Abstracts of Publications from the Keiderling Group - 1997
160. P. Bour, J. Sopkova, L. Bednarova, P. Malon and T. A. Keiderling. Transfer of molecular property tensors in cartesian coordinates-- a new algorithm for simulation of vibrational spectra. J. Computational Chemistry. 18(1997)646-659.
ABSTRACT
A direct transfer of Cartesian molecular force fields (FF) and electric property tensors is tested on model systems and compared to transfer in internal coordinates with an aim to improve simulation of vibrational spectra for larger molecules. This Cartesian transformation can be implemented easily and offers greater flexibility in practical computations. It can be also applied for transfer of anharmonic derivatives. The results for model calculations of the force field and vibrational frequencies for N-methylacetamide show that our method removes errors associated with numerical artifacts caused by nonlinearity of the otherwise required Cartesian to internal coordinate transformation. For determination of IR absorption and vibrational circular dichroism intensities, atomic polar and axial tensors were also transferred in the Cartesian representation. For the latter, which are dependent upon the magnetic dipole operator, a distributed origin gauge is used to avoid an origin dependence. Comparison of the results of transferring ab initio FF and intensity parameters from an amide dimer fragment onto a tripeptide with those from a conventionally determined tripeptide FF document some limitations of the transfer method and its possible applications in the vibrational spectroscopy. Finally, application to determination of the FF and spectra for helical heptapeptide are presented and compared to experimental results. (C) 1997 by John Wiley & Sons, Inc.
C161. "Vibrational Circular Dichroism Techniques and Application to Nucleic Acids" T. A. Keiderling, In "Biomolecular Structure and Dynamics", NATO ASI series, Series E: Applied Sciences- Vol.342, Eds: G. Vergoten and T. Theophanides, Kl uwer Academic Publ ishers, Dordrecht, The Netherlands, 299-317 (1997).
163. P. Malon and T. A. Keiderling. Theoretical simulation of a polarization modulator based on mechanical rotation of a polarizing element. Applied Optics 36(1997)6141-6148.
ABSTRACT
The properties of three alternative designs for a polarization modulator of potential use for the measurement of vibrational circular dichroism (VCD) are evaluated and compared by use of Mueller calculus. The analysis shows that the combination of a fixed polarizer plus either a photoelastic modulator or a rotating quarter-wave plate possesses nearly the same capability for 1 generation of time-varying, circularly polarized light. However, a modulator composed of a rotating polarizer plus a fixed birefringent plate entails considerable theoretical and experimental difficulties for use in the measurement of VCD spectra. While VCD spectra obtained with the rotating devices can be calibrated in the same manner as spectra obtained with a photoelastic modulator, Mueller analysis shows that the form of the resultant calibration signal will have a different shape. The relevant expressions for VCD and linear dichroism as well as the calibration signals are presented, and consequences for practical realization of these experiments are discussed. (C) 1997 Optical Society of America.
164. S. C. Lee and T. A. Keiderling. Multiphoton Ionization (MPI) spectroscopy of tungsten hexafluoride - exprimental observation of molecular bands. J. Korean Physical Society. 30(1997)434-439.
ABSTRACT
Multiphoton ionization (MPI) spectra of WF6 has been measured with a tunable dye laser excitation and ionization of the molecules in a pulsed free jet molecular beam. The three-photon resonant, six-photon ionization process resulted in better resolved molecular spectra than previously obtained with one-photon absorption of gas phase samples. Temperature variation and power dependency studies were done over the wavelength range from 450 nm to 495 nm. Most bands observed in MPI spectra correlate well with one-photon absorption and electron impact results.
165. C. N. Tam, P. Bour and T. A. Keiderling. An experimental comparison of vibrational circular dichroism and Raman optical activity with 1-amino-2-propanol and 2-amino-1-propanol as model compounds. J. Am. Chem. Soc. 119(1997)7061-7064.
ABSTRACT
Mid-IR vibrational circular dichroism (VCD) and the corresponding Raman optical activity (ROA) spectra of 1-amino-2-propanol and 2-amino-1-propanol in neat solution are compared to yield insight into the dominant structural sensitivity of each technique. The ROA spectra for these isomeric compounds are quite similar while their VCD spectra are substantially different. The contrast between the results with these two techniques can be empirically interpreted to imply that VCD is more sensitive to the overall chirality of a molecule, conformation plus configuration, while ROA is more dependent on the nature of the local environment, or the configuration, of the functional groups. This observation would correlate with VCD having a significant dipolar coupling contribution that is highly dependent on conformation. This distinction between VCD and ROA sensitivities would be expected to be most appropriate for high dipole strength transitions in conformationally unconstrained, open-chain molecules. These observations directly reflect the contrast between current applications of VCD and ROA to biomolecular conformational analyses.
C166. "Novel Approaches to Protein Structural Analyses using Combinations of Optical Spectroscopic Methods (Electronic and vibrational circular dichroism a nd FTIR studies)" P. Pancoska, V. Janota, T. A. Keiderling, Spectroscopy of Biological Molecules: Mo dern Trends, Ed. P. Carmona, R. Navarro, A. Hernanz, Kluwer Acad. Pub., Netherlands (1997) pp. 13-14
C167. "Vibrational Circular Dichroism Characteriz ation of Alanine-Rich Peptides." Gorm Yoder and Timothy A. Keiderling, "Spectroscopy of Biological Molecules: Modern Trends," Ed. P. Carmona, R. Navarro, A. Hernanz, Kluwer Acad. Pub., Netherlands (1997) p p. 27-28
C168. "Measurement of Amide III Vibrational Circular Dichroism of Proteins. Correlation of Spectra to Secondary Structure by Similarity Algorithm" Bernoli I. Baello, Petr Pancoska and Timothy A. Keiderling, "Spectroscopy of Biological Molecules: Modern T rends," Ed. P. Carmona, R. Navarro , A. Hernanz, Kluwer Acad. Pub., Netherlands (1997) pp. 25-26
169. B. I. Baello, P. Pancoska and T. A. Keiderling. Vibrational Circular Dichroism Spectra of Proteins in the Amide III Region- Measurement and Correlation of Bandshape to Secondary Structure. Analytical Biochemistry 250(1997)212-221.
ABSTRACT
Vibrational circular dichroism (VCD) spectra have been measured for 23 globular proteins dissolved in H2O/phosphate buffer over the 1400 to 1100 em(-1) region which encompasses the amide III mode. Spectral responses characteristic of the dominant secondary structure type were found as broad features at similar to 1300 cm(-1), with the extreme forms having positive VCD for highly helical proteins and negative VCD for highly sheet-containing proteins. Quantitative correlation with secondary structure was carried out using previously developed factor analysis and restricted multiple regression (FA/RMR) techniques. Since the absorbance Intensity of the amide III mode is difficult to determine due to overlap with other transitions, an alternative, absolute intensity-independent, simple structural analysis method was used. A linear regression was developed between the fractional components of secondary structure for the protein set and the overlap integrals of the normalized spectra from the set with that of a selected protein. The results of this simple method are quite comparable to those of the FA/RMR approach for analysis with amide III VCD. On the other hand, test calculations with the new method when used with electronic CD spectra are not as good as FA/RMR due to its more intensity-dependent relationship with secondary structure. (C) 1997 Academic Press.
170. S. Wi, P. Pancoska, and T. A. Keiderling. Predictions of Protein Secondary Structures using Factor Analysis using Factor Analysis on Fourier Transform Infrared Spectra. Effect of Self-Deconvolution of the Amide I and Amide II bands. (submitted to Biospectroscopy)
ABSTRACT
Fourier Self Deconvolution (FSD) was performed on the amide I and II regions of Fourier Transform Infrared (FTIR) spectra to test if the resultant increased band shape variation would lead to improvements in protein secondary structure prediction with a Factor Analysis (FA) based method. The FTIR spectra of 23 proteins dissolved in H2O were measured in 6 mm path length cell. Before deconvolution all spectra were normalized to a constant amide I peak absorbance. The deconvolved spectra were renormalized by area so that the deconvolved spectra sets had the same area as before. The factor analysis was done on the deconvolved spectra sets and then a selective multiple linear regression of the coefficients was used to fit to the X-ray-determined fractional components (FC) of secondary structures. Because FA works as a filter for the noise, improvements in the predictions of both helical and sheet fractions were observed even though some noise was retained in the spectra. The best fit and prediction for helix usually occurred with the linear combinations of 3~6 subspectra but the linear combinations of only 2 or 3 subspectra proved best for the sheet. From comparison of different degrees (parameters) of deconvolution, it was found that the helical predictions show slight improvement even in those underdeconvolved sets but loses any advantage from deconvolution rapidly on increasing the filtering in well deconvolved sets. On the other hand, sheet predictions begin to show improvement only in well deconvolved sets of spectra and retains it after filtering.
171. G. Yoder, R. A. G. D. Silva, T. A. Keiderling, A. Polese, F. Formaggio, M. Crisma, C. Toniolo, Q. B. Broxterman, and J. Kamphuis. Conformational Characterization of Terminally Blocked L-(alpha-methyl)valine homo-peptides using Vibrational and Electronic Circular Dichroism. 310 Helical Stabilization by Peptide-peptide Interaction. J. Am. Chem. Soc. 119(1997)10278-10285.
ABSTRACT
Vibrational and electronic circular dichroism (VCD and ECD) and Fourier transform infrared (FTIR) spectra of the homo-oligopeptide series Z-[L-(aMe)Val]n-OtBu (n=3 to 8) and selected Ac-[L-(aMe)Val]n-OtBu oligomers (n = 4, 6, and 8) are presented. This is the first VCD study of a complete homo-peptide series formed exclusively by Ca-methylated amino acids. VCD spectra were measured for the oligomers in TFE and CDCl3 over the amide I and amide II spectral regions (1750-1475 cm-1). These oligopeptides, irrespective of the N-terminal group, were found to indicate formation of at least a partially 310-helical conformation for main-chain lengths as short as n = 4 and fully developed 310-helix by n = 6 at high peptide concentrations. A 310-helical conformation for the octamer is consistent with previous spectroscopic studies and crystallographic results. The ECD spectra were measured for the oligomer series in TFE and HFIP over the 260-190 nm region. The ECD spectra, again for both Na-blocking groups, indicate a helical structure for the octamer, a mixed ordered/unordered structure at n = 6, and a predominantly coil form for n = 4. The octamer ECD bandshape and FTIR absorption maximum are concentration dependent. At higher concentrations the ECD mimics that which has been associated with a 310-helical conformation, while at lower concentrations the ECD is more typical of an a-helix. In the FTIR, the amide I absorbance maximum in TFE shifts from 1661 to 1638 cm-1 on increased dilution. A study of the octamer in HFIP indicates a gradual transition from the 310-like to a-helical like ECD spectra with time. These data are the first evidence of a 310-helix to a-helix equilibrium shift induced by peptide-peptide interactions.
C174. "In search of the earliest events of hCGâ folding: structural studies of the 60-87 peptide fragment" S. Sherman, L. Kirnarsky, O. Prakash, H. M. Rogers, R.A.G.D. Silva, T.A. Keiderling, D. Smith, A.M. Hanly, F. Perini, and R.W. Ruddon, American Pep tide Symposium Proceedings, 1997 (submitted)
C175. "Vibrational and Electronic Circular Dichroism Study of 310-Helical Stabilization in Blocked (aplpha-Me)-Val Based Peptides" Gorm Yoder, T. A. Keiderling, Alessandra Polese, Fe rnando Formaggio, Marco Crisma, Claudio Toniolo, Q. B. Broxterman and J ohan Kamphuis, American Peptide Symposium Proceedings, 1997 (submitted)
C176. "Cold Denaturation Studies of (LKELPKEL)n Peptide Using Vibrational Circular Dichroism and FTIR". R. A. G. D. Silva, Vladimir Baumruk, Petr Pancoska, T. A. Keiderling, Eric Lacassie, and Yves Trudelle, American Peptide Symposium Proceedings, 1997 (submitted)
- updated 2 February 2000