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Number of items: 73.

Conference Proceedings

Patel, Siddharth and Indu, S and Ramakrishnan, C and Varadarajan, Raghavan (2013) PROTEIN DISULFIDE ANALYSIS AND DESIGN. In: Conference on Biomolecular Forms and Functions - A Celebration of 50 Years of the Ramachandran Map, JAN, 2013, Indian Inst Sci, Bangalore, INDIA, pp. 296-311.

Journal Article

Rathore, Ujjwal and Kesavardhana, Sannula and Mallajosyula, Vamsee Aditya V and Varadarajan, Raghavan (2014) Immunogen design for HIV-1 and influenza. In: BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1844 (11, SI). pp. 1891-1906.

Mallajosyula, Vamsee VA and Citron, Michael and Ferrara, Francesca and Lu, Xianghan and Callahan, Cheryl and Heidecker, Gwendolyn J and Sarma, Siddhartha P and Flynn, Jessica A and Temperton, Nigel J and Liang, Xiaoping and Varadarajan, Raghavan (2014) Influenza hemagglutinin stem-fragment immunogen elicits broadly neutralizing antibodies and confers heterologous protection. In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111 (25). E2514-E2523.

Tripathi, Arti and Dewan, Pooja C and Siddique, Shahbaz A and Varadarajan, Raghavan (2014) MazF-induced Growth Inhibition and Persister Generation in Escherichia coli. In: JOURNAL OF BIOLOGICAL CHEMISTRY, 289 (7). pp. 4191-4205.

Tripathi, Arti and Varadarajan, Raghavan (2014) Residue specific contributions to stability and activity inferred from saturation mutagenesis and deep sequencing. In: CURRENT OPINION IN STRUCTURAL BIOLOGY, 24 . pp. 63-71.

Kesavardhana, Sannula and Varadarajan, Raghavan (2014) Stabilizing the Native Trimer of HIV-1 Env by Destabilizing the Heterodimeric Interface of the gp41 Postfusion Six-Helix Bundle. In: JOURNAL OF VIROLOGY, 88 (17). pp. 9590-9604.

Tan, Kuan Pern and Khare, Shruti and Varadarajan, Raghavan and Madhusudhan, Mallur Srivatsan (2014) TSpred: a web server for the rational design of temperature-sensitive mutants. In: NUCLEIC ACIDS RESEARCH, 42 (W1). W277-W284.

Jain, Pankaj C and Varadarajan, Raghavan (2014) A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library. In: ANALYTICAL BIOCHEMISTRY, 449 . pp. 90-98.

Tan, Kuan Pern and Nguyen, Thanh Binh and Patel, Siddharth and Varadarajan, Raghavan and Madhusudhan, MS (2013) Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pK(a) of ionizable residues in proteins. In: Nucleic Acids Research, 41 (W1). W314-W321.

Singh, Pranveer and Sharma, Likhesh and Kulothungan, Rajendra S and Adkar, Bharat V and Prajapati, Ravindra Singh and Ali, Shaik Syed P and Krishnan, Beena and Varadarajan, Raghavan (2013) Effect of signal peptide on stability and folding of escherichia coli thioredoxin. In: PLOS One, 8 (5). e63442_1-e63442_14.

Bhattacharyya, Sanchari and Singh, Pranveer and Rathore, Ujjwal and Purwar, Mansi and Wagner, Denise and Arendt, Heather and DeStefano, Joanne and LaBranche, Celia C and Montefiori, David C and Phogat, Sanjay and Varadarajan, Raghavan (2013) Design of an Escherichia coli expressed HIV-1 gp120 fragment Immunogen that binds to b12 and induces broad and potent neutralizing antibodies. In: Journal of Biological Chemistry, 288 (14). pp. 9815-9825.

Mallajosyula, Vamsee Aditya V and Citron, Michael and Lu, Xianghan and ter Meulen, Jan and Varadarajan, Raghavan and Liang, Xiaoping (2013) In vitro and in vivo characterization of designed immunogens derived from the CD-helix of the stem of influenza hemagglutinin. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81 (10). pp. 1759-1775.

Shembekar, Nachiket and Mallajosyula, Vamsee Aditya V and Mishra, Arpita and Yeolekar, Leena and Dhere, Rajeev and Kapre, Subhash and Varadarajan, Raghavan and Gupta, Satish Kumar (2013) Isolation of a High Affinity Neutralizing Monoclonal Antibody against 2009 Pandemic H1N1 Virus That Binds at the `Sa' Antigenic Site. In: PLOS ONE, 8 (1).

Reichenwallner, Joerg and Chakour, Mohammed and Indu, S and Varadarajan, Raghavan and Trommer, Wolfgang E (2013) Maltose Binding Protein Is Partially Structured in Its Molten Globule State. In: APPLIED MAGNETIC RESONANCE, 44 (8). pp. 983-995.

Bhattacharyya, Sanchari and Varadarajan, Raghavan (2013) Packing in molten globules and native states. In: CURRENT OPINION IN STRUCTURAL BIOLOGY, 23 (1). pp. 11-21.

Tripathi, Arti and Dewan, Pooja C and Barua, Bipasha and Varadarajan, Raghavan (2012) Additional role for the ccd operon of F-plasmid as a transmissible persistence factor. In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109 (31). pp. 12497-12502.

Gautam, Saurabh and Dubey, Priyanka and Singh, Pranveer and Kesavardhana, S and Varadarajan, Raghavan and Gupta, Munishwar N (2012) Smart polymer mediated purification and recovery of active proteins from inclusion bodies. In: Journal of Chromatography A, 1235 . pp. 10-25.

Saha, Piyali and Bhattacharyya, Sanchari and Kesavardhana, Sannula and Miranda, Edward Roshan and Ali, Shaik Syed P and Sharma, Deepak and Varadarajan, Raghavan (2012) Designed Cyclic Permutants of HIV-1 gp120: Implications for Envelope Trimer Structure and Immunogen Design. In: Biochemistry, 51 (9). pp. 1836-1847.

Adkar, Bharat V and Tripathi, Arti and Sahoo, Anusmita and Bajaj, Kanika and Goswami, Devrishi and Chakrabarti, Purbani and Swarnkar, Mohit K and Gokhale, Rajesh S and Varadarajan, Raghavan (2012) Protein Model Discrimination Using Mutational Sensitivity Derived from Deep Sequencing. In: Structure, 20 (2). pp. 371-381.

Hu, Xuebo and Saha, Piyali and Chen, Xiaoyue and Kim, Dogeun and Devarasetty, Mahesh and Varadarajan, Raghavan and Jin, Moonsoo M. (2012) Cell Surface Assembly of HIV gp41 Six-Helix Bundles for Facile, Quantitative Measurements of Hetero-oligomeric Interactions. In: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134 (36). pp. 14642-14645.

Gautam, Saurabh and Dubey, Priyanka and Singh, Pranveer and Varadarajan, Raghavan and Gupta, Munishwar N (2012) Simultaneous refolding and purification of recombinant proteins by macro-(affinity ligand) facilitated three-phase partitioning. In: Analytical Biochemistry, 430 (1). pp. 56-64.

Saha, Piyali and Barua, Bipasha and Bhattacharyya, Sanchari and Balamurali, MM and Schief, William R and Baker, David and Varadarajan, Raghavan (2011) Design and Characterization of Stabilized Derivatives of Human CD4D12 and CD4D1. In: Biochemistry, 50 (37). pp. 7891-7900.

Aggarwal, Vasudha and Kulothungan, Rajendra S and Balamurali, MM and Saranya, SR and Varadarajan, Raghavan and Ainavarapu, Sri Rama Koti (2011) Ligand-modulated Parallel Mechanical Unfolding Pathways of Maltose-binding Proteins. In: Journal of Biological Chemistry, 286 (32). pp. 28056-28065.

Tan, Kuan Pern and Varadarajan, Raghavan and Madhusudhan, MS (2011) DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins. In: Nucleic Acids Research, 39 (2). W242-W248.

Indu, S and Kochat, V and Thakurela, S and Ramakrishnan, C and Varadarajan, Raghavan (2011) Conformational analysis and design of cross-strand disulfides in antiparallel beta-sheets. In: Proteins: Structure, Function, and Genetics, 79 (1). pp. 244-260.

Haimann, Michaela M and Akdogan, Yasar and Philipp, Reinhard and Varadarajan, Raghavan and Hinderberger, Dariush and Trommer, Wolfgang E (2011) Conformational changes of the chaperone SecB upon binding to a model substrate - bovine pancreatic trypsin inhibitor (BPTI). In: Biological Chemistry, 392 (10). pp. 849-858.

Bhattacharyya, Sanchari and Rajan, Roshan Elizabeth and Swarupa, Yalla and Rathore, Ujjwal and Verma, Anjali and Udaykumar, Ranga and Varadarajan, Raghavan (2010) Design of a Non-glycosylated Outer Domain-derived HIV-1 gp120 Immunogen That Binds to CD4 and Induces Neutralizing Antibodies. In: Journal of Biological Chemistry, 285 (35). pp. 27100-27110.

Bommakanti, Gayathri and Citron, Michael P and Hepler, Robert W and Callahan, Cheryl and Heidecker, Gwendolyn J and Najar, Tariq Ahmad and Lu, Xianghan and Joyce, Joseph G and Shiver, John W and Casimiro, Danilo R and ter Meulen, Jan and Liang, Xiaoping and Varadarajan, Raghavan (2010) Design of an HA2-based Escherichia coli expressed influenza immunogen that protects mice from pathogenic challenge. In: Proc Natl Acad Sci Unit States Am, 107 (31). pp. 13701-13706.

Indu, S and Kumar, Senthil T and Thakurela, Sudhir and Gupta, Mansi and Bhaskara, Ramachandra M and Ramakrishnan, C and Varadarajan, Raghavan (2010) Disulfide conformation and design at helix N-termini. In: Proteins: Structure, Function, and Genetics, 78 (5). pp. 1228-1242.

Kulothungan, Rajendra S and Das, Mili and Johnson, Madrid and Ganesh, Chandramowli and Varadarajan, Raghavan (2009) Effect of Crowding Agents, Signal Peptide, and Chaperone SecB on the Folding and Aggregation of E. coli Maltose Binding Protein. In: Langmuir, 25 (12). pp. 6637-6648.

Krishnan, Beena and Kulothungan, Rajendra S and Patra, Ashish K and Udgaonkar, Jayant B and Varadarajan, Raghavan (2009) SecB-Mediated Protein Export Need Not Occur via Kinetic Partitioning. In: Journal of Molecular Biology, 385 (4). pp. 1243-1256.

Bajaj, Kanika and Dewan, Pooja C and Chakrabarti, Purbani and Goswami, Devrishi and Barua, Bipasha and Baliga, Chetana and Varadarajan, Raghavan (2008) Structural Correlates of the Temperature Sensitive Phenotype Derived from Saturation Mutagenesis Studies of CcdB. In: Biochemistry, 47 (49). pp. 12964-12973.

Raghava, Smita and Barua, Bipasha and Singh, Pradeep K and Das, Mili and Madan, Lalima and Bhattacharyya, Sanchari and Bajaj, Kanika and Gopal, B and Varadarajan, Raghavan and Gupta, Munishwar N (2008) Refolding and simultaneous purification by three-phase partitioning of recombinant proteins from inclusion bodies. In: Protein Science, 17 (11). pp. 1987-1997.

Raghava, Smita and Aquil, Samina and Bhattacharyya, Sanchari and Varadarajan, Raghavan and Gupta, Munishwar N (2008) Strategy for purifying maltose binding protein fusion proteins by affinity precipitation. In: Journal of Chromatography A, 1194 (1). pp. 90-95.

Bajaj, Kanika and Madhusudhan, MS and Adkar, Bharat V and Chakrabarti, Purbani and Ramakrishnan, C and Sali, Andrej and Varadarajan, Raghavan (2007) Stereochemical Criteria for Prediction of the Effects of Proline Mutations on Protein Stability. In: PLoS Computational Biology, 3 (12). pp. 2465-2475.

Mondal, Kajari and VijayRaghavan, K and Varadarajan, Raghavan (2007) Design and Utility of Temperature-Sensitive Gal4 Mutants for Conditional Gene Expression in Drosophila. In: Fly, 1 (5). pp. 282-286.

Das, Mili and Kobayashi, Masanori and Yamada, Yusuke and Sreeramulu, Sridhar and Ramakrishnan, C and Wakatsuki, Soichi and Kato, Ryuichi and Varadarajan, Raghavan (2007) Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts. In: Journal of Molecular Biology, 372 (5). pp. 1278-1292.

Prajapati, Ravindra Singh and Indu, S and Varadarajan, Raghavan (2007) Identification and thermodynamic characterization of molten globule states of periplasmic binding proteins. In: Biochemistry, 46 (36). pp. 10339-10352.

Mondal, Kajari and Dastidar, Antara Ghosh and Singh, Guramrit and Madhusudhanan, S and Gande, Santosh Lakshmi and VijayRaghavan, K and Varadarajan, Raghavan (2007) Design and Isolation of Temperature-sensitive Mutants of Gal4 in Yeast and Drosophila. In: Journal of Molecular Biology, 370 (5). pp. 939-950.

Mondal, Kalyani and Raghava, Smita and Barua, Bipasha and Varadarajan, Raghavan and Gupta, Munishwar N (2007) Role of Stimuli-Sensitive Polymers in Protein Refolding: \alpha-Amylase and CcdB (Controller of Cell Division or Death B) as Model Proteins. In: Langmuir, 23 (1). pp. 70-75.

Prajapati, Ravindra S and Sirajuddin, Minhajuddin and Durani, Venuka and Sreeramulu, Sridhar and Varadarajan, Raghavan (2006) Contribution of Cation-\pi Interactions to Protein Stability. In: Biochemistry, 45 (50). pp. 15000-15010.

Chakraborty, Kausik and Durani, Venuka and Roshan Miranda, Edward and Citron, Michael and Liang, Xiaoping and Schleif, William and Joyce, Joseph G and Varadarajan, Raghavan (2006) Design of immunogens that present the crown of the HIV-1 V3 loop in a conformation competent to generate 447-52D-like antibodies. In: Biochemical Journal, 399 . pp. 483-491.

Bajaj, Kanika and Chakrabarti, Purbani and Varadarajan, Raghavan (2005) Mutagenesis-based definitions and probes of residue burial in proteins. In: Proceedings of The National Academy of Sciences of The United States of America, 102 (45). pp. 16221-16226.

Chakraborty, Kausik and Shivakumar, P and Raghothama, S and Varadarajan, Raghavan (2005) NMR structural analysis of a peptide mimic of the bridging sheet of HIV-1 gp120 in methanol and water. In: Biochemical Journal, 390 (Part 2). pp. 573-581.

Das, Mili and Rao, Bharathi Vasudeva and Ghosh, Sanjukta and Varadarajan, Raghavan (2005) Attempts to Delineate the Relative Contributions of Changes in Hydrophobicity and Packing to Changes in Stability of Ribonuclease S Mutants. In: Biochemistry, 44 (15). pp. 5923-5930.

Varadarajan, Raghavan and Sharma, Deepak and Chakraborty, Kausik and Patel, Mayuri and Citron, Michael and Sinha, Prem and Yadav, Ramkishor and Rashid, Umar and Kennedy, Sarah and Eckert, Debra and Geleziunas, Romas and Bramhill, David and Schleif, William and Liang, Xiaoping and Shiver, John (2005) Characterization of gp120 and its Single-Chain Derivatives, $gp120-CD4_D_1_2$ and gp120-M9: Implications for Targeting the $CD4_i$ Epitope in Human Immunodeficiency Virus Vaccine Design. In: Journal of Virology, 79 (3). pp. 1713-1723.

Sharma, Deepak and Balamurali, MM and Chakraborty, Kausik and Kumaran, Sowmini and Jeganathan, Sadasivam and Rashid, Umar and Ingallinella, Paolo and Varadarajan, Raghavan (2005) Protein Minimization of the gp120 Binding Region of Human CD4 \dagger. In: Biochemistry, 44 (49). pp. 16192-16202.

Chakraborty, Kausik and Thakurela, Sudhir and Prajapati, Ravindra Singh and Indu, S and Ali, Shaik Syed P and Ramakrishnan, C and Varadarajan, Raghavan (2005) Protein Stabilization by Introduction of Cross-Strand Disulfides. In: Biochemistry, 44 (44). pp. 14638-14646.

Chakshusmathi, Ghadiyaram and Mondal, Kajari and Lakshmi, Santosh G and Singh, Guramrit and Roy, Ankita and Babu, Ravindra Ch and Madhusudhanan, S and Varadarajan, Raghavan (2004) Design of temperature-sensitive mutants solely from amino acid sequence. In: Proceedings of the National Academy of Sciences, 101 (21). pp. 7925-7930.

Bajaj, Kanika and Chakshumathi, Ghadiyaram and Bachhawat-Sikder, Kiran and Surolia, Avadhesha and Varadarajan, Raghavan (2004) Thermodynamic characterization of monomeric and dimeric forms of CcdB (controller of cell division or death B protein). In: Biochemical Journal, 380 (2). 409–417.

Padmakumar, VC and Varadarajan, Raghavan (2003) A gradient PCR-based screen for use in site-directed mutagenesis. In: Analytical Biochemistry, 314 (2). pp. 310-315.

Dani, Vardhan S and Ramakrishnan, C and Varadarajan, Raghavan (2003) MODIP revisited: re-evaluation and refinement of an automated procedure for modeling of disulfide bonds in proteins. In: Protein Engineering,, 16 (3). pp. 187-193.

Prajapati, RS and Lingaraju, GM and Bacchawat, Kiran and Surolia, Avadhesha and Varadarajan, Raghavan (2003) Thermodynamic Effects of Replacements of Pro Residues in Helix Interiors of Maltose-Binding Protein. In: Proteins: Structure, Function, and Genetics, 53 (4). pp. 863-871.

Chakravarty, Suvobrata and Bhinge, Akshay and Varadarajan, Raghavan (2002) A Procedure for Detection and Quantitation of Cavity Volumes in Proteins. In: Journal of Biological Chemistry, 277 (35). pp. 31345-31353.

Chakravarty, Suvobrata and Varadarajan, Raghavan (2002) Elucidation of Factors Responsible for Enhanced Thermal Stability of Proteins: A Structural Genomics Based Study. In: Biochemistry, 41 (25). pp. 8152-8161.

Chakravarty, Suvobrata and Bhinge, Akshay and Varadarajan, Raghavan (2002) A procedure for detection and quantitation of cavity volumes in proteins. Application to measure the strength of the hydrophobic driving force in protein folding. In: Journal of Biological Chemistry, 277 (35). pp. 31345-31353.

Panse, Vikram G and Beena, K and Philipp, Reinhard and Trommer, Wolfgang E and Vogel, Pia D and Varadarajan, Raghavan (2001) Electron Spin Resonance and Fluorescence Studies of the Bound-state Conformation of a Model Protein Substrate to the Chaperone SecB. In: Journal of Biological Chemistry, 276 (36). pp. 33681-33688.

Ganesh, C and Zaidi, Faisal N and Udgaonkar, Jayant B and Varadarajan, Raghavan (2001) Reversible formation of on-pathway macroscopic aggregates during the folding of maltose binding protein. In: Protein Science, 10 (8). 1635 -1644.

Chakravarty, Suvobrata and Mitra, Nivedita and Queitsch, Iris and Surolia, Avadhesha and Varadarajan, Raghavan and Dubel, Stefan (2000) Protein stabilization through phage display. In: FEBS Letters, 476 (3). pp. 296-300.

Panse, Vikram G and Vogel, Pia and Trommer, Wolfgang E and Varadarajan, Raghavan (2000) A Thermodynamic Coupling Mechanism for the Disaggregation of a Model Peptide Substrate by Chaperone SecB. In: Journal of Biological Chemistry, 275 (25). pp. 18698-18703.

Chakravarty, Suvobrata and Varadarajan, Raghavan (2000) Elucidation of determinants of protein stability through genome sequence analysis. In: FEBS Letters, 470 (1). pp. 65-69.

Panse, Vikram G and Swaminathan, Chittor P and Aloor, Jim J and Surolia, Avadhesha and Varadarajan, Raghavan (2000) Unfolding Thermodynamics of the Tetrameric Chaperone, SecB. In: Biochemistry, 39 (9). 2362 -2369.

Panse, Vikram G and Swaminathan, Chittoor P and Surolia, Avadhesha and Varadarajan, Raghavan (2000) Thermodynamics of Substrate Binding to the Chaperone SecB. In: Biochemistry, 39 (9). 2420 -2427.

Ganesh, C and Banerjee, Antara and Shah, Aseema and Varadarajan, Raghavan (1999) Disordered N-terminal residues affect the folding thermodynamics and kinetics of maltose binding protein. In: FEBS Letters, 454 (3). pp. 307-311.

Ganesh, C and Eswar, Narayanan and Srivastava, Sarika and Ramakrishnan, Chandrasekharan and Varadarajan, Raghavan (1999) Prediction of the maximal stability temperature of monomeric globular proteins solely from amino acid sequence. In: FEBS Letters, 454 (1-2). pp. 31-36.

Chakravarty, Suvobrata and Varadarajan, Raghavan (1999) Residue depth: A novel parameter for the analysis of protein structure and stability. In: Structure, 7 (7). pp. 723-732.

Ghoshal, Alokesh K and Swaminathan, Chittoor P and Thomas, Celestine J and Surolia, Avadhesha and Varadarajan, Raghavan (1999) Thermodynamic and kinetic analysis of the Escherichia coli thioredoxin-C fragment complementation system. In: Biochemical Journal, 339 . pp. 721-727.

Panse, Vikram G and Udgaonkar, Jayant B and Varadarajan, Raghavan (1998) SecB binds only to a late native-like intermediate in the folding pathway of barstar and not to the unfolded state. In: Biochemistry, 37 (41). pp. 14477-14483.

Ganesh, C and Shah, Aseema N and Swaminathan, CP and Surolia, Avadhesha and Varadarajan, Raghavan (1997) Thermodynamic characterization of the reversible, two-state unfolding of maltose binding protein, a large two-domain protein. In: Biochemistry, 36 (16). pp. 5020-5028.

Varadarajan, Raghavan and Nagarajaram, HA and Ramakrishnan, C (1996) A procedure for the prediction of temperature-sensitive mutants of a globular protein based solely on the amino acid sequence. In: Proceedings of The National Academy of Sciences of The United States of America, 93 (24). pp. 13908-13913.

Nadig, Gautham and Ratnaparkhi, Girish S and Varadarajan, Raghavan and Vishveshwara, Saraswathi (1996) Dynamics of ribonuclease A and ribonuclease S: Computational and experimental studies. In: Protein Science, 05 (10). pp. 2104-2114.

Thomson, James and Ratnaparkhi, Girish S and Varadarajan, Raghavan and Sturtevant, Julian M and Richards, Frederic M (1994) Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S. In: Biochemistry, 33 (28). pp. 8587-8593.

Editorials/Short Communications

Rathore, Ujjwal and Saha, Piyali and Kesavardhana, Sannula and Kumar, Aditya A and Mascola, John R and Varadarajan, Raghavan (2014) N-linked Glycosylation of HIV-1 core gp120 is Not Required for Native Trimer Formation or Viral Infectivity. In: PROTEIN SCIENCE, 23 (1).

This list was generated on Fri Nov 28 18:41:57 2014 IST.