Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics

© 2018, Springer Nature Switzerland AG. We present a new coarse-grained (CG) model of cholesterol (CHOL) for the electrostatic-based ELBA force field. A distinguishing feature of our CHOL model is that the electrostatics is modeled by an explicit point dipole which interacts through an ideal vacuum permittivity. The CHOL model parameters were optimized in a systematic fashion, reproducing the electrostatic and nonpolar partitioning free energies of CHOL in lipid/water mixtures predicted by full-detailed atomistic molecular dynamics simulations. The CHOL model has been validated by comparison to structural, dynamic and thermodynamic properties with experimental and atomistic simulation reference data. The simulation of binary DPPC/cholesterol mixtures covering the relevant biological content of CHOL in mammalian membranes is shown to correctly predict the main lipid behavior as observed experimentally

Molecular Modeling and Simulation of Membrane Lipid-Mediated Effects on GPCRs

Functioning of G protein-coupled receptors (GPCRs) is tightly linked to the membrane environment, but a molecular level understandingof the modulation of GPCR by membrane lipids is not available. However, specific receptor-lipid interactions as well as unspecificeffects mediated by the bulk properties of the membrane (thickness, curvature, etc.) have been proposed to be key regulators ofGPCR modulation. In this review, we examine computational efforts made towards modeling and simulation of (i) the complex behaviorof membrane lipids, (ii) membrane lipid-GPCR interactions as well as membrane lipid-mediated effects on GPCRs and (iii) GPCR oligomerizationin a native-like membrane environment. We propose that, from the perspective of computational modeling, all three ofthese components need to be addressed in order to achieve a deeper understanding of GPCR functioning. Presently, we are able to simulatenumerous lipid properties applying advanced computational techniques, although some barriers, such as the time-length of thesesimulations, need to be overcome. Implementing three-dimensional structures of GPCRs in such validated membrane systems can givenovel insights in membrane-dependent receptor modulation and formation of higher order receptor complexes. Finally, more realisticGPCR-membrane models would provide a very useful tool in studying receptor behavior and its modulation by small drug-like ligands, arelevant issue for drug discovery.[...

The antioxidant resveratrol acts as a non-selective adenosine receptor agonist

Resveratrol (RSV) is a natural polyphenolic antioxidant with a proven protective role in several human diseases involving oxidative stress, although the molecular mechanism underlying this effect remains unclear. The present work tried to elucidate the molecular mechanism of RSV's role on signal transduction modulation. Our biochemical analysis, including radioligand binding, real time PCR, western blotting and adenylyl cyclase activity, and computational studies provide insights into the RSV binding pathway, kinetics and the most favored binding pose involving adenosine receptors, mainly A2A subtype. In this study, we show that RSV target adenosine receptors (AdoRs), affecting gene expression, receptor levels, and the downstream adenylyl cyclase (AC)/PKA pathway. Our data demonstrate that RSV activates AdoRs. Moreover, RSV activate A2A receptors by directly binding to the classical orthosteric binding site. Intriguingly, RSV-induced receptor activation can stimulate or inhibit AC activity depending on concentration and exposure time. Such subtle and multifaceted regulation of the AdoRs/AC/PKA pathway might contribute to the protective role of RSV. Our findings suggest that RSV molecular action is mediated, at least in part, by activation of adenosine receptors and create the opportunity to interrogate the therapeutic use of RSV in pathological conditions involving AdoRs, such as Alzheimer

Fractal dimension as a measure of surface roughness of G protein-coupled receptors: implications for structure and function

Protein surface roughness is a structural property associated with ligand-protein and protein-protein binding interfaces. In this work we apply for the first time the concept of surface roughness, expressed as the fractal dimension, to address structure and function of G protein-coupled receptors (GPCRs) which are an important group of drug targets. We calculate the exposure ratio and the fractal dimension for helix-forming residues of the β(2) adrenergic receptor (β(2)AR), a model system in GPCR studies, in different conformational states: in complex with agonist, antagonist and partial inverse agonists. We show that both exposure ratio and roughness exhibit periodicity which results from the helical structure of GPCRs. The pattern of roughness and exposure ratio of a protein patch depends on its environment: the residues most exposed to membrane are in general most rough whereas parts of receptors mediating interhelical contacts in a monomer or protein complex are much smoother. We also find that intracellular ends (TM3, TM5, TM6 and TM7) which are relevant for G protein binding and thus receptor signaling, are exposed but smooth. Mapping the values of residual fractal dimension onto receptor 3D structures makes it possible to conclude that the binding sites of orthosteric ligands as well as of cholesterol are characterized with significantly higher roughness than the average for the whole protein. In summary, our study suggests that identification of specific patterns of roughness could be a novel approach to spot possible binding sites which could serve as original drug targets for GPCRs modulation

Membrane cholesterol access into a G-protein-coupled receptor

Cholesterol is a key component of cell membranes with a proven modulatory role on the function and ligand-binding properties of G-protein-coupled receptors (GPCRs). Crystal structures of prototypical GPCRs such as the adenosine A2A receptor (A2AR) have confirmed that cholesterol finds stable binding sites at the receptor surface suggesting an allosteric role of this lipid. Here we combine experimental and computational approaches to show that cholesterol can spontaneously enter the A2AR-binding pocket from the membrane milieu using the same portal gate previously suggested for opsin ligands. We confirm the presence of cholesterol inside the receptor by chemical modification of the A2AR interior in a biotinylation assay. Overall, we show that cholesterol’s impact on A2AR-binding affinity goes beyond pure allosteric modulation and unveils a new interaction mode between cholesterol and the A2AR that could potentially apply to other GPCRs