scholarly journals A molecular sensor for cholesterol in the human serotonin1A receptor

2021 ◽  
Vol 7 (30) ◽  
pp. eabh2922
Author(s):  
G. Aditya Kumar ◽  
Parijat Sarkar ◽  
Tomasz Maciej Stepniewski ◽  
Md. Jafurulla ◽  
Shishu Pal Singh ◽  
...  
Keyword(s):  
Transmembrane Helix ◽  
Conformational Dynamics ◽  
Structural Features ◽  
Receptor Interaction ◽  
Specific Sequence ◽  
Cholesterol Levels ◽  
Extracellular Loops ◽  
Dynamics Simulations ◽  
Key Residues ◽  
G Protein Coupled

The function of several G protein–coupled receptors (GPCRs) exhibits cholesterol sensitivity. Cholesterol sensitivity of GPCRs could be attributed to specific sequence and structural features, such as the cholesterol recognition/interaction amino acid consensus (CRAC) motif, that facilitate their cholesterol-receptor interaction. In this work, we explored the molecular basis of cholesterol sensitivity exhibited by the serotonin1A receptor, the most studied GPCR in the context of cholesterol sensitivity, by generating mutants of key residues in CRAC motifs in transmembrane helix 2 (TM2) and TM5 of the receptor. Our results show that a lysine residue (K101) in one of the CRAC motifs is crucial for sensing altered membrane cholesterol levels. Insights from all-atom molecular dynamics simulations showed that cholesterol-sensitive functional states of the serotonin1A receptor are associated with reduced conformational dynamics of extracellular loops of the receptor. These results constitute one of the first reports on the molecular mechanism underlying cholesterol sensitivity of GPCRs.

scholarly journals Conformational dynamics of a G protein–coupled receptor helix 8 in lipid membranes

2020 ◽  
Vol 6 (33) ◽  
pp. eaav8207 ◽  
Author(s):  
Patricia M. Dijkman ◽  
Juan C. Muñoz-García ◽  
Steven R. Lavington ◽  
Patricia Suemy Kumagai ◽  
Rosana I. dos Reis ◽  
...  
Keyword(s):  
G Protein ◽  
Protein Interactions ◽  
Lipid Membranes ◽  
Transmembrane Helix ◽  
Conformational Dynamics ◽  
Paramagnetic Resonance ◽  
Lipid Protein Interactions ◽  
Dynamics Simulations ◽  
Neurotensin Receptor 1 ◽  
G Protein Coupled

G protein–coupled receptors (GPCRs) are the largest and pharmaceutically most important class of membrane proteins encoded in the human genome, characterized by a seven-transmembrane helix architecture and a C-terminal amphipathic helix 8 (H8). In a minority of GPCR structures solved to date, H8 either is absent or adopts an unusual conformation. The controversial existence of H8 of the class A GPCR neurotensin receptor 1 (NTS1) has been examined here for the nonthermostabilized receptor in a functionally supporting membrane environment using electron paramagnetic resonance, molecular dynamics simulations, and circular dichroism. Lipid-protein interactions with phosphatidylserine and phosphatidylethanolamine lipids, in particular, stabilize the residues 374 to 390 of NTS1 into forming a helix. Furthermore, introduction of a helix-breaking proline residue in H8 elicited an increase in ß-arrestin–NTS1 interactions observed in pull-down assays, suggesting that the structure and/or dynamics of H8 might play an important role in GPCR signaling.

A study on the structural features of SELK, an over-expressed protein in hepatocellular carcinoma, by molecular dynamics simulations in a lipid–water system

2016 ◽  
Vol 12 (10) ◽  
pp. 3209-3222 ◽  
Author(s):  
Andrea Polo ◽  
Stefano Guariniello ◽  
Giovanni Colonna ◽  
Gennaro Ciliberto ◽  
Susan Costantini
Keyword(s):  
Hepatocellular Carcinoma ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Dynamics ◽  
Water System ◽  
Structural Features ◽  
System P ◽  
Dynamics Simulations

Terminal regions in SELK present different conformational dynamics being coupled complicatedly through the membrane.

scholarly journals Insights from Molecular Dynamics Simulations for GPCR Drug Discovery

2019 ◽  
Author(s):  
Ye Zou ◽  
John Ewalt ◽  
Ho-Leung Ng
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
G Protein ◽  
Drug Targets ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Protein Activation ◽  
Downstream Signaling ◽  
Dynamics Simulations ◽  
G Protein Coupled

G protein-coupled receptors (GPCRs) are critical drug targets. GPCRs convey signals from the extracellular to the intracellular environment through G proteins. There is evidence that some ligands that bind to the GPCRs activate different downstream signaling pathways. G protein activation or -arrestin biased signaling involves ligands binding to receptors and stabilizing conformations that trigger a specific pathway. Molecular dynamics (MD) simulations are especially valuable for obtaining detailed mechanistic information, including identification of allosteric sites and understanding modulators' interactions between receptors and ligands. Here, we highlight recent simulation studies and methods used to study biased G protein-coupled receptor signaling and their conformational dynamics. We also highlight applications of MD simulations to drug discovery.

scholarly journals The N-Terminal Juxtamembrane Segment of the V1a Vasopressin Receptor Provides Two Independent Epitopes Required for High-Affinity Agonist Binding and Signaling

2005 ◽  
Vol 19 (11) ◽  
pp. 2871-2881 ◽  
Author(s):  
Stuart R. Hawtin ◽  
Victoria J. Wesley ◽  
John Simms ◽  
Cymone C. H. Argent ◽  
Khalid Latif ◽  
...  
Keyword(s):  
G Protein ◽  
Arginine Vasopressin ◽  
Transmembrane Helix ◽  
Receptor Interaction ◽  
Vasopressin Receptor ◽  
Agonist Binding ◽  
Alanine Scanning Mutagenesis ◽  
High Affinity ◽  
Antagonist Binding ◽  
G Protein Coupled

Abstract It is fundamentally important to define how agonist-receptor interaction differs from antagonist-receptor interaction. The V1a vasopressin receptor (V1aR) is a member of the neurohypophysial hormone subfamily of G protein-coupled receptors. Using alanine-scanning mutagenesis of the N-terminal juxtamembrane segment of the V1aR, we now establish that Glu54 (1.35) is critical for arginine vasopressin binding. The mutant [E54A]V1aR exhibited decreased arginine vasopressin affinity (1700-fold) and disrupted signaling, but antagonist binding was unaffected. Mutation of Glu54 had an almost identical pharmacological effect as mutation of Arg46, raising the possibility that agonist binding required a mutual interaction between Glu54 and Arg46. The role of these two charged residues was investigated by 1) substituting Glu54; 2) inserting additional Glu/Arg in transmembrane helix (TM) 1; 3) repositioning the Glu/Arg in TM1; and 4) characterizing the reciprocal mutant [R46E/E54R]V1aR. We conclude that 1) the positive/negative charges need to be precisely positioned in this N terminus/TM1 segment; and 2) Glu54 and Arg46 function independently, providing two discrete epitopes required for high-affinity agonist binding and signaling. This study explains why Glu and Arg, part of an -R(X3)L/V(X3)E(X3)L- motif, are conserved at these loci throughout this G protein-coupled receptor subfamily and provides molecular insight into key differences between agonist and antagonist binding requirements.

NMR studies of CCK-8/CCK1 complex support membrane-associated pathway for ligand-receptor interaction

2002 ◽  
Vol 80 (5) ◽  
pp. 383-387 ◽  
Author(s):  
Craig Giragossian ◽  
Maria Pellegrini ◽  
Dale F Mierke
Keyword(s):  
G Protein ◽  
Structural Features ◽  
G Protein Coupled Receptors ◽  
Peptide Ligands ◽  
Receptor Interaction ◽  
Peptide Ligand ◽  
Receptor Subtype ◽  
Nmr Studies ◽  
Receptor Complexes ◽  
G Protein Coupled

The interaction of peptide ligands with their associated G-protein-coupled receptors has been examined by a number of different experimental approaches over the years. We have been developing an approach utilizing high-resolution NMR to determine the structural features of the peptide ligand, well-designed fragments of the receptor, and the ligand–receptor complexes formed upon titration of the peptide hormone. The results from these investigations provide evidence for a membrane-associated pathway for the initial interaction of peptide ligands with the receptor. Here, our results from the investigation of the interaction of CCK-8 with the CCK1 receptor are described. Our spectroscopic results clearly show that both CCK-8 and the regions of CCK1 with which it interacts are closely associated with the zwitterionic interface of the lipids utilized in our solution spectroscopic studies.Key words: G-protein-coupled receptors, NMR structural characterization, cholecystokinin, CCK-8, cholecystokinin receptor, subtype 1, CCK1, peptide hormones.

scholarly journals Decay of an active GPCR: Conformational dynamics govern agonist rebinding and persistence of an active, yet empty, receptor state

2016 ◽  
Vol 113 (42) ◽  
pp. 11961-11966 ◽  
Author(s):  
Christopher T. Schafer ◽  
Jonathan F. Fay ◽  
Jay M. Janz ◽  
David L. Farrens
Keyword(s):  
Time Lag ◽  
Transmembrane Helix ◽  
Conformational Dynamics ◽  
Base Hydrolysis ◽  
Fluorescence Labeling ◽  
Time Resolved ◽  
Inactive Conformation ◽  
Agonist Concentration ◽  
G Protein Coupled

Here, we describe two insights into the role of receptor conformational dynamics during agonist release (all-trans retinal, ATR) from the visual G protein-coupled receptor (GPCR) rhodopsin. First, we show that, after light activation, ATR can continually release and rebind to any receptor remaining in an active-like conformation. As with other GPCRs, we observe that this equilibrium can be shifted by either promoting the active-like population or increasing the agonist concentration. Second, we find that during decay of the signaling state an active-like, yet empty, receptor conformation can transiently persist after retinal release, before the receptor ultimately collapses into an inactive conformation. The latter conclusion is based on time-resolved, site-directed fluorescence labeling experiments that show a small, but reproducible, lag between the retinal leaving the protein and return of transmembrane helix 6 (TM6) to the inactive conformation, as determined from tryptophan-induced quenching studies. Accelerating Schiff base hydrolysis and subsequent ATR dissociation, either by addition of hydroxylamine or introduction of mutations, further increased the time lag between ATR release and TM6 movement. These observations show that rhodopsin can bind its agonist in equilibrium like a traditional GPCR, provide evidence that an active GPCR conformation can persist even after agonist release, and raise the possibility of targeting this key photoreceptor protein by traditional pharmaceutical-based treatments.

scholarly journals Electron Transfer Coupled to Conformational Dynamics in Cell Respiration

2021 ◽  
Vol 8 ◽  
Author(s):  
Marco Reidelbach ◽  
Christoph Zimmer ◽  
Brigitte Meunier ◽  
Peter R. Rich ◽  
Vivek Sharma
Keyword(s):  
Electron Transfer ◽  
Proton Transfer ◽  
Conformational Changes ◽  
Transmembrane Helix ◽  
Conformational Dynamics ◽  
Atp Synthesis ◽  
Redox Activity ◽  
Cellular Respiration ◽  
Detailed Knowledge ◽  
Dynamics Simulations

Cellular respiration is a fundamental process required for energy production in many organisms. The terminal electron transfer complex in mitochondrial and many bacterial respiratory chains is cytochrome c oxidase (CcO). This converts the energy released in the cytochrome c/oxygen redox reaction into a transmembrane proton electrochemical gradient that is used subsequently to power ATP synthesis. Despite detailed knowledge of electron and proton transfer paths, a central question remains as to whether the coupling between electron and proton transfer in mammalian mitochondrial forms of CcO is mechanistically equivalent to its bacterial counterparts. Here, we focus on the conserved span between H376 and G384 of transmembrane helix (TMH) X of subunit I. This conformationally-dynamic section has been suggested to link the redox activity with the putative H pathway of proton transfer in mammalian CcO. The two helix X mutants, Val380Met (V380M) and Gly384Asp (G384D), generated in the genetically-tractable yeast CcO, resulted in a respiratory-deficient phenotype caused by the inhibition of intra-protein electron transfer and CcO turnover. Molecular aspects of these variants were studied by long timescale atomistic molecular dynamics simulations performed on wild-type and mutant bovine and yeast CcOs. We identified redox- and mutation-state dependent conformational changes in this span of TMH X of bovine and yeast CcOs which strongly suggests that this dynamic module plays a key role in optimizing intra-protein electron transfers.

Molecular Basis of Glucose Transport Mechanism in Plants

2019 ◽  
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Transport Mechanism ◽  
Conformational Dynamics ◽  
Site Directed Mutagenesis ◽  
Free Energy Barrier ◽  
Transport Cycle ◽  
Dynamics Simulations

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>

Schistosomal Sulfotransferase Interaction with Oxamniquine Involves Hybrid Mechanism of Induced-fit and Conformational Selection

2020 ◽  
Vol 16 (4) ◽  
pp. 451-459 ◽  
Author(s):  
Fortunatus C. Ezebuo ◽  
Ikemefuna C. Uzochukwu
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Binding Energy ◽  
Binding Site ◽  
Conformational Dynamics ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Conformational Selection ◽  
Hybrid Mechanism ◽  
Dynamics Simulations

Background: Sulfotransferase family comprises key enzymes involved in drug metabolism. Oxamniquine is a pro-drug converted into its active form by schistosomal sulfotransferase. The conformational dynamics of side-chain amino acid residues at the binding site of schistosomal sulfotransferase towards activation of oxamniquine has not received attention. Objective: The study investigated the conformational dynamics of binding site residues in free and oxamniquine bound schistosomal sulfotransferase systems and their contribution to the mechanism of oxamniquine activation by schistosomal sulfotransferase using molecular dynamics simulations and binding energy calculations. Methods: Schistosomal sulfotransferase was obtained from Protein Data Bank and both the free and oxamniquine bound forms were subjected to molecular dynamics simulations using GROMACS-4.5.5 after modeling it’s missing amino acid residues with SWISS-MODEL. Amino acid residues at its binding site for oxamniquine was determined and used for Principal Component Analysis and calculations of side-chain dihedrals. In addition, binding energy of the oxamniquine bound system was calculated using g_MMPBSA. Results: The results showed that binding site amino acid residues in free and oxamniquine bound sulfotransferase sampled different conformational space involving several rotameric states. Importantly, Phe45, Ile145 and Leu241 generated newly induced conformations, whereas Phe41 exhibited shift in equilibrium of its conformational distribution. In addition, the result showed binding energy of -130.091 ± 8.800 KJ/mol and Phe45 contributed -9.8576 KJ/mol. Conclusion: The results showed that schistosomal sulfotransferase binds oxamniquine by relying on hybrid mechanism of induced fit and conformational selection models. The findings offer new insight into sulfotransferase engineering and design of new drugs that target sulfotransferase.

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