Biology subjects

Monje, V.

Publications and source records attributed to Monje, V..

5 recordsLinked to original sources

bioRxiv2026

Mechanistic Insights into MLKL Activation via Allosteric Pathways Identified Through Molecular Models

The mixed lineage kinase domain-like protein (MLKL) is responsible for plasma membrane (PM) permeabilization during the last stage of necroptosis, a pro-inflammatory programmed cell death pathway. MLKL contains three domains: the pseudokinase domain (PsKD), the brace region, and the four-helical bundle (4HB). Phosphorylation of PsKD at amino acids S345 and S347 is essential for MLKL function as it triggers conformational changes that expose the 4HB and enables protein oligomerization and sub-sequent PM permeabilization. Understanding the molecular mechanisms of this allosteric signal is critical for the rational design of ligands that modulate cell death via necroptosis as terapeutic alternatives for neurodegenerative and inflammatory disorder. We simulated the wild-type, phosphorylated, and mutant MLKL proteoforms to build a Markov state model that revealed three dominant macrostates corresponding to the open, transition, and closed conformations. Hydrogen-bond/Hydrophobic network analysis, with a novel clustering approach, identified a switch in the allosteric path-ways that favors the open state. Based on this model, we identified and tested computationally an MLKL mutant that facilitates 4HB exposure, and could favor protein oligomerization and compromise plasma membrane integrity. We present a comprehensive all-atom molecular dynamics study to characterize the conformational changes that enable exposure of the 4HB at the molecular level.

biophysics↗

bioRxiv2026

Cholesteryl Esters Modulate Lipid Droplet Rigidity and Monolayer Organization during Liver Cancer Progression

In mammalian cells, lipid monolayers support the integrity of lipid droplets (LDs), organelles that function as storage for neutral lipids. Liver-targeting illnesses such as liver cancer interrupt normal LD metabolism and prompt changes in the chemical content of these organelles, which can have effects on structural and organizational behavior of the lipids. In LDs, liver cancer induces concentric crystalline phases of cholesteryl esters (CEs) and triglycerides near the NL-monolayer interface, which become more pronounced as CE concentration increases. Yet, there is little known about how this phenomenon may link to persistence of undigested LDs in liver cancer patients. To shed light on this, all-atom molecular dynamics simulations were used to model LD micropipette aspiration experiments and gain insight into the effect of CE concentration on partitioning, structural, and mechanical properties of LDs. We successfully model micropipette aspiration by application of constant surface tension laterally, which stretches lipid bilayers and monolayers as the magnitude increased. The results show increased phospholipid packing due to insertion of CE fatty tails into the monolayer. Increasing CE concentration induces a non-linear change in surface packing defects on the LDs, notable rigidification, and stiffness. Taken together, these insights improve our understanding of the physical properties at the LD monolayer-core interface during liver cancer progression.

biophysics↗

bioRxiv2025

Sterols govern membrane susceptibility to saponin-induced lysis

Saponins are natural detergents that interact with cellular membranes, causing deterioration leading to membrane disruption. The magnitude of these effects depends on both the saponin structure and target membrane composition, where sterols play a key modulating role in saponin-membrane interaction. We investigated the influence of different sterol classes on saponin-induced membrane lysis. The bioactive, cytotoxic saponin -hederin induced permeability in membranes containing zoosterol and mycosterol, whereas phytosterol-containing membranes were resistant to lysis in vitro. Similarly, in yeast, -hederin caused significant cell lysis, while in the ergosterol-deficient erg3{Delta} and pdr18{Delta} mutants, cell lysis was minimal. Supplementing phytosterols to yeast provided resistance to -hederin-induced lysis. Molecular dynamics simulations provide novel mechanistic insights, showing that the efficacy of the activity of -hederin is proportional to the sterol type in the membrane. Our findings reveal that while zoosterols and mycosterols render membranes vulnerable to bioactive saponins, phytosterols protect membranes from saponin-induced lysis in vitro, in vivo and in silico.

molecular biology↗

bioRxiv2025

Lipid-Driven Alignment and Binding of p7 Dimers in Early Oligomer Assembly

Proteins engage in interactions with lipid membranes to facilitate important cellular processes that form the basis of healthy or sick biological conditions. Transmembrane proteins such as ion channels are often made up of bound monomers that engage in specific contacts within the bilayer. However, molecular mechanistic information related to how these channel structures form is scarce. Understanding the role of lipids in driving this process have the potential to close knowledge gaps regarding the assembly behavior of oligomeric proteins which are often clinical targets for disease treatment. Using the hepatitis C virus p7 hexamer as a case study, this work focuses on characterizing the interactions that dictate the beginnings of dimerization using molecular dynamics simulations. Results comparing dimers formed in aqueous solution to those at the surface of a lipid membrane model reveal that protein-lipid interactions are critical in aiding the proper alignment and binding of inter-protein residues. Hydrophobic protein-lipid interactions and hydrogen bonding of key residues to phosphatidylcholine and phosphatidylinositol membrane lipids drive the characteristic inter-protein helix interactions that underlie p7 oligomerization. This increases favorable binding between hydrophobic protein residues, particularly for the first helix of the p7 monomers. This study provides evidence that membrane lipids are a necessary and dynamic factor that contributes to appropriate binding and association of proteins for channel formation within cellular membranes.

biophysics↗

bioRxiv2025

2Danalysis: A toolbox for analysis of lipid membranes and biopolymers in two-dimensional space

Molecular simulations expand our ability to learn about the interplay of biomolecules. Biological membranes, composed of diverse lipids with varying physicochemical properties, are highly dynamic environments involved in cellular functions. Proteins, nucleic acids, glycans and bio-compatible polymers are the machinery of cellular processes both in the cytosol and at the lipid membrane interface. Lipid species directly modulate membrane properties, and affect the interaction and function of other biomolecules. Natural molecular diffusion results in changes of local lipid distribution, affecting the membrane properties. Projecting biophysical and structural membrane and biopolymer properties to a two-dimensional plane can be beneficial to quantify molecular signatures in a reduced dimensional space to identify relevant interactions at the interface of interest, i.e. the membrane surface or biopolymer-surface interface. Here, we present a toolbox designed to project membrane and biopolymer properties to a two-dimensional plane to characterize patterns of interaction and spatial correlations between lipid-lipid and lipid-biopolymer interfaces. The toolbox contains two hubs implemented using MDAKits architecture, one for membranes and one for biopolymers, that can be used independently or together. Three case studies demonstrate the versatility of the toolbox with detailed tutorials in GitHub. The toolbox and tutorials will be periodically updated with other functionalities and resolutions to expand our understanding of the structure-function relationship of biomolecules in two-dimensions. SIGNIFICANCE2Danalysis is a significant contribution for the systematic analysis of membrane and biopolymers simulations at planar interfaces. Developed under the open-source MDAKit framework, it enables efficient analysis of trajectories and provides versatile tools for projecting biophysical properties onto a two-dimensional plane. These capabilities enhance the visualization of spatial and temporal changes in membrane characteristics, such as order parameters, and support the study of biopolymer-surface interactions by analyzing adsorption and confinement mechanisms at 2D interfaces. The users can customize the toolbox to study complex 2D phenomena from molecular simulation.

biophysics↗