Dynamics of Various Metal-Octaethylporphyrins in Solution Studied by Resonance Raman and Low-Temperature Optical Absorption Spectroscopies. Role of the Central Metal

A Long Journey into the Investigation of the Structure–Dynamics–Function Paradigm in Proteins through the Activities of the Palermo Biophysics Group

An overview of the biophysics activity at the Department of Physics and Chemistry Emilio Segrè of the University of Palermo is given. For forty years, the focus of the research has been on the protein structure–dynamics–function paradigm, with the aim of understanding the molecular basis of the relevant mechanisms and the key role of solvent. At least three research lines are identified; the main results obtained in collaboration with other groups in Italy and abroad are presented. This review is dedicated to the memory of Professors Massimo Ugo Palma, Maria Beatrice Palma Vittorelli, and Lorenzo Cordone, which were the founders of the Palermo School of Biophysics. We all have been, directly or indirectly, their pupils; we miss their enthusiasm for scientific research, their deep physical insights, their suggestions, their strict but always constructive criticisms, and, most of all, their friendship. This paper is dedicated also to the memory of Prof. Hans Frauenfelder, whose pioneering works on nonexponential rebinding kinetics, protein substates, and energy landscape have inspired a large part of our work in the field of protein dynamics.

Water-Mediated Electronic Structure of Oligopeptides Probed by Their UV Circular Dichroism, Absorption Spectra, and Time-Dependent DFT Calculations

We investigate the UV absorption spectra of a series of cationic GxG peptides (where x denotes a guest residue) in aqueous solution and find that only a subset of these spectra show a strong dependence with temperature. To explore whether or not this observation reflects conformational dependencies, we carry out time-dependent density functional calculations for the polyproline II (pPII) and β-strand conformations in implicit and explicit water. We find that the calculated CD spectra for pPII can qualitatively account for the experimental spectra irrespective of the water model. The β-strand UV-CD spectra, however, require the explicit consideration of water. Contrary to conventional wisdom, we find that both the NV₁ and NV₂ band are the envelopes of contributions from multiple transitions that involve more than just the HOMOs and LUMOs of the peptide groups. A natural transition orbital analysis reveals that some of the transitions have a charge-transfer character. The overall manifold of transitions depends on the peptide's backbone conformation, peptide hydration, and side chain of the guest residue. Our results reveal that peptide groups, side chains, and hydration shells must be considered as an entity for a physically valid characterization of UV absorbance and circular dichroism.

Soret Band of the Gas-Phase Ferri-Cytochrome c

We report the first visible spectrum of a heme-protein in the gas phase. The aim of this work was to provide a reference for the optical absorption of an isolated heme-protein to better understand the influence of protein conformation and fluctuation and of solvent on its optical properties. After laser irradiation of gas-phase cytochrome c (cyt c), electron emission is observed. Electron photodetachment yield of cyt c 6- was recorded in the region of the Soret band of the porphyrin group, showing a maximum at 410 nm. Our results are compared with optical spectra of gas-phase heme and of cyt c in solution. We discuss the influence of the polypeptide chain and of the solvent on both the position and the broadening of the Soret band. Action spectrum of gas-phase cyt c is close to the absorption of native cyt c in solution, suggesting an efficient protection of the heme group from solvent accessibility by the polypeptide chain and similar interactions between the two moieties in solution and the gas phase.

Real-time vibrational dynamics in chlorophyll a studied with a few-cycle pulse laser

We use a 6.8-fs laser as the light source for broad-band femtosecond pump-probe real-time vibrational spectroscopy to investigate both electronic relaxation and vibrational dynamics of the Q(y)-band of Chl-a at 293 K. More than 25 vibrational modes coupled to the Q(y) transition are observed. Eleven of them have been clarified predominantly due to the excited state, and six of them are concluded to be nearly exclusively resulting from the ground-state wave-packet motion. Moreover, thanks to the broad-band detection over 5000 cm⁻¹, the modulated signals due to the excited state vibrational coherence are observed on both sides of the 0-0 transition with equal separation. The corresponding nonlinear process has been studied using a three-level model, from which the probe wavelength dependence of the phase of the periodic modulation can be calculated. The probe wavelength dependence of the vibrational amplitude is interpreted in terms of the interaction between the "pump" or "laser," Stokes, and anti-Stokes field intermediated by the molecular vibrations. In addition, an excited state absorption peak at ~709 nm has been observed. To the best of our knowledge, this is the first study of broad-band real-time vibrational spectroscopy in Chl-a.

Conformational substates of ferricytochrome c revealed by combined optical absorption and electronic circular dichroism spectroscopy at cryogenic temperature

We have investigated the heterogeneity of the Fe(III)-Met80 linkage of horse heart ferricytochrome c by probing the 695nm charge transfer band with absorption and electronic circular dichroism (ECD) spectroscopy. In order to verify the connection between conformational substates of the Fe(III)-Met80 linkage and the 695nm band spectral heterogeneity, we have performed experiments as a function of pH (neutral and acidic) and temperature (room and 20K). At room temperature, the ECD spectrum is blue shifted with respect to the absorption one; the shift is more pronounced at acidic pH and is compatible with the presence of sub-bands. ECD measurements at 20K highlighted the heterogeneous nature of the 695nm band and provided direct experimental evidence for the presence of sub-bands. Indeed, while the absorption spectra remained deceivingly unstructured, the ECD spectra showed well resolved peaks and shoulders. A consistent fit of the 20K absorption and ECD spectra showed that five Gaussians (each centered at the same frequency in the absorption and ECD spectrum) are able to reproduce the observed lineshapes. A careful analysis of frequency shifts and intensity ratios of these sub-bands enabled us to identify at least three distinct sub-bands arising from taxonomic conformational substates of the Fe(III)-Met80 linkage. In view of the major influence of the Fe(III)-Met80 linkage on the redox potential of ferricytochrome c, we speculate that these spectrally distinguishable substates may have different functional roles.

The importance of vibronic perturbations in ferrocytochrome c spectra: a reevaluation of spectral properties based on low-temperature optical absorption, resonance Raman, and molecular-dynamics simulations

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 Q(0) and Q(upsilon) bands. The spectra were first decomposed into the individual split vibronic sidebands assignable to B(1g) (nu15) and A(2g) (nu19, nu21, and nu22) Herzberg-Teller active modes due to their strong intensity in resonance Raman spectra acquired with Q(0) and Q(upsilon) 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 B(2g) 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.

Spectral broadening of the Soret band in myoglobin: an interpretation by the full spectrum of low-frequency modes from a normal modes analysis

In this work the temperature dependence of the Soret band line shape in carbon-monoxy myoglobin is re-analyzed by using both the full correlator approach in the time domain and the frequency domain approach. The new analyses exploit the full density of vibrational states of carbon-monoxy myoglobin available from normal modes analysis, and avoid the artificial division of the entire set of vibrational modes coupled to the Soret transition into "high-frequency" and "low-frequency" subsets; the frequency domain analysis, however, makes use of the so-called short-times approximation, while the time domain one avoids it. Time domain and frequency domain analyses give very similar results, thus supporting the applicability of the short-times approximation to the analysis of hemeprotein spectra; in particular, they clearly indicate the presence of spectral heterogeneity in the Soret band of carbon-monoxy myoglobin. The analyses also show that a temperature dependence of the Gaussian width parameter steeper than the hyperbolic cotangent law predicted by the Einstein harmonic oscillator and/or a temperature dependence of inhomogeneous broadening are not sufficient to obtain quantitative information on the magnitude of an-harmonic contributions to the iron-heme plane motion. However, the dependence of the previous two quantities may be used to obtain semiquantitative information on the overall coupling of the Soret transition to the low-frequency modes and therefore on the dynamic properties of the heme pocket in different states of the protein.

The calculated in vitro and in vivo chlorophyll a absorption bandshape

The room temperature absorption bandshape for the Q transition region of chlorophyll a is calculated using the vibrational frequency modes and Franck-Condon (FC) factors obtained by line-narrowing spectroscopies of chlorophyll a in a glassy (Rebane and Avarmaa, Chem. Phys. 1982; 68:191-200) and in a native environment (Gillie et al., J. Phys. Chem. 1989; 93:1620-1627) at low temperatures. The calculated bandshapes are compared with the absorption spectra of chlorophyll a measured in two different solvents and with that obtained in vivo by a mutational analysis of a chlorophyll-protein complex. It is demonstrated that the measured distributions of FC factors can account for the absorption bandshape of chlorophyll a in a hexacoordinated state, whereas, when pentacoordinated, reduced FC coupling for vibrational frequencies in the range 540-850 cm(-1) occurs. The FC factor distribution for pentacoordinated chlorophyll also describes the native chlorophyll a spectrum but, in this case, either a low-frequency mode (nu < 200 cm(-1)) must be added or else the 262-cm(-1) mode must increase in coupling by about one order of magnitude to describe the skewness of the main absorption bandshape.