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.

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    P.V.Balaji       Department of Biosciences & Bioengineering       IIT Bombay