Biology subjects

Frezza, E.

Publications and source records attributed to Frezza, E..

5 recordsLinked to original sources

bioRxiv2023

The dynamics of protein-RNA interfaces using all-atom molecular dynamics simulations

Facing the current challenges raised by human health diseases requires the understanding of cell machinery at a molecular level. The interplay between proteins and RNA is key for any physiological phenomenon, as well protein-RNA interactions. To understand these interactions many experimental techniques have been developed, spanning a very wide range of spatial and temporal resolutions. In particular, the knowledge of tridimensional structures of protein-RNA complexes provides structural, mechanical and dynamical pieces of information essential to understand their functions. To get insights into the dynamics of protein-RNA complexes, we carried out all-atom molecular dynamics simulations in explicit solvent on nine different protein-RNA complexes with different functions and interface size by taking into account the bound and unbound forms. First, we characterized structural changes upon binding and for the RNA part the change in the puckering. Second, we extensively analyzed the in-terfaces, their dynamics and structural properties, and the structural waters involved in the binding, as well as the contacts mediated by them. Based on our analysis, the interfaces rearranged during the simulation time showing alternative and stable residue-residue contacts with respect to the experimental structure.

biochemistry↗

bioRxiv2022

Internal Normal Mode Analysis applied to RNA flexibility and conformational changes

We investigated the capability of internal normal modes to reproduce RNA dynamics and predict observed RNA conformational changes, and, notably, those induced by the formation of RNA-protein and RNA-ligand complexes. Here, we extended our iNMA approach developed for proteins to study RNA molecules using a simplified representation of RNA structure and its potential energy. Three datasets were also created to investigate different aspects. Despite all the approximations, our study shows that iNMA is a suitable method to take into account RNA flexibility and describe its conformational changes opening the route to its applicability in any integrative approach where these properties are crucial.

biophysics↗

bioRxiv2021

Biasing RNA coarse-grained folding simulations with Small--Angle X--ray Scattering (SAXS) data

RNA molecules can easily adopt alternative structures in response to different environmental conditions. As a result, a molecules energy landscape is rough and can exhibits a multitude of deep basins. In the absence of a high-resolution structure, Small Angle X-ray Scattering data (SAXS) can narrow down the conformational space available to the molecule and be used in conjunction with physical modeling to obtain high-resolution putative structures to be further tested by experiments. Because of the low-resolution of this data, it is natural to implement the integration of SAXS data into simulations using a coarse-grained representation of the molecule, allowing for much wider searches and faster evaluation of SAXS theoretical intensity curves than with atomistic models. We present here the theoretical framework and the implementation of a simulation approach based on our coarse-grained model HiRE-RNA combined with SAXS evaluations "on-the-fly" leading the simulation toward conformations agreeing with the scattering data, starting from partially folded structures as the ones that can easily be obtained from secondary structures predictions based tools. We show on three benchmark systems how our approach can successfully achieve high-resolution structures with remarkable similarity with the native structure recovering not only the overall shape, as imposed by SAXS data, but also the details of initially missing base pairs.

biophysics↗

bioRxiv2020

Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design

Having claimed over 1 million lives worldwide to date, the ongoing COVID-19 pandemic has created one of the biggest challenges to develop an effective drug to treat infected patients. Among all the proteins expressed by the virus, RNA helicase is a fundamental protein for viral replication, and it is highly conserved among the coronaviridae family. To date, there is no high-resolution structure of helicase bound with ATP and RNA. We present here structural insights and molecular dynamics (MD) simulation results of the SARS-CoV-2 RNA helicase both in its apo form and in complex with its natural substrates. Our structural information of the catalytically competent helicase complex provides valuable insights for the mechanism and function of this enzyme at the atomic level, a key to develop specific inhibitors for this potential COVID-19 drug target.

biochemistry↗

bioRxiv2020

Allosteric inhibition of adenylyl cyclase type 5 by G-protein: a molecular dynamics study

Adenylyl cyclases (ACs) have a crucial role in many signal transduction pathways, in particular in the intricate control of cyclic AMP (cAMP) generation from adenosine triphosphate (ATP). Using homology models developed from existing structural data and docking experiments, we have carried out all-atom, microsecond-scale molecular dynamics simulations on the AC5 isoform of adenylyl cyclase bound to the inhibitory G-protein subunit Gi in the presence and in the absence of ATP. The results show that Gi have significant effects on the structure and flexibility of adenylyl cyclase, as observed earlier for the binding of ATP and Gs. New data on Gi bound to the C1 domain of AC5 help to explain how Gi inhibits enzyme activity and to get insight on its regulation. Simulations also suggest a crucial role of ATP in the regulation of stimulation and inhibition of AC5. Author summaryThe neurons that compose the human brain are able to respond to multiple inputs from other neurons. The chemical "integration" of these inputs then decides whether a given neuron passes on a signal or not. External chemical messages act on neurons via proteins in their membranes that trigger cascades of reactions within the cell. One key molecule in these signaling cascades is cyclic adenosine monophosphate (cAMP) that is chemically synthesized from adenosine triphosphate (ATP) by the enzyme adenylyl cyclase (AC). We are investigating the mechanisms that control how much cAMP is produced as a function of the signals received by the neuron. In particular, we have studied the inhibition effect of a key protein, termed Gi, on AC, and we compare it with the stimulator effect of another key protein termed Gs. Using microsecond molecular simulations, we have been able to show how binding Gi to AC changes its structure and its dynamics so that its enzymatic activity is quenched and that ATP seems to have a crucial role in the regulation of stimulation and inhibition of AC5.

molecular biology↗