Normal mode calculation and infrared spectroscopy of proteins in water solution: Relationship between amide I transition dipole strength and secondary structure.

Dipole Strength (DS) of the amides has gained a renewed interest in chemical physics since it provides an important tool to disclose the on-site vibrational energy distributions. Apart from earlier experimental efforts on polypeptides, little is still known about DS in complex proteins. We accurately measured the Fourier Transform Infrared absorption spectra of nine proteins in water solution obtaining their Molar Extinction Coefficient in the amide I and II spectral region. Our results show that the amide I DS value depends on the protein secondary structure, being that of the α-rich and unstructured proteins lower by a factor of 2 than that of the ß-rich proteins. The average DS for amino acids in α and ß secondary structures confirms this finding. Normal Mode calculation and Molecular Dynamics were performed and used as tools for data analysis and interpretation. The present outcomes corroborate the hypothesis that antiparallel ß-sheet environment is more prone to delocalize the on-site CO stretching vibration through coupling mechanisms between carbonyl groups, whereas α-helix structures are energetically less stable to permit vibrational mode delocalization.

The Puzzling Problem of Cardiolipin Membrane-Cytochrome c Interactions: A Combined Infrared and Fluorescence Study.

The interaction of cytochrome c (cyt c) with natural and synthetic membranes is known to be a complex phenomenon, involving both protein and lipid conformational changes. In this paper, we combined infrared and fluorescence spectroscopy to study the structural transformation occurring to the lipid network of cardiolipin-containing large unilamellar vesicles (LUVs). The data, collected at increasing protein/lipid ratio, demonstrate the existence of a multi-phase process, which is characterized by: (i) the interaction of cyt c with the lipid polar heads; (ii) the lipid anchorage of the protein on the membrane surface; and (iii) a long-distance order/disorder transition of the cardiolipin acyl chains. Such effects have been quantitatively interpreted introducing specific order parameters and discussed in the frame of the models on cyt c activity reported in literature.

Proton Dynamics in Palladium-Silver: An Inelastic Neutron Scattering Investigation.

Proton dynamics in Pd77Ag23 membranes is investigated by means of various neutron spectroscopic techniques, namely Quasi Elastic Neutron Scattering, Incoherent Inelastic Neutron Scattering, Neutron Transmission, and Deep Inelastic Neutron Scattering. Measurements carried out at the ISIS spallation neutron source using OSIRIS, MARI and VESUVIO spectrometers were performed at pressures of 1, 2, and 4 bar, and temperatures in the 330-673 K range. The energy interval spanned by the different instruments provides information on the proton dynamics in a time scale ranging from about 102 to 10-4 ps. The main finding is that the macroscopic diffusion process is determined by microscopic jump diffusion. In addition, the vibrational density of states of the H atoms in the metal lattice has been determined for a number of H concentrations and temperatures. These measurements follow a series of neutron diffraction experiments performed on the same sample and thus provide a complementary information for a thorough description of structural and dynamical properties of H-loaded Pd-Ag membranes.

Pressure effects on collective density fluctuations in water and protein solutions.

Neutron Brillouin scattering and molecular dynamics simulations have been used to investigate protein hydration water density fluctuations as a function of pressure. Our results show significant differences between the pressure and density dependence of collective dynamics in bulk water and in concentrated protein solutions. Pressure-induced changes in the tetrahedral order of the water HB network have direct consequences for the high-frequency sound velocity and damping coefficients, which we find to be a sensitive probe for changes in the HB network structure as well as the wetting of biomolecular surfaces.