Insights into the binding mode of lipid a to the anti-lipopolysaccharide factor ALFPm3 from penaeus monodon: an in silico study through MD simulations

The globally expanding threat of antibiotic resistance calls for the development of new strategies for abating Gram-negative bacterial infections. The use of extracorporeal blood cleansing devices with affinity sorbents to selectively capture bacterial lipopolysaccharide (LPS), which is the major constituent of Gram-negative bacterial outer membranes and the responsible agent for eliciting an exacerbated innate immune response in the host during infection, has received outstanding interest. For that purpose, molecules that bind tightly to LPS are required to functionalize the affinity sorbents. Particularly, anti-LPS factors (ALFs) are promising LPS-sequestrating molecules. Hence, in this work, molecular dynamics (MD) simulations are used to investigate the interaction mechanism and binding pose of the ALF isoform 3 from Penaeus monodon (ALFPm3), which is referred to as "AL3" for the sake of simplicity, and lipid A (LA, the component of LPS that represents its endotoxic principle). We concluded that hydrophobic interactions are responsible for AL3-LA binding and that LA binds to AL3 within the protein cavity, where it buries its aliphatic tails, whereas the negatively charged phosphate groups are exposed to the medium. AL3 residues that are key for its interaction with LA were identified, and their conservation in other ALFs (specifically Lys39 and Tyr49) was also analyzed. Additionally, based on the MD-derived results, we provide a picture of the possible AL3-LA interaction mechanism. Finally, an in vitro validation of the in silico predictions was performed. Overall, the insights gained from this work can guide the design of novel therapeutics for treating sepsis, since they may be significantly valuable for designing LPS-sequestrating molecules that could functionalize affinity sorbents to be used for extracorporeal blood detoxification.Financial support from the Spanish Ministry of Science, Innovation and Universities under the project RTI2018- 093310-B-I00 is gratefully acknowledged. C.G.F. also thanks the Spanish Ministry of Universities for the Margarita Salas postdoctoral fellowship (grants for the requalification of the Spanish university system for 2021−2023, University of Cantabria), funded by the European Union-NextGenerationEU

Exploring the Macroscopic Properties of Humic Substances Using Modeling and Molecular Simulations

Soil organic matter (SOM) is composed of a complex and heterogeneous mixture of organic compounds, which poses a challenge in understanding it on an atomistic level. Based on the progress of molecular dynamics simulations and our efforts to create molecular systems that resemble SOM, in this work, we expanded our knowledge of SOM through the use of humic substances (HSs). Specifically, we studied the standardized samples of HS of the International Humic Substances Society (IHSS). This society provided the elemental and organic composition used as input parameters for our Vienna Soil Organic Matter Modeler 2 (VSOMM2). We modeled and simulated different HS samples from various sources, including soil, peat, leonardite, and blackwater river. In order to compare between different HS, we reduced the organic composition information to two principal components, which are associated principally with the amount of carboxyl and aromatic groups in the HS, denominated as PCacid and PCarom, respectively. We performed a plethora of analyses to characterize the structure and dynamics of the systems, including the total potential energy, density, diffusion, preferential solvation, hydrogen bonds, and salt bridges. In general terms, at the water content value of 0.2, we observed that most properties depend on the carboxyl group protonation state. The Coulombic interactions from this ionic specie and the interaction with cations determine the overall behavior of the studied systems. Furthermore, the type of cations and the pH influence those properties. This study exemplifies the importance of molecular dynamics to explain macroscopic properties from the structure and dynamics of the molecules modeled, such as the interaction network, i.e., hydrogen bonds or salt bridges of molecules presented in the system and their mobility

On biophysical properties and sensitivity to gap junction blockers of connexin 39 hemichannels expressed in hela cells

© 2017 Vargas, Cisterna, Saavedra-Leiva, Urrutia, Cea, Vielma, Gutierrez-Maldonado, Martin, Pareja-Barrueto, Escalona, Schmachtenberg, Lagos, Perez-Acle and Sáez. Although connexins (Cxs) are broadly expressed by cells of mammalian organisms, Cx39 has a very restricted pattern of expression and the biophysical properties of Cx39-based channels [hemichannels (HCs) and gap junction channels (GJCs)] remain largely unknown. Here, we used HeLa cells transfected with Cx39 (HeLa-Cx39 cells) in which intercellular electrical coupling was not detected, indicating the absence of GJCs. However, functional HCs were found on the surface of cells exposed to conditions known to increase the open probability of other Cx HCs (e.g., extracellular divalent cationic-free solution (DCFS), extracellular alkaline pH, mechanical stimulus and depolarization to positive membrane potentials). Cx39 HCs were blocked by some traditional Cx HC blockers, but not by others or a pannexin1 channel blocker. HeLa-Cx39 ce