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Biochemistry, Biophysics and Bioinformatics
   J A Y A N T    B    U D G A O N K A R
RESEARCH I LAB MEMBERS I PUBLICATIONS I TRAINING & POSITIONS
 
 

Publications:

Dasgupta A. and Udgaonkar, J.B. (2010)

 Evidence for initial non-specific polypeptide chain collapse during the refolding of the SH3 domain of PI3 kinase
  J. Mol. Biol. (In press)
  Jain, S. and Udgaonkar, J.B. (2010)
 Salt-induced modulation of the pathway of amyloid fibril formation by the mouse prion protein
  Biochemistry, 49, 7615-7624
 Jha, S.K. and Udgaonkar, J.B. (2010)
 Free energy barriers in protein folding and unfolding
 Curr. Sci., 99, 457-475  (PDF File)
 

Kumar, S. and Udgaonkar, J.B. (2010)

 Mechanisms of amyloid fibril formation by proteins
 Curr. Sci., 96,1053-1070  (PDF File)
 Wani, A.H. and Udgaonkar, J.B. (2009)
 Native state dynamics drive the unfolding of the SH3 domain of PI3 kinase at high denaturant concentration.
 Proc. Natl. Acad. Sci. USA, 106, 20711-20716 (PDF File)
 Jha, A., Udgaonkar, J.B. and Krishnamoorthy, G. (2009)
 Characterization of the heterogeneity and specificity of inter-polypeptide interactions in amyloid protofibrils by measurement of site-specific fluorescence anisotropy decay kinetics.
 J. Mol. Biol. 393, 735-752 (PDF File)
 Kumar, S. and Udgaonkar J.B. (2009)
 Structurally distinct amyloid protofibrils form on separate pathways of aggregation of a small protein.
 Biochemistry, 48, 6441-6449 (PDF File)
 Jha, S.K. and Udgaonkar, J.B. (2009)
 Direct evidence for a dry molten globule intermediate during the unfolding of a small protein.
 Proc. Natl. Acad. Sci. USA, 106, 12289-12294 (PDF File)
 Jha, S.K., Dhar, D., Krishnamoorthy, G. and Udgaonkar, J.B.(2009)
 Continuous dissolution of structure during the unfolding of a small protein.
 Proc. Natl. Acad. Sci. USA, 106, 11113-1118 (PDF File) 
 Patra, A.K. & Udgaonkar, J. B. (2009)
 GroEL can unfold late intermediates populated on the folding pathways of monellin.
 J. Mol. Biol. 389, 759-775 (PDF File)
 Sinha, K. K. and Udgaonkar, J. B. (2009)
 Early Events in Protein Folding.
 Curr. Sci. Vol. 96, No. 8, 1053-1070 (PDF File)
 Wani, A. H. and Udgaonkar, J. B. (2009)
 Revealing a concealed intermediate that forms after the rate-limiting step of refolding of the SH3 domain of PI3 kinase .
 J. Mol. Biol. 387, 348-362 (PDF File)
 Kumar S. & Udgaonkar, J.B. (2009)
 Conformational conversion may precede or follow aggregate elongation on alternative pathways of amyloid protofibril formation.
 J. Mol. Biol. 385, 1266-1276 (PDF File)
 Beena K., Kulothungan, R., Patra, A.K., Udgaonkar, J.B. & Varadarajan, R. (2009)
 SecB mediated protein export need not occur via kinetic partitioning.
 J. Mol. Biol. 385, 1243-1256 (PDF File)
 Jain, S. & Udgaonkar, J.B. (2008)
 Evidence for step-wise formation of amyloid fibrils by the mouse prion protein.
 J. Mol. Biol. 382, 1228-1241 (PDF File)
 Udgaonkar, J.B. (2008)
 Multiple routes and structural heterogeneity in protein folding.
 Annual Reviews of Biophysics. 37, 489-510 (PDF File)
 Sinha, K.K. & Udgaonkar, J.B. (2008)
 Barrier-less evolution of structure during the sub-ms folding reaction of a small protein.
 Proc. Natl. Acad. Sci. USA,105, 7998-8003 (PDF File)
 

Jha, S.K. and Udgaonkar, J.B. (2007)

 Exploring the cooperativity of the fast folding reaction of a small protein using pulsed thiol labeling and mass spectrometry.
 J. Biol. Chem 2007,Vol. 282, No.52,37479-37491 (PDF File)
 Patra, A.K. and Udgaonkar, J.B. (2007)
 Characterization of the folding and unfolding reactions of single-chain monellin: evidence for multiple intermediates and competing pathways.
 Biochemistry, 46, 11727-11743 (PDF File)
 Sinha, K.K. & Udgaonkar, J.B. (2007)
 Dissecting the non-specific and specific components of the initial folding reaction of barstar by multi-site FRET measurements.
 J. Mol. Biol., Vol. 370, No. 2, 385-405 (PDF File)
 Saxena, A.M., Krishnamoorthy, G., Udgaonkar, J.B. and Periasamy, N. (2007)
 Identification of intermediate species in protein folding by quantitative analysis of amplitudes in time-domain fluorescence spectroscopy.
 J. Chem Sci., Vol.119 No.2, 61-69 (PDF File)
 Kumar, S., Mohanty, S.K. & Udgaonkar, J.B. (2007)
 Mechanism of formation of amyloid protofibrils of barstar from soluble oligomers: evidence for multiple steps and lateral association coupled to conformational conversion
 J. Mol. Biol. 2007, 367, No. 4, 1186-1204 (PDF File)
 Pradeep, L. & Udgaonkar, J.B. (2006)
 Diffusional barrier in the unfolding of a small protein.
 J. Mol. Biol. 2006, 366, No 3, 1016-1028 (PDF File)
 Wani, A. H. & Udgaonkar, J. B. (2006).
 HX-ESI-MS and Optical Studies of the Unfolding of Thioredoxin Indicate Stabilization of a Partially Unfolded, Aggregation-Competent Intermediate at Low pH.
 Biochemistry, 2006, 45, 11226-11238 (PDF File)
 Saxena, A.M., Udgaonkar, J.B. & Krishnamoorthy, G. (2006).
 Characterization of intra-molecular distances and site-specific dynamics in chemically unfolded barstar: evidence for denaturant-dependent non-random structure.
 J. Mol. Biol. 2006, 359, 174-189 (PDF File)
 Mukhopadhyay, S, Nayak, P, Udgaonkar, JB and Krishnamoorthy, G. (2006).
 Characterization of the Formation of Amyloid Protofibrils from Barstar by Mapping Residue-Specific Fluorescence Dynamics.
 J. Mol. Biol. 2006, 358, 935-942 (PDF File)
 Sinha, K.K. & Udgaonkar, J.B.
 Dependence of the size of the initially collapsed form during the folding of barstar on denaturant
concentration: evidence for a continuous transition.
 J. Mol. Biol. 2005, 353, 704-718. (PDF File)
 Saxena, A.M., Udgaonkar, J.B. & Krishnamoorthy, G.
 Protein dynamics control proton transfer from bulk solvent to protein interior: a case study with green fluorescent protein.
 Protein Science, 2005, 14, 1787-1799. (PDF File)
 Bhavesh, N.S., Juneja, J., Udgaonkar, J.B. & Hosur, R.V.
 Native and non-native conformational preferences in the urea-unfolded state of barstar.
 Protein Science, 2004, 13, 3085-3091, (PDF File)
 Pradeep, L. & Udgaonkar, J.B.
 Osmolytes induce structure in an early intermediate on the folding pathway of barstar.
 J. Biol. Chem., 2004, 279, 40303-40313 (PDF File)
 Pradeep, L. & Udgaonkar, J.B.
 Effect of salt on the urea-unfolded form of barstar probed by m value measurements.
 Biochemistry, 2004, 43, 11393-11402, (PDF File)
 Beena, K., Udgaonkar, J. B., and Varadarajan, R.
 Effect of signal peptide on the stability and folding kinetics of maltose binding protein.
 Biochemistry, 2004, 43, 3608-3619 (PDF File)
 Sridevi, K., Lakshmikanth, G., Krishnamoorthy, G. & Udgaonkar, J.B.
 Increasing stability reduces conformational heterogeneity in a protein folding
intermediate ensemble.
 J. Mol. Biol. (2004) .337, 699–711 (PDF File)
 Mallik, R., Udgaonkar, J.B. & Krishnamoorthy, G.
 Kinetics of proton transfer in a green fluorescent protein: a laser-induced pH jump study.
 Proc. Ind. Acad. Sci. (Chemical Sciences). 2003, 115(4); 307-317 (PDF File)
 Bhutani, N. & Udgaonkar, J.B.
 Folding sub-domains of thioredoxin identified by native-state hydrogen exchange. (PDF File)
 Protein Science, 2003, 12, 1719-1731
 Rami, B.R., Krishnamoorthy, G. and Udgaonkar, J.B.
 Dynamics of the core tryptophan during the formation of a productive molten globule intermediate of barstar. (PDF File)
 Biochemistry, 2003, 42(26); 7986-8000
 Sridevi, K. & Udgaonkar, J.B.
 Surface expansion is independent of and occurs faster than core solvation during the unfolding of barstar. (PDF File)
 Biochemistry, 2003 Feb.18; 42(6) 1551-1563
 Pradeep, L and Udgaonkar, JB
 Differential salt-induced stabilization of structure in the initial folding intermediate ensemble of barstar (PDF File)
 Journal of Molecular Biology, 2002, 324, 331–347.
 
Juneja J, Bhavesh NS, Udgaonkar JB, Hosur RV.
 NMR Identification and Characterization of the Flexible Regions in the 160 kD Molten Globule-Like Aggregate of Barstar at Low pH. (PDF File)
 Biochemistry. 2002 Aug 6;41(31):9885-99.
 Juneja J, Udgaonkar JB.
 Characterization of the unfolding of ribonuclease a by a pulsed hydrogen exchange study: evidence for competing pathways for unfolding. (PDF File)
 Biochemistry. 2002 Feb 26;41(8):2641-54.
 Rami BR, Udgaonkar JB.
 Mechanism of formation of a productive molten globule form of barstar. (PDF File)
 Biochemistry. 2002 Feb 12;41(6):1710-6.
 Sridevi K, Udgaonkar JB.
 Unfolding rates of barstar determined in native and low denaturant conditions indicate the presence of intermediates. (PDF File)
 Biochemistry. 2002 Feb 5;41(5):1568-78.
 Bhutani N, Udgaonkar JB.
 GroEL channels the folding of thioredoxin along one kinetic route. (PDF File)
 J Mol Biol. 2001 Dec 14;314(5):1167-79.
 Rami BR, Udgaonkar JB.
 pH-jump-induced folding and unfolding studies of barstar: evidence for multiple folding and unfolding pathways. (PDF File)
 Biochemistry. 2001 Dec 18;40(50):15267-79.
 Bhuyan AK, Udgaonkar JB.
 Folding of horse cytochrome c in the reduced state. (PDF File)
 J Mol Biol. 2001 Oct 5;312(5):1135-60.
 Lakshmikanth GS, Sridevi K, Krishnamoorthy G, Udgaonkar JB.
 Structure is lost incrementally during the unfolding of barstar. (PDF File)
 Nat Struct Biol. 2001 Sep;8(9):799-804.
 Ganesh C, Zaidi FN, Udgaonkar JB, Varadarajan R.
 Reversible formation of on-pathway macroscopic aggregates during the folding of maltose binding protein. (PDF File)
 Protein Sci. 2001 Aug;10(8):1635-44.
 Sahu SC, Bhuyan AK, Udgaonkar JB, Hosur RV.
 Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study. (PDF File)
 J Biomol NMR. 2000 Oct;18(2):107-18.
 Sahu SC, Bhuyan AK, Majumdar A, Udgaonkar JB.
 Backbone dynamics of barstar: a (15)N NMR relaxation study. (PDF File)
 Proteins: Structure Function and Genetics. 2000 Dec 1;41(4):460-74.
 Sridevi K, Juneja J, Bhuyan AK, Krishnamoorthy G, Udgaonkar JB.
 The slow folding reaction of barstar: the core tryptophan region attains tight packing before substantial secondary and tertiary structure formation and final compaction of the polypeptide chain. (PDF File)
 J Mol Biol. 2000 Sep 15;302(2):479-95.
 Bhutani N, Udgaonkar JB.
 A thermodynamic coupling mechanism can explain the GroEL-mediated acceleration of the folding of barstar. (PDF File)
 J Mol Biol. 2000 Apr 14;297(5):1037-44.
 Ramachandran S, Rami BR, Udgaonkar JB.
 Measurements of cysteine reactivity during protein unfolding suggest the presence of competing pathways. (PDF File)
 J Mol Biol. 2000 Mar 31;297(3):733-45.
 Bhuyan, A.K. & Udgaonkar, J.B.
 Venkatesha, B., Udgaonkar, J.B., Appaji Rao, N. & Savitri, H.S.
 Guanidine hydrochloride-induced reversible unfolding of sheep liver serine hydroxymethyl transferase.
 Journal of Bioscience, 1999, 24, 69-77.
 Bhuyan AK, Udgaonkar JB.
 Observation of multistate kinetics during the slow folding and unfolding of barstar. (PDF File)
 Biochemistry. 1999 Jul 13;38(28):9158-68.
 Panse VG, Udgaonkar JB, Varadarajan R.
 SecB binds only to a late native-like intermediate in the folding pathway of barstar and not to the unfolded state. (PDF File)
 Biochemistry. 1998 Oct 13;37(41):14477-83.
 Bhuyan AK, Udgaonkar JB.
 Stopped-flow NMR measurement of hydrogen exchange rates in reduced horse cytochrome c under strongly destabilizing conditions. (PDF File)
 Proteins. 1998 Aug 1;32(2):241-7.
 Bhuyan AK, Udgaonkar JB.
 Multiple kinetic intermediates accumulate during the unfolding of horse cytochrome c in the oxidized state. (PDF File)
 Biochemistry. 1998 Jun 23;37(25):9147-55.
 Ratnaparkhi GS, Ramachandran S, Udgaonkar JB, Varadarajan R.
 Discrepancies between the NMR and X-ray structures of uncomplexed barstar: analysis suggests that packing densities of protein structures determined by NMR are unreliable. (PDF File)
 Biochemistry. 1998 May 12;37(19):6958-66.
 Venkatesha B, Udgaonkar JB, Rao NA, Savithri HS.
 Reversible unfolding of sheep liver tetrameric serine hydroxymethyltransferase. (PDF File)
 Biochim Biophys Acta. 1998 Apr 23;1384(1):141-52.
 Bhuyan AK, Udgaonkar JB.
 Two structural subdomains of barstar detected by rapid mixing NMR measurement of amide hydrogen exchange. (PDF File)
 Proteins. 1998 Feb 15;30(3):295-308.
 Zaidi FN, Nath U, Udgaonkar JB.
 Multiple intermediates and transition states during protein unfolding.
 Nat Struct Biol. 1997 Dec;4(12):1016-24.
 Schoppe A, Hinz HJ, Agashe VR, Ramachandran S, Udgaonkar JB.
 DSC studies of the conformational stability of barstar wild-type. (PDF file)
 Protein Sci. 1997 Oct;6(10):2196-202.
 Agashe VR, Schmid FX, Udgaonkar JB.
 Thermodynamics of the complex protein unfolding reaction of barstar. (PDF file)
 Biochemistry. 1997 Oct 7;36(40):12288-95.
 Nath U, Udgaonkar JB.
 Folding of tryptophan mutants of barstar: evidence for an initial hydrophobic collapse on the folding pathway. (PDF File)
 Biochemistry. 1997 Jul 15;36(28):8602-10.
 Nath U, Agashe VR, Udgaonkar JB.
 Initial loss of secondary structure in the unfolding of barstar.
 Nat Struct Biol. 1996 Nov;3(11):920-3.
 Swaminathan R, Nath U, Udgaonkar JB, Periasamy N, Krishnamoorthy G.
 Motional dynamics of a buried tryptophan reveals the presence of partially structured forms during denaturation of barstar. (PDF File)
 Biochemistry. 1996 Jul 16;35(28):9150-7.
 Ramachandran S, Udgaonkar JB.
 Stabilization of barstar by chemical modification of the buried cysteines. (PDF File)
 Biochemistry. 1996 Jul 2;35(26):8776-85.
 Agashe VR, Shastry MC, Udgaonkar JB.
 Initial hydrophobic collapse in the folding of barstar.
 Nature. 1995 Oct 26;377(6551):754-7. (PDF Files)
 Khurana R, Hate AT, Nath U, Udgaonkar JB.
 pH dependence of the stability of barstar to chemical and thermal denaturation. (PDF file)
 Protein Sci. 1995 Jun;4(6):1133-44.
 Shastry MCR, Udgaonkar JB.
 The folding mechanism of barstar: evidence for multiple pathways and multiple intermediates. (PDF File)
 J Mol Biol. 1995 Apr 14;247(5):1013-27.
 Udgaonkar JB, Baldwin RL.
 Nature of the early folding intermediate of ribonuclease A. (PDF File)
 Biochemistry. 1995 Mar 28;34(12):4088-96.
 Agashe VR, Udgaonkar JB.
 Thermodynamics of denaturation of barstar: evidence for cold denaturation and evaluation of the interaction with guanidine hydrochloride. (PDF File)
 Biochemistry. 1995 Mar 14;34(10):3286-99.
 Nath U, Udgaonkar JB.
 Perturbation of a tertiary hydrogen bond in barstar by mutagenesis of the sole His residue to Gln leads to accumulation of at least one equilibrium folding intermediate. (PDF File)
 Biochemistry. 1995 Feb 7;34(5):1702-13.
 Swaminathan, R., Periasamy, N., Udgaonkar, J.B. & Krishnamoorthy, G.
 Molten globule-like conformation of barstar: a study by fluorescence dynamics. (PDF File)
 J. Phys. Chem.1994, 98, 9270-9278.
 Raghunathan V, Khurana S, Gupta V, Khurana R, Udgaonkar JB, Salunke DM.
 Crystallization and molecular packing analysis of barstar crystals. (PDF File)
 J Mol Biol. 1994 Oct 28;243(3):533-6.
 Shastry MC, Agashe VR, Udgaonkar JB.
 Quantitative analysis of the kinetics of denaturation and renaturation of barstar in the folding transition zone. (PDF file)
 Protein Sci. 1994 Sep;3(9):1409-17.
 Khurana R, Udgaonkar JB.
 Equilibrium unfolding studies of barstar: evidence for an alternative conformation which resembles a molten globule. (PDF File)
 Biochemistry. 1994 Jan 11;33(1):106-15.
 Udgaonkar JB, Baldwin RL.
 Early folding intermediate of ribonuclease A. (PDF File)
 Proc Natl Acad Sci U S A. 1990 Nov;87(21):8197-201.
 Milburn T, Matsubara N, Billington AP, Udgaonkar JB, Walker JW, Carpenter BK, Webb WW, Marque J, Denk W, McCray JA, et al.
 Synthesis, photochemistry, and biological activity of a caged photolabile acetylcholine receptor ligand. (PDF File)
 Biochemistry. 1989 Jan 10;28(1):49-55.
 Udgaonkar JB, Baldwin RL.
 NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A.
 Nature. 1988 Oct 20;335(6192):694-9. (PDF File)
 Udgaonkar JB, Hess GP.
 Chemical kinetic measurements of a mammalian acetylcholine receptor by a fast-reaction technique. (PDF File)
 Proc Natl Acad Sci U S A. 1987 Dec;84(24):8758-62.
 Udgaonkar JB, Hess GP.
 Acetylcholine receptor: channel-opening kinetics evaluated by rapid chemical kinetic and single-channel current measurements.
 Biophys J. 1987 Nov;52(5):873-83.
 Takeyasu K, Shiono S, Udgaonkar JB, Fujita N, Hess GP.
 Acetylcholine receptor: characterization of the voltage-dependent regulatory (inhibitory) site for acetylcholine in membrane vesicles from Torpedo californica electroplax. (PDF File)
 Biochemistry. 1986 Apr 8;25(7):1770-6.
 Pasquale EB, Udgaonkar JB, Hess GP.
 Single-channel current recordings of acetylcholine receptors in electroplax isolated from the Electrophorus electricus Main and Sachs' electric organs.
 J Membr Biol. 1986;93(2):195-204.
 Shiono S, Takeyasu K, Udgaonkar JB, Delcour AH, Fujita N, Hess GP.
 Regulatory properties of acetylcholine receptor: evidence for two different inhibitory sites, one for acetylcholine and the other for a noncompetitive inhibitor of receptor function (procaine). (PDF File)
 Biochemistry. 1984 Dec 18;23(26):6889-93.
 Takeyasu K, Udgaonkar JB, Hess GP.
 Acetylcholine receptor: evidence for a voltage-dependent regulatory site for acetylcholine. Chemical kinetic measurements in membrane vesicles using a voltage clamp. (PDF File)
 Biochemistry. 1983 Dec 6;22(25):5973-8.
 Pasquale EB, Takeyasu K, Udgaonkar JB, Cash DJ, Severski MC, Hess GP.
 Acetylcholine receptor: evidence for a regulatory binding site in investigations of suberyldicholine-induced transmembrane ion flux in Electrophorus electricus membrane vesicles.
 Biochemistry. 1983 Dec 6;22(25):5967-73. (PDF File)
  
  
 Juneja, J. & Udgaonkar, J.B.
 NMR studies of protein folding. (PDF File)
 Current Science, 2003, 84, No. 2, 157-172
 Bhutani N and Udgaonkar, JB
 Chaperonins as protein folding machines. (PDF File)
 Current Science, 2002, 83 1337-1351.
 Udgaonkar, J.B.
 Entropy in Biology. (PDF File)
 Resonance, 2001, 6, 61-66.
 Bhuyan, A.K. & Udgaonkar, J.B.
 Real-time NMR measurements of protein folding and hydrogen exchange dynamics. (PDF File)
 Current Science, 1999, 77, 942-950.
 Nath, U. & Udgaonkar, J.B.
 How do proteins fold?
 Current Science, 72, 180-191.
 Udgaonkar, J.B.
 Folding in an unfolded protein
 Current Science, 1993, 64, 7-9.
 Udgaonkar, J.B. & Hess, G.P.
 Acetylcholine receptor: isosteric properties
 Trends in Pharm. Sci., 1987, 8, 190-192.
 Hess GP, Udgaonkar JB, Olbricht WL.
 Chemical kinetic measurements of transmembrane processes using rapid reaction techniques: acetylcholine receptor.
 Annu Rev Biophys Biophys Chem. 1987;16:507-34. Review.
 Udgaonkar JB, Hess GP.
 Acetylcholine receptor kinetics: chemical kinetics.
 J Membr Biol. 1986;93(2):93-109.
  
 Saxena, A.M., Udgaonkar, J.B. & Krishnamoorthy, G.
 Protein dynamics and protein folding dynamics revealed by time-resolved fluorescence.
 In Fluorescence Spectroscopy in Biology (eds. Hof, M., Hutterer, R. & Fidler, V.) Springer, 2005,
 Relevance of burst phase changes in optical signals of polypeptides during protein folding.
 In Perspectives in Structural Biology (ed: Vijayan, M., Yathindra, N. & Kolaskar, A.S.), Universities Press, Hyderabad, 1999, 293-303.
 Bhuyan, A.K. & Udgaonkar, J.B.
 Multi-state kinetics of folding and unfolding of barstar.
 Excerpta Medica International Congress Series (ICS), 24th Taniguchi International Symposium, Elsevier Science, 1999, 261-270.
 Hess, G.P., Kolb, H.-A., Lauger, P., Schoffeniels, E., Schwartze, W., Udgaonkar, J.B. & Pasquale, E.B.
 in Molecular Basis of Nerve Activity (eds. Changeux, J.-P., Hucho, F. Maelicke, A. & Neumann, E.) 1985, pp. 317-334, Walter de Gruyter, New York.rajesh