Biology subjects

Bordin, J. R.

Publications and source records attributed to Bordin, J. R..

3 recordsLinked to original sources

bioRxiv2026

Interaction-Range Control of Synapsin Aggregation in a Coarse-Grained Model

Synapsin-1 is a multidomain neuronal protein containing extensive intrinsically disordered regions and is a key component of synaptic-vesicle condensates. Direct residue-level simulation of the collective organization of thousands of synapsin molecules remains computationally demanding. Here, we develop a coarse-grained description that connects residue-level CALVADOS 3 simulations to a one-particle-per-protein model. A potential of mean force between two synapsin molecules is obtained by umbrella sampling and represented by an isotropic effective interaction containing a short-range attractive region and a weak outer repulsive contribution. We compare two treatments of this interaction that differ only in the retention of the outer tail. Langevin dynamics simulations of effective proteins show aggregation upon cooling and compression in both models, but with markedly different collective organization. The shorter-ranged model progressively coarsens toward a single dense domain, whereas retaining the outer repulsive contribution favors the persistence of multiple mesoscale aggregates. The two models also display distinct relationships between aggregate size and particle mobility at low temperature. These results show that weak features of an effective protein-protein interaction can have pronounced consequences for collective synapsin organization at mesoscopic scales. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/745062v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@854288org.highwire.dtl.DTLVardef@d2fc52org.highwire.dtl.DTLVardef@1b37d5aorg.highwire.dtl.DTLVardef@eac583_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2019

Adhesion modulates cell morphology and migration within dense fibrous networks

One of the most fundamental abilities required for the sustainability of complex life forms is active cell migration, since it is essential in diverse processes from morphogenesis to leukocyte chemotaxis in immune response. The movement of a cell is the result of intricate mechanisms, that involve the coordination between mechanical forces, biochemical regulatory pathways and environmental cues. In particular, epithelial cancer cells have to employ mechanical strategies in order to migrate through the tissues basement membrane and infiltrate the bloodstream during the invasion stage of metastasis. In this work we explore how mechanical interactions such as spatial restriction and adhesion affect migration of a self-propelled droplet in dense fibrous media. We have performed a systematic analysis using a phase-field model and we propose a novel approach to simulate cell migration with Dissipative Particle Dynamics (DPD) modelling. With this purpose we have measured the cells velocity and quantified its morphology as a function of the fibre density and of its adhesiveness to the matrix fibres. Furthermore, we have compared our results to a previous in vitro migration assay of fibrosacorma cells in fibrous matrices. The results are model independent and show good agreement between the two methodologies and experiments in the literature, which indicates that these minimalist descriptions are able to capture the main features of the system. Our results indicate that adhesiveness is critical for cell migration, by modulating cell morphology in crowded environments and by enhancing cell velocity. In addition, our analysis suggests that matrix metalloproteinases (MMPs) play an important role as adhesiveness modulators. We propose that new assays should be carried out to address the role of adhesion and the effect of different MMPs in cell migration under confined conditions.

biophysics↗

bioRxiv2019

All-atom Molecular Dynamics model for mycobacterial plasma membrane

Phosphatidyl-myo-inositol mannosides (PIMs) are an essential component of the cell envelope and the most predominant at the inner membrane (IM) of M. tuberculosis. In this work, we propose an Molecular Dynamics (MD) M. tuberculosis IM model composed of PIM2 lipids. The study was divided in three parts: influence of the temperature in the PIM2 membrane stability, self-assembly abilities of the PIM2 lipid and the behavior when a trans membrane protein is inserted in PIM2 membrane. Our results show that the model is able to reproduce the gel phase observed at 310 K and the transition to a fluid phase at 328.15 K. Also, the spontaneous self-assembly of randomly distributed lipids in a vesicular aggregate was observed. Finally, we observe that the PIM2 membrane is more stable than DPPC membranes when a Tap protein is inserted. Once Tap eflux pump is related to multidrug resistance of M. tuberculosis, this result indicated that the use of the proper lipid model is essential to the proper depiction and modeling of these systems.\n\nGraphical TOC Entry\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC=\"FIGDIR/small/788299v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (37K):\norg.highwire.dtl.DTLVardef@1409b8dorg.highwire.dtl.DTLVardef@a46772org.highwire.dtl.DTLVardef@183ab3eorg.highwire.dtl.DTLVardef@15fadaa_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗