Publications

D. R. Turner and J. Kubelka, Infrared and vibrational CD spectra of partially solvated alpha-helices: DFT-based simulations with explicit solvent. J. Phys. Chem B. (in press).

 J. Kim, R. Huang, J. Kubelka, P. Bour and T.A. Keiderling, Simulation of IR spectra of ß-hairpin peptides stabilized by Aib-Gly turn sequence: Correlation between conformational fluctuations and vibrational coupling. J. Phys. Chem. B., 110: 23590-23602, 2006.

J. Kubelka, J. Kim, P. Bour and T.A. Keiderling, Contribution of Transition Dipole Coupling to Amide Coupling in IR Spectra of Peptide Secondary Structures. Vibr. Spectrosc. 42: 63-73, 2006.

C. Magg, J. Kubelka, G. Holtermann, E. Hass, E. and F. X. Schmidt, Specificity of the initial collapse in the folding of the cold shock protein. J. Mol. Biol. 360: 1067-1080, 2006.

J. Kubelka, T. K. Chiu, D. R. Davies, W. A.  Eaton and J. Hofrichter,  Sub-microsecond protein folding. J. Mol. Biol. 359: 546-553, 2006.

T. A. Keiderling, J. Kubelka and J. Hilario, Vibrational circular dichroism of biopolymers. Summary of methods and applications.” In Vibrational Spectroscopy of Biologic and Polymeric Materials, Braiman, M. and Gregoriou, V. (eds.), CRC Taylor & Francis, Boca Raton, FL, pp. 253-324, 2006.

T. A. Keiderling, R. Huang, J. Kubelka, P.  Bour, V.  Setnicka, R. P. Hammer, M. A. Etienne, R. A. G. D. Silva, and S. M. Decatur, Isotopically labeled peptides provide site-resolved structural data with infrared spectra. Probing the structural limit of optical spectroscopy, In Collections Symposium Series, 8 (Volume title: Biologically Active Peptides), pp. 42-49, 2005.

T. Chiu, J. Kubelka, R. Herbst-Irmer, W. A. Eaton, J. Hofrichter, and D. Davies, High-resolution X-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein. Proc. Natl. Acad. Sci. U.S.A.,102: 7517-7522, 2005.

J. Kubelka, M.  Buscaglia, J.  Hofrichter and W. A. Eaton, Ultrafast kinetic studies and the protein folding ‘speed limit’. In Structure, Function, and Dynamics of Biological Macromolecules and Assemblies, NATO Science Series: Life and Behavioral Sciences, Puglisi, J. D. (ed.), IOS Press, Amsterdam, pp. 1-10, 2005.

J. Kubelka, R. Huang, and T. A. Keiderling, Solvent effects on IR and VCD spectra of helical peptides: DFT-based static spectral simulations with explicit water. J. Phys.Chem. B., 109: 8231-8243, 2005.

V. Setnicka, R. Huang, C. L. Thomas, M. A. Etienne, J. Kubelka, R. P. Hammer, and T. A. Keiderling, IR study of cross-strand coupling in a ß-hairpin peptide using isotopic labels. J. Am. Chem. Soc., 127: 4992-4993, 2005.

M. Buscaglia, J. Kubelka, J. Hofrichter, and W. A. Eaton, Determination of ultrafast protein folding rates from loop formation dynamics. J. Mol. Biol., 347: 657-664, 2005.

J. Kubelka, W. A. Eaton, and J. Hofrichter, The protein folding ‘speed limit’. Curr. Opin. Struct. Biol., 14: 76-88, 2004.

R. Huang, J. Kubelka, W. Barber-Armstrong, R. A. G. D. Silva, S. M. Decatur, and T. A. Keiderling, Nature of vibrational coupling in helical peptides: An isotopic labeling study. J. Am. Chem. Soc., 126: 2346-2354, 2004.

J. Kubelka, W. A. Eaton, and J. Hofrichter, Experimental tests of villin subdomain folding simulations. J. Mol. Biol., 329: 625-630, 2003.

J. Hilario, J. Kubelka, and T. A. Keiderling, Optical spectroscopic investigations of model ß-sheet hairpins in aqueous solutions. J. Am. Chem. Soc., 125: 7562-7574, 2003.

R. A. G. D. Silva, S. Yasui, J. Kubelka, F. Formaggio, M. Crisma, C. Toniolo, and T. A. Keiderling, Discriminating 3₁₀- from alpha-helices: Vibrational and electronic CD and IR absorption study of related Aib-containing oligopeptides. Biopolymers, 65: 299-243, 2002.

P. Bour, J. Kubelka, and T. A. Keiderling, Ab initio models of peptide helices and their vibrational spectra. Biopolymers, 65: 45-59, 2002.

J. Kubelka and T. A. Keiderling, Discrimination between peptide 3₁₀- and alpha-helices. Theoretical analysis of the impact of alpha-methyl substitution on experimental spectra. J. Am. Chem. Soc., 124: 5325-5332, 2002.

J. Hilario, J. Kubelka, F. A. Syud, S. H. Gellman, and T. A. Keiderling, Spectroscopic characterization of selected ß-sheet models. Biospectroscopy, 67: 233-236, 2002.

J. Kubelka, P. Bour, R. A. G. D. Silva, S. M. Decatur, and T. A. Keiderling, Chirality in peptide vibrations. Ab initio computational studies of length, solvation, hydrogen bond, dipole coupling and isotope effects. In The Physical Chemistr of Chirality. ACS Symposium Series 810, Hicks J. (ed.), pp. 50-64, Oxford University Press, New York (2002).

J. Kubelka and T. A. Keiderling, Ab initio calculation of amide carbonyl stretch vibrational frequencies in solution with modified basis sets. I. N-methyl acetamide. J. Phys. Chem. A 105: 10922-10928, 2001.

J. Kubelka and T. A. Keiderling, Differentiation of ß-sheet forming structures: Ab initio based simulations of IR absorption and Vibrational CD for model peptide and protein b-sheets. J. Am. Chem. Soc. 123: 12048-12058, 2001.

J. Kubelka and T. A. Keiderling, The anomalous infrared amide I intensity distribution in ¹³C isotopically labeled peptide ß-sheets comes from extended, multiple-stranded structures. An ab initio study. J. Am. Chem. Soc. 123: 6142-6150, 2001.

R. A. G. D. Silva, J. Kubelka, P. Bour, S. M. Decatur, and T. A. Keiderling, Site-specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution. Proc. Natl. Acad. Sci. U. S. A. 97: 8318-8323, 2000.

P. Bour, J. Kubelka, and T. A. Keiderling, Theoretical simulations of oligopeptide vibrational circular dichroism. Effect of isotopic labeling. Biopolymers 53: 380-395, 2000.

J. Kubelka, P. Pancoska, and T. A. Keiderling, Protein spectra-structure relationship by novel modification of 2D correlation analysis. VCD applications. In Spectroscopy of Biological Molecules: New Directions, Greve, J. Puppels, G. J. Otto, C. (eds.), pp. 67-68, Dordrecht, Kluwer Academic Publishers, (1999).

P. Pancoska, J. Kubelka, and T. A. Keiderling, Novel use of a static modification of two-dimensional correlation analysis. Part I: Comparison of the secondary structure sensitivity of electronic circular dichroism, FT-IR, and Raman spectra of proteins. Appl. Spectrosc. 53: 655-665, 1999.

J. Kubelka, P. Pancoska, and T. A. Keiderling, Novel use of a static modification of two-dimensional correlation analysis. Part II: Hetero-spectral correlations of protein Raman, FT-IR, and circular dichroism spectra. Appl. Spectrosc. 53: 666-671, 1999.

A. A. El-Azhary, H. U. Suter, and  J. Kubelka, Experimental and theoretical investigation of the geometry and vibrational frequencies of 1,2,3-triazole, 1,2,4-triazole and tetrazole anions. J. Phys. Chem. 102: 620-629, 1998.

J. Kubelka, M. Burian, and M. Hajek, Development of the protocol for quantitative in vivo MR spectroscopy. J. Magn. Reson. Anal. 3: 93-98, 1997.

J. Kubelka and M. Hajek, Quality control for quantitative in vivo magnetic resonance spectroscopy, Quart. Magn. Res. Biol. Med. 3: 139-149, 1996.