Abstracts of Publications from the Keiderling Group
157. J. J. Yang, B. Vandenberg, M. Pitkeathly, L.J. Smith, K. A. Bolin, T. A. Keiderling, C. Redfield, C. M. Dobson and S. E. Radford. Native-like secondary structure in a peptide from the alpha-domain of hen lysozyme. Folding and Design. 1(1996)473-484.
ABSTRACT
Background: To gain insight into the local and nonlocal interactions that contribute to the stability of hen lysozyme, we have synthesized two peptides that together comprise the entire alpha-domain of the protein. One peptide (peptide 1-40) corresponds to the sequence that forms two alpha-helices, a loop region, and a small beta-sheet in the N-terminal region of the native protein. The other (peptide 84-129) makes up the C-terminal part of the alpha-domain and encompasses two alpha-helices and a 3(10) helix in the native protein. Results: As judged by CD and a range of NMR parameters, peptide 1-40 has little secondary structure in aqueous solution and only a small number of local hydrophobic interactions, largely in the loop region. Peptide 84-129, by contrast, contains significant helical structure and is partially hydrophobically collapsed. More specifically, the region corresponding to helix C in native lysozyme is disordered, whereas regions corresponding to the D and 3(10) helices in the native protein are helical in this peptide. The structure in peptide 84-129 is at least partly stabilized by interactions between residues in the two helical regions, as suggested by further NMR analysis of three short peptides corresponding to the individual helices in this region of the native protein. Conclusions: Stabilization of structure in the sequence 1-40 appears to be facilitated predominantly by long-range interactions between this region and the sequence 84-129. In native lysozyme, the existence of two disulphide bonds between the N- and C-terminal halves of the alpha-domain is likely to be a major factor in their stabilization. The data show, however, that native-like secondary structure can be generated in the C-terminal portion of the alpha-domain by nonspecific and nonnative interactions within a partially collapsed state. (C) Current Biology Ltd.
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.
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.
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.
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.
155. P. Bour, C. N. Tam, M. Shaharuzzaman, J. S. Chickos and T. A. Keiderling. Vibrational optical activity study of trans-succinic-d2-anhydride. J. Phys. Chem. 100(1996)15041-15048.
ABSTRACT
The (R-,R-) and (S-,S-) enantiomers of the trans-dideuteriosuccinic anhydride were synthesized, and their infrared absorption, vibrational circular dichroism (VCD), and Raman spectra were measured. Ab initio quantum mechanical harmonic force fields (FFs) were calculated at the SCF (6-31G**), MP2, and density functional (DFT) levels, transition frequencies were generated, and the fundamental vibrational transitions were assigned. Anharmonic corrections to the SCF and DFT FFs were generated using numerical differentiation to obtain cubic and selected quartic terms. Good overall agreement was observed for the vibrational frequencies and the IR absorption intensities between experimental and calculated results. Computations of the Raman and VCD intensities were carried out at the SCF level, the latter using the magnetic field perturbation method of Stephens and co-workers. The computed Raman intensities are in qualitative agreement with the main experimental features. For the mid-IR VCD transitions, full sign agreement was obtained between the experiment and computations for the (S,S) isomer, enabling the absolute configuration of the title compound to 1 be determined unambiguously.
145. P. Bour, C. N. Tam, B. Wang and T. A. Keiderling. Rotationally resolved magnetic vibrational circular dichroism- 1. Exprimental spectra and theoretical simulation for diamagnetic molecules. Mol. Phys. 87(1996)299-318.
ABSTRACT
The rotationally resolved magnetic vibrational circular dichroism (RR MVCD) spectra of the diamagnetic molecules DCl and NH3 are analysed on the basis of theoretical simulation. Basic theoretical equations are derived for the RR MVCD dispersed intensity pattern from the conventional rovibrational energy level expression. This provides a convenient method for interpretation of MVCD spectra in terms of fundamental spectroscopic parameters. Good agreement was obtained between the simulated and the experimental data measured for DCl and NH3. Minor deviations from the theory occur in the dipole strength distribution for DCl, but this is corrected by measuring the A(1)/D-0 ratio, from which the molecular g value can be determined for resolved transitions. Although magnetic properties of DCl and NH3 are known, this study demonstrates the ability of MVCD to provide an alternate method of determining molecular g-values as compared to classical microwave studies of the Zeeman effect. The data further show that experimentally observed RR MVCD spectra are fully explained using the conventional theory for rovibrational transitions under Zeeman perturbation. Variations of magnetic parameters of the ground and excited vibrational states of these molecules cause characteristic changes of the MVCD band intensity patterns. These variations are used to evaluate approximations made in previous moment analyses of RR MVCD spectra and to delimit the sensitivity of the RR MVCD technique to differences in ground and excited state g-values.
ABSTRACT
The sign and approximate magnitude of the gyromagnetic ratio for the nu(5) doubly degenerate bending mode of acetylene are determined by use of rotationally resolved magnetic dichroism measurement of transitions to the singly excited vibrational state. By analysis of the J-dependence of the apparent g-value for this transition, the vibrational g-factor was determined from the experimental spectrum by moment analysis to be g(nu) = 0.48(25). This is the first such determination of g(nu) in a degenerate state of a linear molecule using MVCD and the first determination of g(nu) for the nu(5) mode in acetylene. Simulated MVCD spectra based on the accepted ground state rotational g-value and this determination of g(nu) agree with the observed intensity pattern, confirming the analysis.
146. C. N. Tam, P. Bour and T. A. Keiderling. Observations of rotational magnetic moments in the ground some excited vibrational sigma states of C2H2, C2HD and C2D2 by magnetic vibrational circular dichroism. J. Chem. Phys. 104(1996)1813-1824.
ABSTRACT
Magnetic vibrational circular dichroism (MVCD) spectra of acetylene and its deuterated isotopomers have been recorded for the following Sigma symmetry combination and overtone bands of C2H2: nu(4)+nu(5); C2HD: nu(4)+nu(5); 2 nu(4), 2 nu(5); C2D2: nu(4)+nu(5): the nu(3) fundamental for C2HD and C2D2; and the nu(4)-->2 nu(4)+nu 5 and nu(5)-->nu(4)+2 nu(5) hot bands for C2H2. For a Sigma(g)-->Sigma(u) 1 transition, the MVCD A terms observed must arise primarily from the rotational Zeeman effect. These negative A(1)/D-0 values for low J '' transitions confirm that the sign of the rotational g-value for acetylene is positive. The rotational magnetic moments in both the lower and upper vibrational states were determined by comparison of moment analyses of experimental and simulated MVCD spectra obtained with a model Hamiltonian for acetylene. The g(J) values in all the excited bending combination and overtone vibrational levels observed are smaller than those in the ground and the first excited stretching vibrational levels. This observation has been confirmed by theoretical simulation of the MVCD spectra of the nu(4)+nu(5) combination band of C2H2. From these MVCD results, for C2H2, g(J)(ground) = +0.0535+/-0.0033 and Delta g(nu(4)+nu(5)) = -0.0061+/-0.0004; for C2HD, g(J)(ground)similar to g(J)(nu(3)) = +0.0363+/-0.0048, Delta g(nu(4)+nu(5)) = -0.0052+/-0.0031; and for C2HD, g(J)(ground)similar to g(J)(nu(3)) = +0.0409 +/- 0.0069. These are the first quantitative, MVCD determinations of nondegenerate excited state g values distinctly different from the ground state. The decrease in g value correlates with off-axis deformation of the linear C2H2 rotation. (C) 1996 American Institute of Physics.
150. M. Shaharuzzaman, J. Chickos, C. N. Tam and T. A. Keiderling. Convenient synthesis of chiral succinic acid-d2 by catalytic assymetic reduction using a ruthenium binap catalyst. Tetrahedron Assym. 6(1995)2929-2932.
ABSTRACT
The synthesis of (2R,3R) and (2S,3S) dideuteriosuccinic acid in 63 +/- 10% enantiomeric excess by reduction of the half acid ester of ethyl fumarate from (R) and (S) BINAP ruthenium (II) diacetate complex, respectively, is reported. (2R,3R) and (2S,3S)-Dideuteriosuccinic acid has also been prepared from (R)-BINAP ruthenium (II) dicarboxylate complex directly in similar optical purity by reversing the sequence of introduction of the isotopic label.
148. P. Bour, C. N. Tam and T. A. Keiderling. Ab Initio calculation of the vibrational magnetic dipole moment. J. Phys. Chem. 99(1995)17810-17813.
ABSTRACT
To theoretically explain the vibrational magnetic dipole moment of a molecule with degenerate vibrational levels, it is necessary to go beyond the Born-Oppenheimer approximation. To obtain a nonzero electronic contribution to the vibrational g factor, electronic excited states must be included. Moreover, the usual perturbation expression for the vibrational magnetic moment becomes zero for degenerate vibrational states, unless higher order perturbation terms are included. For ab initio computation of these magnetic moments two simplified models have been tested by calculating the molecular g factors for the C2H2, HCN, OCS, and NH3 molecules and comparing them to experimental values.
144. C. N. Tam and T. A. Keiderling. Direct measurement of the rotational g-value in the ground vibrational state of acetylene by magnetic vibrational circular dichroism. Chem. Phys. Lett. 243(1995)55-58.
ABSTRACT
The magnetic vibrational circular dichroism (MVCD) spectra of the upsilon(4) + upsilon(5) combination band of acetylene was measured. From the result for the P(J('') = 1 --> J' = 0) rotational transition, the g(j)-value in the ground vibrational state for C2H2 was determined to be + 0.049 (+ 0.005). The sign of the g(j)-value 1 measured by MVCD confirms that the correct sign is positive as found in a revised molecular beam magnetic resonance experiment and predicted on the basis of molecular Zeeman studies of other molecules and magnetic effects on heat flow in acetylene. MVCD offers an exceptionally simple method of determining the sign of molecular g-values for both the ground and excited states.
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. 3-10 Helical Stabilization by Peptide-peptide Interaction. (submitted to Journal of the American Chemical Society)
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.
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.
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.
159. M. Urbanova, T. A. Keiderling and P. Pancoska. Conformational Study of some Milk Proteins- Comparison of the Results of Electronic Circular Dichroism and Vibrational Circular Dichroism. Bioelectrochemistry and Bioenergetics 41(1996)77-80.
ABSTRACT
Solutions of proteins in D2O were measured using vibrational circular dichroism and electronic circular dichroism spectroscopy. The high sensitivity of vibrational circular dichroism spectra to conformational changes of proteins was demonstrated for the spectra of alpha-lactalbumin, beta-lactoglobulin and alpha-casein. Variations of the secondary structure were studied using the difference spectra obtained numerically from the spectra of solutions at different pH and different contents of alcohol. Enhancements of the alpha-helical fraction at pH 2 and the extended structure at pH 12 in alpha-lactalbumin were observed. The differences between the spectra of alpha-casein in the native state and in alcohol-containing solutions indicated a decrease in the beta-sheet fraction. Analogous variations of the solution pH and alcohol content caused negligible spectral changes in beta-lactoglobulin. This type of conformational study of proteins in solutions is extremely useful for electrochemical research of enzyme activities and electrochemical analysis of biomolecules.
156. C. N. Tam, P. Bour and T. A. Keiderling. Vibrational Optical Activity of (3S,6S)-3,6-dimethyl-1,4-dioxane-2,5-dione. J. Am. Chem. Soc. 118(1996)10285-10293.
ABSTRACT
Vibrational circular dichroism (VCD), absorption, Raman, and Raman optical activity (ROA) spectra for the title compound, a cyclic dimer, were measured in non-aqueous solution. The vibrational normal modes are assigned based on the result from ab initio force field calculation. Harmonic frequencies and atomic polar tensors for simulation of IR absorption were calculated both on the (Hartree-Fock SCF) HF/6-31G** level and using density functional theory (DFT) methods with the Becke3/LYP hybrid functional. Magnetic transition dipole derivatives were calculated on the HF/6-31G level, and the ROA polarizability tensors were calculated on the HF/4-31G level. Excellent agreement between the DFT calculated and experimental frequencies was obtained without a need for scaling. Furthermore, using the DFT force field, the correct VCD sign and intensity patterns were reproduced as compared to the experimental mid-IR spectra. Reasonable near-IR VCD and mid-IR ROA sign patterns for the intense peaks were also calculated. The excellent agreement for the mid-IR VCD results shows that medium-sized, biologically relevant molecules can have their spectra simulated using quantum mechanical techniques to a high level, certainly one suitable for conformational analyses by direct comparison of theory to experimental results. Comparison of DFT and HF level calculations suggests that the improvement found using DFT methods is primarily due to the force field and not to the intensity parameters. DFT atomic polar tensors were systematically weaker than the HF generated ones. Weak coupling between the subunits of this dimer implies dominance by local interactions which suggests that useful extension of these calculational techniques to larger oligomers might be accomplished by transfer of parameters.
154. P. Pancoska, H. Fabian, G. Yoder, V. Baumruk, and T. A. Keiderling. Protein Structural Segments and their Interconnections Derived from Optical Spectra- Thermal Unfolding of Ribonuclease T1 as an Example. Biochemistry 35(1996)13094-13106.
ABSTRACT
A novel descriptor for protein structure is examined here that goes beyond predictions of the average fractional components (FC) of a few conformational types and represents the number and interconnection of segments of continuous, well-defined secondary structural elements such as alpha-helices and beta-sheets. This matrix descriptor can be predicted from optical spectra using neural network methods. The new matrix plus traditional FC descriptors can be quickly and generally obtained to provide a level of detail not previously derived from optical spectra and a discrimination between proteins that might otherwise be viewed as being very similar using just the FC descriptor. As an example of its potential utilization, this matrix descriptor approach was applied to an analysis of both the native state and the reversible thermal denaturation of ribonuclease T-1 in H2O. Analyses of the FTIR spectral data indicate initial loss of the major helical segment at 50-55 degrees C but with little accompanying change in the number of sheet segments or the sheet FC values, Circular dichroism (CD) and vibrational CD data are also used to support this interpretation based on FC changes with temperature. Parallel analysis of the corresponding data for this protein in D2O demonstrates that the method is sensitive to the match between the degree of H-D exchange used to prepare samples for the unknown and the reference data set.
153. V. Baumruk, P. Pancoska and T. A. Keiderling. Predictions of Secondary Structure Using Statistical Analyses of Electronic and Vibrational Circular Dichroism and Fourier Transform Infrared Spectra of Proteins in H2O. J. Mol. Biol. 259(1996)774-791.
ABSTRACT
Vibrational circular dichroism (VCD) and Fourier transform IR (FTIR) methods for prediction of protein secondary structure are systematically compared using selective regression analysis. VCD and FTIR spectra over the amide I and II bands of 23 proteins dissolved in H2O were analyzed using the principal component method of factor analysis (PC/FA) and regression fits to fractional components (FC) of secondary structure. Predictive capability was determined by computing structures for proteins sequentially left out of the regression. All possible combinations of PC/FA spectral parameters (coefficients) were used to form a full set of restricted multiple regressions (RMR) of PC/FA coefficients with FC values, both independently for each spectral data set as well as for the VCD and FTIR sets grouped together and with similarly obtained electronic CD (ECD) data. The distribution of predictive error for a set of the best RMR relationships that use a given number of spectral coefficients was used to select the optimal prediction algorithm. Minimum predictive error resulted for a small subset (three to six) of spectral coefficients, which is consistent with our earlier findings using VCD measured for proteins in (H2O)-H-2 and ECD data. Subtracting the average absorption spectrum from all the training set FTIR spectra before analysis yields more variance in the FTIR band shape and improves the predictive ability of the best PC/FA RMR to near that for the VCD. Both methods (FTIR and VCD) using data for proteins in H2O are somewhat better predictors than amide I' (in (H2O)-H-2) VCD alone and, for helix, worse than ECD alone. Combining FTIR and VCD data did not dramatically change the prediction results. Predictions are improved by combining both with ECD data, indicating that the improvement is due to using their very different structural sensitivities. The coupled H2O-based spectral analyses and the mixed amide I' + II VCD plus ECD analysis are comparable for the helix and sheet components, indicating that partial deuteration is not a major source of prediction error. (C) 1996 Academic Press Limited
152. P. Malon and T. A. Keiderling. Spinning quarter-wave plate polarization modulator -- test of feasibility for vibrational circular dichroism measurements. Applied Spectroscopy 50(1996)669-674.
ABSTRACT
A novel polarization modulator design based on a rotating quarter-wave plate and preliminary results of its application for vibrational circular dichroism (VCD) are presented. The device permits quarter-wave retardation in the infrared with alternating senses so that the resultant components of circular polarization can be modulated at frequencies on the order of 100 Hz. We have been able to apply this device to measure VCD with a step-scan FT-IR spectrometer by incorporating a stressed ZnSe optical element as the rotating quarter-wave plate. VCD of alpha-pinene and camphor were obtained. While these test spectra were of low signal-to-noise ratio (S/N), they exhibited the correct VCD spectral features for these chiral molecules. While not yet of competitive, practical utility, this design is potentially adaptable to extension into the far-IR with alternative optical elements, permits variable-frequency polarization modulation, and should be capable of improved S/N with modifications to increase rotation frequency.
151. P. Pancoska, V. Janota and T. A. Keiderling. Interconvertibility of electronic and vibrational circular dichroism spectra of proteins -- a test of principle using neural network mapping. Applied Spectroscopy 50(1996)658-668.
ABSTRACT
Electronic circular dichroism (ECD) and vibrational circular dichroism (VCD) are compared with respect to their interconvertibility For protein structural studies. ECD and amide I' VCD spectra of 28 proteins were used with a backpropagation projection neural network with one hidden layer to develop a mapping between the two special types. After the network converged, the number of neurons in the hidden layer was optimized by principal component analysis of the synaptic weights of the pilot network topology with redundant hidden neurons, actual prediction of one spectrum kern the other for individual proteins was tested by retraining these networks with 28 reduced training sets having one protein systematically left out. Comparison of network-predicted spectra with experimental ones is used to identify those spectral features which are unique in each method. Similarly, the VCD spectra of 23 proteins measured in both D2O and H2O in the amide I region were mapped onto each other with the use of the same type of neural network calculation. The results show that the effects of partial deuteration on the VCD spectra band shape are predictable From the H2O spectra. An analysis of the synaptic weights of the optimized networks was performed which allowed identification of the linear and nonlinear parts of the obtained mappings. Insight into the details of how the neural networks encode and process the spectroscopic information is derived from a spectral representation of these weight matrices.
149. R. K. Dukor and T. A. Keiderling. Mutarotation Studies of Poly-L-Proline using FTIR, Electronic and Vibrational Circular Dichroism. Biospectroscopy 2(1996)83-100.
ABSTRACT
FTIR, electronic and vibrational circular dichroism (ECD and VCD) are used to follow the mutarotation of poly-L-proline I (PLP I) to poly-L-proline II (PLP II) in D2O solution. While this process is well known, these studies elucidate the nature of the characteristic spectra of each form in an aqueous environment, which can be useful for qualitative structural diagnoses of proteins and peptides using these spectroscopic techniques. Further, our data demonstrate the presence of an intermediate in the transformation, at least in highly concentrated aqueous solution, which is characterized by an absorption band growing in at 1653 cm(-1) and then decaying away as the transformation proceeds. Based on correlations to FTIR and VCD studies on L-proline and D,L alternate proline oligopeptides previously carried out in our laboratories, this intermediate structure can be assigned to there being a distribution of cis-trans linkages in the polymer. This contrasts with the cooperative conformational transition from PLP I to PLP II, proceeding sequentially from end to end, that has been proposed fbr this mutarotation in previous studies, primarily in different environments. Our results are consistent with early inter pretations of hydrodynamic data. Related studies of collagen and poly-L-hydroxyproline indicate that both yield VCD spectra similar in shape to that of PLP II, as expected, and demonstrate that intra-chain, near neighbor interactions dominate the VCD. (C) 1996 John Wiley & Sons, Inc.
141. P. Pancoska, E. Bitto, V. Janota, M. Urbanova, V. P. Gupta and T. A. Keiderling. Comparison of and Limits of Accuracy for Statistical Analyses of Vibrational and Electronic Circular Dichroism Spectra in Terms of Correlations to and Predictions of Protein Secondary Structure. Protein Science 4(1995)1384-1401.
ABSTRACT
This work provides a systematic comparison of vibrational CD (VCD) and electronic CD (ECD) methods for spectral prediction of secondary structure. The VCD and ECD data are simplified to a small set of spectral parameters using the principal component method of factor analysis (PC/FA). Regression fits of these parameters are made to the X-ray-determined fractional components (FC) of secondary structure. Predictive capability is determined by computing structures for proteins sequentially left out of the regression. All possible combinations of PC/FA spectral parameters (coefficients) were used to form a full set of restricted multiple regressions with the FC values, both independently for each spectral data set as well as for the two VCD sets and all the data grouped together. The complete search over all possible combinations of spectral parameters for different types of spectral data is a new feature of this study, and the focus on prediction is the strength of this approach. The PC/FA method was found to be stable in detail to expansion of the training set. Coupling amide II to amide I' parameters reduced the standard deviations of the VCD regression relationships, and combining VCD and ECD data led to the best fits. Prediction results had a minimum error when dependent on relatively few spectral coefficients. Such a limited dependence on spectral variation is the key finding of this work, which has ramifications for previous studies as well as suggests future directions for spectral analysis of structure. The best ECD prediction for helix and sheet uses only one parameter, the coefficient of the first subspectrum. With VCD, the best predictions sample coefficients of both the amide I' and II bands, but error is optimized using only a few coefficients. In this respect, ECD is more accurate than VCD for alpha-helix, and the combined VCD (amide I'=II) predicts the beta-sheet component better than does ECD. Combining VCD and ECD data sets yields exceptionally good predictions by utilizing the strengths of each. However, the residual error, its distribution, and, most importantly, the lack of dependence of the method on many of the significant components derived from the spectra leads to the conclusion that the heterogeneity of protein structure is a fundamental limitation to the use of such spectral analysis methods. The underutilization of these data for prediction of secondary structure suggests spectral data could predict a more detailed descriptor.
140. B. Wang and T. A. Keiderling. Observations on the measurement of vibrational circular dichroism with rapid scan and step-scan FTIR techniques. Applied Spectroscopy 49(1995)1347-1355.
ABSTRACT
Extensive tests to determine an optimal method for using a Bio-Rad FTS-60A spectrometer for measurement of vibrational circular dichroism (VCD) in both step-scan and rapid-scan modes are reported. In the latter case, results of ''fast-scan'' and ''slow-scan'' experiments are also presented for comparison. In step-scan mode, phase modulation (PM) during the polarization-modulation measurements is found to be detrimental to the signal-to-noise ratio (S/N), but is very useful for the normal In measurements at slow step speeds. VCD S/N is improved by doing sequential spectral collection of the polarization-modulated spectrum without PM and the instrument response spectra with phase modulation. Systematic comparative studies are used to identify optimal parameter sets for doing the step-scan VCD measurements. These conditions use more rapid data collection with faster steps than previously suggested, which permits a more realistic evaluation of S/N and reproducibility of the spectra through comparison of spectra collected in blocks. Example VCD spectra are presented for small molecules in nonaqueous solution measured in short times and for proteins in aqueous solution measured over longer times scales. Near-IR FT-VCD measured in step-scan mode at both moderate resolution and high S/N are presented. At this stage, fast-scan, slow-scan, and step-scan techniques are shown to be virtually equivalent in the mid-IR, but the reduction in frequency dependence of the phase correction and the new capability for VCD measurement in the near-In favor continued development of step-scan techniques.
138. W. Mastle, R. K. Dukor, G. Yoder and T. A. Keiderling. Conformational Study of Linear Alternating and Mixed D- and L-Proline Oligomers using Electronic and Vibrational CD and Fourier Transform IR. Biopolymers 36(1995)623-631.
ABSTRACT
Vibrational CD (VCD) spectra of a series of blocked linear, alternating D- and L-proline containing oligopeptides, dissolved in D2O and in CDCl3, are reported For the BoC-LDL-Pro(3) to BOC-DLDLDLDL-Pro(8) oligomers, the VCD spectra in the amide I band is a positive couplet, opposite in sense to that obtained for (L-Pro)(n) oligomers. While this admits the possibility of their favoring a right-handed helical chain conformation, the amide I ir spectra for these DL oligomers in D2O indicate a mixed, apparently alternate, cis-trans conformation that prevents a simple conclusion. Their VCD in D2O evidence no narrowing and has a progressive loss in intensity (measured as Delta AA/A) with an increase in chain length. In CDCl3 a similar pattern of positive VCD couplers decreasing in intensity with length was seen, but the iv spectra are narrower. Their electronic CD (ECD), in the uv, also indicates a loss in intensity with increasing length. Oligomers with odd or even numbers of Pro residues have different ECD patterns, indicating that those spectra are strongly influenced by local contributions arising in the N-terminal groups. The VCD arises from dipolar and vibrational coupling of the amides in the helical structure. All the spectra are consistent with the chiral end groups leading to formation of an excess of one helical handedness. With an increase in length, the influence of this selectiveness is less and the overall CD measured decreases. (C) 1995 John Wiley & Sons, Inc.
137. G. Yoder, T. A. Keiderling, F. Formaggio, M. Crisma, C. Toniolo and J. Kamphuis. Helical screw sense of homo-oligopeptides of C-alpha-methylated-alpha-amino acids as determined with vibrational circular dichroism. Tetrahedron Assym. 6(1995)687-690.
ABSTRACT
Vibrational circular dichroism spectra for three homo-oligopeptides, p-BrBz-`D-(alpha Me)Phe (4,5)-OtBu and p-BrBz-(D-Iva)(5)-OtBu, are presented and interpreted to show that the C-alpha-methylated alpha-amino acids (alpha Me)Phe and Iva of the same optical configuration favor helical conformations of the opposite screw sense. The D-(alpha Me)Phe tetra- and pentapeptides are folded in a right-handed 3(10)-helix, which is consistent with previous findings regarding homo-oligomers of C alpha-methylated amino acids with gamma-branched side chains. On the other hand, the pentapeptide of D-Iva, with a linear side chain, is folded in a left-handed helical sense, in agreement with the behavior of peptides based on the D-enantiomers of protein amino acids.
135. T. A. Keiderling, B. Wang, M. Urbanova, P. Pancoska and R. K. Dukor. Empirical studies of protein secondary structure using vibrational circular dichroism and related techniques. a-lactalbumin and lysozyme as examples. Faraday Discussions 99(1994)263-285.
ABSTRACT
Vibrational circular dichroism (VCD) has been shown to be sensitive to secondary structure in proteins and peptides and has been used as the basis for quantitative secondary-structure-prediction algorithms. However, the accuracy of these algorithms is not matched by the apparent qualitative sensitivity of the VCD spectra. This report provides examples of the use of VCD to follow structural change spectrally and to clarify the qualitative nature of the structural changes underlying the spectral variation. The VCD spectra and the complementary UV electronic CD (ECD) and FTIR spectra of alpha-lactalbumin (LA) have been studied as a function of pH, denaturation, Ca2+ ion and solvent conditions for several species. Spectral data for lysozyme were compared with those of LA because of their very similar crystal structures. In fact, these proteins in D2O-based pH 7 solution have quite different spectra using these optical techniques. Even for the LA proteins, the human differs from the bovine and goat species. Furthermore, under low pH conditions, where the LAs are in a reversibly denatured, molten globule form, the spectra are more similar, species variation is minimal and the 1 spectral differences from lysozyme are in fact smaller. Our data are consistent with native, pH 7, alpha-lactalbumin having a less well organized structure than lysozyme, possibly in a dynamic sense. Conversely, in the low-pH, molten globule form of LA, tertiary structure is lost which could relax constraints that might distort the helical segments in the native form. The differences between the interpretation of our results and those from X-ray and NMR data may be due to motional sampling of various geometries in LA which all contribute to the spectral signatures seen in optical spectra but whose contributions are washed out in NMR or frozen out in the crystal structure. Part of this flexibility may relate to the rather large 3(10)-helical content in the LA protein structure. Fluctionality may have specific functional effects, perhaps allowing LA to bind better to beta-galactosyl transferase and form the biologically active lactose synthetase complex.
134. P. Pancoska, E. Bitto, V. Janota and T. A. Keiderling. Quantitative analysis of vibrational circular dichroism of proteins-- problems and perspectives. Faraday Discussions 99(1994)287-310. [ discussion of this paper included in General Discussion, Faraday Discussions 99(1994)311-326 ]
ABSTRACT
Experimental and computational aspects of the quantitative analysis of vibrational circular dichroism (VCD) of proteins are discussed. Experimentally, the effect of spectral resolution, sample concentration, cell selection and spectral normalization effects are considered. The influence of random intensity variations on the results of quantitative analysis of amide I' VCD are shown to be minor up to a 15% variation in spectral intensity. A computational algorithm, based on factor analysis of the spectra and multiple linear regression calculation of fractions of secondary structures (FC), was designed to analyse quantitatively the details of the VCD spectra-structure relationship It also enabled the results of VCD measured independently for the amide I' and amide II regions to be combined. Our study is based primarily on the optimization of the calculation to predict FC values for proteins not included in the reference data set used for regression. The best prediction is obtained with the function using only part of the observable independent VCD spectral components. Inclusion of all components actually reduces the prediction accuracy of the analysis. Spectroscopic reasons for such behaviour and the consequences of the interdependence of the crystallographic FC values on the spectra-structure analysis are discussed. Finally, the possibility of utilizing VCD spectra to obtain quantitative structural information about the protein beyond the conventional secondary structure composition is explored. A matrix descriptor of super-secondary structure features for proteins is designed, and preliminary results for prediction of this descriptor from amide I' VCD spectra are presented. These latter calculations use a novel design of the back-propagation neural network.
133. G. Yoder, T. A. Keiderling, F. Formaggio, M. Crisma and C. Toniolo. Characterization of Beta-Bend Ribbon Spiral Forming Peptides using Electronic and Vibrational CD. Biopolymers 35(1995)103-111.
ABSTRACT
Terminally blocked (L-Pro-Aib)(n) and Aib-(L-Pro-Aib)(n) sequential oligopeptides are known to form right-handed beta-bend ribbon spirals under a variety of experimental conditions. Here we describe the results of a complete CD and ir characterization of this subtype of 3(10)-helical structure. The electronic CD spectra were obtained in solvents of different polarity in the 260-180 nm region. The vibrational CD and Fourier transform ir (FTIR) spectra were measured in deuterochloroform solution in the amide I and amide II (1750-1500 cm(-1)) regions. The critical chain length for full development of the beta-bend ribbon spiral structure is found to be five to six residues. Spectral effects related to concentration-induced stabilization of the structures of the longer peptides were seen in the resolution-enhanced FTIR spectra. Comparison to previous studies of (Aib)(n) and (Pro)(n) oligomers indicate that the low frequency of the amide I mode is due to the interaction of secondary and tertiary amide bonds and not to a strong difference in conformation from a regular 3(10)-helix. (C) 1995 John Wiley and Sons, Inc.
132. T. B. Freedman, L. A. Nafie and T. A. Keiderling. Vibrational Optical Activity of Oligopeptides. Biopolymers 37(1995)265-279.
ABSTRACT
Vibrational optical activity (VOA) is a relatively new spectroscopic technique, which has two principal manifestations, ir vibrational CD and vibrational Raman optical activity. Progress in the study of oligopeptides using both of these forms of VOA is reviewed from the perspective of theoretical and instrumental techniques, spectral results, and structural interpretations. (C) 1995 John Wiley & Sons, Inc.
129. L. J. Wang, L. G. Yang and T. A. Keiderling. Vibrational Circular Dichroism of A-, B-, and Z-Form Nucleic Acids in the PO2- Strectching Region. Biophysical Journal 67(1994)2460-2467.
ABSTRACT
Vibrational circular dichroism (VCD) spectra were measured for H2O solutions of several natural and model DNAs (single and double strands, oligomers and polymers) in the B-form, poly(dG-dC) poly(dG-dC) in the Z-form, and various duplex RNAs in an A-form over the PO2- stretching region. Only the symmetric PO2- stretch at similar to 1075 cm(-1) yields a significant intensity VCD signal. Differences of the PO2- stretching VCD spectra found for these conformational types are consistent with the spectral changes seen in the base region, but no sequence dependence was seen in contrast to VCD for base modes. The B to Z transition is accompanied by an inversion of the PO2- VCD spectra, which is characteristic of the change in the helical sense of the nucleic acid backbone. A-RNAs give rise to the same sense of couplet VCD as do B-DNAs but have a somewhat different shape because of overlapping ribose modes. These PO2- VCD spectral characteristics have been successfully modeled using simple dipole coupling calculations. The invariability of the symmetric PO2- stretching mode VCD spectra to the base sequence as opposed to that found for the C=O stretching and base deformation modes is evidence that this mode will provide a stable indication of the DNA helical sense.
128. V. Baumruk, D. F. Huo, R. K. Dukor, T. A. Keiderling, D. Lelievre and A. Brack. Conformational Study of Sequential Lys and Leu Based Polymers and Oligomers using Vibrational and Electronic CD Spectra. Biopolymers 34(1994)1115-1121.
ABSTRACT
Vibrational CD (VCD) and electronic CD (ECD) spectra of some sequential Lys and Leu based oligo- and polypeptides were studied as a function of added salt and (for ECD) as a function of concentration in aqueous solution. For these samples, the VCD spectra can only be measured at relatively high concentrations under which the well-known salt-induced transition to a beta-sheet form can be observed for the KL based species, but only the end-state alpha-helical conformation is obvious for the LKKL based samples. ECD concentration dependence demonstrates that, at high concentration with no added or with added salt, LKKL based oligomers and polymers give alpha-helical spectra. These data provide evidence of aggregation induced secondary structure formation in an exceptionally simple peptide system. Similarly, the KL based oligomers and polymers give beta-sheet like spectra at high concentration or at high salt. These systems further provide model systems under ''normal'' aqueous conditions that yield VCD band shapes that correlate to the major secondary structural types of polypeptides. They are in substantial agreement with those spectra obtained on homopolypeptides and on proteins, confirming the relative independence of the VCD technique from side-chain and solvent effects. (C) 1994 John Wiley & Sons, Inc.
127. L. J. Wang, P. Pancoska and T. A. Keiderling. Detection and Characterization of Triple-Helical Pyrimidine-Purine-Pyrimidine Nucleic Acids with Vibrational Circular Dichroism. Biochemistry 33(1994)8428-8435.
ABSTRACT
Vibrational circular dichroism (VCD) spectra were measured in the C=O stretching region for poly(U)*poly(A).poly(U), poly(dT)*poly(dA).poly(dT), and poly(U)*poly(dA).poly(dT). These VCD spectra of the triple-helical structure were dramatically different from those of the corresponding duplexes. The VCD indicates that a very similar base-pair structure is present in these triplexes. The same sign pattern was found for poly(C+)*poly(I).poly(C), which implies a generality of structure than can result from the steric constraint of the triple helix conformation. By contrast, the corresponding duplexes are quite different in terms of their VCD. The transitions between triplex, duplex, and single-stranded forms were studied as a function of temperature and interpreted using factor analysis. The relative stabilities of the triplexes lie in the order RNA > DNA > hybrid. Nondegenerate dipole-coupling calculations for a U*A.U oligomer were carried out for the C=O stretching modes to model the spectral changes observed. The experimental absorbance spectra indicate that the bases have nonequivalent H-bonds which can be achieved if a reverse Hoogsteen base-pairing scheme is assumed. The computational VCD results with such a scheme were in better qualitative agreement with experiment than those using the expected Hoogsteen base-pairing scheme.
121. M. Urbanova, P. Pancoska and T. A. Keiderling. Spectroscopic Study of the Temperature-Dependent Conformation of Glucoamylase. Biochimica et Biophysica Acta 1203(1993)290-294.
ABSTRACT
Vibrational circular dichroism, electronic circular dichroism and infrared absorption with Fourier self-deconvolution have been used for a conformational study of the small form, G2, of glucoamylase, 1,4-alpha-D-glucan glucohydrolase from Aspergillus niger (EC 3.2.1.3) in aqueous solution. From the temperature dependence of spectra measured from 25 degrees C to 60 degrees C it was seen that the helical content is relatively constant to 50 degrees C and then sharply decreases by a factor of more than three by 60 degrees C. This decrease in helix is primarily compensated by a rise in the fraction of beta-sheet; but bend, turn and 'other' components also increase. By comparison of the three techniques, it was determined that the electronic CD analysis was quantitatively in error due to interference by glycosidic residues. The inherent resolution of the vibrational techniques, FTIR and VCD, avoids such interference.