个人简介

Ph.D., Physical Chemistry, 2002, University of Illinois at Chicago Postdoctoral Fellow, National Institutes of Health

研究领域

Physical Chemistry

Research in Kubelka group is centered on problems of protein structure and dynamics, along with the development of new sensitive spectroscopic methods for their study. Our main goal is to understand the molecular mechanism of protein folding. We focus on small and structurally simple model proteins. Isotopically-edited infrared (IR) spectroscopy is used to selectively probe the structure of particular regions of the studied proteins during folding or unfolding processes. In combination with mutational studies, insights into the roles of sequence specific interactions and physical origins of the folding mechanism are obtained. In parallel, infrared spectroscopic studies on model small molecules and quantum density functional theory calculations help understand and interpret the complex protein vibrational spectra.

近期论文

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Anderson, B. A., Literati, A., Ball, B. and Kubelka, J. (2014) "Temperature dependence of C-terminal carboxylic group absorptions in the amide I' region Spectrochim. Acta, Part A Mol. Biomol. Spectros. 134, 473-483. Kota, P. ,Buchner, G. S., Chakraborty, H., Dang, Y. L. He, H., Garcia, G. J. M., Kubelka, J., Gentzch, M., Sutz, M. J. and Dokholyan, N. V. (2014) "The N-terminal domain allosterically regulates cleavage and activation of the epithelial sodium channel." J. Biol. Chem. 289, 23029-23042. Kubelka, G. S. and Kubelka, J. (2014) "Site-specific thermodynamic stability and unfolding of a de novo designed protein structrual motif mapped by C-13 isotopically edited IR spectroscopy." J. Am. Chem. Soc. 136, 6037-6048. Anderson, B. A., Literati, A., Ball, B. and Kubelka, J. (2014) "Temperature dependence of amino acid side-chain IR absorptions in the amide I' region." Biopolymers 101, 536-548. Sargsyan, G., Leonard, B. M., Kubelka, J. and Balaz, M. (2014) "Supramolecular ssDNA templated porphyrin and metalloporphyrin nanoassemblies with tunable helicity." Chem. Eur. J. 20, 1878-1892. Tohgha, U., Deol, K. K., Porter, A. G., Bartko, S. G., Choi, J. K., Leonard, B. M., Varga, K., Kubelka, J., Muller, G. and Balaz, M. (2013) "Ligand induced circular dichroism and circularly polarized luminescence in CdSe quantum dots." ACS Nano 7, 11094-11102. Chi, H., Welch, W. R. W., Kubelka, J. and Keiderling, T. A. (2013) "Insight into the packing pattern of b2 fibrils. A model study of glutamic acid rich oligomers with 13C isotopic edited vibrational spectroscopy." Biomacromolecules, 14, 3880-3891. Kubelka, J. (2013) "Multivariate analysis of spectral data with frequency shifts: Application to temperature dependent infrared spectra of peptides and proteins." Anal. Chem. 85, 9588-9595. Welch, W. R. W., Keiderling, T. A. and Kubelka, J. (2013) "Structural analyses of experimental 13C edited amide I' IR and VCD for peptide b-sheet aggregates and fibrils using DFT-based spectral simulations." J. Phys. Chem. B., 117, 10359-10369. Welch, W. R. W., Kubelka, J. and Keiderling, T. A. (2013) "Infrared, VCD and Raman spectral simulations for b-sheet structures with various isotopic labels, inter-strand and stacking arrangements using Density Functional Theory." J. Phys. Chem. B., 117, 10343-10358. Sedghi, M., Goual, L., Welch, W.R.W. and Kubelka, J. (2013) "Effect of asphaltene structure on association and aggregation using molecular dynamics." J. Phys. Chem. B., 117, 5765-5776. Topchyi, E., Armstrong, G. S., Boswell, K. I., Buchner, G. S., Kubelka, J. and Lehmann, T. E. (2013) "T1BT* structrual strudy of an anti-plasmoidal peptide through NMR and molecular dynamics." Malaria J. 12, 104. Sargsyan, G., Schatz, A. A., Kubelka, J. and Balaz, M. (2013) 揊ormation and helicity control of ssDNA templated porphyrin nanoassemblies.� Chem. Comm. 10, 1020-1022. Buchner, G. S., Shih, N., Niebling, S., Reece, A. E. and Kubelka, J. (2012) 揢nusual cold denaturation of a small protein domain.� Biochemistry 51, 6496-6498. Welch, W. R. W. and Kubelka, J. (2012) 揇FT-Based Simulations of Amide I ' IR Spectra of a small protein in solution using empirical electrostatic map with a continuum solvent model.� J. Phys. Chem. B 116, 10739-10747. Lai, J., Lin, J., Kubelka, J. and Liberles, D. A. (2012) "A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function." J. Mol. Biol.422 442-459. Grahnen, J. A., Nandakumar, P., Kubelka, J. and Liberles, D. A. (2011) 揃iophysical and structural considerations for protein sequence evolution." BMC Evol. Biol. 11, 361-378. Amunson, K. E., Anderson, B. A. and Kubelka J. (2011) "Temperature effects on the optical path length of infrared liquid transmission cells." Appl. Spectrosc. 65, 1307-1313. Grahnen, J. A., Kubelka, J. and Liberles, D. A. (2011) "Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effect of mutation during evolution." J. Mol. Evol. 73, 23-33. Kaminsky, J., Kubelka, J. and Bour, P. (2011) "Theoretical modeling of peptide a-helical circular dichroism in aqueous solution." J. Phys. Chem. A 115, 1734-1742.