Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium.

SARS-CoV-2 contains four structural proteins in its genome. These proteins aid in the assembly and budding of new virions at the ER-Golgi intermediate compartment (ERGIC). Current fundamental research efforts largely focus on one of these proteins - the spike (S) protein.

Identification of electroporation sites in the complex lipid organization of the plasma membrane.

The plasma membrane of a biological cell is a complex assembly of lipids and membrane proteins, which tightly regulate transmembrane transport. When a cell is exposed to strong electric field, the membrane integrity becomes transiently disrupted by formation of transmembrane pores. This phenomenon termed electroporation is already utilized in many rapidly developing applications in medicine including gene therapy, cancer treatment, and treatment of cardiac arrhythmias.

Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor.

Nanobody binding stabilizes G-protein-coupled receptors (GPCR) in a fully active state and modulates their affinity for bound ligands. However, the atomic-level basis for this allosteric regulation remains elusive. Here, we investigate the conformational changes induced by the binding of a nanobody (Nb80) on the active-like β2 adrenergic receptor (β2AR) via enhanced sampling molecular dynamics simulations.

Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel.

As the first potassium channel with an x-ray structure determined, and given its homology to eukaryotic channels, the pH-gated prokaryotic channel KcsA has been extensively studied. Nevertheless, questions related, in particular, to the allosteric coupling between its gates remain open. The many currently available x-ray crystallography structures appear to correspond to various stages of activation and inactivation, offering insights into the molecular basis of these mechanisms.

Combining EXAFS and Computer Simulations to Refine the Structural Description of Actinyls in Water.

EXAFS spectroscopy is one of the most used techniques to solve the structure of actinoid solutions. In this work a systematic analysis of the EXAFS spectra of four actinyl cations, [UO], [NpO], [NpO] and [PuO] has been carried out by comparing experimental results with theoretical spectra. These were obtained by averaging individual contributions from snapshots taken from classical Molecular Dynamics simulations which employed a recently developed [AnO] -HO force field based on the hydrated ion model using a quantum-mechanical (B3LYP) potential energy surface.

Network analysis reveals how lipids and other cofactors influence membrane protein allostery.

Many membrane proteins are modulated by external stimuli, such as small molecule binding or change in pH, transmembrane voltage, or temperature. This modulation typically occurs at sites that are structurally distant from the functional site. Revealing the communication, known as allostery, between these two sites is key to understanding the mechanistic details of these proteins.

A general study of actinyl hydration by molecular dynamics simulations using ab initio force fields.

A set of new ab initio force fields for aqueous [AnO] (An = Np(vi,v), Pu(vi), Am(vi)) has been developed using the Hydrated Ion (HI) model methodology previously used for [UO]. Except for the non-electrostatic contribution of the HI-bulk water interaction, the interaction potentials are individually parameterized. Translational diffusion coefficients, hydration enthalpies, and vibrational normal mode frequencies were calculated from the MD simulations.

Extracting the Americyl Hydration from an Americium Cationic Mixture in Solution: A Combined X-ray Absorption Spectroscopy and Molecular Dynamics Study.

Am(VI) solution chemistry differs from that of lighter actinoids, as U, Pu, and Np, where the actinyl [AnO] is the most stable form and plays an important role in nuclear fuel technology. The behavior of americium in solution shows the trend to stabilize lower oxidation states, mainly Am(III). Riddle and co-workers recently reported the EXAFS and first XANES spectra of an americium-containing aqueous solution where the americyl species is detected in a mixture.

A hydrated ion model of [UO] in water: Structure, dynamics, and spectroscopy from classical molecular dynamics.

A new ab initio interaction potential based on the hydrated ion concept has been developed to obtain the structure, energetics, and dynamics of the hydration of uranyl in aqueous solution. It is the first force field that explicitly parameterizes the interaction of the uranyl hydrate with bulk water molecules to accurately define the second-shell behavior. The [UO(HO)] presents a first hydration shell U-O average distance of 2.