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J Kubelka

Publications and source records attributed to J Kubelka.

9 recordsLinked to original sources
PubMed2001

Differentiation of beta-sheet-forming structures: ab initio-based simulations of IR absorption and vibrational CD for model peptide and protein beta-sheets.

Ab initio quantum mechanical computations of force fields (FF) and atomic polar and axial tensors (APT and AAT) were carried out for triamide strands Ac-A-A-NH-CH(3) clustered into single-, double-, and triple-strand beta-sheet-like conformations. Models with phi, psi, and omega angles constrained to values appropriate for planar antiparallel and parallel as well as coiled antiparallel (two-stranded) and twisted antiparallel and parallel sheets were computed. The FF, APT, and AAT values were transferred to corresponding larger oligopeptide beta-sheet structures of up to five strands of eight residues each, and their respective IR and vibrational circular dichroism (VCD) spectra were simulated. The antiparallel planar models in a multiple-stranded assembly give a unique IR amide I spectrum with a high-intensity, low-frequency component, but they have very weak negative amide I VCD, both reflecting experimental patterns seen in aggregated structures. Parallel and twisted beta-sheet structures do not develop a highly split amide I, their IR spectra all being similar. A twist in the antiparallel beta-sheet structure leads to a significant increase in VCD intensity, while the parallel structure was not as dramatically affected by the twist. The overall predicted VCD intensity is quite weak but predominantly negative (amide I) for all conformations. This intrinsically weak VCD can explain the high variation seen experimentally in beta-forming peptides and proteins. An even larger variation was predicted in the amide II VCD, which had added complications due to non-hydrogen-bonded residues on the edges of the model sheets.

Circular Dichroism↗
PubMed2001

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.

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 substituted (Ac-A(12)-NH-CH(3))(n)() peptides clustered in an antiparallel beta-sheet conformation having a varying number of strands, n = 2-5. The results demonstrate that the anomalous intensity previously reported for the isotopically shifted amide I in (13)C labeled peptides is due to formation of multistranded beta-sheet structures in this conformation. Computations show that the characteristic widely split amide I mode for beta-sheet polypeptides as well as this anomalous intensity enhancement in isotopically substituted beta-sheet peptides grows with increasing sheet size. For sheets of five strands, qualitative and near quantitative agreement with experimental amide I intensity patterns is obtained for both labeled and unlabeled peptides. The strongest transitions primarily represent in-phase coupled modes of the (13)C labeled, next nearest neighbor amides on the inner strands of the multistranded beta-sheet. Long-range transition dipole coupling interactions do not promote the (13)C amide I intensity enhancement. Understanding of the IR intensity mechanisms with this level of detail for the isotopically labeled peptides permits design of site-specific probes of beta-sheet folding and unfolding dynamics.

Alanine↗
PubMed2000

Site-specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution.

Understanding the detailed mechanism of protein folding requires dynamic, site-specific stereochemical information. The short time response of vibrational spectroscopies allows evaluation of the distribution of populations in rapid equilibrium as the peptide unfolds. Spectral shifts associated with isotopic labels along with local stereochemical sensitivity of vibrational circular dichroism (VCD) allow determination of the segment sequence of unfolding. For a series of alanine-rich peptides that form alpha-helices in aqueous solution, we used isotopic labeling and VCD to demonstrate that the alpha-helix noncooperatively unwinds from the ends with increasing temperature. For these blocked peptides, the C-terminal is frayed at 5 degrees C. Ab initio level theoretical simulations of the IR and VCD band shapes are used to analyze the spectra and to confirm the conformation of the labeled components. The VCD signals associated with the labeled residues are amplified by coupling to the nonlabeled parts of the molecule. Thus small labeled segments are detectable and stereochemically defined in moderately large peptides in this report of site-specific peptide VCD conformational analysis.

Amino Acid Sequence↗
PubMed2000

Simulations of oligopeptide vibrational CD: effects of isotopic labeling.

Simulated ir absorption and vibrational CD (VCD) spectra of four alanine-based octapeptides, each having its main chain constrained to a different secondary structure conformation, were analyzed and compared with experimental results for several different peptides. The octapeptide simulations were based on transfer of property tensors from a series of ab initio calculations for a short L-alanine based segment containing 3 peptide bonds with relative straight phi, psi angles fixed to those appropriate for alpha-helix, 3(10)-helix, ProII-like helix, and beta-sheet-like strand. The tripeptide force field (FF) and atomic polar tensors were obtained with density functional theory techniques at the BPW91/6-31G** level and the atomic axial tensor at the mixed BPW91/6-31G**/HF/6-31G level. Allowing for frequency correction due to the FF limitations, the octapeptide results obtained are qualitatively consistent with experimental observations for ir and VCD spectra of polypeptides and oligopeptides in established conformations. In all cases, the correct VCD sign patterns for the amide I and II bands were predicted, but the intensities did have some variation from the experimental patterns. Predicted VCD changes upon deuteration of either the peptide or side-chains as well as for (13)C isotopic labeling of the amide C=O at specific sites in the peptide chain were computed for analysis of experimental observations. A combination of theoretical modeling with experimental data for labeled compounds leads both to enhanced resolution of component transitions and added conformational applicability of the VCD spectra.

Alanine↗
PubMed1998

Noncontact Er:YAG laser ablation: clinical evaluation.

OBJECTIVE: The aim of this study is to evaluate the quality of laser ablation in comparison with the classical drilling preparation. METHODS: For the experiment, the Er:YAG laser drilling machine was used. The system had a laser head, water cooler, and power supply with automatic control. Spot size of 300-350 microns was used for the preparation. Repetition rate of 1-4 Hz, and pulse energies of 100-400 mJ with water spray were chosen. Cavity shape in comparison with classical drill, time of preparation, and influence of cavity shape on filling materials retention in accordance with the U.S. Public Health Service System were used. The evaluation criteria for noncontact Er:YAG ablation were done. RESULTS: The cavity shape is irregular, but spot surface has larger area and microretentive appearance. Caries of enamel and dentin were treated with a noncontact preparation. It was possible to remove the old insufficient fillings, except for amalgam or metal alloys. The average number of pulses was 111.22 (SE 67.57). Vibrations of microexplosions during preparation were felt by patients on 14 cavities; however, nobody felt unpleasant pain. The qualities of filling materials in laser cavities were very stable; however, cavo surface margin discoloration of 82-86% of Alfa rating could be a problem. Changes of the color and anatomic form of the tooth were observed in 4-8%. CONCLUSIONS: In comparison with the classical treatment, it could be said that the retention and quality of filling materials is the same or very similar.

Adult↗
PubMed1997

Dentin and pulp response to Erbium:YAG laser ablation: a preliminary evaluation of human teeth.

OBJECTIVE: We determined the real effect of Erbium:YAG laser ablation on human teeth in vivo. SUMMARY BACKGROUND DATA: We advocated the idea that overheating of teeth, specially pulp damage can be avoided if correct laser parameters are used. METHODS: We evaluated human premolars scheduled for extraction during orthodontic treatment. Before tooth extraction, an oval cavity preparation was made with a pulsed Er:YAG laser. After extraction, the teeth were decalcified for 6 weeks. Routine staining with haematoxylin and eosin was performed on longitudinal section. One hundred seventy-two sections were prepared and examined in a light microscope. RESULTS: Under Er:YAG laser application, reduction of the dentin layer was observed. Dentinal tubules had a radial course up to the surface. No cracks or structural injury were observed. Inflammatory reaction in the pulp was not found. The vascularity of the pulp was normal. The odontoblasts were of the usual spindle-like or star-like cell shape. The cementum and epithelial attachment were healthy. No changes of structure or indications of inflammation were observed. CONCLUSIONS: The results of this in vivo experiment on human teeth confirm safety of Er:YAG laser ablation of enamel and dentin under the conditions described.

Adolescent↗