Biology subjects

Maiani, E.

Publications and source records attributed to Maiani, E..

4 recordsLinked to original sources

bioRxiv2023

Phosphorylation-induced rewiring of intermolecular interactions with LC3B: local and long-range effects on short linear motifs

Short Linear Motifs (SLiMs) play a pivotal role in mediating interactions between intrinsically disordered proteins and their binding partners. SLiMs exhibit sequence degeneracy and undergo regulation through post-translational modifications, including phosphorylation. The flanking regions surrounding the core motifs also exert a crucial role in shaping the modes of interaction. In this study, we aimed to integrate biomolecular simulations, in silico high-throughput mutational scans, and biophysical experiments to elucidate the structural details of phospho-regulation in a class of SLiMs crucial for autophagy, known as LC3 interacting regions (LIRs). As a case study, we investigated the interaction between optineurin and LC3B. Optineurin LIR perfectly exemplify a class of LIR where there is a complex interplay of different phosphorylations and a N-terminal helical flanking region to be disentangled. Our work unveils the unexplored role of the N-terminal flanking region upstream of the LIR core motif in contributing to the interaction interface. The results offer an atom-level perspective on the structural mechanisms and conformational alterations induced by phosphorylation in optineurin and LC3B recognition, along with of effects of mutations on the background of the phosphorylated form of the protein. Additionally, we assessed the impact of disease-related mutations on optineurin, accounting for different functional features. Notably, we established an approach based on Microfluidic Diffusional Sizing as a novel method to investigate the binding affinity of SLiMs to target proteins, enabling precise measurements of the dissociation constant for a selection of variants identified in the in silico mutational screening. Overall, our work provides a versatile toolkit to characterize other LIR-containing proteins and their modulation by phosphorylation or other phospho-regulated SLiMs, thereby advancing the understanding of important cellular processes.

biochemistry↗

bioRxiv2022

MIADE metadata guidelines: Minimum Information About a Disorder Experiment

An unambiguous description of an experimental setup and analysis, and the subsequent biological observation is vital for accurate data interpretation and reproducible results. Consequently, experimental analyses should be described in a concise, unequivocal, and digestible manner. The aim of minimum information guidelines is to define the fundamental complement of data that can support an unambiguous conclusion on experimental observations. In this document, we present the Minimum Information About Disorder Experiments (MIADE) guidelines to define the minimal fundamental parameters required for non-experts to understand the key findings of an experiment studying intrinsically disordered proteins (IDPs) or intrinsically disordered protein regions (IDRs). MIADE guidelines provide recommendations for data producers to describe the results of their experiments at source, for curators to annotate experimental data to community resources and for database developers maintaining community resources to disseminate the data. We give examples of the application of these guidelines in common use cases and describe the implementation of an update to the DisProt IDP database to allow MIADE-compliant annotation. The MIADE guidelines will improve the interpretability of experimental results for data consumers, facilitate direct data submission, simplify data curation, improve data exchange among repositories and standardise the dissemination of the key metadata on an IDP experiment by IDP data sources.

scientific communication and education↗

bioRxiv2019

MutateX: an automated pipeline for in-silico saturation mutagenesis of protein structures and structural ensembles

Mutations resulting in amino acid substitution influence the stability of proteins along with their binding to other biomolecules. A molecular understanding of the effects induced by protein mutations are both of biotechnological and medical relevance. The availability of empirical free energy functions that quickly estimate the free energy change upon mutation ({Delta}{Delta}G) can be exploited for systematic screenings of proteins and protein complexes. Indeed, in silico saturation mutagenesis can guide the design of new experiments or rationalize the consequences of already-known mutations at the atomic level. Often software such as FoldX, while fast and reliable, lack the necessary automation features to make them useful in high-throughput scenarios. Here we introduce MutateX, a software which aims to automate the prediction of {Delta}{Delta}Gs associated with the systematic mutation of each available residue within a protein or protein complex to all other possible residue types, by employing the FoldX energy function. MutateX also supports {Delta}{Delta}G calculations over protein ensembles and the estimation of the changes in free energy upon post-translational modifications. At the heart of MutateX lies an automated pipeline engine that handles input preparation, performs parallel runs with FoldX and outputs publication-ready figures. We here illustrate the MutateX protocol applied to the study of the mutational landscape of cancer-related proteins, industrial enzymes and protein-protein interfaces. The results of the high-throughput scan provided by our tools could help in different applications, such as the analysis of disease-associated mutations, or in the design of protein variants for experimental studies or industrial applications. MutateX is a collection of Python tools that relies on Open Source libraries and requires the FoldX software to be installed beforehand. It is available free of charge and under the GNU General Public License from https://github.com/ELELAB/mutatex.

bioinformatics↗

bioRxiv2019

Kinase-independent inhibition of cyclophosphamide-induced pathways protects the ovarian reserve and prolongs fertility

Premature ovarian failure and infertility are adverse effects of cancer therapies. The mechanism underlying chemotherapy-mediated depletion of the ovarian reserve remains unclear. Here, we aim to identify the signaling pathways involved in the loss of the ovarian reserve to prevent the damaging effects of chemotherapy. We evaluated the effects of cyclophosphamide, one of the most damaging chemotherapeutic drugs, against follicle reserve. In vivo studies showed that the cyclophosphamide-induced loss of ovarian reserve occurred through a sequential mechanism. Cyclophosphamide exposure induced the activation of both DNAPK-{gamma}H2AX-checkpoint kinase 2 (CHK2)-p53/TAp63 isoform and protein kinase B (AKT)-forkhead box O3 (FOXO3a) signaling axes in the nucleus of oocytes. Concomitant administration of an allosteric ABL inhibitor and cyclophosphamide modulated both pathways while protecting the ovarian reserve from chemotherapy assaults. As a consequence, the fertility of the treated mice was prolonged. On the contrary, the administration of an allosteric ABL activator enhanced the lethal effects of cyclophosphamide while shortening mouse fertility. Therefore, kinase-independent inhibition may serve as an effective ovarian-protective strategy in women under chemotherapy.

cell biology↗