PUBLICATIONS

    1. Ghoshal B, Chakraborty D, Nag M, Varadarajan R and Jhunjhunwala S. (2024) Ex Vivo Delivery of mRNA to Immune Cells via a Nonendosomal Route Obviates the Need for Nucleoside Modification. ACS Bio & Med Chem Au. doi: 10.1021/acsbiomedchemau.4c00057.


    2. Kanjo, K., Chakshusmathi, G., Varadarajan, R. (2024) Vaccine Research and Development in India for COVID-19 and Influenza. In: John, G., Panda, A.K. (eds) Biotechnology in India - Reworking A Strategy. Springer, Singapore. Proteins. doi: 10.1007/978-981-97-0896-3_6.


    3. Sharma A, Singh N, Bhasin M, Tiwari P , Chopra P, Varadarajan R and Singh R. (2024) Deciphering the role of VapBC13 and VapBC26 toxin antitoxin systems in the pathophysiology of Mycobacterium tuberculosis. Communications Biology. (Manuscript Accepted).


    4. Nanda, B., Bhowmick, J., Varadarajan, R., & Sarma, S. P. (2024) Backbone assignment of CcdB_G100T toxin from E.coli in complex with the toxin binding C-terminal domain of its cognate antitoxin CcdA. Biomolecular NMR assignments. Advance online publication. . doi:10.1007/s12104-024-10201-6. PMID: 39276296.


    5. Ganesan S, Mittal N, Bhat A, Adiga RS, Ganesan A, Nagarajan D, Varadarajan R. (2024) Improved Prediction of Stabilizing Mutations in Proteins by Incorporation of Mutational Effects on Ligand Binding. Proteins. doi: 10.1002/prot.26738. PMID: 39166462.


    6. Liang Z, Lin X, Sun L, Edwards KM, Song W, Sun H, Xie Y, Lin F, Ling S, Liang T, Xiao B, Wang J, Li M, Leung CY, Zhu H, Bhandari N, Varadarajan R, Levine MZ, Peiris M, Webster R, Dhanasekaran V, Leung NHL, Cowling BJ, Webby RJ, Ducatez M, Zanin M, Wong SS. (2024) A(H2N2) and A(H3N2) influenza pandemics elicited durable cross-reactive and protective antibodies against avian N2 neuraminidases. Nat Commun. doi: 10.1038/s41467-024-49884-9. PMID: 38961067; PMCID: PMC11222539.


    7. Jia JZ, Cohen CA, Gu H, McLean MR, Varadarajan R, Bhandari N, Peiris M, Leung GM, Poon LLM, Tsang T, Chung AW, Cowling BJ, Leung NHL, Valkenburg SA. (2024) Influenza antibody breadth and effector functions are immune correlates from acquisition of pandemic infection of children. Nat Commun. doi: 10.1038/s41467-024-47590-0. PMID: 38615070; PMCID: PMC11016072.


    8. Khan MS, Jakob V, Singh R, Rajmani RS, Kumar S, Lemoine C, Kleanthous H, Ringe RP, Dubois PM, Varadarajan R. (2023) Enhancing Immunogenicity of a Thermostable, Efficacious SARS-CoV-2 Vaccine Formulation through Oligomerization and Adjuvant Choice. Pharmaceutics. doi: 10.3390/pharmaceutics15122759. PMID: 38140101; PMCID: PMC10747592.


    9. Bajaj P, Bhasin M, Varadarajan R. (2023) Molecular bases for strong phenotypic effects of single synonymous codon substitutions in the E. coli ccdB toxin gene. BMC Genomics. doi: 10.1186/s12864-023-09817-0.


    10. Mittal N, Kumar S, Rajmani RS, Singh R, Lemoine C, Jakob V, Bj S, Jagannath N, Bhat M, Chakraborty D, Pandey S, Jory A, Sa SS, Kleanthous H, Dubois P, Ringe RP, Varadarajan R. (2023) Enhanced protective efficacy of a thermostable RBD-S2 vaccine formulation against SARS-CoV-2 and its variants. NPJ Vaccines. doi: 10.1038/s41541-023-00755-2. PMID: 37880298; PMCID: PMC10600342.


    11. Kumar S, Delipan R, Chakraborty D, Kanjo K,Singh R, Singh N, Siddiqui S, Tyagi A, Jha V, Thakur KG, Pandey R, Varadarajan R, Ringe RP. (2023) Mutations in S2 subunit of SARS-CoV-2 Omicron spike strongly influence its conformation, fusogenicity, and neutralization sensitivity. J Virol. doi: 10.1128/jvi.00922-23 . PMID: 37861334.


    12. Bhowmick J, Chandra S, Varadarajan R. (2023) Deep mutational scanning to probe specificity determinants (Chapter). Structure and Intrinsic Disorder in Enzymology, Academic Press. doi: 10.1016/B978-0-323-99533-7.00005-4.


    13. Bhowmick J, Nag M, Ghosh P, Rajmani RS, Chatterjee R, Karmakar K, Chandra K, Chatterjee J, Chakravortty D, Varadarajan R. (2023) A CcdB toxin-derived peptide acts as a broad-spectrum antibacterial therapeutic in infected mice. EMBO Rep. doi: 10.15252/embr.202255338. PMID: 37166011; PMCID: PMC10328072.


    14. Kumar N, Taily IM, Singh C, Kumar S, Rajmani RS, Chakraborty D, Sharma A, Singh P, Thakur KG, Varadarajan R, Ringe RP, Banerjee P, Banerjee I. (2023) Identification of diphenylurea derivatives as novel endocytosis inhibitors that demonstrate broad-spectrum activity against SARS-CoV-2 and influenza A virus both in vitro and in vivo. PLoS Pathog. doi: 10.1371/journal.ppat.1011358. PMID: 37126530; PMCID: PMC10174524.


    15. Kanjo K, Chattopadhyay G, Malladi SK, Singh R, Jayatheertha S, Varadarajan R. (2023) Biophysical Correlates of Enhanced Immunogenicity of a Stabilized Variant of the Receptor Binding Domain of SARS-CoV-2. J Phys Chem B. doi: 10.1021/acs.jpcb.2c07262. PMID: 6790910; PMCID: PMC9942533.


    16. Chandra S, Manjunath K, Asok A, Varadarajan R. (2023) Mutational scan inferred binding energetics and structure in intrinsically disordered protein CcdA. Protein Sci. doi: 10.1002/pro.4580. PMID: 36714997; PMCID: PMC9951195.


    17. Khaleeq S, Sengupta N, Kumar S, Patel UR, Rajmani RS, Reddy P, Pandey S, Singh R, Dutta S, Ringe RP, Varadarajan R. (2023) Neutralizing Efficacy of Encapsulin Nanoparticles against SARS-CoV2 Variants of Concern. Viruses. doi: 10.3390/v15020346. PMID: 36851560; PMCID: PMC9961482.


    18. Chattopadhyay G, Ahmed S, Srilatha NS, Asok A, Varadarajan R. (2023) Ter-Seq: A high-throughput method to stabilize transient ternary complexes and measure associated kinetics. Protein Sci. doi: 10.1002/pro.4514. PMID: 36382921; PMCID: PMC9793979.


    19. Chandra S, Gupta K, Khare S, Kohli P, Asok A, Mohan SV, Gowda H, Varadarajan R. (2022) The High Mutational Sensitivity of ccdA Antitoxin Is Linked to Codon Optimality. Mol Biol Evol. doi: 10.1093/molbev/msac187. PMID: 36069948; PMCID: PMC9555053.


    20. Sahoo A, Jones AT, Cheedarla N, Gangadhara S, Roy V, Styles TM, Shiferaw A, Walter KL, Williams LD, Shen X, Ozorowski G, Lee WH, Burton S, Yi L, Song X, Qin ZS, Derdeyn CA, Ward AB, Clements JD, Varadarajan R, Tomaras GD, Kozlowski PA, Alter G, Amara RR. (2022) A clade C HIV-1 vaccine protects against heterologous SHIV infection by modulating IgG glycosylation and T helper response in macaques. Sci Immunol. doi: 10.1126/sciimmunol.abl4102 . PMID: 35867800; PMCID: PMC9410801.


    21. Kar U, Khaleeq S, Garg P, Bhat M, Reddy P, Vignesh VS, Upadhyaya A, Das M, Chakshusmathi G, Pandey S, Dutta S, Varadarajan R. (2022) Comparative Immunogenicity of Bacterially Expressed Soluble Trimers and Nanoparticle Displayed Influenza Hemagglutinin Stem Immunogens. Front Immunol. doi: 10.3389/fimmu.2022.890622 . PMID: 35720346; PMCID: PMC9204493.


    22. Chattopadhyay G, Bhasin M, Ahmed S, Gosain TP, Ganesan S, Das S, Thakur C, Chandra N, Singh R, Varadarajan R. (2022) Functional and Biochemical Characterization of the MazEF6 Toxin-Antitoxin System of Mycobacterium tuberculosis. J Bacteriol. doi: 10.1128/jb.00058-22 . PMID: 35357163; PMCID: PMC9053165.


    23. Jansen van Vuren P, McAuley AJ, Kuiper MJ, Singanallur NB, Bruce MP, Riddell S, Goldie S, Mangalaganesh S, Chahal S, Drew TW, Blasdell KR, Tachedjian M, Caly L, Druce JD, Ahmed S, Khan MS, Malladi SK, Singh R, Pandey S, Varadarajan R, Vasan SS. (2022) Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice. Viruses. doi: 10.3390/v14040800 . PMID: 35458530; PMCID: PMC9031315.


    24. Ahmed S, Chattopadhyay G, Manjunath K, Bhasin M, Singh N, Rasool M, Das S, Rana V, Khan N, Mitra D, Asok A, Singh R, Varadarajan R.(2022) Combining cysteine scanning with chemical labeling to map protein-protein interactions and infer bound structure in an intrinsically disordered region. Front Mol Biosci. doi: 10.3389/fmolb.2022.997653. PMID: 36275627; PMCID: PMC9585320.


    25. Chandra S, Gupta K, Khare S, Kohli P, Asok A, Mohan SV, Gowda H, Varadarajan R. (2022) The high mutational sensitivity of ccdA antitoxin is linked to codon optimality. Mol Biol Evol. doi: 10.1093/molbev/msac187. PMID: 36069948; PMCID: PMC9555053..


    26. Sahoo A, Jones AT, Cheedarla N, Gangadhara S, Roy V, Styles TM, Shiferaw A, Walter KL, Williams LD, Shen X, Ozorowski G, Lee WH, Burton S, Yi L, Song X, Qin ZS, Derdeyn CA, Ward AB, Clements JD, Varadarajan R, Tomaras GD, Kozlowski PA, Alter G, Amara RR. (2022) A clade C HIV-1 vaccine protects against heterologous SHIV infection by modulating IgG glycosylation and T helper response in macaques. Sci Immunol. doi: 10.1126/sciimmunol.abl4102. PMID: 35867800; PMCID: PMC9410801.


    27. Chattopadhyay G, Bhowmick J, Manjunath K, Ahmed S, Goyal P, Varadarajan R. (2022). Mechanistic insights into global suppressors of protein folding defects. PLoS genetics. doi: 10.1371/journal.pgen.1010334. PMID: 36037221; PMCID: PMC9491731.


    28. Bajaj P, Manjunath K, Varadarajan R. (2022) Structural and functional determinants inferred from deep mutational scans. Protein Science. doi:10.1002/pro.4357. PMID: 35762712; PMCID: PMC9202547.


    29. Khatri B, Pramanick I, Malladi SK, Rajmani RS, Kumar S, Ghosh P, Sengupta N, Rahisuddin R, Kumar N, Kumaran S, Ringe RP, Varadarajan R, Dutta S, Chatterjee J. (2022) A proteomimetic prevents SARS-CoV-2 infection by dimerizing the spike protein. Nat. Chem. Biol. doi: 10.1038/s41589-022-01060-0. PMID: 35654847; PMCID: PMC9512702.


    30. Van Vuren PJ, McAuley AJ, Kuiper MJ, Singanallur NB, Bruce MP, Riddell S, Goldie S, Mangalaganesh S, Chahal S, Drew TW, Blasdell KR, Tachedjian M, Caly L, Druce JD, Ahmed S, Khan MS, Malladi SK, Singh R, Pandey S, Varadarajan R, Vasan SS. (2022) Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies Against Delta and Omicron in Mice. Viruses. doi: 10.3390/v14040800. PMID: 35458530; PMCID: PMC9031315.


    31. Chattopadhyay G, Bhasin M, Ahmed S, Gosain TP, Ganesan S, Das S, Thakur C, Chandra N, Singh R, Varadarajan, R. (2022). Functional and Biochemical Characterization of the MazEF6 Toxin-Antitoxin System of Mycobacterium tuberculosis. Journal of bacteriology. doi: 10.1128/jb.00058-22. PMID: 35357163; PMCID: PMC9053165.


    32. Ahmed S, Manjunath K, Chattopadhyay G, Varadarajan R. (2022) Identification of stabilizing point mutations through mutagenesis of destabilized protein libraries. J Biol Chem. doi: 10.1016/j.jbc.2022.101785. PMID: 35247389; PMCID: PMC8971944.


    33. Ahmed S, Bhasin M, Manjunath K, Varadarajan R. (2021) Prediction of residue-specific contributions to binding and thermal stability using yeast surface display. Front Mol Biosci. doi: 10.3389/fmolb.2021.800819. PMID: 35127820; PMCID: PMC8814602.


    34. Ahmed S, Khan MS, Gayathri S, Singh R, Kumar S, Patel UR, Malladi SK, Rajmani RS, van Vuren PJ, Riddell S, Goldie S, Girish N, Reddy P, Upadhyaya A, Pandey S, Siddiqui S, Tyagi A, Jha S, Pandey R, Khatun O, Narayan R, Tripathi S, McAuley A, Balasubramanian NS, Vasan SS, Ringe RP, Varadarajan R. (2021) A stabilized, monomeric, Receptor Binding Domain elicits high-titer neutralizing antibodies against all SARS-CoV-2 variants of concern. Frontiers in Immunology. doi: 10.3389/fimmu.2021.765211. PMID: 34956193; PMCID: PMC8695907.


    35. Chandra S, Chattopadhyay G, Varadarajan R. (2021) Rapid Identification of Secondary Structure and Binding Site Residues in an Intrinsically Disordered Protein Segment. Frontiers in Genetics. doi: 10.3389/fgene.2021.755292. PMID: 34795695; PMCID: PMC8593223.


    36. Mittal N, Sengupta N, Malladi SK, Reddy P, Bhat M, Rajmani RS, Sedeyn K, Saelens X, Dutta S, Varadarajan R. (2021) Protective Efficacy of Recombinant Influenza Hemagglutinin Ectodomain Fusions. Viruses. doi: 10.3390/v13091710 . PMID: 34578291; PMCID: PMC8473191.


    37. Malladi SK, Patel UR, Rajmani RS, Singh R, Pandey S, Kumar S, Khaleeq S, van Vuren PJ, Riddell S, Goldie S, Gayathri S, Chakraborty D, Kalita P, Pramanick I, Agarwal N, Reddy P, Girish N, Upadhyaya A, Khan MS, Kanjo K, Bhat M, Mani S, Bhattacharyya S, Siddiqui S, Tyagi A, Jha S, Pandey R, Tripathi S, Dutta S, McAuley AJ, Singanallur NB, Vasan SS, Ringe RP, Varadarajan R. (2021) Immunogenicity and Protective Efficacy of a Highly Thermotolerant, Trimeric SARS-CoV-2 Receptor Binding Domain Derivative. ACS infectious diseases. doi: 10.1021/acsinfecdis.1c00276. PMID: 34260218; PMCID: PMC8996237.


    38. Bhasin M, Varadarajan R. (2021) Prediction of Function Determining and Buried Residues Through Analysis of Saturation Mutagenesis Datasets. Front Mol Biosci. doi: 10.3389/fmolb.2021.635425. PMID: 33778004; PMCID: PMC7991590.


    39. Datta R, Roy Chowdhury R, Manjunath K, Hanna LE, Varadarajan R. (2020) A facile method of mapping HIV-1 neutralizing epitopes using chemically masked cysteines and deep sequencing. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.2010256117. PMID: 33168755; PMCID: PMC7703538.


    40. Malladi SK, Singh R, Pandey S, Gayathri S, Kanjo K, Ahmed S, Khan MS, Kalita P, Girish N, Upadhyaya A, Reddy P, Pramanick I, Bhasin M, Mani S, Bhattacharyya S, Joseph J, Thankamani K, Raj VS, Dutta S, Singh R, Nadig G, Varadarajan R. (2020) Design of a highly thermotolerant, immunogenic SARS-CoV-2 spike fragment. Journal of Biological Chemistry. doi: 10.1074/jbc.RA120.016284. PMID: 33154165; PMCID: PMC7832000.


    41. Mallajosyula VA, Swaroop S & Varadarajan R. (2020) Influenza Hemagglutinin Head Domain Mimicry by Rational Design. The Protein Journal. doi: 101007/s10930-020-09930-z. PMID: 33068234; PMCID: PMC7704708.


    42. Sharma A, Chattopadhyay G, Chopra P, Bhasin M, Thakur C, Agarwal S, Ahmed S, Chandra N, Varadarajan R, Singh R. (2020) VapC21 Toxin Contributes to Drug-Tolerance and Interacts With Non-cognate VapB32 Antitoxin in Mycobacterium tuberculosis. Front Microbiol. doi: 10.3389/fmicb.2020.02037. PMID: 33042034; PMCID: PMC7517352.


    43. Nickolaus C, Vargas C, Reichenwallner J, Chakour M, Selmke B, Chakraborty R, Varadarajan R, Keller S, Trommer WE. (2020) The Molten Globule State of Maltose-Binding Protein: Structural and Thermodynamic Characterization by EPR Spectroscopy and Isothermal Titration Calorimetry. Appl Magn Reson. doi: 0.1007/s00723-020-01232-y.


    44. Das R, Datta R, Varadarajan R. (2020) Probing the structure of the HIV-1 Envelope trimer using Aspartate Scanning Mutagenesis. J Virol. doi:10.1128/JVI.01426-20 . PMID: 32817217; PMCID: PMC7565623.


    45. Malladi SK, Schreiber D, Pramanick I, Sridevi MA, Goldenzweig A, Dutta S, Fleishman SJ, Varadarajan R. (2020) One-step sequence and structure-guided optimization of HIV-1 envelope gp140. Current Research in Structural Biology. doi: 10.1016/j.crstbi.2020.04.001. PMID: 33688632; PMCID: PMC7939140


    46. Agarwal S, Sharma A, Bouzeyen R, Deep A, Sharma H, Mangalaparthi KK, Datta KK, Kidwai S, Gowda H, Varadarajan R, Sharma RD, Thakur KG, Singh R. (2020) VapBC22 toxin-antitoxin system from Mycobacterium tuberculosis is required for pathogenesis and modulation of host immune response. Sci Adv. doi: 10.1126/sciadv.aba6944. PMID: 32537511; PMCID: PMC7269643


    47. Aghera NK, Prabha J, Tandon H, Chattopadhyay G, Vishwanath S, Srinivasan N, Varadarajan R. (2020) Mechanism of CcdA-Mediated Rejuvenation of DNA Gyrase. Structure. doi: 10.1016/j.str.2020.03.006. PMID: 32294467.


    48. Tandon H, Sharma A, Wadhwa S, Varadarajan R, Singh R, Srinivasan N, & Sandhya S (2019). Bioinformatic and mutational studies of related toxin-antitoxin pairs in Mycobacterium tuberculosis predict and identify key functional residues. J Biol Chem. doi: 10.1074/jbc.RA118.006814. PMID: 31018964; PMCID: PMC6556569.


    49. Chattopadhyay G, Varadarajan R. (2019) Facile measurement of protein stability and folding kinetics using a nano differential scanning fluorimeter. Protein Sci. doi: 10.1002/pro.3622. PMID: 30993730; PMCID: PMC6511731.


    50. Tripathi A, Swaroop S, Varadarajan R (2019) Molecular determinants of temperature-sensitive phenotypes. Biochemistry. doi: 10.1021/acs.biochem.8b00964. PMID: 30843689.


    51. Baliga C, Selmke B, Worobiew I, Borbat P, Sarma SP, Trommer WE, Varadarajan R, Aghera N. (2019) CcdB at pH 4 forms a partially unfolded state with a dry core. Biophysical Journal. doi: 10.1016/j.bpj.2019.01.026. PMID: 30777307; PMCID: PMC6401195.


    52. Jones AT, Shen X, Walter KL, LaBranche CC, Wyatt LS, Tomaras G, Montefiori DC, Moss B, Barouch DH, Clements JD, Kozlowski PA, Varadarajan R, Amara RR (2019) Needle-free delivery of an HIV-1 vaccine to the oral mucosae induces strong systemic and mucosal antibody responses in rhesus macaques. Nat Comm. doi: 10.1038/s41467-019-08739-4.


    53. Khare S, Bhasin M, Sahoo A, Varadarajan R. (2019) Protein model discrimination attempts using mutational sensitivity, predicted secondary structure, and model quality information. Proteins. doi: 10.1002/prot.25654. PMID: 30615225.


    54. Raghunandanan S, Ramachandran R, Gomez RL, Sivasankar D, Bommakanti A, Kondapi AK,Varadarajan R, Kumar AR. (2018) Rv0474 is a copper-responsive transcriptional regulator that negatively regulates expression of RNA polymerase β subunit in Mycobacterium tuberculosis. FEBS J. doi: 10.1111/febs.14637. PMID: 30120904.


    55. Rathore U, Purwar M, Vignesh VS, Das  R, Kumar AA, Bhattacharyya S, Arendt H, DeStefano J, Wilson A, Parks C, La Branche CC, Montefiori DC, Varadarajan R (2018)   Bacterially expressed HIV-1 gp120 outer-domain fragment immunogens with improved stability and affinity for CD4 binding site neutralizing antibodies. J Biol Chem. doi: 10.1074/jbc.RA118.005006. PMID: 30093409; PMCID: PMC6166733.


    56. Purwar M, Pokorski J, Singh P, Bhattacharyya S, Arendt H, DeStefano J, La Branche CC, Montefiori DC, Finn MG, Varadarajan R (2018). Design, display and immunogenicity of HIV1 gp120 fragment immunogens on virus-like particles. Vaccine. doi: 10.1016/j.vaccine.2018.07.032. PMID: 30220462; PMCID: PMC6364316.


    57. Selmke B, Borbat P, Nickolaus C, Varadarajan R, Freed J, Trommer W. (2018) Open and Closed Form of Maltose Binding Protein in Its Native and Molten Globule State as Studied by EPR Spectroscopy. Biochemistry. doi: 10.1021/acs.biochem.8b00322. PMID: 30004675; PMCID: PMC6211580.


    58. Najar TA, Kar U, Flynn J, Varadarajan R (2018) Isolation of an in vitro affinity-matured, thermostable "Headless" HA stem fragment that binds broadly neutralizing antibodies with high affinity Biochemistry. doi: 10.1021/acs.biochem.8b00267. PMID: 29863853.


    59. Najar TA, Khare S, Varadarajan R (2018) Rapid mapping of protein binding sites and conformational epitopes by coupling yeast surface display to chemical labeling and deep sequencing. Methods Mol Biol. doi: 10.1007/978-1-4939-7841-0_6. PMID: 29714013.


    60. Cheedarla N, Hemalatha B, Anangi B, Muthuramalingam K, Selvachithiram M, Sathyamurthi P, Kailasam N, Varadarajan R, Swaminathan S, Tripathy S P, Vaniambadi S K, D. Vadakkupattu R and Hanna L E (2018) Evolution of Neutralization Response in HIV-1 Subtype C-Infected Individuals Exhibiting Broad Cross-Clade Neutralization of HIV-1 Strains. Front. Immunol. doi: 10.3389/fimmu.2018.00618. PMID: 29662494; PMCID: PMC5890096.


    61. Gupta K and Varadarajan R (2018)  Insights into protein structure, stability and function from saturation mutagenesis. Curr Opin Struct Biol. doi: 10.1016/j.sbi.2018.02.006. PMID: 29505936; PMCID: PMC6078801.


    62. Jones AT, Chamcha V, Kesavardhana S, Shen X, Beaumont D, Das R, Wyatt LS, LaBranche CC, Stanfield-Oakley S, Ferrari G, Montefiori DC, Moss B, Tomaras GD, Varadarajan R, Amara RR (2017) A trimeric HIV-1 envelope gp120 immunogen induces potent and broad anti-V1V2 loop antibodies against HIV-1 in rabbits and rhesus macaques. J Virol. doi: 10.1128/JVI.01796-17.PMID: 29237847; PMCID: PMC5809733.


    63. Sutton TC, Chakraborty S, Mallajosyula VVA, Lamirande EW, Ganti K, Bock KW, Moore IN,Varadarajan R, Subbarao K (2017) Protective efficacy of influenza group 2 hemagglutinin stem-fragment immunogen 2 vaccines. npj Vaccines. doi: 10.1038/s41541-017-0036-2. PMID: 29263889; PMCID: PMC5732283.


    64. Gupta K, Tripathi A, Sahu A,  Varadarajan R.  (2017) Contribution of the chromosomal ccdAB operon to bacterial drug tolerance. J Bacteriol. doi: 10.1128/JB.00397-17. PMID: 28674066; PMCID: PMC5585702..


    65. Rathore U, Saha P, Kesavardhana S, Kumar AA, Datta R, Devanarayanan S, Das R, Mascola JR, Varadarajan R. (2017) Glycosylation of the core of the HIV-1 envelope subunit protein gp120 is not required for native trimer formation or viral infectivity. J Biol Chem. doi: 10.1074/jbc.M117.788919. PMID: 28446609; PMCID: PMC5473224.


    66. Khan L, Kumar R, Thiruvengadam R, Parray HA, Makhdoomi MA, Kumar S, Aggarwal  H, Mohata M, Hussain AW, Das R, Varadarajan R, Bhattacharya J, Vajpayee M, Murugavel KG, Solomon S, Sinha S, Luthra K. (2017) Cross-neutralizing anti-HIV-1 human single chain variable fragments(scFvs) against CD4 binding site and N332 glycan identified from a recombinant phage library. Sci Rep. doi: 10.1038/srep45163. PMID: 28332627; PMCID: PMC5362912.


    67. Najar TA, Khare S, Pandey R, Gupta SK, Varadarajan R. (2017) Mapping Protein Binding Sites and Conformational Epitopes Using Cysteine Labeling and Yeast Surface Display. Structure. doi: 10.1016/j.str.2016.12.016. PMID: 28132782.


    68. Kesavardhana S, Das R, Citron M, Datta R, Ecto L, Srilatha NS, DiStefano D, Swoyer R, Joyce JG, Dutta S, LaBranche CC, Montefiori DC, Flynn JA, Varadarajan R. (2017) Structure based design of cyclically permuted HIV-1 gp120 trimers that elicit neutralizing antibodies. J Biol Chem. doi: 10.1074/jbc.M116.725614. PMID: 27879316; PMCID: PMC5217686.


    69. Tawfik DS, Varadarajan R. (2016)  Editorial overview: Engineering and design. Curr Opin Struct Biol. doi: 10.1016/j.sbi.2016.08.004. PMID: 27595363.


    70. Malik A, Mallajosyula V, Mishra NN, Arukha AP, Varadarajan R, Gupta SK. (2016) Generation and characterisation of monoclonal antibodies specific to avian influenza H7N9 haemagglutinin protein. Indian J Med Microbiol. doi: 10.4103/0255-0857.195366. PMID: 27934828.


    71. Vijaykrishnaa N, Melangatha.G, Kumara. R, Khandeliaa P, Bawaa P, Varadarajan R, Vijayraghavana U. (2016) The fission yeast pre-mRNA processing factor 18  (prp18+) has intron-specific splicing functions with links to G1-S cell cycle progression. J Biol Chem. doi: 10.1074/jbc.M116.751289. PMID: 27875300; PMCID: PMC5207164.


    72. Baliga C, Varadarajan R, Aghera N (2016) The homodimeric E. coli toxin CcdB (Controller of Cell Division or Death B protein) folds via parallel pathways. Biochemistry. doi: 10.1021/acs.biochem.6b00726. PMID: 27696818.


    73. Tripathi A, Gupta K, Khare S, Jain P. C, Patel S, Kumar P, Pulianmackal A. J, Aghera N, Varadarajan, R. (2016) Molecular determinants of mutant phenotypes, inferred from saturation mutagenesis data. Mol Biol Evol. doi: 10.1093/molbev/msw182. PMID: 27563054; PMCID: PMC5062330.


    74. Shembekar N,  Mallajosyula VA,  Malik A, Saini A, Varadarajan R, Gupta SK (2016) Neutralization and binding profile of monoclonal antibodies generated against influenza A H1N1 viruses. Monoclon. Antib. Immunodiagn. Immunother. doi: 10.1089/mab.2016.0015. PMID: 27463230.


    75. Baliga C , Majhi S, Mondal K , Bhattacharjee A, VijayRaghavan K, Varadarajan R (2016) Rational elicitation of cold sensitive phenotypes Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1604190113. PMID: 27091994; PMCID: PMC4983833.


    76. Valkenburg SA, Mallajosyula VV, Li OT, Chin AW, Carnell G, Temperton N, Varadarajan R, Poon LL. (2016) Stalking influenza by vaccination with pre-fusion headless HA mini-stem. Sci Rep. doi: 10.1038/srep22666. PMID: 26947245; PMCID: PMC4780079.


    77. Srinivasan S, Ghosh M, Maity S, Varadarajan R, (2016) Broadly neutralizing antibodies for therapy of viral infections. Antibody Technology Journal. doi: 10.2147/ANTI.S92190.


    78. Sahoo A, Khare S, Devanarayanan S, Jain P, Varadarajan R. (2015) Residue proximity information and protein model discrimination using saturation-suppressor  mutagenesis. Elife. doi: 10.7554/eLife.09532. PMID: 26716404; PMCID: PMC4758949.


    79. Malik A , Mallajosyula VV, Mishra NN, Varadarajan R and Gupta SK (2015) Generation and characterization of monoclonal antibodies specific to avian influenza H5N1 hemagglutinin protein. Monoclon. Antib. Immunodiagn. Immunother. doi: 10.1089/mab.2015.0047. PMID: 26683184.


    80. Mallajosyula VA, Citron M, Ferrara F, Temperton NJ, Liang X, Flynn JA and Varadarajan R (2015). Hemagglutinin sequence conservation guided stem immunogen design from influenza A H3 subtype. Front. Immunol. doi: 10.3389/fimmu.2015.00329. PMID: 26167164; PMCID: PMC4481277.


    81. Shembekar N, Mallajosyula VV, Chaudhary P, Upadhyay V, Varadarajan R, Gupta S.K. (2014) Humanized antibody neutralizing 2009 pandemic H1N1 virus. Biotechnol J. doi: 10.1002/biot.201400083. PMID: 25044602.


    82. Kesavardhana S, Varadarajan R. (2014) Stabilizing the native trimer of HIV-1 Env by destabilizing the heterodimeric interface of the gp41 post-fusion six helix bundle. J Virol. doi: 10.1128/JVI.00494-14. PMID: 24920800; PMCID: PMC4136328.


    83. Rathore U, Kesavardhana S, Mallajosyula VV, Varadarajan R. (2014) Immunogen Design for HIV-1 and Influenza. BBA - Proteins and Proteomics. doi: 10.1016/j.bbapap.2014.05.010. PMID: 24892211.


    84. Mallajosyula V, Citron M, Ferrara F, Lu X, Callahan C, Heidecker GJ; Sarma SP; Flynn JA, Temperton NJ, Liang X, Varadarajan R. (2014) Influenza hemagglutinin stem-fragment immunogen elicits broadly neutralizing antibodies and confers heterologous protection. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1402766111. PMID: 24927560; PMCID: PMC4078824.


    85. Tan KP, Khare S, Varadarajan R, Madhusudhan M.S. (2014) TSpred: a web server for the rational design of temperature-sensitive mutants. Nucleic Acids Res. 42(Web Server issue): W277-84: doi: 10.1093/nar/gku319. PMID: 24782523; PMCID: PMC4086094.


    86. Tripathi A, Dewan PC, Siddique SA, Varadarajan R. (2014) MazF induced growth inhibition and persister generation in Escherichia coli. J Biol Chem. doi: 10.1074/jbc.M113.510511. PMID: 24375411; PMCID: PMC3924284.


    87. Tripathi A and Varadarajan R. (2014) Residue specific contributions to stability and activity inferred from saturation mutagenesis and deep sequencing Curr Opin Struct Biol. doi: 10.1016/j.sbi.2013.12.001. PMID: 24721454.


    88. Jain PC and Varadarajan R. (2014) A rapid, efficient and economical inverse PCR-based method for generating a Site-Saturation Mutant library. Anal Biochem. doi: 10.1016/j.ab.2013.12.002. PMID: 24333246.


    89. Sridharamurthy R, Doraiswamy H, Patel S, Varadarajan R, and Natarajan V. (2013) Extraction of robust voids and pockets in proteins. EuroVis doi:10.2312/PE.EuroVisShort.EuroVisShort2013.067-071.


    90. Reichenwallner J, Chakour M, Indu S, Varadarajan R, Trommer WE. (2013) Maltose Binding Protein Is Partially Structured in Its Molten Globule State. Appl Magn Reson. doi: 10.1007/s00723-013-0468-4


    91. Tan KP, Nguyen T, Patel S, Varadarajan R, Madhusudhan M.S.(2013) Depth: A Web server to compute depth, cavity sizes, detect potential small-molecule binding cavities and predict the pKa of ionizable residues in proteins. Nucleic Acids Res. doi: 10.1093/nar/gkt503. PMID: 23766289; PMCID: PMC3692129.


    92. Singh P, Sharma L , Kulothungan S.R, Adkar BV, Prajapati RS, Ali PSS, Krishnan B, Varadarajan R. (2013) Effect of Signal Peptide on Stability and Folding of Escherichia coli Thioredoxin. PLoS One. doi: 10.1371/journal.pone.0063442. PMID: 23667620; PMCID: PMC3646739.


    93. Mallajosyula VV, Citron MP, Lu X, Ter Meulen J, Varadarajan R, Liang X. (2013) In vitro and in vivo characterization of designed immunogens derived from CD-helix of the stem of influenza hemagglutinin. Proteins. doi: 10.1002/prot.24317. PMID: 23625724.


    94. Bhattacharyya S, Singh P, Rathore U, Purwar M, Wagner D, Arendt H, Destefano J, Labranche CC, Montefiori D.C, Phogat S, Varadarajan R. (2013) Design of an E. coli expressed HIV-1 gp120 fragment immunogen that binds to b12 and induces broad and potent neutralizing antibodies. J Biol Chem. doi: 10.1074/jbc.M112.425959. PMID: 23430741; PMCID: PMC3617282.


    95. Shembekar N, Mallajosyula VV, Mishra A, Yeolekar L, Dhere R, Kapre S, Varadarajan R, Gupta S.K. (2013) Isolation of a High Affinity Neutralizing Monoclonal Antibody against 2009 Pandemic H1N1 Virus That Binds at the 'Sa' Antigenic Site. PLoS One. doi: 10.1371/journal.pone.0055516. PMID: 23383214; PMCID: PMC3561186.


    96. Bhattacharyya S and Varadarajan R. (2013) Packing in molten globules and native states. Curr Opin Struct Biol. doi: 10.1016/j.sbi.2012.10.010. PMID: 23270864.


    97. Gautam S, Dubey P, Varadarajan R, Gupta MN. (2012) Role of smart polymers in protein purification and refolding. Bioengineered. doi: 10.4161/bioe.21372. PMID: 22892577; PMCID: PMC3477697.


    98. Bommakanti G, Lu X, Citron M.P, Najar T.A, Heidecker G.J, Ter Meulen J, Varadarajan R, Liang X. (2012) Design of E. coli expressed stalk domain immunogens of H1N1 HA that protect mice from lethal challenge. J. Virol. doi: 10.1128/JVI.01429-12. PMID: 23015722; PMCID: PMC3503045.


    99. Hu X, Saha P, Chen X, Kim D, Devarasetty M, Varadarajan R, Jin MM. (2012) Cell Surface assembly of HIV gp41 six-helix bundles for facile, quantitative measurement of hetero-oligomeric interactions. J.Am. Chem. Soc. doi: 10.1021/ja301099s. PMID: 22888993; PMCID: PMC3731752.


    100. Gautam S, Dubey P, Singh P, Varadarajan R, Gupta MN. (2012) Simultaneous refolding and purification of recombinant rpoteins by macro-(affinity ligand) facilitated threel-phase partitioning (MLFTPP). Anal. Biochem. doi: 10.1016/j.ab.2012.07.028. PMID: 22885237.


    101. Tripathi A, Dewan PC, Barua B, Varadarajan R. (2012) An additional role for the ccd operon of F-plasmid as a transmissible persistence factor. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1121217109. PMID: 22802647; PMCID: PMC3412025.


    102. Saha P, Bhattacharyya S, Kesavardhana S, Miranda ER, Ali PS, Sharma D and Varadarajan R. (2012) Designed cyclic permutants of HIV-1 gp120: implications for envelope trimer structure and immunogen design. Biochemistry. doi: 10.1021/bi300003v. PMID: 22329717.


    103. Gautam S, Dubey P, Singh P, Kesavardana S, Varadarajan R and Gupta M.N. (2012) Smart Polymer Mediated Purification and Recovery of Active Proteins from Inclusion Bodies. Journal of Chromatography A. doi: 10.1016/j.chroma.2012.02.048. PMID: 22425208.


    104. Adkar BV, Tripathi A, Sahoo A, Bajaj K, Goswami D, Chakrabarti P, Swarnkar MK, Gokhale RS and Varadarajan R. (2012) Protein model discrimination using mutational sensitivity derived from deep sequencing. Structure. doi: 10.1016/j.str.2011.11.021. PMID: 22325784.


    105. Tan KP, Varadarajan R and Madhusudhan MS. (2011) DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins. Nucleic Acids Res. doi: 10.1093/nar/gkr356. PMID: 21576233; PMCID: PMC3125764.


    106. Saha P, Barua B, Bhattacharyya S, Balamurali MM, Schief WR, Baker D and Varadarajan R. (2011) Design and characterization of stabilized derivatives of human CD4D12 and CD4D1. Biochemistry. doi: 10.1021/bi200870r. PMID: 21827143.


    107. Indu S, Kochat V, Thakurela S, Ramakrishnan C, and Varadarajan R. (2011) Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets. Proteins. doi: 10.1002/prot.22878. PMID: 21058397.


    108. Haimann MM, Akdogan Y, Philipp R, Varadarajan R, Hinderberger D, and Trommer WE. (2011) Conformational changes of the chaperone SecB upon binding to a model substrate--bovine pancreatic trypsin inhibitor (BPTI). Biol Chem. doi: 10.1515/BC.2011.151. PMID: 21848506.


    109. Aggarwal V, Kulothungan SR, Balamurali MM, Saranya SR, Varadarajan R and Ainavarapu SR. (2011) Ligand-modulated parallel mechanical unfolding pathways of maltose-binding proteins. J Biol Chem. doi: 10.1074/jbc.M111.249045. PMID: 21659518; PMCID: PMC3151051.


    110. Indu S, Kumar ST, Thakurela S, Gupta M, Bhaskara RM, Ramakrishnan C and Varadarajan R. (2010) Disulfide conformation and design at helix N-termini. Proteins. doi: 10.1002/prot.22641. PMID: 19938155; PMCID: PMC7167797.


    111. Bommakanti G, Citron MP, Hepler RW, Callahan C, Heidecker GJ, Najar TA, Lu X, Joyce JG, Shiver JW, Casimiro DR, ter Meulen J, Liang X, and Varadarajan R. (2010) Design of an HA2-based Escherichia coli expressed influenza immunogen that protects mice from pathogenic challenge. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1007465107. PMID: 20615991; PMCID: PMC2922242.


    112. Bhattacharyya S, Rajan RE, Swarupa Y, Rathore U, Verma A, Udaykumar R, and Varadarajan R. (2010) Design of a non-glycosylated outer domain-derived HIV-1 gp120 immunogen that binds to CD4 and induces neutralizing antibodies. J Biol Chem. doi: 10.1074/jbc.M110.152272. PMID: 20558728; PMCID: PMC2930709.


    113. Kulothungan SR, Das M, Johnson M, Ganesh C, and Varadarajan R. (2009) Effect of Crowding Agents, Signal Peptide, and Chaperone SecB on the Folding and Aggregation of E. coli Maltose Binding Protein. Langmuir. doi: 10.1021/la900198h. PMID: 19358587.


    114. Krishnan B, Kulothungan SR, Patra AK, Udgaonkar J. B, and Varadarajan R. (2009) SecB-mediated protein export need not occur via kinetic partitioning. J Mol Biol. doi: 10.1016/j.jmb.2008.10.094. PMID: 19028503.


    115. Bhattacharya S, and Varadarajan R. (2009) Emerging trends at the interface of Chemistry and Biology: Applications to the design of human therapeutics. J Chem Sci, Indian Academy of Sciences, Platinum Jubilee P1, 1-11. 10.1007/s12039-010-0034-7.


    116. Raghava S, Barua B, Singh P. K, Das M, Madan L, Bhattacharyya S, Bajaj K, Gopal B, Varadarajan R, and Gupta M. N. (2008) Refolding and simultaneous purification by three-phase partitioning of recombinant proteins from inclusion bodies. Protein Sci. doi: 10.1110/ps.036939.108. PMID: 18780821; PMCID: PMC2578805.


    117. Raghava S, Aquil S, Bhattacharyya S, Varadarajan R, and Gupta M. N. (2008) Strategy for purifying maltose binding protein fusion proteins by affinity precipitation. J Chromatogr A. doi: 10.1016/j.chroma.2008.04.029. PMID: 18466911.


    118. Das A, Sood AK, Maiti PK, Das M, Varadarajan R, and Rao C. N. R. (2008) Binding of nucleobases with single-walled carbon nanotubes: Theory andexperiment. Chem Phys Lett. doi: 10.1016/j.cplett.2008.01.057.


    119. Bajaj K, Dewan PC, Chakrabarti P, Goswami D, Barua B, Baliga C, and Varadarajan R. (2008) Structural correlates of the temperature sensitive phenotype derived from saturation mutagenesis studies of CcdB. Biochemistry. doi: 10.1021/bi8014345. PMID: 19006334.


    120. Prajapati RS, Indu S, and Varadarajan R. (2007) Identification and thermodynamic characterization of molten globule states of periplasmic binding proteins. Biochemistry. doi: 10.1021/bi700577m. PMID: 17696409.


    121. Prajapati RS, Das M, Sreeramulu S, Sirajuddin M, Srinivasan S, Krishnamurthy V, Ranjani R, Ramakrishnan C, and Varadarajan R. (2007) Thermodynamic effects of proline introduction on protein stability. Proteins. doi: 10.1002/prot.21215. PMID: 17034035.


    122. MondalK, VijayRaghavan K, and Varadarajan R. (2007) Design and utility of temperature-sensitive Gal4 mutants for conditional gene expression in Drosophila. Fly (Austin). doi: 10.4161/fly.5251. PMID: 18836309.


    123. MondalK, Raghava S, Barua B, Varadarajan R and Gupta MN. (2007) Role of stimuli-sensitive polymers in protein refolding: alpha-amylase and CcdB (controller of cell division or death B) as model proteins. Langmuir. doi: 10.1021/la0616799. PMID: 17190487.


    124. Mondal K, Dastidar AG, Singh G, Madhusudhanan S, Gande SL, Vijayraghavan K, and Varadarajan R. (2007) Design and Isolation of Temperature-sensitive Mutants of Gal4 in Yeast and Drosophila. J Mol Biol. doi: 10.1016/j.jmb.2007.05.035. PMID: 17553522.


    125. Das M, Kobayashi M, Yamada Y, Sreeramulu S, Ramakrishnan C, Wakatsuki S, Kato R, and Varadarajan R. (2007) Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts. J Mol Biol. doi: 10.1016/j.jmb.2007.07.033. PMID: 17727880.


    126. Bajaj K, Madhusudhan MS, Adkar BV, Chakrabarti P, Ramakrishnan C, Sali A, and Varadarajan R. (2007) Stereochemical criteria for prediction of the effects of proline mutations on protein stability. PLoS Comput Biol. doi: 10.1371/journal.pcbi.0030241. PMID: 18069886; PMCID: PMC2134964.


    127. Prajapati RS, Sirajuddin M, Durani V, Sreeramulu S, and Varadarajan R. (2006) Contribution of cation-pi interactions to protein stability. Biochemistry. doi: 10.1021/bi061275f. PMID: 17154537.


    128. Chakraborty K, Durani V, Miranda E. R, Citron M, Liang X, Schleif W, Joyce JG, and Varadarajan R. (2006) Design of immunogens that present the crown of the HIV-1 V3 loop in a conformation competent to generate 447-52D-like antibodies. Biochem J. doi: 10.1042/BJ20060588. PMID: 16827663; PMCID: PMC1615908.


    129. Varadarajan R, Sharma D, Chakraborty K, Patel M, Citron M, Sinha P, Yadav R, Rashid U, Kennedy S, Eckert D, Geleziunas R, Bramhill D, Schleif W, Liang X, and Shiver J. (2005) Characterization of gp120 and its single-chain derivatives, gp120-CD4D12 and gp120-M9: implications for targeting the CD4i epitope in human immunodeficiency virus vaccine design. J Virol. doi: 10.1128/JVI.79.3.1713-1723.2005. PMID: 15650196; PMCID: PMC544110.


    130. Sharma D, Balamurali MM, Chakraborty K, Kumaran S, Jeganathan S, Rashid U,Ingallinella P, and Varadarajan R. (2005) Protein minimization of the gp120 binding region of human CD4. Biochemistry. doi: 10.1021/bi051120s. PMID: 16331979.


    131. Das M, Rao B. V, Ghosh S, and Varadarajan R. (2005) Attempts to delineate the relative contributions of changes in hydrophobicity and packing tochanges in stability of ribonuclease S mutants. Biochemistry. doi: 10.1021/bi050001+. PMID: 15823052.


    132. Chakraborty K, Thakurela S, Prajapati RS, Indu S, Ali PS, Ramakrishnan C, and Varadarajan R. (2005) Protein stabilization by introduction of cross-strand disulfides. Biochemistry. doi: 10.1021/bi050921s. PMID: 16262263.


    133. Chakraborty K, Shivakumar P, Raghothama S, and Varadarajan R. (2005) NMR structural analysis of a peptide mimic of the bridging sheet of HIV-1 gp120 in methanol and water. Biochem J. doi: 10.1042/BJ20050442. PMID: 15896194; PMCID: PMC1198937.


    134. Bajaj K, Chakrabarti P, and Varadarajan R. (2005) Mutagenesis-based definitions and probes of residue burial in proteins. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.0505089102. PMID: 16251276; PMCID: PMC1283427.


    135. Chakshusmathi G, Mondal K, Lakshmi GS, Singh G, Roy A, Ch RB, Madhusudhanan S, and Varadarajan R. (2004) Design of temperature-sensitive mutants solely from amino acid sequence. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.0402222101. PMID: 15148363; PMCID: PMC419533.


    136. Bhinge A, Chakrabarti P, Uthanumallian K, Bajaj K, Chakraborty K, and Varadarajan R. (2004) Accurate detection of protein:ligand binding sites using molecular dynamics simulations. Structure. doi: 10.1016/j.str.2004.09.005. PMID: 15530363.


    137. Beena K, Udgaonkar JB, and Varadarajan R. (2004) Effect of signal peptide on the stability and folding kinetics of maltose binding protein. Biochemistry. doi: 10.1021/bi0360509. PMID: 15035631.


    138. Bajaj K, Chakshusmathi G, Bachhawat-Sikder K, Surolia A, and Varadarajan R. (2004) Thermodynamic characterization of monomeric and dimeric forms of CcdB (controller of cell division or death B protein). Biochem J. doi: 10.1042/BJ20031528. PMID: 14763902; PMCID: PMC1224168.


    139. Prajapati RS, Lingaraju GM, Bacchawat K, Surolia A, and Varadarajan R. (2003) Thermodynamic effects of replacements of Pro residues in helix interiors of maltose-binding protein. Proteins. doi: 10.1002/prot.10488. PMID: 14635128.


    140. Padmakumar VC, and Varadarajan R. (2003) A gradient PCR-based screen for use in site-directed mutagenesis. Anal Biochem. doi: 10.1016/s0003-2697(02)00688-7. PMID: 12654318.


    141. Dani VS, Ramakrishnan C, and Varadarajan R. (2003) MODIP revisited: re-evaluation and refinement of an automated procedure for modeling of disulfide bonds in proteins. Protein Eng. doi: 10.1093/proeng/gzg024. PMID: 12702798.


    142. Rudresh JR, Dani V, Mitra A, Srivastava S, Sarma SP, Varadarajan R, and Ramakumar S. (2002) Structural consequences of replacement of an alpha-helical Pro residue in Escherichia coli thioredoxin. Protein Eng. doi: 10.1093/protein/15.8.627. PMID: 12364576.


    143. Chakshusmathi G, and Varadarajan R. (2002) Protein misfolding and inclusion body resolubilization. PINSA-A. doi: 10.1016/s0168-1656(02)00033-0. PMID: 12142139.


    144. Chakravarty S, and Varadarajan R. (2002) Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. Biochemistry. doi: 10.1021/bi025523t. PMID: 12069608.


    145. Chakravarty S, Bhinge A, and Varadarajan R. (2002) A procedure for detection and quantitation of cavity volumes proteins. Application to measure the strength of the hydrophobic driving force in protein folding. J Biol Chem. doi: 10.1074/jbc.M201373200. PMID: 12070144.


    146. Ratnaparkhi GS, and Varadarajan R. (2001) Osmolytes stabilize ribonuclease S by stabilizing its fragments S protein and S peptide to compact folding-competent states. J Biol Chem. doi: 10.1074/jbc.M101906200. PMID: 11373282.


    147. Panse VG, Beena K, Philipp R, Trommer WE, Vogel PD, and Varadarajan R. (2001) Electron spin resonance and fluorescence studies of the bound-state conformation of a model protein substrate to the chaperone SecB. J Biol Chem. doi: 10.1074/jbc.M104466200. PMID: 11435433.


    148. Ganesh C, Zaidi FN, Udgaonkar JB, and Varadarajan R. (2001) Reversible formation of on-pathway macroscopic aggregates during the folding of maltose binding protein. Protein Sci. doi: 10.1110/ps.8101. PMID: 11468360; PMCID: PMC2374092.


    149. Ratnaparkhi GS, and Varadarajan R. (2000) Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics. Biochemistry. doi: 10.1021/bi000775k. PMID: 11015216.


    150. Ratnaparkhi GS, Awasthi SK, Rani P, Balaram P, and Varadarajan R. (2000) Structural and thermodynamic consequences of introducing alpha-aminoisobutyric acid in the S peptide of ribonuclease S. ProteinEng. doi: 10.1093/protein/13.10.697. PMID: 11112508.


    151. Panse VG, Vogel P, Trommer WE, and Varadarajan R. (2000) A thermodynamic coupling mechanism for the disaggregation of a model peptide substrate by chaperone secB. J Biol Chem. doi:10.1074/jbc.275.25.18698.


    152. Panse VG, Swaminathan CP, Surolia A, and Varadarajan R. (2000) Thermodynamics of substrate binding to the chaperone SecB. Biochemistry. doi: 10.1021/bi992065o. PMID: 10694412.


    153. Panse VG, Swaminathan CP, Aloor JJ, Surolia A, and Varadarajan R. (2000) Unfolding thermodynamics of the tetrameric chaperone, SecB. Biochemistry. doi: 10.1021/bi992484l. PMID: 10694404.


    154. Chakravarty S, and Varadarajan R. (2000) Elucidation of determinants of protein stability through genome sequence analysis. FEBS Lett. doi: 10.1016/s0014-5793(00)01267-9. PMID: 10722847.


    155. Chakravarty S, Mitra N, Queitsch I, Surolia A, Varadarajan R, and Dubel S. (2000) Protein stabilization through phage display. FEBS Lett. doi: 10.1016/s0014-5793(00)01725-7. PMID: 10913631.


    156. Sheshadri S, Lingaraju G. M, and Varadarajan R. (1999) Denaturant mediated unfolding of both native and molten globule states of maltose binding protein are accompanied by large deltaCp's. Protein Sci. doi: 10.1110/ps.8.8.1689. PMID: 10452613; PMCID: PMC2144416.


    157. Ratnaparkhi GS, and Varadarajan R. (1999) X-ray crystallographic studies of the denaturation of ribonuclease S. Proteins. PMID: 10409822.


    158. Ghoshal AK, Swaminathan CP, Thomas CJ, Surolia A, and Varadarajan R. (1999) Thermodynamic and kinetic analysis of the Escherichia coli thioredoxin-C' fragment complementation system. Biochem J. PMID: 10215612; PMCID: PMC1220209.


    159. Ganesh C, and Varadarajan R. (1999) Human Myoglobin, VCH, Weinheim, Germany.


    160. Ganesh C, and Varadarajan R. (1999) The size dependence of protein folding thermodynamics, Indian Academy of Sciences and University Press, Hyderabad.


    161. Ganesh C, Eswar N, Srivastava S, Ramakrishnan C, and Varadarajan R. (1999) Prediction of the maximal stability temperature of monomeric globular proteins solely from amino acid sequence. FEBS Lett. doi: 10.1016/s0014-5793(99)00758-9. PMID: 10413090.


    162. Ganesh C, Banerjee A, Shah A, and Varadarajan R. (1999) Disordered N-terminal residues affect the folding thermodynamics and kinetics of maltose binding protein. FEBS Lett. doi: 10.1016/s0014-5793(99)00826-1. PMID: 10431828.


    163. Chakshusmathi G, Ratnaparkhi GS, Madhu PK, and Varadarajan R. (1999) Native-state hydrogen-exchange studies of a fragment complex can provide structural information about the isolated fragments. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.96.14.7899. PMID: 10393919; PMCID: PMC22159.


    164. Chakravarty S, and Varadarajan R. (1999) Residue depth: a novel parameter for the analysis of protein structure and stability. Structure. doi: 10.1016/s0969-2126(99)80097-5. PMID: 10425675.


    165. Chakrabarti A, Srivastava S, Swaminathan CP, Surolia A, and Varadarajan R. (1999) Thermodynamics of replacing an alpha-helical Pro residue in the P40S mutant of Escherichia coli thioredoxin. Protein Sci. doi: 10.1110/ps.8.11.2455. PMID: 10595549; PMCID: PMC2144191.


    166. Ratnaparkhi GS, Ramachandran S, Udgaonkar JB, and Varadarajan R. (1998) Discrepancies between the NMR and X-ray structures of uncomplexed barstar: analysis suggests that packing densities of protein structures determined by NMR are unreliable. Biochemistry. doi: 10.1021/bi972857n. PMID: 9578582.


    167. Panse VG, Udgaonkar JB, and Varadarajan R. (1998) SecB binds only to a late native-like intermediate in the folding pathway of barstar and not to the unfolded state. Biochemistry. doi: 10.1021/bi980777t. PMID: 9772175.


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