University of Wyoming
Department of Chemistry

Kubelka Group
Protein Folding - Biomolecular Spectroscopy - Computational Chemistry


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Publications


Journal Articles:

2014:

Anderson, B. A., Literati, A., Ball, B. and Kubelka, J. (2014) "Temperature dependence of C-terminal carboxylic group absorptions in teh 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.

2013:

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) “Formation and helicity control of ssDNA templated porphyrin nanoassemblies.” Chem. Comm. 10, 1020-1022.

2012:

Buchner, G. S., Shih, N., Niebling, S., Reece, A. E. and Kubelka, J. (2012) “Unusual cold denaturation of a small protein domain.” Biochemistry 51, 6496-6498.

Welch, W. R. W. and Kubelka, J. (2012) “DFT-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.

2011:

Grahnen, J. A., Nandakumar, P., Kubelka, J. and Liberles, D. A. (2011) “Biophysical 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.

Buchner, G. S., Murphy R. D., Buchete N.-V. and Kubelka, J. (2011) "Dynamics of protein folding: Probing the kinetic network of folding-unfolding transitions with experiment and theory." BBA Proteins Proteom. 1814, 1001-1020.

Kaminsky, J., Bour, P., and Kubelka, J. (2011) "Simulations of the temperature dependence of the amide I vibration." J. Phys. Chem. A 115, 30-34.

2010:

Grahnen, J., Amunson, K. E. and Kubelka, J. (2010) "DFT-based simulations of IR amide I spectra for a small protein in solution. Comparison of explicit and empirical solvent models." J. Phys. Chem. B 114, 13011-13020.

Paulson, L. O, Kaminsky, J., Bour, P., Anderson D. T. and Kubelka, J. (2010) "Theoretical study of vibrationally averaged dipole moments for the ground and excited C=O stretching states of trans-formic acid". J. Chem. Theor. Comput. 6, 817-827.

2009:

Nettels, D., Muller-Spath, S., Kuster, F., Hofman, H., Haenni, D, Ruegger, S, Reymond, L., Hoffman, A., Kubelka, J., Heinz, B., Gast, K., Best, R. and Schuler, B. (2009) “Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins.” Proc. Natl. Acad. Sci. U.S.A. 106, 20740-20745.

Kubelka, J. (2009) “Time-resolved methods in Biophysics 9: Laser temperature-jump methods for investigation of biomolecular dynamics.” Photochem. Photobiol. Sci. 8, 499-512.

Kubelka, J. and Bour, P. (2009) “Simulation of the vibrational spectra of large molecules by arbitrary time propagation.” J. Chem. Theor. Comput. 5, 200-207.

Murza A. and Kubelka, J. (2009) “Beyond the nearest neighbor Zimm-Bragg model for helix-coil transition in peptides.” Biopolymers 91, 120-131.

Ackels L. A., Stawski, P., Amunson, K. E. and Kubelka, J. (2009) “On the temperature dependence of the amide I infrared intensities of peptides in solution” Vibr. Specrosc. 50, 2-9.

2008:

Kubelka, J., Henry, E. R., Cellmer, T., Hofrichter, J. and Eaton, W. A. (2008) “Chemical, physical and theoretical kinetics of an ultrafast folding protein” Proc. Natl. Acad. Sci. U.S.A. 105, 18655-18662.

Amunson, K. E., Ackels, L. A. and Kubelka, J. (2008) “Site-specific unfolding thermodynamics of a helix-turn-helix protein." J. Am Chem. Soc. 130, 8146-8147.

Godoy-Ruiz, R., Henry, E. R., Kubelka, J., Hofrichter, J., Muñoz ,V., Sanchez-Ruiz, J. M., and Eaton, W. A. (2008) “Estimating free-energy barrier heights for an ultrafast folding protein from calorimetric and kinetic data.” J. Phys. Chem. B. 112, 5938-5949.

2007:

Huang, R., Setnicka, V., Etienne, M. A., Kim, J., Kubelka, J., Hammer, R. P. and Keiderling, T. A. (2007) “Cross-strand coupling of a b-hairpin peptide stabilized with an Aib-Gly turn using isotope-edited IR spectroscopy” J. Am. Chem. Soc. 129, 13592-13603.

Amunson, K. E. and Kubelka, J., (2007) “On the temperature dependence of amide vibrational frequencies of peptides in solution.” J. Phys. Chem. B 111, 9993-9998.

Cellmer, T., Henry, E. R.,Kubelka, J., Hofrichter, J. and Eaton, W. A. (2007) “Relaxation rate for an ultrafast folding protein is independent of chemical denaturant concentration” J. Am. Chem. Soc. 129, 14564-14565.

Turner, D. A. and Kubelka, J., (2007) “Infrared and vibrational CD spectra of partially solvated a-helices: DFT-based simulations with explicit solvent.” J. Phys. Chem. B 111, 1834-1845.

2006:

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

Kubelka, J., Kim, J., Bour P. and Keiderling T. A. (2006) “Contribution of transition dipole coupling to amide coupling in IR spectra of peptide secondary structures.” Vibr. Spectrosc. 42, 63-73.

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

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

2005:

Chiu, T., Kubelka, J., Herbst-Irmer, R., Eaton, W. A., Hofrichter, J. and Davies, D. (2005) “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.

Kubelka, J., Huang, R. and Keiderling, T. A. (2005) “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.

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

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

Ancient History:

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

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

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

Hilario, J., Kubelka, J. and Keiderling, T. A. (2003) “Optical spectroscopic investigations of model b-sheet hairpins in aqueous solutions.” J. Am. Chem. Soc. 125, 7562-7574.

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

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

Kubelka, J. and Keiderling T.A. (2002) “Discrimination between peptide 310- from a-helices. Theoretical analysis of the impact of a-methyl substitution on experimental spectra.” J. Am. Chem. Soc. 124, 5325-5332.

Hilario, J., Kubelka, J., Syud, F. A., Gellman, S. H. and Keiderling, T. A.(2002) “Spectroscopic characterization of selected b-sheet models.” Biospectroscopy 67, 233-236,.

Kubelka, J. and Keiderling, T. A. (2001) “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,.

Kubelka, J. and Keiderling, T. A. (2001) “Differentiation of b-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.

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

Silva, R. A. G. D., Kubelka, J., Bour, P., Decatur, S. M. and Keiderling, T. A.(2000) “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.

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

Pancoska, P., Kubelka, J. and Keiderling, T. A.(1999) “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.

Kubelka, J., Pancoska, P. and Keiderling, T. A. (1999) “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.

El-Azhary, A. A., Suter, H. U. and Kubelka, J. (1998) “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.

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

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

Book Chapters:

Buchner, G. S. and Kubelka, J. (2012) "Isotope-Edited Infrared Spectroscopy." In Intrinsically Disordered Protein Analysis: Vol. 2, Methods and Experimental Tools (Methods in Molecular Biology), Uversky, V. N. and Dunker, A. K. (eds.), Springer NY, pp. 347-358.

Kubelka, J., Bour, P. and Keiderling, T. A. (2009) “Quantum mechanical calculations of peptide vibrational force fields and spectral intensities.” In Biomedical Applications of Infrared Spectroscopy, Barth, A. and Haris, P. I. (eds.), IOS Press, Amsterdam, pp. 178-223.

Keiderling, T. A., Kubelka, J. and Hilario, J. (2006) “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.

Keiderling, T. A., Huang, R., Kubelka, J., Bour, P., Setnicka, V., Hammer, R. P., Etienne, M. A., Silva, R. A. G. D. and Decatur, S. M. (2005) "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.

Kubelka, J., Buscaglia, M., Hofrichter, J. and Eaton, W. A (2005) “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.

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

Kubelka, J., Pancoska, P. and Keiderling, T. A. (1999) “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.), Dordrecht, Kluwer Academic Publishers, pp. 67-68.


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