Terahertz vibrations in proteins: experimental and numerical investigation

The principal goal of this Doctorate thesis is to study high frequency vibrations (in the range between Gigahertz and Terahertz) in nanoscopic biological structures such as proteins. In particular, the idea of this thesis is to found, by means of experimental sessions and numerical simulations, natural frequencies of entire proteins or of large portions of that. The mechanical behaviour of proteins is receiving an increasing attention from the scientific community. Recently it has been suggested that mechanical vibrations play a crucial role in controlling structural configuration changes (folding) which govern proteins biological function. The mechanism behind protein folding is still not completely understood, and many efforts are being made to investigate this phenomenon. Complex Molecular Dynamics simulations and sophisticated experimental measurements are conducted to investigate protein dynamics and to perform protein structure predictions; however, these are two related, although quite distinct, approaches. Here we investigate the linearly free dynamics (frequencies and modes) of proteins by Modal Analysis. The input mechanical parameters are taken from the literature. We first give an estimate of the order of magnitude of the natural frequencies of protein crystals by considering both classical wave mechanics and structural dynamics formulas. Afterwards, we perform modal analyses of some relevant chemical groups and of the full lysozyme and Na-K ATPase proteins. The numerical results are compared to experimental data, obtained from both in-house and literature Raman measurements. Our present investigations are devoted to understand if stimulating protein samples with a laser that excites resonant mechanical vibrations (say, in the THz range) may induce variations in the vibrational spectra due to possible conformational changes of protein structure.