We have developed, implemented and applied a computational approach to compute the amide I band (i.e., the band arising from the stretching of the backbone C=O group) in peptides and proteins. The amide I is a particularly diagnostic band for the investigation of the structure and dynamics of proteins and its calculation can provide relevant information with atomistic detail. More recently, the approach has been further developed to model time-dependent IR signals for the study of protein folding, to model the infrared bands arising from sidechain absorption and to study the effects of the electric field polarization on the amide I band. This approach will also be applied to model the vibrational spectroscopic features of macromolecular systems made up of supercoiled DNA in interaction with proteins in the framework of a EU-EIC project.
We also address the calculation of UV–VIS spectra of chromophores in solution and inside proteins, with the aim of clarifying how the interaction with the environment affects the chromophore excited states. The investigation of chromophores of biological relevance is addressed, such as flavins and porphyrins. Concerning the latter, we investigated porphyrin-based flexible molecular cages that showed to be able to encapsulate guest substrates.
| People | Stefano Corni, Laura Zanetti Polzi* |
| Keywords | Infrared spectra, protein folding, UV-VIS spectra |
| Methods, techniques | Hybrid quantum/classical computational approaches, all-atoms molecular dynamics simulations |
| Granted projects | Granted projects: HORIZON-EIC-2021-PATHFINDEROPEN-01, Project 101046920- iSenseDNA |
| Collaborations | University of L’Aquila, CNR ISOF |
| Publications | |
| SMV Pinto, N Tasinato, V Barone, A Amadei, L Zanetti-Polzi, I Daidone Modeling amino-acid side chain infrared spectra: the case of carboxylic residues Phys Chem Chem Phys 2020 | |
| L Zanetti-Polzi, A Amadei, R Djemili, S Durot, L Schoepff, V Heitz, B Ventura, I Daidone Interpretation of experimental soret bands of porphyrins in flexible covalent cages and in their related Ag (I) fixed complexes J Phys Chem C 2019 | |
| V Giliberti, R Polito, E Ritter, M Broser, P Hegemann, L Puskar, U Schade, L Zanetti-Polzi, I Daidone, S Corni, F Rusconi, P Biagioni, L Baldassarre, M Ortolani Tip-enhanced infrared difference-nanospectroscopy of the proton pump activity of bacteriorhodopsin in single purple membrane patches Nano Lett 2019 | |
| CM Davis, L Zanetti-Polzi, M Gruebele, A Amadei, RB Dyer, I Daidone A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy Chem Sci 2018 |