Biology subjects

Parisini, E.

Publications and source records attributed to Parisini, E..

6 recordsLinked to original sources

bioRxiv2025

Mechanistic Insights into Cross-β Sheet Formation in the HIV-Associated Amyloidogenic Peptide PAP248-286 from Unbiased All-Atom Molecular Dynamics Simulation

Semen-derived enhancer of viral infection (SEVI) fibrils, assembled from the peptide fragment PAP248-286, enhance HIV transmission by promoting viral attachment to host cells. However, the molecular basis of SEVI nucleation and early aggregation remains unclear. Here, we conducted 80 independent all-atom molecular dynamics (MD) simulations spanning a total of 40 s, together with 100 independent steered MD and umbrella sampling runs, to explore the dimerization and dissociation of PAP248-286 Our results show that hydrogen bonding is the dominant stabilizing force driving {beta}-sheet formation during peptide association. Residue-level analyses identified Arg10, Val17, Glu19, and Ile20 as key contributors to inter-peptide binding, consistent with steric zipper motifs described in other amyloid systems. Steered MD revealed mechanically resilient dimers with average rupture forces of [~]20 kcal/mol/[A] and multi-barrier unbinding behavior. Umbrella sampling estimated a peptide dissociation free energy of [~]8.7 kcal/mol, highlighting a clear thermodynamic separation between bound and unbound states. Together, these findings suggest that small {beta}-sheet nuclei in PAP248-286 dimers act as cooperative intermediates that seed the formation of full-length cross-{beta} structures, providing atomistic insights into the earliest steps of SEVI fibril assembly.

biochemistry↗

bioRxiv2024

Development of a highly active engineered PETase enzyme for polyester degradation

Polyethylene terephthalate (PET) accounts for {approx}6% of global plastic production, contributing considerably to the global solid waste stream and environmental plastic pollution. Since the discovery of PET-depolymerizing enzymes, enzymatic PET recycling has been regarded as a promising method for plastic disposal, particularly in the context of a circular economy strategy. However, as the PET degrading enzymes developed so far suffer from relatively limited thermostability, low catalytic efficiency, as well as degradation intermediate-induced inhibition, their large scale industrial applications are still largely hampered. To overcome these limitations, we used in silico protein design methods to develop an engineered Leaf-branch Compost Cutinase (LCC), named DRK3, that features enhanced thermal stability and PETase activity relative to the current gold standard LCC enzyme (LCC-ICCG). DRK3 features a 4.1{degrees}C increase in melting temperature relative to the LCC-ICCG enzyme. Under optimal reaction conditions (68{degrees}C), the DRK3 enzyme hydrolyzes amorphous PET material into TPA with a 2-fold higher efficiency compared to LCC-ICCG. Owing to its enhanced properties, DRK3 may be a promising candidate for future applications in industrial PET recycling processes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/602061v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@125688eorg.highwire.dtl.DTLVardef@f360f8org.highwire.dtl.DTLVardef@634486org.highwire.dtl.DTLVardef@127f622_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

Investigating the effect of POPC-POPG Lipid Bilayer Composition on PAP248-286 Binding using CG Molecular Dynamics Simulations

PAP248-286 is a fusogenic peptide derived from prostatic acid phosphatase, commonly found in human semen, and is known to mediate HIV fusion with cell membranes. In this study, we performed 120 independent coarse-grained molecular dynamics simulations to investigate the spontaneous binding of PAP248-286 monomers, considering both charged and neutral histidine (His) residues, to membrane bilayers composed of different lipid compositions: 100% POPC, 70% POPC-30% POPG, and 50% POPC-50% POPG. Our simulations revealed that PAP248-286 displayed spontaneous binding to the membrane, with increased binding observed in the presence of anionic lipid POPG. Specifically, in systems containing 30% and 50% POPG lipids, monomer residues, particularly in the systems containing charged histidine (His) residues, exhibited prolonged binding with the membrane. Furthermore, our simulations indicated that PAP248-286 adopted a parallel orientation with the membrane, exposing its positively charged residues to the lipid bilayer. Interestingly, systems containing charged His residues showed higher lipid occupancy around the peptide. These findings are consistent with previous experimental data, suggesting that PAP248-286 binding is enhanced in membranes with charged His residues, resembling the conditions found in the acidic vaginal pH environment. The results of our study provide further insights into the molecular mechanisms underlying the membrane binding of PAP248-286, contributing to our understanding of its potential role in HIV fusion and infection.

biochemistry↗

bioRxiv2022

A Coarse-Grained Molecular Dynamics Investigation on Spontaneous Binding of Aβ9-40 Fibril with Cholesterol-mixed DPPC Bilayer

Alzheimers disease is the most common form of dementia. Its aetiology is characterized by the misfolding and aggregation of amyloid-{beta} (A{beta}) peptides into {beta}-sheet-rich A{beta} oligomers/fibrils. Whereas experimental studies have suggested that A{beta} oligomers/fibrils interact with the cell membranes and perturb their structures and dynamics, the molecular mechanism of this interaction is still not fully understood. In the present work, we have performed a total of 120 s-long simulations to investigate the interaction between trimeric or hexameric A{beta}1-40 fibrils with either a 100% DPPC bilayer, a 70% DPPC-30% cholesterol bilayer or a 50% DPPC-50 % cholesterol bilayer. Our simulation data capture the spontaneous binding of the aqueous A{beta}1-40 fibrils with the membranes and show that the central hydrophobic amino acid cluster, the lysine residue adjacent to it and the C-terminal hydrophobic residues are all involved in the process. Moreover, our data show that while the A{beta}1-40 fibril does not bind to the 100% DPPC bilayer, its binding affinity for the membrane increases with the amount of cholesterol. Overall, our data suggest that two clusters of hydrophobic residues and one lysine help A{beta}1-40 fibrils establish stable interactions with a cholesterol-rich DPPC bilayer. These residues are likely to represent potential target regions for the design of inhibitors, thus opening new avenues in structure-based drug design against A{beta} oligomer/fibril-membrane interaction.

biochemistry↗

bioRxiv2022

Targeting triple-negative breast cancer with β1-integrin binding aptamer

Targeted therapies have increased the treatment options for triple-negative breast cancer patients. However, the paucity of targetable biomarkers and tumour heterogeneity have limited the ability of precision-guided interventions to live up to their full potential. As affinity targeting ligands, aptamers show high selectivity towards target molecules. Compared to antibodies, aptamers have lower molecular weight, increased stability during transportation, reduced immunogenicity, and increased tissue uptake. Recently, we reported the discovery of GreenB1 aptamer that is internalized in cultured triple-negative MDA-MB-231 human breast cancer cells. We show that the GreenB1 aptamer specifically targets {beta}1-integrin, a protein previously linked to breast cancer cell invasiveness and migration. Aptamer binds to {beta}1-integrin with low nanomolar affinity. GreenB1 homes in the orthotopic 4T1 triple-negative breast cancer lesions modelled in mice. Our findings suggest potential applications for the GreenB1-guided precision agents for the diagnosis and therapy of triple-negative breast cancer.

molecular biology↗

bioRxiv2022

Early Stages of Misfolding of PAP248-286 at two different pH values: An Insight from Molecular Dynamics Simulations

PAP248-286 peptides, which are highly abundant in human semen, aggregate and form amyloid fibrils that enhance HIV infection. Previous experimental studies have shown that the infection-promoting activity of PAP248-286 begins to increase well before amyloid formation takes place and that pH plays a key role in the enhancement of PAP248-286-related infection. Hence, understanding the early stages of misfolding of the PAP2482-86 peptide is crucial. To this end, we have performed 60 independent MD simulations for a total of 24 s at two different pH values (4.2 and 7.2). Our data shows that misfolding of the PAP248-286 peptide is a multistage process and that the first step of the process is a transition from an "I-shaped" structure to a "U-shaped" structure. We further observed that the structure of PAP248-286 at the two different pH values shows significantly different features. At pH 4.2, the peptide has less intra-molecular H-bonds and a reduced -helical content than at pH 7.2. Moreover, differences in intra-peptide residues contacts are also observed at the two pH values. Finally, free energy landscape analysis shows that there are more local minima in the energy surface of the peptide at pH 7.2 than at pH 4.2. Overall, the present study elucidates the early stages of misfolding of the PAP248-286 peptide at the atomic level, thus possibly opening new avenues in structure-based drug discovery against HIV infection.

biochemistry↗