Permeation through a lamellar stack of lipid mixtures

We study material transport and permeation through a lamellar stack of multi-component lipid membranes by performing Monte Carlo simulations of a stacked two-dimensional Ising model in presence of permeants. In the model, permeants are transported through the stack via in-plane lipid clusters, which are inter-connected in the vertical direction. These clusters are formed transiently by concentration fluctuations of the lipid mixture, and the permeation process is affected, especially close to the critical temperature of the binary mixture. We show that the permeation rate decays exponentially as function of temperature and permeant lateral size, whereas the dependency on the characteristic waiting time obeys a stretched exponential function. The material transport through such lipid clusters can be significantly affected around physiological temperatures.Comment: Accepted versio

Digging into Lipid Membrane Permeation for Cardiac Ion Channel Blocker d-Sotalol with All-Atom Simulations.

Interactions of drug molecules with lipid membranes play crucial role in their accessibility of cellular targets and can be an important predictor of their therapeutic and safety profiles. Very little is known about spatial localization of various drugs in the lipid bilayers, their active form (ionization state) or translocation rates and therefore potency to bind to different sites in membrane proteins. All-atom molecular simulations may help to map drug partitioning kinetics and thermodynamics, thus providing in-depth assessment of drug lipophilicity. As a proof of principle, we evaluated extensively lipid membrane partitioning of d-sotalol, well-known blocker of a cardiac potassium channel Kv11.1 encoded by the hERG gene, with reported substantial proclivity for arrhythmogenesis. We developed the positively charged (cationic) and neutral d-sotalol models, compatible with the biomolecular CHARMM force field, and subjected them to all-atom molecular dynamics (MD) simulations of drug partitioning through hydrated lipid membranes, aiming to elucidate thermodynamics and kinetics of their translocation and thus putative propensities for hydrophobic and aqueous hERG access. We found that only a neutral form of d-sotalol accumulates in the membrane interior and can move across the bilayer within millisecond time scale, and can be relevant to a lipophilic channel access. The computed water-membrane partitioning coefficient for this form is in good agreement with experiment. There is a large energetic barrier for a cationic form of the drug, dominant in water, to cross the membrane, resulting in slow membrane translocation kinetics. However, this form of the drug can be important for an aqueous access pathway through the intracellular gate of hERG. This route will likely occur after a neutral form of a drug crosses the membrane and subsequently re-protonates. Our study serves to demonstrate a first step toward a framework for multi-scale in silico safety pharmacology, and identifies some of the challenges that lie therein

Structural basis of control of inward rectifier Kir2 channel gating by bulk anionic phospholipids

Inward rectifier potassium (Kir) channel activity is controlled by plasma membrane lipids. Phosphatidylinositol-4,5-bisphosphate (PIP(2)) binding to a primary site is required for opening of classic inward rectifier Kir2.1 and Kir2.2 channels, but interaction of bulk anionic phospholipid (PL(−)) with a distinct second site is required for high PIP(2) sensitivity. Here we show that introduction of a lipid-partitioning tryptophan at the second site (K62W) generates high PIP(2) sensitivity, even in the absence of PL(−). Furthermore, high-resolution x-ray crystal structures of Kir2.2[K62W], with or without added PIP(2) (2.8- and 2.0-Å resolution, respectively), reveal tight tethering of the C-terminal domain (CTD) to the transmembrane domain (TMD) in each condition. Our results suggest a refined model for phospholipid gating in which PL(−) binding at the second site pulls the CTD toward the membrane, inducing the formation of the high-affinity primary PIP(2) site and explaining the positive allostery between PL(−) binding and PIP(2) sensitivity

Domain Growth, Budding, and Fission in Phase Separating Self-Assembled Fluid Bilayers

A systematic investigation of the phase separation dynamics in self-assembled multi-component bilayer fluid vesicles and open membranes is presented. We use large-scale dissipative particle dynamics to explicitly account for solvent, thereby allowing for numerical investigation of the effects of hydrodynamics and area-to-volume constraints. In the case of asymmetric lipid composition, we observed regimes corresponding to coalescence of flat patches, budding, vesiculation and coalescence of caps. The area-to-volume constraint and hydrodynamics have a strong influence on these regimes and the crossovers between them. In the case of symmetric mixtures, irrespective of the area-to-volume ratio, we observed a growth regime with an exponent of 1/2. The same exponent is also found in the case of open membranes with symmetric composition

Molecular modeling to study dendrimers for biomedical applications

© 2014 by the authors; licensee MDPI; Basel; Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/). Date of Acceptance: 17/11/2014Molecular modeling techniques provide a powerful tool to study the properties of molecules and their interactions at the molecular level. The use of computational techniques to predict interaction patterns and molecular properties can inform the design of drug delivery systems and therapeutic agents. Dendrimers are hyperbranched macromolecular structures that comprise repetitive building blocks and have defined architecture and functionality. Their unique structural features can be exploited to design novel carriers for both therapeutic and diagnostic agents. Many studies have been performed to iteratively optimise the properties of dendrimers in solution as well as their interaction with drugs, nucleic acids, proteins and lipid membranes. Key features including dendrimer size and surface have been revealed that can be modified to increase their performance as drug carriers. Computational studies have supported experimental work by providing valuable insights about dendrimer structure and possible molecular interactions at the molecular level. The progress in computational simulation techniques and models provides a basis to improve our ability to better predict and understand the biological activities and interactions of dendrimers. This review will focus on the use of molecular modeling tools for the study and design of dendrimers, with particular emphasis on the efforts that have been made to improve the efficacy of this class of molecules in biomedical applications.Peer reviewedFinal Published versio

Effects of different slipping methods on the mortality of sardine, Sardina pilchardus, after purse-seine capture off the Portuguese Southern coast (Algarve)

The effects of two different slipping methods on the survival, physical and physiological response of sardines, Sardina pilchardus, captured in a purse-seine fishery were investigated in southern Portugal. Sardines were collected and transferred into holding tanks onboard a commercial fishing vessel after being captured, crowded and deliberately released using two slipping procedures: standard and modified. The standard slipping procedure aggregated fish at high densities and made them "roll over" the floatline, while the modified procedure aggregated the fish at moderate densities and enabled them to escape through an opening created by adding weights to the floatline. Both slipping methods were compared with minimally harmed non-slipped sardines (sardines collected from the loose pocket of the purse seine). Survival rates were monitored in captivity over 28 days using three replicates for each treatment. The estimated survival of sardines was 43.6% for the non-slipped fish, 44.7% for the modified slipping and 11.7% for the standard slipping treatments. Scale loss indicated the level of physical impact experienced, with dead fish from the non-slipped and modified slipping technique showing significantly lower scale loss than those fish from the standard slipping treatment within the same period. Of the physiological indicators of stress measured, cortisol, glucose, lactate and osmolality attained peak values during slipping and up to the first hours after introduction to captivity. This work indicates that although delayed mortality after release may be substantial, appropriately modified slipping techniques significantly enhance survival of slipped sardines.FCT [SFRH/BPD/116307/2016]; European Commission's Horizon 2020 Research and Innovation Programme [634495

The conduction pathway of potassium channels is water free under physiological conditions.

Ion conduction through potassium channels is a fundamental process of life. On the basis of crystallographic data, it was originally proposed that potassium ions and water molecules are transported through the selectivity filter in an alternating arrangement, suggesting a "water-mediated" knock-on mechanism. Later on, this view was challenged by results from molecular dynamics simulations that revealed a "direct" knock-on mechanism where ions are in direct contact. Using solid-state nuclear magnetic resonance techniques tailored to characterize the interaction between water molecules and the ion channel, we show here that the selectivity filter of a potassium channel is free of water under physiological conditions. Our results are fully consistent with the direct knock-on mechanism of ion conduction but contradict the previously proposed water-mediated knock-on mechanism