Biology subjects

Melo, M. N.

Publications and source records attributed to Melo, M. N..

7 recordsLinked to original sources

bioRxiv2026

Ceramides disrupt hexokinase HKI-VDAC complex assembly and modulate VDAC tilting

Ceramides bind voltage-dependent anion channels (VDACs) to promote mitochondrial apoptosis. However, the underlying mechanism is unclear. Ceramide binding relies on a charged, bilayer-facing glutamate that also controls complex formation between VDACs and pro-survival hexokinase HKI, suggesting that ceramides may exert their pro-apoptotic activity by displacing HKI from VDACs. Here, we challenged this model using coarse-grain molecular dynamics simulations. We show that ceramides impair VDAC-HKI complex assembly, but not via direct competition with HKI for binding to the crucial glutamate. Instead, we find that ceramides disrupt the membrane thinning capacity of polar channel residues adjacent to the glutamate, thereby congesting a low-energy passageway used by HKI for efficient complex formation. We also demonstrate that VDACs are tilted in the membrane and that ceramides act as modulators of channel tilt by neutralizing the hydrophobic mismatch imposed by the polar channel residues. We postulate that this ceramide action further modulates the oligomerization propensity of VDACs. Altogether, our data reveal a mechanistic basis for how ceramides may trigger apoptotic cell death.

biophysics↗

bioRxiv2025

Key determinants of VDAC-hexokinase I complex assembly revealed by a minimal vesicle-based interaction assay

Binding of hexokinase HKI to mitochondrial voltage-dependent anion channels (VDACs) regulates the metabolic fate of glucose and promotes cell survival in hyperglycolytic tumors. Computer simulations indicated that complex assembly relies on intimate contacts between the N-terminal -helix of HKI and a charged bilayer-facing glutamate on the outer wall of VDACs. Protonation of this residue blocks complex formation in silico, explaining the release of HKI from mitochondria observed upon cytosolic acidification. To validate these findings, we here developed an in vitro assay for interrogating HKI binding to VDAC1 reconstituted in vesicles captured on a functionalized surface. TIRF-based quantitative interaction studies with a fluorescent peptide comprising the N-terminal -helix of HKI revealed a crucial role of the bilayer-facing glutamate in complex assembly and recapitulated an exquisite sensitivity of HKI-VDAC binding to fluctuations in pH. Our assay opens up important opportunities to investigate the impact of membrane environment on HKI-VDAC complex assembly and may benefit the development of therapeutics that target pathogenic imbalances in this process.

biophysics↗

bioRxiv2024

Hexokinase-I directly binds to a charged membrane-buried glutamate of mitochondrial VDAC1 and VDAC2

Binding of hexokinase HKI to mitochondrial voltage-dependent anion channels (VDACs) has far-reaching physiological implications. However, the structural basis of this interaction is unclear. Combining computer simulations with experiments in cells, we here show that complex assembly relies on intimate contacts between the N-terminal -helix of HKI and a charged membrane-buried glutamate on the outer wall of VDAC1 and VDAC2. Protonation of this residue blocks complex formation in silico while acidification of the cytosol causes a reversable release of HKI from mitochondria. Membrane insertion of HKI occurs adjacent to the bilayer-facing glutamate where a pair of polar channel residues mediates a marked thinning of the cytoplasmic leaflet. Disrupting the membrane thinning capacity of VDAC1 dramatically impairs its ability to bind HKI in silico and in cells. Our data reveal key topological and mechanistic insights into HKI-VDAC complex assembly that may benefit the development of therapeutics to counter pathogenic imbalances in this process.

biochemistry↗

bioRxiv2024

GoMartini 3: From large conformational changes in proteins to environmental bias corrections

Coarse-grained modeling has become an important tool to supplement experimental measurements, allowing access to spatio-temporal scales beyond all-atom based approaches. The G[o]Martini model combines structure- and physics-based coarse-grained approaches, balancing computational efficiency and accurate representation of protein dynamics with the capabilities of studying proteins in different biological environments. This paper introduces an enhanced G[o]Martini model, which combines a virtual-site implementation of G[o] models with Martini 3. The implementation has been extensively tested by the community since the release of the new version of Martini. This work demonstrates the capabilities of the model in diverse case studies, ranging from protein-membrane binding to protein-ligand interactions and AFM force profile calculations. The model is also versatile, as it can address recent inaccuracies reported in the Martini protein model. Lastly, the paper discusses the advantages, limitations, and future perspectives of the Martini 3 protein model and its combination with G[o] models.

biophysics↗

bioRxiv2022

Xport-A functions as a chaperone by stabilizing the first 5 transmembrane domains of Rhodopsin-1

Rhodopsin-1 (Rh1), the main photo-sensitive protein of Drosophila, is a seven transmembrane domain protein, which is inserted co-translationally in the endoplasmic reticulum (ER) membrane. Maturation of Rh1 occurs in the ER, where various chaperones interact with Rh1 to aid in its folding and subsequent transport in the secretory pathway. Xport-A has been shown to be a chaperone/ transport factor for Rh1, but the exact molecular mechanism for Xport-A activity upon Rh1 is not known. Here, based on computational predictions, we propose a model where Xport-A functions as a chaperone in the biosynthesis of Rh1 by stabilizing the first 5 transmembrane domains of Rh1, but not the full length Rh1 protein.

cell biology↗

bioRxiv2021

SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 5 million people and is causing a devastating social and economic impact all over the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss vaccine and natural immunity, and increased transmissibility. All circulating VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes, via its receptor binding domain (RBD) that binds to angiotensin-converting enzyme 2 (ACE2). In an attempt to understand the effect of RBD mutations in circulating VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis is limited, since it ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some VOCs mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of three circulating VOCs (alpha, beta, and delta). Our results show that in solution, wt RBD presents two distinct conformations: an "open" conformation where it is free to bind ACE2; and a "closed" conformation, where the RBM ridge blocks the binding surface. The alpha and beta variants significantly impact the open/closed equilibrium, shifting it towards the open conformation by roughly 20%. This shift likely increases ACE2 binding affinity. Simulations of the currently predominant delta variant RBD were extreme in this regard, in that a closed conformation was never observed. Instead, the system alternated between the before mentioned open conformation and an alternative "reversed" one, with a significantly changed orientation of the RBM ridge flanking the RBD. This alternate conformation could potentially provide a fitness advantage not only due to increased availability for ACE2 binding, but also by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the delta variant, impact RBD conformational dynamics in a direction that simultaneously promotes efficient binding to ACE2 and antibody escape.

biophysics↗

bioRxiv2017

Lipid-protein interactions are unique fingerprints for membrane proteins

Cell membranes contain hundreds of different proteins and lipids in an asymmetric arrangement. Understanding the lateral organization principles of these complex mixtures is essential for life and health. However, our current understanding of the detailed organization of cell membranes remains rather elusive, owing to the lack of experimental methods suitable for studying these fluctuating nanoscale assemblies of lipids and proteins with the required spatiotemporal resolution. Here, we use molecular dynamics simulations to characterize the lipid environment of ten membrane proteins. To provide a realistic lipid environment, the proteins are embedded in a model plasma membrane, where more than 60 lipid species are represented, asymmetrically distributed between leaflets. The simulations detail how each protein modulates its local lipid environment through local lipid composition, thickness, curvature and lipid dynamics. Our results provide a molecular glimpse of the complexity of lipid-protein interactions, with potentially far reaching implications for the overall organization of the cell membrane.

biophysics↗