylcholine into cylindrical micelle and bilayer from the same starting conformation.
In Mathematical Biology: Recent Trends. Proceedings of the International Conference on Mathematical Biology ICMB-2004 (Chandra, P. and Kumar, B.V.R., eds.), pp 199-205, Anamaya Publishers, New Delhi.
Sujatha, M.S. and Balaji, P.V. (2006)
Binding site features of galactose-specific proteins are fuzzy.
In Mathematical Biology: Recent Trends. Proceedings of the International Conference on Mathematical Biology ICMB-2004 (Chandra, P. and Kumar, B.V.R., eds.), pp 181-186, Anamaya Publishers, New Delhi.
Seshu Kumar, K.V., Nagaraja, G. and Balaji, P.V. (2002)
Locally aligned terminal distinguishable languages and identification of proteins.
In Artificial Intelligence: Theory and Practice. Proceedings of the International
Conference KBCS-2002 (Sasikumar et al., eds.), pp 311-321, Vikas Publishing House
Pvt. Ltd., New Delhi.
PS file
SYMPOSIUM ABSTRACTS PUBLISHED IN JOURNALS
Qasba, P.K., Ramakrishnan, B. and Balaji, P.V.
(2002)
Oligosaccharide binding site of b1,4-galactosyltransferases (Gal-Ts)
defined by docking various glycan substrates in the binding site.
223rd Am. Chem. Soc. National Meeting on Carbohydrates and
Therapeutics Glycoproteins (Code: CARB).
Abstract
Vasudevan, S.V. and Balaji, P.V. (1999)
Headgroup dynamics of GM1 anchored in dodecylphosphocholine micelle.
J. Biosci. 24, Suppl. 1, 497.
Boeggeman, E.E., Balaji, P.V. and Qasba, P.K. (1995)
Functional domains of bovine beta1->4-galactosyltransferase.
Glycoconj. J., 12, 451-452.
Qasba, P.K., Balaji, P.V. and Rao, V.S.R. (1995)
Conformations of oligosaccharides accessed by molecular dynamics simulations and
selected in the lectin-carbohydrate complexes.
Glycoconj. J., 12, 430.
Qasba, P.K., Balaji, P.V. and Rao, V.S.R. (1995)
Molecular dynamics simulations of oligosaccharides and their conformation in lectin-
carbohydrate complexes.
Abs. Am. Chem. Soc., 209, 101.
Balaji, P.V., Qasba, P.K. and Rao, V.S.R. (1994)
Molecular dynamics simulations of high mannose oligosaccharides:
possible pathways for processing of Man9GlcNAc2 to Man5GlcNAc2.
J. Cell. Biochem., 18D, s269.
Qasba, P.K., Masibay, A.S., Boeggeman, E.E. and
Balaji, P.V. (1993)
Study of the functional domains of beta1->4-galactosyltransferase through the
expression of the deletion constructs of cDNA in E. coli and mammalian cells:
disulphide bond between Cys134 and Cys247 is required for folding and enzyme
activity while the transmembrane domain is essential for stable expression in
mammalian cells.
Prot. Engng., 6, s99.