Biology subjects

Chamorro, V. C.

Publications and source records attributed to Chamorro, V. C..

3 recordsLinked to original sources

bioRxiv2024

Challenges in the Accurate Modelling of Lipid Dynamics in Monolayers and Bilayers

Recent advances in hydrodynamic theory have revealed the severe effect of periodic boundary conditions (PBCs) on the diffusive dynamics of lipid membranes in molecular dynamics simulations. Even when accounting for PBC effects, the corrected lipid diffusion coefficients often severely overshoot the experimental estimates. Here, we investigate the underlying reasons for the exaggerated dynamics, and suggest potential ways for improvement. To this end, we examine the diffusion of four lipid types in both bilayers and monolayers using the CHARMM36 force field. We account for PBC effects using the full hydrodynamic treatment: for bilayers we use non-equilibrium simulations to extract the interleaflet friction parameter used in the correction; whereas monolayer hydrodynamics are treated by setting this parameter to zero. Our results suggest that the dynamics of bilayers are too fast, even if interleaflet friction is accounted for. However, the change of the water model to OPC leads to an excellent agreement with experiments. For monolayers, the dynamics with the TIP3P water model agree well with experiments, whereas they are undershot with OPC. As OPC and TIP3P differ in both shear viscosity and surface tension, we develop two new mass-scaled water models to clarify the roles of the thermodynamic and kinetic properties of the water model on lipid dynamics. Our results indicate that both of these quantities play a major role in lipid dynamics. Moreover, it seems that the accurate description of diffusion in both lipid bilayers and monolayers cannot be accounted for by changes in the water model alone, but likely also requires modifications in the lipid model.

biophysics↗

bioRxiv2023

Influence of Electronic Polarization on the Binding of Anions to a Chloride-Pumping Rhodopsin

The functional properties of some biological ion channels and membrane transport proteins are proposed to exploit anion-hydrophobic interactions. Here, we investigate a chloride-pumping rhodopsin (ClR) as an example of a membrane protein known to contain a defined anion binding site composed predominantly of hydrophobic residues. Using molecular dynamics simulations, we explore Cl- binding to this hydrophobic site and compare the dynamics arising when electronic polarization is neglected (CHARMM36 (c36) fixed-charge force field), included implicitly (via the prosECCo force field), or included explicitly (through the polarizable force field, AMOEBA). Free energy landscapes of Cl- moving out of the binding site and into bulk solution demonstrate that the inclusion of polarization results in stronger ion binding and a second metastable binding site in ClR. Simulations focused on this hydrophobic binding site also indicate longer binding durations and closer ion proximity when polarization is included. Furthermore, simulations reveal that Cl- within this binding site interacts with an adjacent loop to facilitate rebinding events that are not observed when polarization is neglected. These results demonstrate how the inclusion of polarization can influence the behavior of anions within protein binding sites and thereby reveal novel mechanisms. Statement of SignificanceMolecular simulations based on classical (Newtonian) mechanics represent the most common method of visualizing the behavior of water and ions within channels and nanopores. Although computationally efficient, many of the approximations required mean that these simulations often do not fully capture the complex and dynamic interactions involved. Here, we use the prosECCo force field that offers an improved electronic description whilst maintaining computational efficiency. We show that using this method to include the effects of polarization greatly influences the binding dynamics of anions to a protein binding site and yields results similar to more accurate but computationally demanding methods.

biophysics↗

bioRxiv2020

Sweet taste of heavy water

Hydrogen to deuterium isotopic substitution has only a minor effect on physical and chemical properties of water and, as such, is not supposed to influence its neutral taste. Here we conclusively demonstrate that humans are, nevertheless, able to distinguish D2O from H2O by taste. Indeed, highly purified heavy water has a distinctly sweeter taste than same-purity normal water and adds to perceived sweetness of sweeteners. In contrast, mice do not prefer D2O over H2O, indicating that they are not likely to perceive heavy water as sweet. HEK 293T cells transfected with the TAS1R2/TAS1R3 heterodimer and chimeric G-proteins are activated by D2O but not by H2O. Lactisole, which is a known sweetness inhibitor acting via the TAS1R3 monomer of the TAS1R2/TAS1R3, suppresses the sweetness of D2O in human sensory tests, as well as the calcium release elicited by D2O in sweet taste receptor-expressing cells. The present multifaceted experimental study, complemented by homology modelling and molecular dynamics simulations, resolves a long-standing controversy about the taste of heavy water, shows that its sweet taste is mediated by the human TAS1R2/TAS1R3 taste receptor, and opens way to future studies of the detailed mechanism of action. One sentence summaryHeavy water elicits sweet taste for humans via the TAS1R2/TAS1R3 taste receptor.

biochemistry↗