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The respective band profile of horse heart ferri-cytochrome c was measured as a function of temperature between 283 K and 333 K. It was found that the decrease of the absorptivity is wavenumber-dependent and exhibits a biphasic behavior.

The mutations of yeast iso-1-cytochrome c that replace polar by nonpolar residues in the heme vicinity investigated by employing Raman dispersion was observed to show most pronounced effect for Y67F which increases the triclinic [B.sub.2g] deformation of the heme group.

We measured the Soret band of deoxymyoglobin (deoxyMb), myoglobin cyanide (MbCN), and aquo-metmyoglobin (all from horse heart) with absorption and circular dichroism (CD) spectroscopies. A clear non-coincidence was observed between the absorption and CD profiles of deoxyMb and MbCN, with the CD profiles red- and blueshifted with respect to the absorption band position, respectively. On the contrary, the CD and absorption profiles of aquametMb were nearly identical. The observed noncoincidence indicates a splitting of the excited B state due to heme-protein interactions. CD and absorption profiles of deoxyMb and MbCN were self-consistently analyzed by employing a perturbation approach for weak vibronic coupling as well as the relative intensities and depolarization ratios of seven bands in the respective resonance Raman spectra measured with B-band excitation. The respective By component was found to dominate the observed Cotton effect of both myoglobin derivatives. The different signs of the noncoincidences between CD and absorption bands observed for deoxyMb and MbCN are due to different signs of the respective matrix elements of A1g electronic interstate coupling, which reflects an imbalance of Gouterman’s 50:50 states. The splitting of the B band reflects contributions from electronic and vibronic perturbations of B1g symmetry. The results of our analysis suggest that the broad and asymmetric absorption band of deoxyMb results from this band splitting rather than from its dependence on heme doming. Thus, we are able to explain recent findings that the temperature dependences of CO rebinding to myoglobin and the Soret band profile are uncorrelated[Ormos et al., Proc. Natl. Acad. Sci U.S.A. 95, 6762 (1998)]. [ABSTRACT FROM AUTHOR]

We have measured and analyzed the low-temperature (T=10 K) absorption spectrum of reduced horse heart and yeast cytochrome c. Both spectra show split and asymmetric Q0 and Qv bands. The spectra were first decomposed into the individual split vibronic sidebands assignable to B1g (ν15) and A2g (ν19, ν21, and ν22) Herzberg-Teller active modes due to their strong intensity in resonance Raman spectra acquired with Q0 and Qv excitations. The measured band splittings and asymmetries cannot be rationalized solely in terms of electronic perturbations of the heme macrocycle. On the contrary, they clearly point to the importance of considering not only electronic perturbations but vibronic perturbations as well. The former are most likely due to the heterogeneity of the electric field produced by charged side chains in the protein environment, whereas the latter reflect a perturbation potential due to multiple heme-protein interactions, which deform the heme structure in the ground and excited states. Additional information about vibronic perturbations and the associated ground-state deformations are inferred from the depolarization ratios of resonance Raman bands. The results of our analysis indicate that the heme group in yeast cytochrome c is more nonplanar and more distorted along a B2g coordinate than in horse heart cytochrome c. This conclusion is supported by normal structural decomposition calculations performed on the heme extracted from molecular-dynamic simulations of the two investigated proteins. Interestingly, the latter are somewhat different from the respective deformations obtained from the x-ray structures. [ABSTRACT FROM AUTHOR]

Vibrational (IR, Raman, and VCD) were combined with NMR spectroscopy to explore the conformational distributions sampled by the central amino acid residue in short host-guest peptides, such as GxG tripeptides. The intrinsic propensities of eight amino acid residues (x = A, V, F, L, S, E, K, and M) in GxG peptides which were determined as mole fractions of theses subensembles showed that alanine adopted primarily a polyproline II (PPII)-like conformation, while valine and phenylalanine were found to sample PPII and [beta]-strand-like conformations equally.

The pH dependence of the 695 nm charge transfer band of horse heart ferricytochrome c at low ion concentrations is determined. The various steps involved in the transition of the ferricytochrome c compound from the native to its alkaline states are also discussed.

Charge transfer (CT) transitions between the C-terminal carboxylate and peptide group are investigated for alanyl-X and X-alanine dipeptides by far-ultraviolet (UV) absorption and electronic circular dichroism (ECD) spectroscopy (where X represented different amino acid residues). The ECD technique is also used as a convenient tool to detect the influence of the negatively charged side chains on the pK value and the structure of the C-terminal carboxylate group.

The temperature dependent electronic circular dichroism (ECD) spectra of AX, XA, and XG dipeptides in D2O were measured. The spectra of all XA and AX peptides indicate a substantial population of the polyproline II (PPII) conformation while the ECD spectra of LG, KG, PG and AG were found to be quantitatively different from the alanine based dipeptides.

A study was conducted to show that two peptides, salmon calcitonin and amyloid beta, with amyloidogenic capacity adopt different conformational manifolds in their unfolded states. The results emphasize the belief that individual structural propensities of amino acid residues give rise to structural differences between the unfolded states of even long peptide chains, at variance with expectations based on a random or statistical coil model.

A series of AX and XA dipeptides in D(sub 2)O were investigated by FTIR, isotropic, and anisotropic Raman spectroscopy at acidic, neutral, and alkaline pD, to probe the influence of amino acid side chains on the amide I' band. A set of spectral parameters were obtained for each peptide, including intensities, wavenumbers, half-widths, and dipole moments, and it was found that these amide I' parameters were dependent on the side chain.

Local structure in unfolded proteins, especially turn segments, has been suggested to initiate the hierarchical protein-folding process. To determine the intrinsic propensity to form such turn structures, amide I' band profiles of the Raman, IR, and vibrational circular dichroism (VCD) spectra, and several structure-sensitive NMR J-coupling constants, have been measured for a series of GxG (x=D, N, T, C) peptides, in which the central x residues are abundant in various turn motifs in folded proteins. In addition, we revisited earlier measured GSG experimental data. To check whether this relatively high propensity for these residues to sample turns reflects an intrinsic propensity, the experimental data were analyzed in terms of conformational distributions that can be described as a superposition of two-dimensional Gaussian distributions associated with different so-called mesostates. The analysis reveals that the investigated residues sample dihedral angles similar to those found in the corner residues of various turns, namely, type I/I', II/II', and IV β-turns. Aspartic acid (D) was found to predominantly sample regions attributed to turns, including distributions at the upper border of the upper-right quadrant of the Ramachandran plot, which bear some resemblance to asx-turns observed in proteins. This conformation enables hydrogen bonding between the side-chain carboxylate and the C-terminal amide group. Altogether, the study shows that the high propensity for T, S, C, N, and D to be located in turn motifs reflects, to a substantial degree, an intrinsic property and supports the role of these residues as initiation sites for hierarchical folding processes that can lead to compact structures in the unfolded state of peptides and proteins., (Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Over the last 50 years cytochrome c has been used as a model system for studying electron transfer and protein folding processes. Recently, convincing evidence has been provided that this protein is also involved in other biological processes such as the apoptosis and α-synuclein aggregation. Numerous lines of evidence suggest that the diversity of the functional properties of cytochrome c is linked to its conformational plasticity. This chapter introduces circular dichroism and absorption spectroscopy, as an ideal tool to explore this protein's conformational in solution. Besides assisting in distinguishing different conformations and in obtaining the equilibrium thermodynamics of the transitions between them, the two spectroscopies can also be used to explore details of heme-protein interaction, for example, the influence of the external electric field on the prosthetic heme group., (Copyright © 2009 Elsevier Inc. All rights reserved.)

We measured the temperature-dependent electronic circular dichroism (ECD) spectra of AX, XA, and XG dipeptides in D2O. The spectra of all XA and AX peptides indicate a substantial population of the polyproline II (PPII) conformation, while the ECD spectra of LG, KG, PG, and AG were found to be quantitatively different from the alanine-based dipeptides. Additional UV absorption data indicate that the ECD spectra of the XG peptides stem from electronic coupling between the peptide and the C-terminal group, and that spectral differences reflect different orientations of the latter. We also measured the 1H NMR spectra of the investigated dipeptides to determine the 3JHalphaNH coupling constants for the C-terminal residue. The observed temperature dependence of the ECD spectra and the respective room-temperature 3JHalphaNH coupling constants were analyzed by a two-state model encompassing PPII and a beta-like conformation. The PPII propensity of alanine in the XA series is only slightly modulated by the N-terminal side chain, and is larger than 50%. As compared to AA, XA peptides containing L, P, S, K V, E, T, and I all cause a relative stabilization of the extended beta-strand conformation. The PPII fractions of XA peptides varied between 0.64 for AA and 0.58 for DA, whereas the PPII fractions of AX peptides were much lower. From the investigated AX peptides, only AL and AQ showed the expected PPII propensity. We found that AT, AI, and AV clearly prefer an extended beta-strand conformation. A quantitative comparison of AA, AAA, and AAAA revealed a hierarchy AAAA > AAA approximately AA for the PPII population, in agreement with predictions from MD calculations and results from Raman optical activity studies (McColl et al. J. Am. Chem. Soc. 2004, 126, 5076).