Search Results - "Kubelka, J"

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 by Kubelka, J, Keiderling, T A

“…Ab initio based calculations of force fields and atomic polar tensors are used to simulate amide I infrared absorption spectra for a series of isotopically…”
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Differentiation of β-Sheet-Forming Structures:  Ab Initio-Based Simulations of IR Absorption and Vibrational CD for Model Peptide and Protein β-Sheets by Kubelka, Jan, Keiderling, Timothy A

“…Ab initio quantum mechanical computations of force fields (FF) and atomic polar and axial tensors (APT and AAT) were carried out for triamide strands…”
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Spectroscopic characterization of selected β- sheet hairpin models by Hilario, Jovencio, Kubelka, Jan, Syud, Faisal A., Gellman, Samuel H., Keiderling, Timothy A.

“…The IR and vibrational circular dichroism (VCD) spectra of a model two‐stranded β hairpin are compared to those of a related cyclic two‐stranded model, which…”
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The protein folding ‘speed limit’ by Kubelka, Jan, Hofrichter, James, Eaton, William A

“…How fast can a protein possibly fold? This question has stimulated experimentalists to seek fast folding proteins and to engineer them to fold even faster…”
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Experimental and Theoretical Investigation of the Geometry and Vibrational Frequencies of 1,2,3-Triazole, 1,2,4-Triazole, and Tetrazole Anions by El-Azhary, A. A, Suter, H. U, Kubelka, J

“…Optimized geometries, vibrational frequencies, scale factors, and IR absorption intensities were calculated for the 1,2,3-triazole anion (1) at the B3LYP, LDA,…”
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Experimental Tests of Villin Subdomain Folding Simulations by Kubelka, Jan, Eaton, William A., Hofrichter, James

“…We have used laser temperature-jump to investigate the kinetics and mechanism of folding the 35 residue subdomain of the villin headpiece. The relaxation…”
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Ab Initio Calculation of Amide Carbonyl Stretch Vibrational Frequencies in Solution with Modified Basis Sets. 1. N-Methyl Acetamide by Kubelka, Jan, Keiderling, Timothy A

“…Density functional theory DFT(BPW91) level calculations with modified 6-31G(d) basis sets are tested for a small amide, N-methyl acetamide (NMA), as an…”
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High-Resolution X-Ray Crystal Structures of the Villin Headpiece Subdomain, an Ultrafast Folding Protein by Chiu, Thang K., Kubelka, Jan, Herbst-Irmer, Regine, Eaton, William A., Hofrichter, James, Davies, David R.

“…The 35-residue subdomain of the villin headpiece (HP35) is a small ultrafast folding protein that is being intensely studied by experiments, theory, and…”
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Solvent Effects on IR and VCD Spectra of Helical Peptides:  DFT-Based Static Spectral Simulations with Explicit Water by Kubelka, Jan, Huang, Rong, Keiderling, Timothy A

“…Simulations of IR and VCD spectra are carried out for model α-helical, 310-helical, and 31-helical (polyProII-like) oligopeptides, with up to 21 amide groups,…”
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Optical Spectroscopic Investigations of Model β-Sheet Hairpins in Aqueous Solution by Hilario, Jovencio, Kubelka, Jan, Keiderling, Timothy A

“…In this contribution we report optical spectroscopic data on a series of designed β hairpins previously shown by NMR to contain a substantial population of…”
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Ab initio quantum mechanical models of peptide helices and their vibrational spectra by Bour, Petr, Kubelka, Jan, Keiderling, Timothy A.

“…Structural parameters for standard peptide helices (α, 310, 31 left‐handed) were fully ab initio optimized for Ac–(L‐Ala)9–NHMe and for Ac–(L‐Pro)9–NHMe…”
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Nature of Vibrational Coupling in Helical Peptides:  An Isotopic Labeling Study by Huang, Rong, Kubelka, Jan, Barber-Armstrong, Wendy, Silva, R. A. G. D, Decatur, Sean M, Keiderling, Timothy A

“…Infrared (IR) and vibrational circular dichroism (VCD) spectra were measured for a series of isotopically (13C on two or more amide CO) labeled, 25 residue,…”
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Discrimination between peptide 3(10)- and alpha-helices. Theoretical analysis of the impact of alpha-methyl substitution on experimental spectra by Kubelka, Jan, Silva, R A Gangani D, Keiderling, Timothy A

“…Detailed spectral simulations based on ab initio density functional theory computations of the amide I and II infrared (IR) and vibrational circular dichroism…”
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Determination of Ultrafast Protein Folding Rates from Loop Formation Dynamics by Buscaglia, Marco, Kubelka, Jan, Eaton, William A., Hofrichter, James

“…Quenching of the triplet state of tryptophan by contact with cysteine can be used to measure the kinetics of loop formation in unfolded proteins. Here we show…”
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Specificity of the Initial Collapse in the Folding of the Cold Shock Protein by Magg, Christine, Kubelka, Jan, Holtermann, Georg, Haas, Elisha, Schmid, Franz X.

“…The two-state folding reaction of the cold shock protein from Bacillus caldolyticus ( Bc-Csp) is preceded by a rapid chain collapse. A fast shortening of…”
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Site-Specific Conformational Determination in Thermal Unfolding Studies of Helical Peptides Using Vibrational Circular Dichroism with Isotopic Substitution by R. A. G. D. Silva, Kubelka, Jan, Bour, Petr, Decatur, Sean M., Keiderling, Timothy A.

“…Understanding the detailed mechanism of protein folding requires dynamic, site-specific stereochemical information. The short time response of vibrational…”
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IR Study of Cross-Strand Coupling in a β-Hairpin Peptide Using Isotopic Labels by Setnička, Vladimír, Huang, Rong, Thomas, Catherine L, Etienne, Marcus A, Kubelka, Jan, Hammer, Robert P, Keiderling, Timothy A

“…Model β-hairpin peptides can be used to develop understanding of fundamental elements of β-sheet secondary structure formation and stability. We have studied…”
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Discriminating 3(10)- from alpha-helices: vibrational and electronic CD and IR absorption study of related Aib-containing oligopeptides by Silva, R A Gangani D, Yasui, Sritana C, Kubelka, Jan, Formaggio, Fernando, Crisma, Marco, Toniolo, Claudio, Keiderling, Timothy A

“…Model peptides based on -(Aib-Ala)(n)-, and (Aib)(n)-Leu-(Aib)(2) sequences, which have varying amounts of 3(10)-helical character, were studied by use of…”
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Simulations of oligopeptide vibrational CD: Effects of isotopic labeling by Bour, Petr, Kubelka, Jan, Keiderling, Timothy A.

“…Simulated ir absorption and vibrational CD (VCD) spectra of four alanine‐based octapeptides, each having its main chain constrained to a different secondary…”
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Q-switching and mode-locking Nd-YAP laser (1.34 μm) with BDN II by JELINEK, M, JELINKOVA, H, KUBELKA, J

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