Jan Kubelka, Ph.D. - Publications

Affiliations: 
2002 University of Illinois at Chicago, Chicago, IL, United States 
Area:
General Biophysics, Physical Chemistry

66 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Choi JK, Haynie BE, Tohgha U, Pap L, Elliott KW, Leonard BM, Dzyuba SV, Varga K, Kubelka J, Balaz M. Chirality Inversion of CdSe and CdS Quantum Dots Without Changing the Stereochemistry of Capping Ligand. Acs Nano. PMID 26938741 DOI: 10.1021/acsnano.6b00567  1
2015 Lai JK, Kubelka GS, Kubelka J. Sequence, structure, and cooperativity in folding of elementary protein structural motifs. Proceedings of the National Academy of Sciences of the United States of America. 112: 9890-5. PMID 26216963 DOI: 10.1073/pnas.1506309112  1
2015 Anderson BA, Literati A, Ball B, Kubelka J. Temperature dependence of C-terminal carboxylic group IR absorptions in the amide I' region. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 134: 473-83. PMID 25036456 DOI: 10.1016/j.saa.2014.06.102  1
2015 Anderson BA, Kubelka GS, Kubelka J. Temperature dependence of peptide carboxylic group IR spectra in the amide I′ region at neutral and acidic pH Vibrational Spectroscopy. 77: 40-50. DOI: 10.1016/j.vibspec.2015.02.005  1
2014 Kota P, Buchner G, Chakraborty H, Dang YL, He H, Garcia GJ, Kubelka J, Gentzsch M, Stutts MJ, Dokholyan NV. The N-terminal domain allosterically regulates cleavage and activation of the epithelial sodium channel. The Journal of Biological Chemistry. 289: 23029-42. PMID 24973914 DOI: 10.1074/jbc.M114.570952  1
2014 Kubelka GS, Kubelka J. Site-specific thermodynamic stability and unfolding of a de novo designed protein structural motif mapped by 13C isotopically edited IR spectroscopy. Journal of the American Chemical Society. 136: 6037-48. PMID 24684597 DOI: 10.1021/ja500918k  1
2014 Sargsyan G, Leonard BM, Kubelka J, Balaz M. Supramolecular ssDNA templated porphyrin and metalloporphyrin nanoassemblies with tunable helicity. Chemistry (Weinheim An Der Bergstrasse, Germany). 20: 1878-92. PMID 24458504 DOI: 10.1002/chem.201304153  1
2014 Anderson BA, Literati A, Ball B, Kubelka J. Temperature dependence of amino acid side chain IR absorptions in the amide I' region. Biopolymers. 101: 536-48. PMID 24122549 DOI: 10.1002/bip.22416  1
2013 Tohgha U, Deol KK, Porter AG, Bartko SG, Choi JK, Leonard BM, Varga K, Kubelka J, Muller G, Balaz M. Ligand induced circular dichroism and circularly polarized luminescence in CdSe quantum dots. Acs Nano. 7: 11094-102. PMID 24200288 DOI: 10.1021/nn404832f  1
2013 Chi H, Welch WR, Kubelka J, Keiderling TA. Insight into the packing pattern of β2 fibrils: a model study of glutamic acid rich oligomers with 13C isotopic edited vibrational spectroscopy. Biomacromolecules. 14: 3880-91. PMID 24053614 DOI: 10.1021/bm401015f  1
2013 Kubelka J. Multivariate analysis of spectral data with frequency shifts: application to temperature dependent infrared spectra of peptides and proteins. Analytical Chemistry. 85: 9588-95. PMID 24028416 DOI: 10.1021/ac402083p  1
2013 Welch WR, Kubelka J, Keiderling TA. Infrared, vibrational circular dichroism, and Raman spectral simulations for β-sheet structures with various isotopic labels, interstrand, and stacking arrangements using density functional theory. The Journal of Physical Chemistry. B. 117: 10343-58. PMID 23924300 DOI: 10.1021/jp4056126  1
2013 Welch WR, Keiderling TA, Kubelka J. Structural analyses of experimental 13C edited amide I' IR and VCD for peptide β-sheet aggregates and fibrils using DFT-based spectral simulations. The Journal of Physical Chemistry. B. 117: 10359-69. PMID 23924239 DOI: 10.1021/jp405613r  1
2013 Sedghi M, Goual L, Welch W, Kubelka J. Effect of asphaltene structure on association and aggregation using molecular dynamics. The Journal of Physical Chemistry. B. 117: 5765-76. PMID 23581711 DOI: 10.1021/jp401584u  1
2013 Topchiy E, Armstrong GS, Boswell KI, Buchner GS, Kubelka J, Lehmann TE. T1BT* structural study of an anti-plasmodial peptide through NMR and molecular dynamics. Malaria Journal. 12: 104. PMID 23506240 DOI: 10.1186/1475-2875-12-104  1
2013 Sargsyan G, Schatz AA, Kubelka J, Balaz M. Formation and helicity control of ssDNA templated porphyrin nanoassemblies. Chemical Communications (Cambridge, England). 49: 1020-2. PMID 23258275 DOI: 10.1039/c2cc38150h  1
2012 Welch WR, Kubelka J. DFT-based simulations of amide I' IR spectra of a small protein in solution using empirical electrostatic map with a continuum solvent model. The Journal of Physical Chemistry. B. 116: 10739-47. PMID 22891757 DOI: 10.1021/jp305387x  1
2012 Buchner GS, Shih N, Reece AE, Niebling S, Kubelka J. Unusual cold denaturation of a small protein domain. Biochemistry. 51: 6496-8. PMID 22871296 DOI: 10.1021/bi300916v  1
2012 Buchner GS, Kubelka J. Isotope-edited infrared spectroscopy. Methods in Molecular Biology (Clifton, N.J.). 895: 347-58. PMID 22760327 DOI: 10.1007/978-1-61779-927-3_20  1
2012 Lai J, Jin J, Kubelka J, Liberles DA. A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function. Journal of Molecular Biology. 422: 442-59. PMID 22651983 DOI: 10.1016/j.jmb.2012.05.028  1
2011 Grahnen JA, Nandakumar P, Kubelka J, Liberles DA. Biophysical and structural considerations for protein sequence evolution. Bmc Evolutionary Biology. 11: 361. PMID 22171550 DOI: 10.1186/1471-2148-11-361  1
2011 Amunson KE, Anderson BA, Kubelka J. Temperature effects on the optical path length of infrared liquid transmission cells. Applied Spectroscopy. 65: 1307-13. PMID 22054091 DOI: 10.1366/11-06405  1
2011 Grahnen JA, Kubelka J, Liberles DA. Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolution. Journal of Molecular Evolution. 73: 23-33. PMID 21800121 DOI: 10.1007/s00239-011-9454-3  1
2011 Kaminský J, Kubelka J, Bour P. Theoretical modeling of peptide α-helical circular dichroism in aqueous solution. The Journal of Physical Chemistry. A. 115: 1734-42. PMID 21322543 DOI: 10.1021/jp110418w  1
2011 Kaminský J, Bouř P, Kubelka J. Simulations of the temperature dependence of amide I vibration. The Journal of Physical Chemistry. A. 115: 30-4. PMID 21141980 DOI: 10.1021/jp1084839  1
2011 Buchner GS, Murphy RD, Buchete NV, Kubelka J. Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory. Biochimica Et Biophysica Acta. 1814: 1001-20. PMID 20883829 DOI: 10.1016/j.bbapap.2010.09.013  1
2010 Paulson LO, Kaminský J, Anderson DT, Bouř P, Kubelka J. Theoretical Study of Vibrationally Averaged Dipole Moments for the Ground and Excited C═O Stretching States of trans-Formic Acid. Journal of Chemical Theory and Computation. 6: 817-27. PMID 26613309 DOI: 10.1021/ct900608t  1
2010 Grahnen JA, Amunson KE, Kubelka J. DFT-based simulations of IR amide I' spectra for a small protein in solution. Comparison of explicit and empirical solvent models. The Journal of Physical Chemistry. B. 114: 13011-20. PMID 20857992 DOI: 10.1021/jp106639s  1
2009 Kubelka J, Bouř P. Simulation of Vibrational Spectra of Large Molecules by Arbitrary Time Propagation. Journal of Chemical Theory and Computation. 5: 200-7. PMID 26609833 DOI: 10.1021/ct800298n  1
2009 Nettels D, Müller-Späth S, Küster F, Hofmann H, Haenni D, Rüegger S, Reymond L, Hoffmann A, Kubelka J, Heinz B, Gast K, Best RB, Schuler B. Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins. Proceedings of the National Academy of Sciences of the United States of America. 106: 20740-5. PMID 19933333 DOI: 10.1073/pnas.0900622106  1
2009 Kubelka J. Time-resolved methods in biophysics. 9. Laser temperature-jump methods for investigating biomolecular dynamics. Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society For Photobiology. 8: 499-512. PMID 19337664 DOI: 10.1039/b819929a  1
2009 Murza A, Kubelka J. Beyond the nearest-neighbor Zimm-Bragg model for helix-coil transition in peptides. Biopolymers. 91: 120-31. PMID 18814306 DOI: 10.1002/bip.21093  1
2009 Kubelka J, Bouř P, Keiderling TA. Quantum mechanical calculations of peptide vibrational force fields and spectral intensities Advances in Biomedical Spectroscopy. 2: 178-223. DOI: 10.3233/978-1-60750-045-2-178  1
2009 Ackels L, Stawski P, Amunson KE, Kubelka J. On the temperature dependence of amide I intensities of peptides in solution Vibrational Spectroscopy. 50: 2-9. DOI: 10.1016/j.vibspec.2008.07.004  1
2008 Kubelka J, Henry ER, Cellmer T, Hofrichter J, Eaton WA. Chemical, physical, and theoretical kinetics of an ultrafast folding protein Proceedings of the National Academy of Sciences of the United States of America. 105: 18655-18662. PMID 19033473 DOI: 10.1073/pnas.0808600105  1
2008 Amunson KE, Ackels L, Kubelka J. Site-specific unfolding thermodynamics of a helix-turn-helix protein. Journal of the American Chemical Society. 130: 8146-7. PMID 18529000 DOI: 10.1021/ja802185e  1
2008 Godoy-Ruiz R, Henry ER, Kubelka J, Hofrichter J, Muñoz V, Sanchez-Ruiz JM, Eaton WA. Estimating free-energy barrier heights for an ultrafast folding protein from calorimetric and kinetic data Journal of Physical Chemistry B. 112: 5938-5949. PMID 18278894 DOI: 10.1021/jp0757715  1
2007 Cellmer T, Henry ER, Kubelka J, Hofrichter J, Eaton WA. Relaxation rate for an ultrafast folding protein is independent of chemical denaturant concentration Journal of the American Chemical Society. 129: 14564-14565. PMID 17983235 DOI: 10.1021/ja0761939  1
2007 Huang R, Setnicka V, Etienne MA, Kim J, Kubelka J, Hammer RP, Keiderling TA. Cross-strand coupling of a beta-hairpin peptide stabilized with an Aib-Gly turn studied using isotope-edited IR spectroscopy. Journal of the American Chemical Society. 129: 13592-603. PMID 17929810 DOI: 10.1021/ja0736414  1
2007 Amunson KE, Kubelka J. On the temperature dependence of amide I frequencies of peptides in solution. The Journal of Physical Chemistry. B. 111: 9993-8. PMID 17676791 DOI: 10.1021/jp072454p  1
2007 Turner DR, Kubelka J. Infrared and vibrational CD spectra of partially solvated alpha-helices: DFT-based simulations with explicit solvent. The Journal of Physical Chemistry. B. 111: 1834-45. PMID 17256894 DOI: 10.1021/jp0666840  1
2006 Kim J, Huang R, Kubelka J, Bou Rcaron P, Keiderling TA. Simulation of infrared spectra for beta-hairpin peptides stabilized by an Aib-Gly turn sequence: correlation between conformational fluctuation and vibrational coupling. The Journal of Physical Chemistry. B. 110: 23590-602. PMID 17107215 DOI: 10.1021/jp0640575  1
2006 Magg C, Kubelka J, Holtermann G, Haas E, Schmid FX. Specificity of the Initial Collapse in the Folding of the Cold Shock Protein Journal of Molecular Biology. 360: 1067-1080. PMID 16815441 DOI: 10.1016/j.jmb.2006.05.073  1
2006 Kubelka J, Chiu TK, Davies DR, Eaton WA, Hofrichter J. Sub-microsecond protein folding. Journal of Molecular Biology. 359: 546-53. PMID 16643946 DOI: 10.1016/j.jmb.2006.03.034  1
2006 Kubelka J, Kim J, Bour P, Keiderling TA. Contribution of transition dipole coupling to amide coupling in IR spectra of peptide secondary structures Vibrational Spectroscopy. 42: 63-73. DOI: 10.1016/j.vibspec.2006.04.003  1
2005 Kubelka J, Huang R, Keiderling TA. Solvent effects on IR and VCD spectra of helical peptides: DFT-based static spectral simulations with explicit water. The Journal of Physical Chemistry. B. 109: 8231-43. PMID 16851962 DOI: 10.1021/jp0506078  1
2005 Chiu TK, Kubelka J, Herbst-Irmer R, Eaton WA, Hofrichter J, Davies DR. High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein. Proceedings of the National Academy of Sciences of the United States of America. 102: 7517-22. PMID 15894611 DOI: 10.1073/pnas.0502495102  1
2005 Setnicka V, Huang R, Thomas CL, Etienne MA, Kubelka J, Hammer RP, Keiderling TA. IR study of cross-strand coupling in a beta-hairpin peptide using isotopic labels. Journal of the American Chemical Society. 127: 4992-3. PMID 15810813 DOI: 10.1021/ja043007f  1
2005 Buscaglia M, Kubelka J, Eaton WA, Hofrichter J. Determination of ultrafast protein folding rates from loop formation dynamics Journal of Molecular Biology. 347: 657-664. PMID 15755457 DOI: 10.1016/j.jmb.2005.01.057  1
2004 Kubelka J, Hofrichter J, Eaton WA. The protein folding 'speed limit' Current Opinion in Structural Biology. 14: 76-88. PMID 15102453 DOI: 10.1016/j.sbi.2004.01.013  1
2004 Huang R, Kubelka J, Barber-Armstrong W, Silva RA, Decatur SM, Keiderling TA. Nature of vibrational coupling in helical peptides: an isotopic labeling study. Journal of the American Chemical Society. 126: 2346-54. PMID 14982438 DOI: 10.1021/ja037998t  1
2003 Hilario J, Kubelka J, Keiderling TA. Optical spectroscopic investigations of model beta-sheet hairpins in aqueous solution. Journal of the American Chemical Society. 125: 7562-74. PMID 12812496 DOI: 10.1021/ja030039e  1
2003 Kubelka J, Eaton WA, Hofrichter J. Experimental tests of villin subdomain folding simulations Journal of Molecular Biology. 329: 625-630. PMID 12787664 DOI: 10.1016/S0022-2836(03)00519-9  1
2002 Silva RA, Yasui SC, Kubelka J, Formaggio F, Crisma M, Toniolo C, Keiderling TA. Discriminating 3(10)- from alpha-helices: vibrational and electronic CD and IR absorption study of related Aib-containing oligopeptides. Biopolymers. 65: 229-43. PMID 12382284 DOI: 10.1002/bip.10241  1
2002 Bour P, Kubelka J, Keiderling TA. Ab initio quantum mechanical models of peptide helices and their vibrational spectra. Biopolymers. 65: 45-59. PMID 12209472 DOI: 10.1002/bip.10224  1
2002 Hilario J, Kubelka J, Syud FA, Gellman SH, Keiderling TA. Spectroscopic characterization of selected beta- sheet hairpin models. Biopolymers. 67: 233-6. PMID 12012436 DOI: 10.1002/bip.10094  1
2002 Kubelka J, Silva RA, Keiderling TA. Discrimination between peptide 3(10)- and alpha-helices. Theoretical analysis of the impact of alpha-methyl substitution on experimental spectra. Journal of the American Chemical Society. 124: 5325-32. PMID 11996573 DOI: 10.1021/ja012685o  1
2002 Kubelka J, Bour P, Silva RAGD, Decatur SM, Keiderling TA. Chirality in peptide vibrations: Ab initio computational studies of length, solvation, hydrogen bond, dipole coupling, and isotope effects on vibrational CD Acs Symposium Series. 810: 50-64.  1
2001 Kubelka J, Keiderling TA. Differentiation of beta-sheet-forming structures: ab initio-based simulations of IR absorption and vibrational CD for model peptide and protein beta-sheets. Journal of the American Chemical Society. 123: 12048-58. PMID 11724613 DOI: 10.1021/ja0116627  1
2001 Kubelka J, Keiderling TA. The anomalous infrared amide I intensity distribution in (13)C isotopically labeled peptide beta-sheets comes from extended, multiple-stranded structures: an ab initio study. Journal of the American Chemical Society. 123: 6142-50. PMID 11414848 DOI: 10.1021/ja010270x  1
2001 Kubelka J, Keiderling TA. Ab initio calculation of amide carbonyl stretch vibrational frequencies in solution with modified basis sets. 1. JV-methyl acetamide Journal of Physical Chemistry A. 105: 10922-10928.  1
2000 Silva RA, Kubelka J, Bour P, Decatur SM, Keiderling TA. Site-specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution. Proceedings of the National Academy of Sciences of the United States of America. 97: 8318-23. PMID 10880566 DOI: 10.1073/pnas.140161997  1
2000 Bour P, Kubelka J, Keiderling TA. Simulations of oligopeptide vibrational CD: effects of isotopic labeling. Biopolymers. 53: 380-95. PMID 10738200 DOI: 10.1002/(SICI)1097-0282(20000415)53:5<380::AID-BIP3>3.0.CO;2-R  1
1999 Kubelka J, Pancoska P, Keiderling TA. 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 Applied Spectroscopy. 53: 666-671.  1
1999 Pancoska P, Kubelka J, Keiderling TA. 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 Applied Spectroscopy. 53: 655-665.  1
1998 El-Azhary AA, Suter HU, Kubelka J. Experimental and theoretical investigation of the geometry and vibrational frequencies of 1,2,3-triazole, 1,2,4-triazole, and tetrazole anions Journal of Physical Chemistry A. 102: 620-629.  1
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