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Najar, TA and Khare, S and Varadarajan, R (2018) Rapid mapping of protein binding sites and conformational epitopes by coupling yeast surface display to chemical labeling and deep sequencing. [Book Chapter]
Raju, N and Trommer, WE and Varadarajan, R and Pause, VG and Beena, K (2004) Conformational changes and bound state conformation of maltose binding protein (MBP) upon interaction with the chaperone SecB: ESR and fluorescence studies. In: 48th Annual Meeting of the Biophysical Society, FEB 14-18, 2004, Baltimore, MD.
Bajaj, P and Bhasin, M and Varadarajan, R (2023) Molecular bases for strong phenotypic effects of single synonymous codon substitutions in the E. coli ccdB toxin gene. In: BMC Genomics, 24 (1).
Chattopadhyay, G and Ahmed, S and Srilatha, NS and Asok, A and Varadarajan, R (2023) Ter-Seq: A high-throughput method to stabilize transient ternary complexes and measure associated kinetics. In: Protein Science, 32 (1).
Bhowmick, J and Nag, M and Ghosh, P and Rajmani, RS and Chatterjee, R and Karmakar, K and Chandra, K and Chatterjee, J and Chakravortty, D and Varadarajan, R (2023) A CcdB toxin-derived peptide acts as a broad-spectrum antibacterial therapeutic in infected mice. In: EMBO Reports .
Kumar, N and Taily, IM and Singh, C and Kumar, S and Rajmani, RS and Chakraborty, D and Sharma, A and Singh, P and Thakur, KG and Varadarajan, R and Ringe, RP and Banerjee, P and Banerjee, I (2023) Identification of diphenylurea derivatives as novel endocytosis inIdentification 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 vivohibitors that demonstrate broad-spectrum activity against SARS-CoV-2 and influenza A virus both in vitro and in vivo. In: PLoS Pathogens, 19 (5).
Chandra, S and Manjunath, K and Asok, A and Varadarajan, R (2023) Mutational scan inferred binding energetics and structure in intrinsically disordered protein CcdA. In: Protein Science, 32 (3).
Khan, MS and Jakob, V and Singh, R and Rajmani, RS and Kumar, S and Lemoine, C and Kleanthous, H and Ringe, RP and Dubois, PM and Varadarajan, R (2023) Enhancing Immunogenicity of a Thermostable, Efficacious SARS-CoV-2 Vaccine Formulation through Oligomerization and Adjuvant Choice. In: Pharmaceutics, 15 (12).
Ahmed, S and Chattopadhyay, G and Manjunath, K and Bhasin, M and Singh, N and Rasool, M and Das, S and Rana, V and Khan, N and Mitra, D and Asok, A and Singh, R and Varadarajan, R (2022) Combining cysteine scanning with chemical labeling to map protein-protein interactions and infer bound structure in an intrinsically disordered region. In: Frontiers in Molecular Biosciences, 9 .
Chattopadhyay, G and Bhowmick, J and Manjunath, K and Ahmed, S and Goyal, P and Varadarajan, R (2022) Mechanistic insights into global suppressors of protein folding defects. In: PLoS Genetics, 18 (8).
Bajaj, P and Manjunath, K and Varadarajan, R (2022) Structural and functional determinants inferred from deep mutational scans. In: Protein Science, 31 (7).
Kar, U and Khaleeq, S and Garg, P and Bhat, M and Reddy, P and Vignesh, VS and Upadhyaya, A and Das, M and Chakshusmathi, G and Pandey, S and Dutta, S and Varadarajan, R (2022) Comparative Immunogenicity of Bacterially Expressed Soluble Trimers and Nanoparticle Displayed Influenza Hemagglutinin Stem Immunogens. In: Frontiers in Immunology, 13 .
Chattopadhyay, G and Bhasin, M and Ahmed, S and Priya Gosain, T and Ganesan, S and Das, S and Thakur, C and Chandra, N and Singh, R and Varadarajan, R (2022) Functional and Biochemical Characterization of the MazEF6 Toxin-Antitoxin System of Mycobacterium tuberculosis. In: Journal of Bacteriology, 204 (4).
Jansen van Vuren, P and McAuley, AJ and Kuiper, MJ and Singanallur, NB and Bruce, MP and Riddell, S and Goldie, S and Mangalaganesh, S and Chahal, S and Drew, TW and Blasdell, KR and Tachedjian, M and Caly, L and Druce, JD and Ahmed, S and Khan, MS and Malladi, SK and Singh, R and Pandey, S and Varadarajan, R and Vasan, SS (2022) Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice. In: Viruses, 14 (4).
Ahmed, S and Manjunath, K and Chattopadhyay, G and Varadarajan, R (2022) Identification of stabilizing point mutations through mutagenesis of destabilized protein libraries. In: Journal of Biological Chemistry, 298 (4).
Kanjo, K and Chattopadhyay, G and Malladi, SK and Singh, RK and Jayatheertha, S and Varadarajan, R (2022) Biophysical Correlates of Enhanced Immunogenicity of a Stabilized Variant of the Receptor Binding Domain of SARS-CoV-2. In: Journal of Physical Chemistry B .
Ahmed, S and Bhasin, M and Manjunath, K and Varadarajan, R (2022) Prediction of Residue-specific Contributions to Binding and Thermal Stability Using Yeast Surface Display. In: Frontiers in Molecular Biosciences, 8 .
Sahoo, A and Jones, AT and Cheedarla, N and Gangadhara, S and Roy, V and Styles, TM and Shiferaw, A and Walter, KL and Williams, LD and Shen, X and Ozorowski, G and Lee, W-H and Burton, S and Yi, L and Song, X and Qin, ZS and Derdeyn, CA and Ward, AB and Clements, JD and Varadarajan, R and Tomaras, GD and Kozlowski, PA and Alter, G and Amara, RR (2022) A clade C HIV-1 vaccine protects against heterologous SHIV infection by modulating IgG glycosylation and T helper response in macaques. In: Science immunology, 7 (73). eabl4102.
Ahmed, S and Khan, MS and Gayathri, S and Singh, R and Kumar, S and Patel, UR and Malladi, SK and Rajmani, RS and van Vuren, PJ and Riddell, S and Goldie, S and Girish, N and Reddy, P and Upadhyaya, A and Pandey, S and Siddiqui, S and Tyagi, A and Jha, S and Pandey, R and Khatun, O and Narayan, R and Tripathi, S and McAuley, AJ and Singanallur, NB and Vasan, SS and Ringe, RP and Varadarajan, R (2021) A Stabilized, Monomeric, Receptor Binding Domain Elicits High-Titer Neutralizing Antibodies Against All SARS-CoV-2 Variants of Concern. In: Frontiers in Immunology, 12 .
Mittal, N and Sengupta, N and Malladi, SK and Reddy, P and Bhat, M and Rajmani, RS and Sedeyn, K and Saelens, X and Dutta, S and Varadarajan, R (2021) Protective efficacy of recombinant influenza hemagglutinin ectodomain fusions. In: Viruses, 13 (9).
Malladi, SK and Patel, UR and Rajmani, RS and Singh, R and Pandey, S and Kumar, S and Khaleeq, S and Van Vuren, PJ and Riddell, S and Goldie, S and Gayathri, S and Chakraborty, D and Kalita, P and Pramanick, I and Agarwal, N and Reddy, P and Girish, N and Upadhyaya, A and Khan, MS and Kanjo, K and Bhat, M and Mani, S and Bhattacharyya, S and Siddiqui, S and Tyagi, A and Jha, S and Pandey, R and Tripathi, S and Dutta, S and McAuley, AJ and Singanallur, NB and Vasan, SS and Ringe, RP and Varadarajan, R (2021) Immunogenicity and Protective Efficacy of a Highly Thermotolerant, Trimeric SARS-CoV-2 Receptor Binding Domain Derivative. In: ACS Infectious Diseases .
Bhasin, M and Varadarajan, R (2021) Prediction of Function Determining and Buried Residues Through Analysis of Saturation Mutagenesis Datasets. In: Frontiers in Molecular Biosciences, 8 .
Malladi, SK and Singh, R and Pandey, S and Gayathri, S and Kanjo, K and Ahmed, S and Khan, MS and Kalita, P and Girish, N and Upadhyaya, A and Reddy, P and Pramanick, I and Bhasin, M and Mani, S and Bhattacharyya, S and Joseph, J and Thankamani, K and Raj, VS and Dutta, S and Singh, R and Nadig, G and Varadarajan, R (2021) Design of a highly thermotolerant, immunogenic SARS-CoV-2 spike fragment. In: Journal of Biological Chemistry, 296 .
Chandra, S and Chattopadhyay, G and Varadarajan, R (2021) Rapid Identification of Secondary Structure and Binding Site Residues in an Intrinsically Disordered Protein Segment. In: Frontiers in Genetics, 12 .
Datta, R and Chowdhury, RR and Manjunath, K and Hanna, LE and Varadarajan, R (2020) A facile method of mapping HIV-1 neutralizing epitopes using chemically masked cysteines and deep sequencing. In: Proceedings of the National Academy of Sciences of the United States of America, 117 (47). pp. 29584-29594.
Malladi, SK and Schreiber, D and Pramanick, I and Sridevi, MA and Goldenzweig, A and Dutta, S and Fleishman, SJ and Varadarajan, R (2020) One-step sequence and structure-guided optimization of HIV-1 envelope gp140. In: Current Research in Structural Biology, 2 . pp. 45-55.
Mallajosyula, VVA and Swaroop, S and Varadarajan, R (2020) Influenza Hemagglutinin Head Domain Mimicry by Rational Design. In: Protein Journal, 39 (5). pp. 434-448.
Nickolaus, C and Vargas, C and Reichenwallner, J and Chakour, M and Selmke, B and Chakraborty, R and Varadarajan, R and Keller, S and Trommer, WE (2020) The Molten Globule State of Maltose-Binding Protein: Structural and Thermodynamic Characterization by EPR Spectroscopy and Isothermal Titration Calorimetry. In: Applied Magnetic Resonance, 51 (9-10). pp. 877-886.
Das, R and Datta, R and Varadarajan, R (2020) Probing the Structure of the HIV-1 Envelope Trimer Using Aspartate Scanning Mutagenesis. In: Journal of Virology, 94 (21).
Sharma, A and Chattopadhyay, G and Chopra, P and Bhasin, M and Thakur, C and Agarwal, S and Ahmed, S and Chandra, N and Varadarajan, R and Singh, R (2020) VapC21 Toxin Contributes to Drug-Tolerance and Interacts With Non-cognate VapB32 Antitoxin in Mycobacterium tuberculosis. In: Frontiers in Microbiology, 11 .
Agarwal, S and Sharma, A and Bouzeyen, R and Deep, A and Sharma, H and Mangalaparthi, KK and Datta, KK and Kidwai, S and Gowda, H and Gowda, H and Varadarajan, R and Sharma, RD and Thakur, KG and Singh, R (2020) VapBC22 toxin-antitoxin system from Mycobacterium tuberculosis is required for pathogenesis and modulation of host immune response. In: Science Advances, 6 (23).
Aghera, NK and Prabha, J and Tandon, H and Chattopadhyay, G and Vishwanath, S and Srinivasan, N and Varadarajan, R (2020) Mechanism of CcdA-Mediated Rejuvenation of DNA Gyrase. In: Structure, 28 (5). 562-572.e4.
Tripathi, A and Swaroop, S and Varadarajan, R (2019) Molecular Determinants of Temperature-Sensitive Phenotypes. In: Biochemistry, 58 (13). pp. 1738-1750.
Baliga, C and Selmke, B and Worobiew, I and Borbat, P and Sarma, SP and Trommer, WE and Varadarajan, R and Aghera, N (2019) CcdB at pH 4 Forms a Partially Unfolded State with a Dry Core. In: Biophysical Journal, 116 (5). pp. 807-817.
Bhattacharya, S and Varadarajan, R (2010) Emerging trends at the interface of chemistry and biology: Applications to the design of human therapeutics. In: Journal of Chemical Sciences, 122 (2). pp. 97-107.
Das, Anindya and Sood, AK and Maiti, Prabal K and Das, Mili and Varadarajan, R and Rao, CNR (2008) Binding of nucleobases with single-walled carbon nanotubes: Theory and experiment. In: Chemical Physics Letters, 453 (4-6). pp. 266-273.
Bhinge, A and Chakrabarti, P and Uthanumallian, K and Bajaj, K and Chakraborty, K and Varadarajan, R (2004) Accurate detection of protein:ligand binding sites using molecular dynamics simulations. In: Structure, 12 (11). pp. 1989-1999.
Beena, K and Udgaonkar, Jayant B and Varadarajan, R (2004) Effect of Signal Peptide on the Stability and Folding Kinetics of Maltose Binding Protein. In: Biochemistry, 43 (12). pp. 3608-3619.
Rudresh, * and Jain, Rinku and Dani, Vardhan and Mitra, Ashima and Srivastava, Sarika and Sarma, Siddhartha P and Varadarajan, R and Ramakumar, S (2002) Structural consequences of replacement of an \alpha-helical Pro residue in Escherichia coli thioredoxin. In: Protein Engineering, 15 (8). pp. 627-633.
Ratnaparkhi, Girish S and Varadarajan, R (2001) Osmolytes stabilize Ribonuclease S by stabilizing its fragments S protein and S peptide to compact folding-competent states. In: Journal of Biological Chemistry, 276 (31). pp. 28789-28798.
Ratnaparkhi, Girish S 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. In: Biochemistry, 39 (40). pp. 12365-12374.
Ratnaparkhi, Girish S and Awasthi, Satish Kumar and Rani, P and Balaram, P and Varadarajan, R (2000) Structural and thermodynamic consequences of introducing alpha-aminoisobutyric acid in the S peptide of ribonuclease S. In: Protein Engineering, 13 (10). pp. 697-702.
Ratnaparkhi, Girish S 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. In: Biochemistry, 39 (40). pp. 12365-12374.
Chakrabarti, A and Srivastava, S and Swaminathan, CP and Surolia, A and Varadarajan, R (1999) Thermodynamics of replacing an alpha-helical Pro residue in the P40S mutant of Escherichia coli thioredoxin. In: Protein Science, 8 (11). pp. 2455-2459.
Sheshadri, S and Lingaraju, GM and Varadarajan, R (1999) Denaturant mediated unfolding of both native and molten globule states of maltose binding protein are accompanied by large $\Delta Cp^'s$. In: Protein Science, 8 (8). pp. 1689-1695.
Ratnaparkhi, Girish S and Varadarajan, R (1999) X-ray Crystallographic Studies of the Denaturation of Ribonuclease S. In: Proteins:Structure, Function, and Genetics, 36 (3). pp. 282-294.
Sheshadri, S and Lingaraju, GM and Varadarajan, R (1999) Denaturant mediated unfolding of both native and molten globule states of maltose binding protein are accompanied by large [Delta]Cp's. In: Protein Science, 8 (8). pp. 1689-1695.
Ratnaparkhi, Girish S and Ramachandran, S and Udgaonkar, Jayant B 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. In: Biochemistry, 37 (19). pp. 6958-6966.
Ratnaparkhi, Girish S and Varadarajan, R (1997) Structural studies of protein unfolding. In: Current Science (Bangalore), 72 (11). pp. 826-830.
