Biology subjects

Mercadante, D.

Publications and source records attributed to Mercadante, D..

13 recordsLinked to original sources

bioRxiv2026

Capturing secondary structure in coarse grained intrinsically disordered proteins with simulations driven by chemical shifts.

A major challenge when investigating intrinsically disordered proteins (IDPs) pertains to understanding how secondary structure formation across otherwise disordered ensembles, relates to function. While coarse-grained (CG) simulation methods are instrumental to describe ensemble-to-function relationships in IDPs, they remain largely incapable of sampling secondary structure. We here present NapshiftC, an artificial neural network capable of modelling NMR chemical shifts from C-mapped CG protein conformations, leveraging its predictions to restrain simulations and yield experimentally-informed IDP ensembles that contain secondary structure. We applied NapshiftC on a large set of proteins in isolation or condensed phase, and found that, when secondary structure is present, CS incorporation yields improved agreements with smFRET spectroscopy and resolves the over-reliance of CG models on near linear conformers. By incorporating observables that are routinely collected for IDPs but never coupled to CG simulations, NapshiftC ultimately informs on both local and global conformational features of function-defining IDP ensembles.

biophysics↗

bioRxiv2025

Integrating NMR restraints into coarse-grained simulations: toward accurate conformational ensembles of complex protein systems

Structural dynamics play critical roles for the biological activity of protein molecules. Characterising the inherent conformational landscapes of these macromolecules remains a major experimental and computational challenge, particularly for heterogeneous and transient systems such as intrinsically disordered proteins, membrane-associated assemblies and disordered fuzzy coats of amyloid aggregates. In this context, coarse-grained (CG) molecular dynamics simulations have enabled accessing to extended timescales and large system sizes, however, their reduced resolution and simplified interaction potentials often limit the structural accuracy. Here, we introduce Martini3-NMR, an integrative framework that incorporates nuclear magnetic resonance (NMR) observables directly into CG protein force fields. Using artificial neural networks to model NMR chemical shifts at the CG level, and integrating these data with NOE restraints, we define an approach to significantly enhance the accuracy of CG simulations while maintaining their elevated sampling efficiency, thereby resulting in a substantially improved description of protein conformational ensembles. We demonstrate the broad applicability of Martini3-NMR by generating CG ensembles for a diverse range of systems and complex processes such as protein folding from misfolded states, oligomer disassembly within lipid bilayers and the topology of disordered fuzzy regions at amyloid fibril surfaces, which were found to display condensate-like structural and dynamical properties. By enabling an experimentally driven and computationally efficient exploration of protein conformational landscapes, Martini3-NMR provides a novel general framework for investigating dynamic, heterogeneous and multiscale biomolecular processes. This approach opens to significant new opportunities for extending CG simulations towards a more quantitative understanding of the relationship between molecular structure, dynamics and biological function.

biophysics↗

bioRxiv2025

Redox-controlled dimerisation regulates ethylene biosynthesis

Ethylene is a central plant hormone that orchestrates growth, development, senescence, and stress responses. Because it is gaseous, ethylene must be synthesised on demand, yet the catalytic and regulatory mechanisms of its biosynthetic enzyme, 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), remain poorly understood. Here, using structural, biophysical, and computational analyses, we uncovered two principles: ACO catalysis relies on an induced-fit mechanism, and disulfide-mediated dimerisation via a conserved cysteine acts as a redox switch toggling ACO between active monomer and inactive dimer. This previously unrecognised regulatory layer positions ACO as a redox sensor in plant cells, revealing a fundamental control point in ethylene biosynthesis. Given ethylenes pivotal role in crop productivity and stress resilience, these findings open new opportunities for precise manipulation of hormone signalling in agriculture and biotechnology.

biochemistry↗

bioRxiv2025

Protease mimicry: dissecting the ester bond crosslinking mechanics in bacterial adhesin proteins

The ester bond crosslink discovered within bacterial adhesin proteins offers a captivating insight into the convergent evolution of enzyme-like machinery. Crystal structures reveal a putative catalytic triad comprising an acid-base-nucleophile combination and an oxyanion-like site that suggest a serine protease-like mechanism drives the crosslinking process. We now provide confirmation of the mechanism, revealing functional catalytic dyads or triads, and the recapitulation of protease machinery from a Pseudomonas bacterium and a human cytomegalovirus related only by convergent evolution. Molecular dynamics simulations show how a conservative threonine-to-serine mutation of the nucleophile induces hydrolysis and eliminates the ester bond crosslink. Collectively, our structural, functional, and computational efforts detail the molecular intricacies of intramolecular ester bond formation and underscore the convergent evolutionary adaptations of bacteria in exploiting enzyme-like machinery to protect essential adhesin proteins from the mechanical, biological, and chemical hostilities of the bacterias replicative niche.

biochemistry↗

bioRxiv2024

Disordered regions of human eIF4B orchestrate a dynamic self-association landscape

Eukaryotic translation initiation factor eIF4B is required for efficient cap-dependent translation, it is overexpressed in cancer cells, and may influence stress granule formation. Due to the high degree of intrinsic disorder, eIF4B is rarely observed in cryo-EM structures of translation complexes and only ever by its single structured RNA recognition motif domain, leaving the molecular details of its large intrinsically disordered region (IDR) unknown. By integrating experiments and simulations we demonstrate that eIF4B IDR orchestrates and fine-tunes an intricate transition from monomers to a condensed phase, in which large-size dynamic oligomers form before mesoscopic phase separation. Single-molecule spectroscopy combined with molecular simulations enabled us to characterize the conformational ensembles and underlying intra- and intermolecular dynamics across the oligomerization transition. The observed sensitivity to ionic strength and molecular crowding in the self-association landscape suggests potential regulation of eIF4B nanoscopic and mesoscopic behaviors such as driven by protein modifications, binding partners or changes to the cellular environment.

biophysics↗

bioRxiv2023

DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2

More than 1600 human transcription factors orchestrate the transcriptional machinery to control gene expression and cell fate. Their function is conveyed through intrinsically disordered regions (IDRs) containing activation or repression domains but lacking quantitative structural ensemble models prevents their mechanistic decoding. Here we integrate single-molecule FRET and NMR spectroscopy with molecular simulations showing that DNA binding can lead to complex changes in the IDR ensemble and accessibility. The C-terminal IDR of pioneer factor Sox2 is highly disordered but its conformational dynamics are guided by weak and dynamic charge interactions with the folded DNA binding domain. Both DNA and nucleosome binding induce major rearrangements in the IDR ensemble without affecting DNA binding affinity. Remarkably, interdomain interactions are redistributed in complex with DNA leading to variable exposure of two activation domains critical for transcription. Charged intramolecular interactions allowing for dynamic redistributions may be common in transcription factors and necessary for sensitive tuning of structural ensembles.

biophysics↗

bioRxiv2022

The structural, dynamical and biochemical characterizations of Verticillium dahliae pectate lyase, VdPelB, highlight its specificities

Pectins, complex polysaccharides and major components of the plant primary cell wall, can be degraded by pectate lyases (PLs). PLs cleave glycosidic bonds of homogalacturonans (HG), the main pectic domain, by {beta}-elimination, releasing unsaturated oligogalacturonides (OGs). To understand the catalytic mechanism and structure/function of these enzymes, we characterized VdPelB from Verticillium dahliae, a plant pathogen. We first solved the crystal structure of VdPelB at 1.2[A] resolution showing that it is a right-handed parallel {beta}-helix structure. Molecular dynamics (MD) simulations further highlighted the dynamics of the enzyme in complex with substrates that vary in their degree of methylesterification, identifying amino acids involved in substrate binding and cleavage of non-methylesterified pectins. We then biochemically characterized wild type and mutated forms of VdPelB. VdPelB was most active on non-methylesterified pectins, at pH 8 in presence of Ca2+ ions. VdPelB-G125R mutant was most active at pH 9 and showed higher relative activity compared to native enzyme. The OGs released by VdPelB differed to that of previously characterized PLs, showing its peculiar specificity in relation to its structure. OGs released from Verticillium-partially tolerant and sensitive flax cultivars differed which could facilitate the identification VdPelB-mediated elicitors of defence responses.

biochemistry↗

bioRxiv2022

Cortical Dynein Drives Centrosome Clustering in Cells with Centrosome Amplification

During cell division, the microtubule nucleating and organizing organelle, known as the centrosome, is critical for the formation of the mitotic spindle. In cells with two centrosomes, each centrosome functions as an anchor point for microtubules, leading to the formation of a bipolar spindle and progression through a bipolar cell division. When extra centrosomes are present, multipolar spindles form and the parent cell may divide into more than two daughter cells. Cells that are born from multipolar divisions are not viable and hence clustering of extra centrosomes and progression to a bipolar division are critical determinants of viability in cells with extra centrosomes. We combine experimental approaches with computational modeling to define a role for cortical dynein in centrosome clustering. We show that centrosome clustering fails and multipolar spindles dominate when cortical dynein distribution or activity is experimentally perturbed. Our simulations further reveal that centrosome clustering is sensitive to the distribution of dynein on the cortex. Together, these results indicate that dyneins cortical localization alone is insufficient for effective centrosome clustering and instead, dynamic relocalization of dynein from one side of the cell to the other throughout mitosis promotes timely clustering and bipolar cell division in cells with extra centrosomes.

cell biology↗

bioRxiv2022

Differences in the structure of plant polygalacturonases specify enzymes dynamics and processivities to fine-tune pectins and root development

The fine-tuning of pectins by polygalacturonases (PGs) plays a key role in modulating plant cell wall chemistry and mechanics, impacting plant development. In plants, the high number of PGs encoded in the genome questions the regulation of pectin depolymerization and the roles of distinct isozymes in the control of development. Here we report the first crystal structures of two PGs from Arabidopsis, PGLR and ADPG2 whose expression overlap in roots. Albeit having overall conserved folds and active sites, PGLR and ADPG2 differed in the structure of their binding grooves and in the amino-acids of the subsites. We determined the structural features that explain the absence of inhibition of the plant PGs by endogenous PG-Inhibiting Proteins (PGIPs). By combining molecular dynamic simulations, analysis of enzymes kinetics and hydrolysis products, we showed that subtle differences in PGLR and ADPG2 structures translated into distinct enzyme-substrate dynamics and enzymes processivities. Using the plant root as a developmental model, exogenous application of purified enzymes showed that these distinct PGLR/ADPG2 processivities ultimately translated into different impacts on development. The highly processive ADPG2 had major effects on both root cell elongation and cell adhesion. Our study suggests that, in plants, gene redundancy is unlikely to reflect redundant biochemical specificities. Isozymes of distinct specificities and processivities are likely to be of major importance for the fine spatial and temporal regulation of pectin structure. Significance StatementPlant polygalacturonases (PG) are enzymes that play a key role in the regulation of cell wall pectin chemistry by controlling the degree of polymerization of the HG chains. The high number of genes encoding PG in Arabidopsis questions the rationale for such abundance. We solved the crystal structure of two PG (PGLR and ADPG2) whose expression overlap in roots and showed, using combined computational and experimental approaches, that they differ in their enzyme-substrate dynamics, leading to distinct processivities. The highly processive ADPG2 can generate digestion products of shorter degree of polymerization, and upon exogenous application on developing roots, induced drastic developmental defects. Our study suggests that gene redundancy is unlikely to reflect redundant biochemical specificities of isozymes.

biochemistry↗

bioRxiv2021

The pH-dependent processivity of Arabidopsis AtPME2 can control cell wall mechanical properties

Pectin methylesterases (PMEs) modify homogalacturonans (HG) chemistry and play a key role in regulating primary cell wall mechanical properties. How PME activity can fine-tune pectin structure in the growing plant has remained elusive. Here we report on the Arabidopsis AtPME2, which we found to be highly expressed during lateral root emergence and dark-grown hypocotyl elongation. We produced the mature active enzyme using heterologous expression in Pichia pastoris and characterized it through the use of a generic plant PME antiserum suitable for detecting recombinant and native enzyme independent of species source. At neutral pH AtPME2 is preferentially active on pectins with a degree of 55-70% methylesterification and can be inhibited by PME inhibitor protein (PMEI). We show that the mode of action for AtPME2 can switch from full processivity (at pH 8), creating large blocks of unmethylated galacturonic acid, to low processivity (at pH 5) and relate these observations to the differences in electrostatic potential of the protein at acidic and alkaline pH. To assess the role of AtPME2 in development, we characterized two knock-out lines. We show that in the context of acidified apoplast, low-processive demethylesterification by AtPME2 can loosen the cell wall, with consequent increase in cell elongation and etiolated hypocotyl length. Our study brings insights into how the pH-dependent regulation by PME activity could affect pectin structure and associated cell wall mechanical properties in expansion. One sentence summaryThe processivity of AtPME2, a pectin methylesterase that fine-tunes cell wall pectins is modulated by pH in vitro and impacts the mechanical properties of the wall, affecting development in planta.

plant biology↗

bioRxiv2020

α-Synuclein plasma membrane localization correlates with cellular phosphatidylinositol polyphosphate levels.

The Parkinsons disease protein -synuclein (Syn) promotes membrane fusion and fission by interacting with various negatively charged phospholipids. Despite postulated roles in endocytosis and exocytosis, plasma membrane (PM) interactions of Syn are poorly understood. Here, we show that phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidylinositol 3,4,5-trisphosphate (PIP3), two highly acidic components of inner PM leaflets, mediate plasma membrane localization of endogenous pools of Syn in A2780, HeLa, SH-SY5Y and SK-MEL-2 cells. We demonstrate that Syn binds reconstituted PIP2-membranes in a helical conformation in vitro and that PIP2 synthesizing kinases and hydrolyzing phosphatases reversibly redistribute Syn in cells. We further delineate that Syn-PM targeting follows phosphoinositide-3 kinase (PI3K)-dependent changes of cellular PIP2 and PIP3 levels, which collectively suggests that phosphatidylinositol polyphosphates contribute to Syns cellular function(s) at the plasma membrane.

cell biology↗

bioRxiv2020

Disordered Proteins Enable Histone Chaperoning on the Nucleosome

Proteins with highly charged disordered regions are abundant in the nucleus, where many of them interact with nucleic acids and control key processes such as transcription. The functional advantages conferred by protein disorder, however, have largely remained unclear. Here we show that disorder can facilitate a remarkable regulatory mechanism involving molecular competition. Single-molecule experiments demonstrate that the human linker histone H1 binds to the nucleosome with ultra-high affinity. However, the large-amplitude dynamics of the positively charged disordered regions of H1 persist on the nucleosome and facilitate the interaction with the highly negatively charged and disordered histone chaperone prothymosin . Consequently, prothymosin can efficiently invade the H1-nucleosome complex and displace H1 via competitive substitution. By integrating experiments and simulations, we establish a molecular model that rationalizes this process structurally and kinetically. Given the abundance of charged disordered regions in the nuclear proteome, this mechanism may be widespread in cellular regulation.

biophysics↗

bioRxiv2018

Aurora A inhibition limits centrosome clustering and promotes mitotic catastrophe in cells with supernumerary centrosomes

The presence of supernumerary centrosomes is prevalent in cancer, where they promote the formation of transient multipolar mitotic spindles. Active clustering of supernumerary centrosomes enables the formation of a functional bipolar spindle that is competent to complete a bipolar division. Disruption of spindle pole clustering in cancer cells promotes multipolar division and generation of non-proliferative daughter cells with compromised viability. Hence molecular pathways required for spindle pole clustering in cells with supernumerary centrosomes, but dispensable in normal cells, are promising therapeutic targets. Here we demonstrate that Aurora A kinase activity is required for spindle pole clustering in cells with extra centrosomes. While cells with two centrosomes are ultimately able to build a bipolar spindle and proceed through a normal cell division in the presence of Aurora A inhibition, cells with supernumerary centrosomes form multipolar and disorganized spindles that are not competent for chromosome segregation. Instead, following a prolonged mitosis, these cells experience catastrophic divisions that result in grossly aneuploid, and non-proliferative daughter cells. Aurora A inhibition in a panel of Acute Myeloid Leukemia cancer cells has a similarly disparate impact on cells with supernumerary centrosomes, suggesting that centrosome number and spindle polarity may serve as predictive biomarkers for response to therapeutic approaches that target Aurora A kinase function.

cancer biology↗