scholarly journals State-Dependent Lipid Interactions with the A2a Receptor Revealed by MD Simulations Using In Vivo-Mimetic Membranes

2018 ◽  
Author(s):  
Wanling Song ◽  
Hsin-Yung Yen ◽  
Carol V. Robinson ◽  
Mark S.P. Sansom
Keyword(s):  
Conformational Dynamics ◽  
Md Simulations ◽  
Receptor Activation ◽  
Active State ◽  
Coarse Grained ◽  
Lipid Interactions ◽  
A2a Receptor ◽  
The Impact ◽  
Specific Lipid

AbstractG protein-coupled receptors (GPCRs) are the largest family of integral membrane proteins and a major class of drug targets. Membranes are known to have modulatory effects on GPCRs via specific lipid interactions. However, the mechanisms of such modulations in cell membranes and how they influence GPCR functions remain unclear. Here we report coarse-grained MD simulations on the Adenosine A2a receptor embedded in an in vivo mimetic membrane model comprised of 10 different lipid species. Three conformational states of the receptor, i.e. the inactive state, the active state, and the active state with a mini-GS protein bound were simulated to study the impact of protein-lipid interactions on the receptor activation. The simulations revealed three specific lipids (GM3, cholesterol and PIP2) that form stable and preferential interactions with the receptor, differentiating these from bulk lipids such as PS, PE and PC. In total, nine specific lipid-binding sites were revealed. The strength of lipid interaction with these sites depends on the conformational state of the receptor, suggesting that these lipids may regulate the conformational dynamics of the receptor. In particular, we revealed a dual role of PIP2 in promoting A2aR activation, which involves stabilization of both the characteristic outward tilt of helix TM6 within receptor and also the association of A2aR and mini-Gs when the activated complex forms. Structural comparisons suggested that PIP2 may facilitate Gα activation. Our results reveal likely allosteric effects of bound lipids in regulating the functional behaviour of GPCRs, providing a springboard for design of allosteric modulators of these biomedically important receptors.

scholarly journals State-dependent Lipid Interactions with the A2a Receptor Revealed by MD Simulations Using In Vivo-Mimetic Membranes

Structure ◽  
2019 ◽  
Vol 27 (2) ◽  
pp. 392-403.e3 ◽  
Author(s):  
Wanling Song ◽  
Hsin-Yung Yen ◽  
Carol V. Robinson ◽  
Mark S.P. Sansom
Keyword(s):  
Md Simulations ◽  
Lipid Interactions ◽  
State Dependent ◽  
A2a Receptor

scholarly journals Conformational entropy of a single peptide controlled under force governs protease recognition and catalysis

2018 ◽  
Vol 115 (45) ◽  
pp. 11525-11530 ◽  
Author(s):  
Marcelo E. Guerin ◽  
Guillaume Stirnemann ◽  
David Giganti
Keyword(s):  
Single Molecule ◽  
Conformational Dynamics ◽  
Conformational Sampling ◽  
Enzymatic Reactions ◽  
Sequence Specificity ◽  
Proteomics Data ◽  
Conformational Entropy ◽  
Substrate Peptide ◽  
The Impact

An immense repertoire of protein chemical modifications catalyzed by enzymes is available as proteomics data. Quantifying the impact of the conformational dynamics of the modified peptide remains challenging to understand the decisive kinetics and amino acid sequence specificity of these enzymatic reactions in vivo, because the target peptide must be disordered to accommodate the specific enzyme-binding site. Here, we were able to control the conformation of a single-molecule peptide chain by applying mechanical force to activate and monitor its specific cleavage by a model protease. We found that the conformational entropy impacts the reaction in two distinct ways. First, the flexibility and accessibility of the substrate peptide greatly increase upon mechanical unfolding. Second, the conformational sampling of the disordered peptide drives the specific recognition, revealing force-dependent reaction kinetics. These results support a mechanism of peptide recognition based on conformational selection from an ensemble that we were able to quantify with a torsional free-energy model. Our approach can be used to predict how entropy affects site-specific modifications of proteins and prompts conformational and mechanical selectivity.

scholarly journals Exploration of inositol 1,4,5-trisphosphate (IP3) regulated dynamics of N-terminal domain of IP3 receptor reveals early phase molecular events during receptor activation

2018 ◽  
Author(s):  
Aneesh Chandran ◽  
Xavier Chee ◽  
David L. Prole ◽  
Taufiq Rahman
Keyword(s):  
Conformational Dynamics ◽  
Md Simulations ◽  
Receptor Activation ◽  
Activation Mechanism ◽  
Ip3 Receptor ◽  
Dynamic Correlation ◽  
Molecular Events ◽  
Binding Core ◽  
Domain Dynamics ◽  
Phosphate Groups

Inositol 1, 4, 5-trisphosphate (IP3) binding at the N-terminus (NT) of IP3 receptor (IP3R) allosterically triggers the opening of a Ca2+-conducting pore located ~ 100 Å away from the IP3-binding core (IBC). However, the precise mechanism of IP3 binding and correlated domain dynamics in the NT that are central to the IP3R activation, remains unknown. Our all-atom molecular dynamics (MD) simulations recapitulate the characteristic twist motion of the suppresser domain (SD) and reveal correlated ‘clam closure’ dynamics of IBC with IP3-binding, complementing existing suggestions on IP3R activation mechanism. Our study further reveals the existence of inter-domain dynamic correlation in the NT and establishes the SD to be critical for the conformational dynamics of IBC. Also, a tripartite interaction involving Glu283-Arg54-Asp444 at the SD – IBC interface seemed critical for IP3R activation. Intriguingly, during the sub-microsecond long simulation, we observed Arg269 undergoing an SD-dependent flipping of hydrogen bonding between the first and fifth phosphate groups of IP3. This seems to play a major role in determining the IP3 binding affinity of IBC in the presence/absence of the SD. Our study thus provides atomistic details of early molecular events occurring within the NT during and following IP3 binding that lead to channel gating.

scholarly journals Computational Study of C-X-C Chemokine Receptor (CXCR)3 Binding with Its Natural Agonists Chemokine (C-X-C Motif) Ligand (CXCL)9, 10 and 11 and with Synthetic Antagonists: Insights of Receptor Activation towards Drug Design for Vitiligo

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4413
Author(s):  
Giovanny Aguilera-Durán ◽  
Antonio Romo-Mancillas
Keyword(s):  
Molecular Dynamics ◽  
Computational Study ◽  
Md Simulations ◽  
Receptor Activation ◽  
Activation Mechanism ◽  
Coarse Grained ◽  
Dimensional Structure ◽  
Cytotoxic Lymphocytes ◽  
Ligand Interaction ◽  
Α Subunit

Vitiligo is a hypopigmentary skin pathology resulting from the death of melanocytes due to the activity of CD8+ cytotoxic lymphocytes and overexpression of chemokines. These include CXCL9, CXCL10, and CXCL11 and its receptor CXCR3, both in peripheral cells of the immune system and in the skin of patients diagnosed with vitiligo. The three-dimensional structure of CXCR3 and CXCL9 has not been reported experimentally; thus, homology modeling and molecular dynamics could be useful for the study of this chemotaxis-promoter axis. In this work, a homology model of CXCR3 and CXCL9 and the structure of the CXCR3/Gαi/0βγ complex with post-translational modifications of CXCR3 are reported for the study of the interaction of chemokines with CXCR3 through all-atom (AA-MD) and coarse-grained molecular dynamics (CG-MD) simulations. AA-MD and CG-MD simulations showed the first activation step of the CXCR3 receptor with all chemokines and the second activation step in the CXCR3-CXCL10 complex through a decrease in the distance between the chemokine and the transmembrane region of CXCR3 and the separation of the βγ complex from the α subunit in the G-protein. Additionally, a general protein–ligand interaction model was calculated, based on known antagonists binding to CXCR3. These results contribute to understanding the activation mechanism of CXCR3 and the design of new molecules that inhibit chemokine binding or antagonize the receptor, provoking a decrease of chemotaxis caused by the CXCR3/chemokines axis.

scholarly journals Functional Analysis of the Murine Cytomegalovirus Chemokine Receptor Homologue M33: Ablation of Constitutive Signaling Is Associated with an Attenuated Phenotype In Vivo

2007 ◽  
Vol 82 (4) ◽  
pp. 1884-1898 ◽  
Author(s):  
Ruth Case ◽  
Emma Sharp ◽  
Tau Benned-Jensen ◽  
Mette M. Rosenkilde ◽  
Nicholas Davis-Poynter ◽  
...  
Keyword(s):  
Cell Surface ◽  
Salivary Glands ◽  
Surface Expression ◽  
Receptor Activation ◽  
Murine Cytomegalovirus ◽  
Cell Surface Expression ◽  
Transmembrane Receptors ◽  
C Terminus ◽  
The Impact

ABSTRACT The murine cytomegalovirus (MCMV) M33 gene is conserved among all betaherpesviruses and encodes a homologue of seven-transmembrane receptors (7TMR) with the capacity for constitutive signaling. Previous studies have demonstrated that M33 is important for MCMV dissemination to or replication within the salivary glands. In this study, we probed N- and C-terminal regions of M33 as well as known 7TMR signature motifs in transmembrane (TM) II and TM III to determine the impact on cell surface expression, constitutive signaling, and in vivo phenotype. The region between amino acids R340 and A353 of the C terminus was found to be important for CREB- and NFAT-mediated signaling, although not essential for phosphatidylinositol turnover. Tagging or truncation of the N terminus of M33 resulted in loss of cell surface expression. Within TM II, an F79D mutation abolished constitutive signaling, demonstrating a role, as in other cellular and viral 7TMR, of TM II in receptor activation. In TM III, the arginine (but not the asparagine) residue of the NRY motif (the counterpart of the common DRY motif in cellular 7TMR) was found to be essential for constitutive signaling. Selected mutations incorporated into recombinant MCMV showed that disruption of constitutive signaling for a viral 7TMR homologue resulted in a reduced capacity to disseminate to or replicate in the salivary glands. In addition, HCMV UL33 was found to partially compensate for the lack of M33 in vivo, suggesting conserved biological roles of the UL33 gene family.

scholarly journals Lipid-mediated Association of the Slg1 Transmembrane Domains in Yeast Plasma Membranes

2021 ◽  
Author(s):  
Azadeh Alavizargar ◽  
Annegret Eltig ◽  
Roland Wedlich Soeldner ◽  
Andreas Heuer
Keyword(s):  
Plasma Membrane ◽  
Protein Interactions ◽  
Plasma Membranes ◽  
Acyl Chain ◽  
Md Simulations ◽  
Receptor Activation ◽  
Transmembrane Domains ◽  
Coarse Grained ◽  
Self Association ◽  
Lipid Protein Interactions

Clustering of transmembrane proteins underlies a multitude of fundamental biological processes at the plasma membrane such as receptor activation, lateral domain formation and mechanotransduction. The self-association of the respective transmembrane domains (TMD) has also been suggested to be responsible for the micron-scaled patterns seen for integral membrane proteins in the budding yeast plasma membrane (PM). However, the underlying interplay between local lipid composition and TMD identity is still not mechanistically understood. In this work we have used coarse-grained molecular dynamics (MD) simulations as well as microscopy experiments (TIRFM) to analyze the behavior of a representative helical yeast TMD (Slg1) within different lipid environments. Via the simulations we evaluated the effect of acyl chain saturation and the presence of anionic lipids head groups on the association of TMDs via simulations. Our simulations revealed that weak lipid-protein interactions significantly affect the configuration of TMD dimers and the free energy of association. Increased amounts of unsaturated phospholipids strongly reduced helix-helix interaction and the presence of phosphatidylserine (PS) lipids only slightly affected the dimer. Experimentally, the network factor, characterizing the association strength on a mesoscopic level, was measured in the presence and absence of PS lipids. Consistently with the simulations, no significant effect was observed. We also found that formation of TMD dimers in turn increased the order parameter of the surrounding lipids and induced long-range perturbations in lipid organization, shedding new light on the lipid-mediated dimerization of TMDs in complex lipid mixtures.

scholarly journals Leukocyte adenosine A2A receptor activation inhibits leukocyte‐endothelial interactions in vivo

2007 ◽  
Vol 21 (5) ◽  
Author(s):  
Rong Tang ◽  
Huan Wang ◽  
Jiang‐Fan Chen ◽  
Joel Linden
Keyword(s):  
Receptor Activation ◽  
Adenosine A2a Receptor ◽  
A2a Receptor ◽  
Adenosine A2a

scholarly journals Unique actions of GABA arising from cytoplasmic chloride microdomains

2020 ◽  
Author(s):  
Negah Rahmati ◽  
Kieran P. Normoyle ◽  
Joseph Glykys ◽  
Volodymyr I. Dzhala ◽  
Kyle P. Lillis ◽  
...  
Keyword(s):  
Fluorescent Protein ◽  
Reversal Potential ◽  
Receptor Activation ◽  
Fluorescence Lifetime Imaging ◽  
Lifetime Imaging ◽  
Electrophysiological Measurements ◽  
Highly Correlated ◽  
Cation Chloride Cotransporters ◽  
The Impact

AbstractDevelopmental, cellular, and subcellular variations in the direction of neuronal Cl− currents elicited by GABAA receptor activation have been frequently reported, and we found a corresponding variance in the reversal potential (EGABA) for individual interneurons synapsing on a single pyramidal cell. These findings suggest a corresponding variance in the cytoplasmic concentration of Cl− ([Cl−i]). We determined [Cl−]i by: 1) two-photon imaging of the Cl− sensitive, ratiometric fluorescent protein SuperClomeleon (sCLM); 2) Fluorescence Lifetime IMaging (FLIM) of the Cl− sensitive fluorophore MEQ; and 3) electrophysiological measurements of EGABA. These methods collectively demonstrated stable [Cl−]i microdomains in individual neurons in vivo. Fluorometric and electrophysiological estimates of local [Cl−]i were highly correlated. [Cl−]i microdomains persisted after pharmacological inhibition of cation-chloride cotransporters (CCCs) but steadily decreased after inhibiting the polymerization of the anionic macromolecule actin. These studies highlight the existence of functionally significant neuronal Cl− microdomains that modify the impact of GABAergic inputs.

scholarly journals A multiscale analysis of DNA phase separation: From atomistic to mesoscale level

2018 ◽  
Author(s):  
Tiedong Sun ◽  
Alexander Mirzoev ◽  
Vishal Minhas ◽  
Nikolay Korolev ◽  
Alexander P. Lyubartsev ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Crystalline ◽  
Coarse Graining ◽  
Md Simulations ◽  
Coarse Grained ◽  
Effective Potentials ◽  
Dna Oligonucleotides ◽  
Hexagonally Ordered ◽  
Dna Packing

ABSTRACTDNA condensation and phase separation is of utmost importance for DNA packing in vivo with important applications in medicine, biotechnology and polymer physics. The presence of hexagonally ordered DNA is observed in virus capsids, sperm heads and in dinoflagellates. Rigorous modelling of this process in all-atom MD simulations is presently difficult to achieve due to size and time scale limitations. We used a hierarchical approach for systematic multiscale coarse-grained (CG) simulations of DNA phase separation induced by the three-valent cobalt(III)-hexammine (CoHex3+). Solvent-mediated effective potentials for a CG model of DNA were extracted from all-atom MD simulations. Simulations of several hundred 100-bp-long CG DNA oligonucleotides in the presence of explicit CoHex3+ ions demonstrated aggregation to a liquid crystalline hexagonally ordered phase. Following further coarse-graining and extraction of effective potentials, we conducted modelling at mesoscale level. In agreement with electron microscopy observations, simulations of an 10.2-kbp-long DNA molecule showed phase separation to either a toroid or a fibre with distinct hexagonal DNA packing. The mechanism of toroid formation is analysed in detail. The approach used here is based only on the underlying all-atom force field and uses no adjustable parameters and may be generalized to modelling chromatin up to chromosome size.

scholarly journals Computational Approaches to Investigate and Design Lipid-binding Domains for Membrane Biosensing

2021 ◽  
Vol 75 (12) ◽  
pp. 1031-1036
Author(s):  
Sriraksha Srinivasan ◽  
Stefano Vanni
Keyword(s):  
Membrane Trafficking ◽  
De Novo ◽  
Md Simulations ◽  
Lipid Binding ◽  
Broad Perspective ◽  
Computational Approaches ◽  
Binding Domains ◽  
Specific Lipid

Association of proteins with cellular membranes is critical for signaling and membrane trafficking processes. Many peripheral lipid-binding domains have been identified in the last few decades and have been investigated for their specific lipid-sensing properties using traditional in vivo and in vitro studies. However, several knowledge gaps remain owing to intrinsic limitations of these methodologies. Thus, novel approaches are necessary to further our understanding in lipid–protein biology. This review briefly discusses lipid-binding domains that act as specific lipid biosensors and provides a broad perspective on the computational approaches such as molecular dynamics (MD) simulations and machine learning (ML)-based techniques that can be used to study protein–membrane interactions. We also highlight the need for de novo design of proteins that elicit specific lipid-binding properties.

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