The main research lines foreseen for the first period of the project focussed particularly on the algorithmic and methodological aspects, with important input coming from the fruitful collaboration established with scientists outside of the group (e.g. M. Scott Shell, UCSB (USA), and Flavio Vella, Free University of Bozen (IT)).
Various papers have been published in this period, which conveyed the main message of the project and related research lines (Diggins et al., JCTC 2019; Giulini and Potestio, Interface Focus 2019; Tarenzi et al., JCTC 2019; Erban et al., Interface Focus 2019; Riccardi et al., Interface Focus 2019; Fiorentini et al., Proteins 2020).
A key milestone of the project has been achieved with the development of the mapping entropy minimisation method (Giulini et al. JCTC 2020; Errica et al., Front. Mol. Biosci 2021), which enables the identification of biologically relevant atoms and residues of proteins through an information theory-based analysis of a molecular dynamics simulation. A manuscript reporting on a generalisation of this method was published on PRE (Holtzman et al., PRE 2022).
Further work was carried out for the development of variable resolution modelling strategies capable of preserving crucial mechanical and dynamical properties of the reference model (Tarenzi et al., Scientific Reports 2021; Tarenzi et al., Applied Sciences 2022).
A modelling strategy has been developed that produces a multiple-resolution model of the system based on user-provided instructions. This approach has been validated on two nontrivial case studies, the adenylate kinase enzyme and the pharmaceutical antibody pembrolizumab. The paper was published shortly after the end of the project (Fiorentini et al., JCIM 2023).
Recently we have employed an approach based on two measures of information content of data, namely resolution and relevance, to investigate the properties of a protein’s conformational space and to identify the optimal strategy to coarse-grain it. This work was accepted for publication in Soft Matter (Mele et al., Soft Matter 2022).
Other works have been carried out in this period, which contributed to establish important relationships among a protein’s structure, its dynamics, and its function, through the usage of the resolution level and distribution of its description as a bridge between these elements. Specifically:
Tarenzi et al., JCTC 2019
Heidari et al., JCP 2020
Baptista et al., JPCM 2021
Menichetti et al., EPJB 2021
Giulini et al., 2021
Tarenzi et al., BBA Biomembranes 2022
Luchi et al., arxiv preprint 2022
Micheloni et al., biorXiv preprint 2022
During the second half of the project we also carried out several activities aimed at communicating science to the general public. The outcomes of the project have been the following:
1. Participation in the European Researcher’s Night 2021.
2. Production of a book containing 36 images related to the group’s research activity.
3. The 36 images were exposed in a dedicated exhibition lasting until February 14, 2022 at the BUC - Central University Library in Trento, Italy.
