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Pirona L, Ballabio F, Alfonso-Prieto M, Capelli R. Calcium-Driven In Silico Inactivation of a Human Olfactory Receptor. J Chem Inf Model 2024; 64:2971-2978. [PMID: 38523266 DOI: 10.1021/acs.jcim.4c00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Conformational changes as well as molecular determinants related to the activation and inactivation of olfactory receptors are still poorly understood due to the intrinsic difficulties in the structural determination of this GPCR family. Here, we perform, for the first time, the in silico inactivation of human olfactory receptor OR51E2, highlighting the possible role of calcium in this receptor state transition. Using molecular dynamics simulations, we show that a divalent ion in the ion binding site, coordinated by two acidic residues at positions 2.50 and 3.39 conserved across most ORs, stabilizes the receptor in its inactive state. In contrast, protonation of the same two acidic residues is not sufficient to drive inactivation within the microsecond timescale of our simulations. Our findings suggest a novel molecular mechanism for OR inactivation, potentially guiding experimental validation and offering insights into the possible broader role of divalent ions in GPCR signaling.
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Affiliation(s)
- Lorenza Pirona
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Federico Ballabio
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, D-54248 Jülich, Germany
| | - Riccardo Capelli
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, I-20133 Milano, Italy
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Madhu MK, Shewani K, Murarka RK. Biased Signaling in Mutated Variants of β 2-Adrenergic Receptor: Insights from Molecular Dynamics Simulations. J Chem Inf Model 2024; 64:449-469. [PMID: 38194225 DOI: 10.1021/acs.jcim.3c01481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The molecular basis of receptor bias in G protein-coupled receptors (GPCRs) caused by mutations that preferentially activate specific intracellular transducers over others remains poorly understood. Two experimentally identified biased variants of β2-adrenergic receptors (β2AR), a prototypical GPCR, are a triple mutant (T68F, Y132A, and Y219A) and a single mutant (Y219A); the former bias the receptor toward the β-arrestin pathway by disfavoring G protein engagement, while the latter induces G protein signaling explicitly due to selection against GPCR kinases (GRKs) that phosphorylate the receptor as a prerequisite of β-arrestin binding. Though rigorous characterizations have revealed functional implications of these mutations, the atomistic origin of the observed transducer selectivity is not clear. In this study, we investigated the allosteric mechanism of receptor bias in β2AR using microseconds of all-atom Gaussian accelerated molecular dynamics (GaMD) simulations. Our observations reveal distinct rearrangements in transmembrane helices, intracellular loop 3, and critical residues R1313.50 and Y3267.53 in the conserved motifs D(E)RY and NPxxY for the mutant receptors, leading to their specific transducer interactions. Moreover, partial dissociation of G protein from the receptor core is observed in the simulations of the triple mutant in contrast to the single mutant and wild-type receptor. The reorganization of allosteric communications from the extracellular agonist BI-167107 to the intracellular receptor-transducer interfaces drives the conformational rearrangements responsible for receptor bias in the single and triple mutants. The molecular insights into receptor bias of β2AR presented here could improve the understanding of biased signaling in GPCRs, potentially opening new avenues for designing novel therapeutics with fewer side-effects and superior efficacy.
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Affiliation(s)
- Midhun K Madhu
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal, Madhya Pradesh 462066, India
| | - Kunal Shewani
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal, Madhya Pradesh 462066, India
| | - Rajesh K Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal, Madhya Pradesh 462066, India
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Vo ADP, Kim SK, Yang MY, Ondrus AE, Goddard WA. Fully activated structure of the sterol-bound Smoothened GPCR-Gi protein complex. Proc Natl Acad Sci U S A 2023; 120:e2300919120. [PMID: 38015850 PMCID: PMC10710022 DOI: 10.1073/pnas.2300919120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 10/22/2023] [Indexed: 11/30/2023] Open
Abstract
Smoothened (SMO) is an oncoprotein and signal transducer in the Hedgehog signaling pathway that regulates cellular differentiation and embryogenesis. As a member of the Frizzled (Class F) family of G protein-coupled receptors (GPCRs), SMO biochemically and functionally interacts with Gi family proteins. However, key molecular features of fully activated, G protein-coupled SMO remain elusive. We present the atomistic structure of activated human SMO complexed with the heterotrimeric Gi protein and two sterol ligands, equilibrated at 310 K in a full lipid bilayer at physiological salt concentration and pH. In contrast to previous experimental structures, our equilibrated SMO complex exhibits complete breaking of the pi-cation interaction between R4516.32 and W5357.55, a hallmark of Class F receptor activation. The Gi protein couples to SMO at seven strong anchor points similar to those in Class A GPCRs: intracellular loop 1, intracellular loop 2, transmembrane helix 6, and helix 8. On the path to full activation, we find that the extracellular cysteine-rich domain (CRD) undergoes a dramatic tilt, following a trajectory suggested by positions of the CRD in active and inactive experimental SMO structures. Strikingly, a sterol ligand bound to a shallow transmembrane domain (TMD) site in the initial structure migrates to a deep TMD pocket found exclusively in activator-bound SMO complexes. Thus, our results indicate that SMO interacts with Gi prior to full activation to break the molecular lock, form anchors with Gi subunits, tilt the CRD, and facilitate migration of a sterol ligand in the TMD to an activated position.
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Affiliation(s)
- Amy-Doan P. Vo
- Materials and Process Simulation Center, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Soo-Kyung Kim
- Materials and Process Simulation Center, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Moon Young Yang
- Materials and Process Simulation Center, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Alison E. Ondrus
- Department of Chemistry, University of Illinois Chicago, Chicago, IL60607
- Department of Pharmaceutical Sciences, University of Illinois Chicago, Chicago, IL60607
| | - William A. Goddard
- Materials and Process Simulation Center, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA91125
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Abrol R, Serrano E, Santiago LJ. Development of enhanced conformational sampling methods to probe the activation landscape of GPCRs. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:325-359. [PMID: 35034722 DOI: 10.1016/bs.apcsb.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
G protein-coupled receptors (GPCRs) make up the largest superfamily of integral membrane proteins and play critical signal transduction roles in many physiological processes. Developments in molecular biology, biophysical, biochemical, pharmacological, and computational techniques aimed at these important therapeutic targets are beginning to provide unprecedented details on the structural as well as functional basis of their pleiotropic signaling mediated by G proteins, β arrestins, and other transducers. This pleiotropy presents a pharmacological challenge as the same ligand-receptor interaction can cause a therapeutic effect as well as an undesirable on-target side-effect through different downstream pathways. GPCRs don't function as simple binary on-off switches but as finely tuned shape-shifting machines described by conformational ensembles, where unique subsets of conformations may be responsible for specific signaling cascades. X-ray crystallography and more recently cryo-electron microscopy are providing snapshots of some of these functionally-important receptor conformations bound to ligands and/or transducers, which are being utilized by computational methods to describe the dynamic conformational energy landscape of GPCRs. In this chapter, we review the progress in computational conformational sampling methods based on molecular dynamics and discrete sampling approaches that have been successful in complementing biophysical and biochemical studies on these receptors in terms of their activation mechanisms, allosteric effects, actions of biased ligands, and effects of pathological mutations. Some of the sampled simulation time scales are beginning to approach receptor activation time scales. The list of conformational sampling methods and example uses discussed is not exhaustive but includes representative examples that have pushed the limits of classical molecular dynamics and discrete sampling methods to describe the activation energy landscape of GPCRs.
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Affiliation(s)
- Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, United States.
| | - Erik Serrano
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, United States
| | - Luis Jaimes Santiago
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, United States
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Abstract
The exchange of vibrational energy in proteins is crucial for their function. Here, we establish a connection between quantities related to it with geometry-based properties such as the proteins' residues coordination number. This relation is proven by molecular simulation in a neuro-pharmacologically relevant transmembrane receptor. The connection demonstrated here paves the way to studies of protein allostery and conformational changes based solely on protein structure.
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Affiliation(s)
- L Maggi
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - P Carloni
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
- Institute for Neuroscience and Medicine INM-11 , Forschungszentrum Jülich , 52428 Jülich , Germany
- Department of Physics , RWTH Aachen University , 52078 Aachen , Germany
- Department of Neurology , University Hospital Aachen , 52078 Aachen , Germany
| | - G Rossetti
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
- Division Computational Science - Simulation Laboratory Biology, Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH , 52428 Jülich , Germany
- Department of Oncology, Hematology and Stem Cell Transplantation, University Hospital Aachen , RWTH Aachen University , 52074 Aachen , Germany
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Lau A, Bourkas M, Lu YQQ, Ostrowski LA, Weber-Adrian D, Figueiredo C, Arshad H, Shoaei SZS, Morrone CD, Matan-Lithwick S, Abraham KJ, Wang H, Schmitt-Ulms G. Functional Amyloids and their Possible Influence on Alzheimer Disease. Discoveries (Craiova) 2017; 5:e79. [PMID: 32309597 PMCID: PMC7159844 DOI: 10.15190/d.2017.9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Amyloids play critical roles in human diseases but have increasingly been recognized to also exist naturally. Shared physicochemical characteristics of amyloids and of their smaller oligomeric building blocks offer the prospect of molecular interactions and crosstalk amongst these assemblies, including the propensity to mutually influence aggregation. A case in point might be the recent discovery of an interaction between the amyloid β peptide (Aβ) and somatostatin (SST). Whereas Aβ is best known for its role in Alzheimer disease (AD) as the main constituent of amyloid plaques, SST is intermittently stored in amyloid-form in dense core granules before its regulated release into the synaptic cleft. This review was written to introduce to readers a large body of literature that surrounds these two peptides. After introducing general concepts and recent progress related to our understanding of amyloids and their aggregation, the review focuses separately on the biogenesis and interactions of Aβ and SST, before attempting to assess the likelihood of encounters of the two peptides in the brain, and summarizing key observations linking SST to the pathobiology of AD. While the review focuses on Aβ and SST, it is to be anticipated that crosstalk amongst functional and disease-associated amyloids will emerge as a general theme with much broader significance in the etiology of dementias and other amyloidosis.
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Affiliation(s)
- Angus Lau
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.,Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - Matthew Bourkas
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.,Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - Yang Qing Qin Lu
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Lauren Anne Ostrowski
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Danielle Weber-Adrian
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Carlyn Figueiredo
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Hamza Arshad
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.,Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - Seyedeh Zahra Shams Shoaei
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Christopher Daniel Morrone
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Stuart Matan-Lithwick
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Karan Joshua Abraham
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Hansen Wang
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - Gerold Schmitt-Ulms
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.,Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
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