Strategy for purifying maltose binding protein fusion proteins by affinity precipitation (2008)
Raghava, Smita, Aquil, Samina, Bhattacharyya, Sanchari, Varadarajan, Raghavan, Gupta, Munishwar N
The maltose binding protein (MBP) affinity tag has been extensively used for protein purification. A commercial grade cationic starch could precipitateMBPor anMBP-tagged protein quantitatively by...
Kanika Bajaj, M. S. Madhusudhan, Bharat V. Adkar, Purbani Chakrabarti, C. Ramakrishnan, Andrej Sali, ...
When incorporated into a polypeptide chain, proline (Pro) differs from all other naturally occurring amino acid residues in two important respects. The ϕ dihedral angle of Pro is constrained to...
Kanika Bajaj, M.S. Madhusudhan, Bharat V Adkar, Purbani Chakrabarti, C Ramakrishnan, Andrej Sali, ...
When incorporated into a polypeptide chain, Proline (Pro) differs from all other naturally occurring amino acid residues in two important respects. The φ dihedral angle of Pro is constrained to...
Mondal, Kalyani, Raghava, Smita, Barua, Bipasha, Varadarajan, Raghavan, Gupta, Munishwar N
Alginate, a calcium-sensitive polymer, could carry out simultaneous purification and refolding of 8 M urea/100 mM dithiothreitol (DTT) denatured and thermally denatured R-amylase present in a...
Thermodynamic Effects of Proline Introduction on Protein Stability (2007)
Prajapati, Ravindra Singh, Das, Mili, Sreeramulu, Sridhar, Sirajuddin, Minhajuddin, Srinivasan, Sankaranarayanan, Krishnamurthy, Vaishnavi, ...
The amino acid Pro is more rigid than other naturally occurring amino acids and, in proteins, lacks an amide hydrogen. To understand the structural and thermodynamic effects of Pro substitutions, it...
Design and Isolation of Temperature-sensitive Mutants of Gal4 in Yeast and Drosophila (2007)
Mondal, Kajari, Dastidar, Antara Ghosh, Singh, Guramrit, Madhusudhanan, S, Gande, Santosh Lakshmi, VijayRaghavan, K, ...
Little is known about mechanisms responsible for the temperature-sensitive (ts) phenotype, or of the transferability of ts mutants of a specific gene between organisms. Using a structure-based...
Bajaj, Kanika, Madhusudhan, MS, Adkar, Bharat V, Chakrabarti, Purbani, Ramakrishnan, C, Sali, Andrej, ...
When incorporated into a polypeptide chain, proline (Pro) differs from all other naturally occurring amino acid residues in two important respects. The \phi dihedral angle of Pro is constrained to...
Das, Mili, Kobayashi, Masanori, Yamada, Yusuke, Sreeramulu, Sridhar, Ramakrishnan, C, Wakatsuki, Soichi, ...
Disulfide bonds play an important role in protein stability and function. Here, we describe a general procedure for generating disulfide-linked dimers and multimers of proteins of known crystal...
Mondal, Kajari, VijayRaghavan, K, Varadarajan, Raghavan
Temperature-sensitive (ts) mutants are valuable tools to study the function of essential genes in vivo. Despite their widespread use, little is known about mechanisms responsible for the...
Contribution of Cation-\pi Interactions to Protein Stability (2006)
Prajapati, Ravindra S, Sirajuddin, Minhajuddin, Durani, Venuka, Sreeramulu, Sridhar, Varadarajan, Raghavan
Calculations predict that cation-\pi interactions make an important contribution to protein stability. While there have been some attempts to experimentally measure strengths of cation-\pi...
Chakraborty, Kausik, Durani, Venuka, Roshan Miranda, Edward, Citron, Michael, Liang, Xiaoping, Schleif, William, ...
gp120 is a subunit of the envelope glycoprotein of HIV-1. The third variable loop region of gp120 (V3 loop) contains multiple immunodominant epitopes and is also functionally important for deciding...
Das, Mili, Rao, Bharathi Vasudeva, Ghosh, Sanjukta, Varadarajan, Raghavan
While the hydrophobic driving force is thought to be a majorcontributor to protein stability, it is difficult to experimentallydissect out its contribution to the overall free energy of folding....
Chakraborty, Kausik, Shivakumar, P, Raghothama, S, Varadarajan, Raghavan
gp120 is a subunit of the Env (viral envelope protein) of HIV-1. The protein consists of inner and outer domains linked by a bridging sheet. Several gp120 residues that bind the neutralizing antibody...
Mutagenesis-based definitions and probes of residue burial in proteins (2005)
Bajaj, Kanika, Chakrabarti, Purbani, Varadarajan, Raghavan
Every residue of the 101-aa Escherichia, coli toxin CcdB was substituted with Ala, Asp, Glu, Lys, and Arg by using site-directed mutagenesis. The activity of each mutant in vivo was characterized as...
Protein Minimization of the gp120 Binding Region of Human CD4 \dagger (2005)
Sharma, Deepak, Balamurali, MM, Chakraborty, Kausik, Kumaran, Sowmini, Jeganathan, Sadasivam, Rashid, Umar, ...
CD4 is an important component of the immune system and is also the cellular receptor for HIV-1. CD4 consists of a cytoplasmic tail, one transmembrane region, and four extracellular domains, D1-D4....
Protein Stabilization by Introduction of Cross-Strand Disulfides (2005)
Chakraborty, Kausik, Thakurela, Sudhir, Prajapati, Ravindra Singh, Indu, S, Ali, Shaik Syed P, Ramakrishnan, C, ...
Disulfides cross-link residues in a protein that are separated in primary sequence and stabilize the protein through entropic destabilization of the unfolded state. While the removal of naturally...
Varadarajan, Raghavan, Sharma, Deepak, Chakraborty, Kausik, Patel, Mayuri, Citron, Michael, Sinha, Prem, ...
Single-chain derivatives of JRFL gp120 linked to the first two domains of human CD4 $(gp120-CD4_D_1_2)$ or to the CD4 miniprotein analog CD4M9 (gp120-M9), have been constructed. Biacore studies...
Design of temperature-sensitive mutants solely from amino acid sequence (2004)
Chakshusmathi, Ghadiyaram, Mondal, Kajari, Lakshmi, Santosh G, Singh, Guramrit, Roy, Ankita, Babu, Ravindra Ch, ...
Temperature-sensitive (Ts) mutants are a powerful tool with which to study gene function in vivo. Ts mutants are typically generated by random mutagenesis followed by laborious screening procedures....
Bajaj, Kanika, Chakshumathi, Ghadiyaram, Bachhawat-Sikder, Kiran, Surolia, Avadhesha, Varadarajan, Raghavan
The protein CcdB (controller of cell division or death B)is an Fplasmid-encoded toxin that acts as an inhibitor of Escherichia coli DNA gyrase. The stability and aggregation state of CcdB have been...
Prajapati, RS, Lingaraju, GM, Bacchawat, Kiran, Surolia, Avadhesha, Varadarajan, Raghavan
Introduction of Pro residues into helix interiors results in protein destabilization. It is currently unclear if the converse substitution (i.e., replacement of Pro residues that naturally occur in...
A Procedure for Detection and Quantitation of Cavity Volumes in Proteins (2002)
Chakravarty, Suvobrata, Bhinge, Akshay, Varadarajan, Raghavan
Accurate identification of cavities is important in the study of protein structure, stability, design, and ligand binding. Identification and quantitation of cavities is a nontrivial problem because...
Chakravarty, Suvobrata, Bhinge, Akshay, Varadarajan, Raghavan
Accurate identification of cavities is important in the study of protein structure, stability, design, and ligand binding. Identification and quantitation of cavities is a nontrivial problem because...
Chakravarty, Suvobrata, Varadarajan, Raghavan
Understanding the molecular basis for the enhanced stability of proteins from thermophiles has been hindered by a lack of structural data for homologous pairs of proteins from thermophiles and...
Panse, Vikram G, Beena, K, Philipp, Reinhard, Trommer, Wolfgang E, Vogel, Pia D, Varadarajan, Raghavan
SecB is a homotetrameric, cytosolic chaperone that forms part of the protein translocation machinery in Escherichia coli. We have investigated the bound-state conformation of a model protein...
Ganesh, C, Zaidi, Faisal N, Udgaonkar, Jayant B, Varadarajan, Raghavan
Maltose binding protein (MBP) is widely used as a model for protein folding and export studies. We show here that macroscopic aggregates form transiently during the refolding of MBP at micromolar...
Thermodynamics of Substrate Binding to the Chaperone SecB (2000)
Panse, Vikram G, Swaminathan, Chittoor P, Surolia, Avadhesha, Varadarajan, Raghavan
The thermodynamics of binding of unfolded polypeptides to the chaperone SecB was investigated in vitro by isothermal titration calorimetry and fluorescence spectroscopy. The substrates were reduced...
Protein stabilization through phage display (2000)
Chakravarty, Suvobrata, Mitra, Nivedita, Queitsch, Iris, Surolia, Avadhesha, Varadarajan, Raghavan, Dubel, Stefan
RNase S consists of two proteolytic fragments of RNase A, residues 1–20 (S20) and residues 21–124 (S pro). A 15-mer peptide (S15p) with high affinity for S pro was selected from a phage display...
Elucidation of determinants of protein stability through genome sequence analysis (2000)
Chakravarty, Suvobrata, Varadarajan, Raghavan
Sequences of putative soluble proteins from complete genomes of eight thermophiles and 12 mesophiles were analyzed to gain insight into determinants of protein thermostability. The predator algorithm...
Unfolding Thermodynamics of the Tetrameric Chaperone, SecB (2000)
Panse, Vikram G, Swaminathan, Chittor P, Aloor, Jim J, Surolia, Avadhesha, Varadarajan, Raghavan
SecB is a cytosolic tetrameric chaperone in Escherichia coli, which maintains polypeptides, destined for export in a translocation competent state. The thermodynamics of unfolding of SecB was studied...
Panse, Vikram G, Vogel, Pia, Trommer, Wolfgang E, Varadarajan, Raghavan
Molecular chaperones prevent protein aggregation in vivo and in vitro. In a few cases, multichaperone systems are capable of dissociating aggregated state(s) of substrate proteins, although little is...
Ghoshal, Alokesh K, Swaminathan, Chittoor P, Thomas, Celestine J, Surolia, Avadhesha, Varadarajan, Raghavan
Escherichia coli thioredoxin was cleaved with CNBr at its single Met residue at position 37, which lies in the middle of a long \alpha -helix. The two fragments, 1–37 and 38–108, were purified...
Residue depth: A novel parameter for the analysis of protein structure and stability (1999)
Chakravarty, Suvobrata, Varadarajan, Raghavan
Accessible surface area is a parameter that is widely used in analyses of protein structure and stability. Accessible surface area does not, however, distinguish between atoms just below the protein...
Ganesh, C, Eswar, Narayanan, Srivastava, Sarika, Ramakrishnan, Chandrasekharan, Varadarajan, Raghavan
Globular protein thermostability is characterized the cold denaturation, maximal stability $(T_{ms})$ and heat denaturation temperatures. For mesophilic globular proteins, $T_{ms}$ typically ranges...
Ganesh, C, Banerjee, Antara, Shah, Aseema, Varadarajan, Raghavan
Maltose binding protein (MBP) exhibits a slow phase of folding at pH 7.4, 298 K. The kinetics of this phase has been characterized as a function of denaturant concentration and temperature....
Thesis (Ph. D.)--Stanford University, 1988.
Design of temperature-sensitive mutants solely from amino acid sequence
Chakshusmathi, Ghadiyaram, Mondal, Kajari, Lakshmi, G. Santosh, Singh, Guramrit, Roy, Ankita, Ch., Ravindra Babu, ...
Temperature-sensitive (Ts) mutants are a powerful tool with which to study gene function in vivo. Ts mutants are typically generated by random mutagenesis followed by laborious screening procedures....
Varadarajan, Raghavan, Sharma, Deepak, Chakraborty, Kausik, Patel, Mayuri, Citron, Michael, Sinha, Prem, ...
Single-chain derivatives of JRFL gp120 linked to the first two domains of human CD4 (gp120-CD4D12) or to the CD4 miniprotein analog CD4M9 (gp120-M9), have been constructed. Biacore studies revealed...
Chakraborty, Kausik, Shivakumar, P., Raghothama, S., Varadarajan, Raghavan
gp120 is a subunit of the Env (viral envelope protein) of HIV-1. The protein consists of inner and outer domains linked by a bridging sheet. Several gp120 residues that bind the neutralizing antibody...
Bajaj, Kanika, Chakshusmathi, Ghadiyaram, Bachhawat-Sikder, Kiran, Surolia, Avadhesha, Varadarajan, Raghavan
The protein CcdB (controller of cell division or death B) is an F-plasmid-encoded toxin that acts as an inhibitor of Escherichia coli DNA gyrase. The stability and aggregation state of CcdB have been...
Mutagenesis-based definitions and probes of residue burial in proteins
Bajaj, Kanika, Chakrabarti, Purbani, Varadarajan, Raghavan
Every residue of the 101-aa Escherichia coli toxin CcdB was substituted with Ala, Asp, Glu, Lys, and Arg by using site-directed mutagenesis. The activity of each mutant in vivo was characterized as a...
Design of temperature-sensitive mutants solely from amino acid sequence
Chakshusmathi, Ghadiyaram, Mondal, Kajari, Lakshmi, G. Santosh, Singh, Guramrit, Roy, Ankita, Ch., Ravindra Babu, ...
Temperature-sensitive (Ts) mutants are a powerful tool with which to study gene function in vivo. Ts mutants are typically generated by random mutagenesis followed by laborious screening procedures....
Varadarajan, Raghavan, Sharma, Deepak, Chakraborty, Kausik, Patel, Mayuri, Citron, Michael, Sinha, Prem, ...
Single-chain derivatives of JRFL gp120 linked to the first two domains of human CD4 (gp120-CD4D12) or to the CD4 miniprotein analog CD4M9 (gp120-M9), have been constructed. Biacore studies revealed...
Chakraborty, Kausik, Shivakumar, P., Raghothama, S., Varadarajan, Raghavan
gp120 is a subunit of the Env (viral envelope protein) of HIV-1. The protein consists of inner and outer domains linked by a bridging sheet. Several gp120 residues that bind the neutralizing antibody...
Bajaj, Kanika, Chakshusmathi, Ghadiyaram, Bachhawat-Sikder, Kiran, Surolia, Avadhesha, Varadarajan, Raghavan
The protein CcdB (controller of cell division or death B) is an F-plasmid-encoded toxin that acts as an inhibitor of Escherichia coli DNA gyrase. The stability and aggregation state of CcdB have been...
Mutagenesis-based definitions and probes of residue burial in proteins
Bajaj, Kanika, Chakrabarti, Purbani, Varadarajan, Raghavan
Every residue of the 101-aa Escherichia coli toxin CcdB was substituted with Ala, Asp, Glu, Lys, and Arg by using site-directed mutagenesis. The activity of each mutant in vivo was characterized as a...
Chakraborty, Kausik, Durani, Venuka, Miranda, Edward Roshan, Citron, Michael, Liang, Xiaoping, Schleif, William, ...
gp120 is a subunit of the envelope glycoprotein of HIV-1. The third variable loop region of gp120 (V3 loop) contains multiple immunodominant epitopes and is also functionally important for deciding...
Stereochemical Criteria for Prediction of the Effects of Proline Mutations on Protein Stability
Bajaj, Kanika, Madhusudhan, M. S, Adkar, Bharat V, Chakrabarti, Purbani, Ramakrishnan, C, Sali, Andrej, ...
When incorporated into a polypeptide chain, proline (Pro) differs from all other naturally occurring amino acid residues in two important respects. The φ dihedral angle of Pro is constrained to...
Ganesh, C., Zaidi, Faisal. N., Udgaonkar, Jayant. B., Varadarajan, Raghavan
Maltose binding protein (MBP) is widely used as a model for protein folding and export studies. We show here that macroscopic aggregates form transiently during the refolding of MBP at micromolar...