Biophysical Society Thematic Meeting | Trieste 2024

Emerging Theoretical Approaches to Complement Single-Particle Cryo-EM

Poster Abstracts

19-POS Board 19 ATOM PROBE TOMOGRAPHY AS NEW TOOL TO DETERMINE THE STRUCTURE OF PROTEINS: A COMPUTATIONAL AND EXPERIMENTAL STUDY Giovanni Novi Inverardi ; 1 University of Trento, Department of Physics, Trento, Italy Atom Probe Tomography (APT) has been recently proposed as an alternative procedure to determine three-dimensional structures of proteins. APT consists of a spatially–resolved mass spectrometry technique, whereby a biological specimen is first embedded by an amorphous silica matrix, and subsequently evaporated under irradiation of short laser pulses, upon application of a strong electric field to direct ejected ions towards a detecting surface. Building on APT, a funded EIC-Pathfinder consortium, named MIMOSA, aims to provide a new approach to 4D microscopy, enabling high spatial resolution and chemical sensitivity by employing terahertz (THz) source lasers. Both the embedding procedure and the subsequent laser irradiation step present several challenges that can be addressed and inspected with the available computational techniques. We have proposed a Molecular Dynamics protocol aimed at depicting the early stages of the embedding process of proteins in a solution of water and polymers of orthosilicic acid, taken as precursor of the silica matrix. APT requires that the silica primer remains bio compatible, keeping the native structural features of the system at hand while condensing into an amorphous, glassy-like coating. If on one hand we observed a negligible influence of orthosilicic acid polymers on the dynamics of stable folded domains, on the other they seem to reduce the fluctuations of intrinsically disordered domains and loops. We have also recently developed a computational protocol based on Time–Dependent Density Functional Theory (TDDFT), aimed at describing the orthosilicic acid under electric field and THz laser irradiation. In fact, the combined effects of electric fields and laser pulses on the matrix complex are still not properly deciphered. We explored different values of electric field and laser frequencies, reconstructing a phase diagram characterizing the ion–field evaporation process of the silanol groups of orthosilicic acid, matching confirmed experimental data.

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