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García-Cuesta EM, Martínez P, Selvaraju K, Ulltjärn G, Gómez Pozo AM, D'Agostino G, Gardeta S, Quijada-Freire A, Blanco Gabella P, Roca C, Hoyo DD, Jiménez-Saiz R, García-Rubia A, Soler Palacios B, Lucas P, Ayala-Bueno R, Santander Acerete N, Carrasco Y, Oscar Sorzano C, Martinez A, Campillo NE, Jensen LD, Rodriguez Frade JM, Santiago C, Mellado M. Allosteric modulation of the CXCR4:CXCL12 axis by targeting receptor nanoclustering via the TMV-TMVI domain. eLife 2024; 13:RP93968. [PMID: 39248648 PMCID: PMC11383527 DOI: 10.7554/elife.93968] [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] [Indexed: 09/10/2024] Open
Abstract
CXCR4 is a ubiquitously expressed chemokine receptor that regulates leukocyte trafficking and arrest in both homeostatic and pathological states. It also participates in organogenesis, HIV-1 infection, and tumor development. Despite the potential therapeutic benefit of CXCR4 antagonists, only one, plerixafor (AMD3100), which blocks the ligand-binding site, has reached the clinic. Recent advances in imaging and biophysical techniques have provided a richer understanding of the membrane organization and dynamics of this receptor. Activation of CXCR4 by CXCL12 reduces the number of CXCR4 monomers/dimers at the cell membrane and increases the formation of large nanoclusters, which are largely immobile and are required for correct cell orientation to chemoattractant gradients. Mechanistically, CXCR4 activation involves a structural motif defined by residues in TMV and TMVI. Using this structural motif as a template, we performed in silico molecular modeling followed by in vitro screening of a small compound library to identify negative allosteric modulators of CXCR4 that do not affect CXCL12 binding. We identified AGR1.137, a small molecule that abolishes CXCL12-mediated receptor nanoclustering and dynamics and blocks the ability of cells to sense CXCL12 gradients both in vitro and in vivo while preserving ligand binding and receptor internalization.
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Affiliation(s)
- Eva M García-Cuesta
- Chemokine Signaling group, Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Pablo Martínez
- Chemokine Signaling group, Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Karthik Selvaraju
- Division of Diagnostics and Specialist Medicine, Department of Health, Medical and Caring Sciences, Linköping University, Linköping, Sweden
| | - Gabriel Ulltjärn
- Division of Diagnostics and Specialist Medicine, Department of Health, Medical and Caring Sciences, Linköping University, Linköping, Sweden
| | | | - Gianluca D'Agostino
- Chemokine Signaling group, Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Sofia Gardeta
- Chemokine Signaling group, Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Adriana Quijada-Freire
- Chemokine Signaling group, Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
| | | | - Carlos Roca
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
| | - Daniel Del Hoyo
- Biocomputing Unit, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Rodrigo Jiménez-Saiz
- Chemokine Signaling group, Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
- Department of Immunology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Madrid, Spain
- Department of Medicine, McMaster Immunology Research Centre (MIRC), Schroeder Allergy and Immunology Research Institute, McMaster University, Hamilton, Canada
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria (UFV), Madrid, Spain
| | | | - Blanca Soler Palacios
- Chemokine Signaling group, Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Pilar Lucas
- Chemokine Signaling group, Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Rosa Ayala-Bueno
- Chemokine Signaling group, Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Noelia Santander Acerete
- Chemokine Signaling group, Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Yolanda Carrasco
- B Lymphocyte Dynamics, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Carlos Oscar Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Ana Martinez
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
- Neurodegenerative Diseases Biomedical Research Network Center (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Nuria E Campillo
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
| | - Lasse D Jensen
- Division of Diagnostics and Specialist Medicine, Department of Health, Medical and Caring Sciences, Linköping University, Linköping, Sweden
| | - Jose Miguel Rodriguez Frade
- Chemokine Signaling group, Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
| | - César Santiago
- X-ray Crystallography Unit, Department of Macromolecules Structure, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Mario Mellado
- Chemokine Signaling group, Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
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Yadav MK, Sarma P, Maharana J, Ganguly M, Mishra S, Zaidi N, Dalal A, Singh V, Saha S, Mahajan G, Sharma S, Chami M, Banerjee R, Shukla AK. Structure-guided engineering of biased-agonism in the human niacin receptor via single amino acid substitution. Nat Commun 2024; 15:1939. [PMID: 38431681 PMCID: PMC10908815 DOI: 10.1038/s41467-024-46239-2] [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: 07/31/2023] [Accepted: 02/18/2024] [Indexed: 03/05/2024] Open
Abstract
The Hydroxycarboxylic acid receptor 2 (HCA2), also known as the niacin receptor or GPR109A, is a prototypical GPCR that plays a central role in the inhibition of lipolytic and atherogenic activities. Its activation also results in vasodilation that is linked to the side-effect of flushing associated with dyslipidemia drugs such as niacin. GPR109A continues to be a target for developing potential therapeutics in dyslipidemia with minimized flushing response. Here, we present cryo-EM structures of the GPR109A in complex with dyslipidemia drugs, niacin or acipimox, non-flushing agonists, MK6892 or GSK256073, and recently approved psoriasis drug, monomethyl fumarate (MMF). These structures elucidate the binding mechanism of agonists, molecular basis of receptor activation, and insights into biased signaling elicited by some of the agonists. The structural framework also allows us to engineer receptor mutants that exhibit G-protein signaling bias, and therefore, our study may help in structure-guided drug discovery efforts targeting this receptor.
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Affiliation(s)
- Manish K Yadav
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Parishmita Sarma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Jagannath Maharana
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Manisankar Ganguly
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Sudha Mishra
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Nashrah Zaidi
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Annu Dalal
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Vinay Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Sayantan Saha
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Gargi Mahajan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Saloni Sharma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Mohamed Chami
- BioEM Lab, Biozentrum, Universität Basel, Basel, Switzerland
| | - Ramanuj Banerjee
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India.
| | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India.
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3
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Jones RD. Information Transmission in G Protein-Coupled Receptors. Int J Mol Sci 2024; 25:1621. [PMID: 38338905 PMCID: PMC10855935 DOI: 10.3390/ijms25031621] [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: 12/30/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of receptors in the human genome and constitute about 30% of all drug targets. In this article, intended for a non-mathematical audience, both experimental observations and new theoretical results are compared in the context of information transmission across the cell membrane. The amount of information actually currently used or projected to be used in clinical settings is a small fraction of the information transmission capacity of the GPCR. This indicates that the number of yet undiscovered drug targets within GPCRs is much larger than what is currently known. Theoretical studies with some experimental validation indicate that localized heat deposition and dissipation are key to the identification of sites and mechanisms for drug action.
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Affiliation(s)
- Roger D Jones
- European Centre for Living Technology, University of Venice, 30123 Venice, Italy
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4
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Simon IA, Bjørn-Yoshimoto WE, Harpsøe K, Iliadis S, Svensson B, Jensen AA, Gloriam DE. Ligand selectivity hotspots in serotonin GPCRs. Trends Pharmacol Sci 2023; 44:978-990. [PMID: 37914598 DOI: 10.1016/j.tips.2023.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023]
Abstract
Serotonin is a neurotransmitter regulating numerous physiological processes also modulated by drugs, for example, schizophrenia, depression, migraine, and obesity. However, these drugs typically have adverse effects caused by promiscuous binding across 12 serotonin and more than 20 homologous receptors. Recently, structures of the entire serotonin receptor family uncovered molecular ligand recognition. Here, we present a map of 19 'selectivity hotspots', that is, nonconserved binding site residues governing selectivity via favorable target interactions or repulsive 'off-target' contacts. Furthermore, we review functional rationale from observed ligand-binding affinities and mutagenesis effects. Unifying knowledge underlying specific probes and drugs is critical toward the functional characterization of different receptors and alleviation of adverse effects.
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Affiliation(s)
- Icaro A Simon
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Walden E Bjørn-Yoshimoto
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Kasper Harpsøe
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Stylianos Iliadis
- Centre for Endocrinology, William Harvey Research Institute, Bart's and the London School of Medicine and Dentistry, University of London, London EC1M 6BQ, UK
| | - Bo Svensson
- SARomics Biostructures AB, Scheelevägen 2, 223 63 Lund, Sweden
| | - Anders A Jensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.
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5
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Guner JZ, Monsivais D, Yu H, Stossi F, Johnson HL, Gibbons WE, Matzuk MM, Palmer S. Oral follicle-stimulating hormone receptor agonist affects granulosa cells differently than recombinant human FSH. Fertil Steril 2023; 120:1061-1070. [PMID: 37532169 PMCID: PMC10659100 DOI: 10.1016/j.fertnstert.2023.07.024] [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: 02/28/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/04/2023]
Abstract
OBJECTIVE To determine whether TOP5300, a novel oral follicle-stimulating hormone (FSH) receptor (FSHR) allosteric agonist, elicits a different cellular response than recombinant human FSH (rh-FSH) in human granulosa cells from patients undergoing in vitro fertilization. DESIGN Basic science research with a preclinical allosteric FSHR agonist. SETTING University hospital. PATIENT(S) Patients with infertility at a single academic fertility clinic were recruited under an Institutional Review Board-approved protocol. Primary granulosa cell cultures were established for 41 patients, of whom 8 had normal ovarian reserve (NOR), 17 were of advanced reproductive age (ARA), 12 had a diagnosis of polycystic ovary syndrome (PCOS), and 4 had a combination of diagnoses, such as ARA and PCOS. INTERVENTION(S) Primary granulosa-lutein (GL) cell cultures were treated with rh-FSH, TOP5300, or vehicle. MAIN OUTCOME MEASURE(S) Estradiol (E2) production using enzyme-linked immunosorbent assay, steroid pathway gene expression of StAR and aromatase using quantitative polymerase chain reaction, and FSHR membrane localization using immunofluorescence were measured in human GL cells. RESULT(S) TOP5300 consistently stimulated E2 production among patients with NOR, ARA, and PCOS. Recombinant FSH was the more potent ligand in GL cells from patients with NOR but was ineffective in cells from patients with ARA or PCOS. The lowest level of FSHR plasma membrane localization was seen in patients with ARA, although FSHR localization was more abundant in cells from patients with PCOS; the highest levels were present in cells from patients with NOR. The localization of FSHR was not affected by TOP5300 relative to rh-FSH in any patient group. TOP5300 stimulated greater expression of StAR and CYP19A1 across cells from all patients with NOR, ARA, and PCOS combined, although rh-FSH was unable to stimulate StAR and aromatase (CYP19A1) expression in cells from patients with PCOS. TOP5300-induced expression of StAR and CYP19A1 mRNA among patients with ARA and NOR was consistently lower than that observed in cells from patients with PCOS. CONCLUSION(S) TOP5300 appears to stimulate E2 production and steroidogenic gene expression from GL cells more than rh-FSH in PCOS, relative to patients with ARA and NOR. It does not appear that localization of FSHR at cell membranes is a limiting step for TOP5300 or rh-FSH stimulation of steroidogenic gene expression and E2 production.
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Affiliation(s)
- Joie Z Guner
- Center for Drug Discovery, Baylor College of Medicine, Houston, Texas; Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California
| | - Diana Monsivais
- Center for Drug Discovery, Baylor College of Medicine, Houston, Texas; Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas
| | - Henry Yu
- CanWell Pharma, Wellesley, Massachusetts
| | - Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas; Integrated Microscopy Core and GCC Center for Advanced Microscopy and Image Informatics, Baylor College of Medicine, Houston, Texas
| | - Hannah L Johnson
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas; Integrated Microscopy Core and GCC Center for Advanced Microscopy and Image Informatics, Baylor College of Medicine, Houston, Texas
| | - William E Gibbons
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Baylor College of Medicine, and Texas Children's Hospital Family Fertility Center, Houston, Texas
| | - Martin M Matzuk
- Center for Drug Discovery, Baylor College of Medicine, Houston, Texas; Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas
| | - Stephen Palmer
- Center for Drug Discovery, Baylor College of Medicine, Houston, Texas; Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas.
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6
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Sadee W. Ligand-Free Signaling of G-Protein-Coupled Receptors: Physiology, Pharmacology, and Genetics. Molecules 2023; 28:6375. [PMID: 37687205 PMCID: PMC10489045 DOI: 10.3390/molecules28176375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) are ubiquitous sensors and regulators of cellular functions. Each GPCR exists in complex aggregates with multiple resting and active conformations. Designed to detect weak stimuli, GPCRs can also activate spontaneously, resulting in basal ligand-free signaling. Agonists trigger a cascade of events leading to an activated agonist-receptor G-protein complex with high agonist affinity. However, the ensuing signaling process can further remodel the receptor complex to reduce agonist affinity, causing rapid ligand dissociation. The acutely activated ligand-free receptor can continue signaling, as proposed for rhodopsin and μ opioid receptors, resulting in robust receptor activation at low agonist occupancy with enhanced agonist potency. Continued receptor stimulation can further modify the receptor complex, regulating sustained ligand-free signaling-proposed to play a role in opioid dependence. Basal, acutely agonist-triggered, and sustained elevated ligand-free signaling could each have distinct functions, reflecting multi-state conformations of GPCRs. This review addresses basal and stimulus-activated ligand-free signaling, its regulation, genetic factors, and pharmacological implications, focusing on opioid and serotonin receptors, and the growth hormone secretagogue receptor (GHSR). The hypothesis is proposed that ligand-free signaling of 5-HT2A receptors mediate therapeutic effects of psychedelic drugs. Research avenues are suggested to close the gaps in our knowledge of ligand-free GPCR signaling.
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Affiliation(s)
- Wolfgang Sadee
- Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- Aether Therapeutics Inc., Austin, TX 78756, USA
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7
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Cao Y, van der Velden WJC, Namkung Y, Nivedha AK, Cho A, Sedki D, Holleran B, Lee N, Leduc R, Muk S, Le K, Bhattacharya S, Vaidehi N, Laporte SA. Unraveling allostery within the angiotensin II type 1 receptor for Gα q and β-arrestin coupling. Sci Signal 2023; 16:eadf2173. [PMID: 37552769 PMCID: PMC10640921 DOI: 10.1126/scisignal.adf2173] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 07/20/2023] [Indexed: 08/10/2023]
Abstract
G protein-coupled receptors engage both G proteins and β-arrestins, and their coupling can be biased by ligands and mutations. Here, to resolve structural elements and mechanisms underlying effector coupling to the angiotensin II (AngII) type 1 receptor (AT1R), we combined alanine scanning mutagenesis of the entire sequence of the receptor with pharmacological profiling of Gαq and β-arrestin engagement to mutant receptors and molecular dynamics simulations. We showed that Gαq coupling to AT1R involved a large number of residues spread across the receptor, whereas fewer structural regions of the receptor contributed to β-arrestin coupling regulation. Residue stretches in transmembrane domain 4 conferred β-arrestin bias and represented an important structural element in AT1R for functional selectivity. Furthermore, we identified allosteric small-molecule binding sites that were enclosed by communities of residues that produced biased signaling when mutated. Last, we showed that allosteric communication within AT1R emanating from the Gαq coupling site spread beyond the orthosteric AngII-binding site and across different regions of the receptor, including currently unresolved structural regions. Our findings reveal structural elements and mechanisms within AT1R that bias Gαq and β-arrestin coupling and that could be harnessed to design biased receptors for research purposes and to develop allosteric modulators.
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Affiliation(s)
- Yubo Cao
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Wijnand J. C. van der Velden
- Department of Computational & Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Yoon Namkung
- Department of Medicine, McGill University Health Center, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Anita K. Nivedha
- Department of Computational & Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Aaron Cho
- Department of Medicine, McGill University Health Center, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Dana Sedki
- Department of Medicine, McGill University Health Center, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Brian Holleran
- Department of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Nicholas Lee
- Department of Medicine, McGill University Health Center, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Richard Leduc
- Department of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Sanychen Muk
- Department of Computational & Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Keith Le
- Department of Computational & Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Supriyo Bhattacharya
- Department of Computational & Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Nagarajan Vaidehi
- Department of Computational & Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Stéphane A. Laporte
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
- Department of Medicine, McGill University Health Center, McGill University, Montréal, Québec H4A 3J1, Canada
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8
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Park HK, Nguyen LP, Nguyen TU, Cho M, Nguyen HT, Hurh S, Kim HR, Seong JY, Lee CS, Ham BJ, Hwang JI. The N-terminus of CXCR4 splice variants determines expression and functional properties. PLoS One 2023; 18:e0283015. [PMID: 37141381 PMCID: PMC10159351 DOI: 10.1371/journal.pone.0283015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/28/2023] [Indexed: 05/06/2023] Open
Abstract
C-X-C motif chemokine ligand 12(CXCL12) is an essential chemokine for organ development and homeostasis in multiple tissues. Its receptor, C-X-C chemokine receptor type 4(CXCR4), is expressed on the surface of target cells. The chemokine and receptor are expressed almost ubiquitously in human tissues and cells throughout life, and abnormal expression of CXCL12 and CXCR4 is observed in pathological conditions, such as inflammation and cancer. CXCR4 is reportedly translated into five splicing variants of different lengths, which each have different amino acids in the N-terminus. As the N-terminus is the first recognition site for chemokines, CXCR4 variants may respond differently to CXCL12. Despite these differences, the molecular and functional properties of CXCR4 variants have not been thoroughly described or compared. Here, we explored the expression of CXCR4 variants in cell lines and analyzed their roles in cellular responses using biochemical approaches. RT-PCR revealed that most cell lines express more than one CXCR4 variant. When expressed in HEK293 cells, the CXCR4 variants differed in protein expression efficiency and cell surface localization. Although variant 2 demonstrated the strongest expression and cell surface localization, variants 1, 3, and 5 also mediated chemokine signaling and induced cellular responses. Our results demonstrate that the N-terminal sequences of each CXCR4 variant determine the expression of the receptor and affect ligand recognition. Functional analyses revealed that CXCR4 variants may also affect each other or interact during CXCL12-stimulated cellular responses. Altogether, our results suggest that CXCR4 variants may have distinct functional roles that warrant additional investigation and could contribute to future development of novel drug interventions.
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Affiliation(s)
- Hee-Kyung Park
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Lan Phuong Nguyen
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Thai Uy Nguyen
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Minyeong Cho
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Huong Thi Nguyen
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Sunghoon Hurh
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Hong-Rae Kim
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Jae Young Seong
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Cheol Soon Lee
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Byung-Joo Ham
- Department of Psychiatry, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Jong-Ik Hwang
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea
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9
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Liessmann F, Künze G, Meiler J. Improving the Modeling of Extracellular Ligand Binding Pockets in RosettaGPCR for Conformational Selection. Int J Mol Sci 2023; 24:7788. [PMID: 37175495 PMCID: PMC10178219 DOI: 10.3390/ijms24097788] [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: 04/03/2023] [Revised: 04/19/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of drug targets and undergo substantial conformational changes in response to ligand binding. Despite recent progress in GPCR structure determination, static snapshots fail to reflect the conformational space of putative binding pocket geometries to which small molecule ligands can bind. In comparative modeling of GPCRs in the absence of a ligand, often a shrinking of the orthosteric binding pocket is observed. However, the exact prediction of the flexible orthosteric binding site is crucial for adequate structure-based drug discovery. In order to improve ligand docking and guide virtual screening experiments in computer-aided drug discovery, we developed RosettaGPCRPocketSize. The algorithm creates a conformational ensemble of biophysically realistic conformations of the GPCR binding pocket between the TM bundle, which is consistent with a knowledge base of expected pocket geometries. Specifically, tetrahedral volume restraints are defined based on information about critical residues in the orthosteric binding site and their experimentally observed range of Cα-Cα-distances. The output of RosettaGPCRPocketSize is an ensemble of binding pocket geometries that are filtered by energy to ensure biophysically probable arrangements, which can be used for docking simulations. In a benchmark set, pocket shrinkage observed in the default RosettaGPCR was reduced by up to 80% and the binding pocket volume range and geometric diversity were increased. Compared to models from four different GPCR homology model databases (RosettaGPCR, GPCR-Tasser, GPCR-SSFE, and GPCRdb), the here-created models showed more accurate volumes of the orthosteric pocket when evaluated with respect to the crystallographic reference structure. Furthermore, RosettaGPCRPocketSize was able to generate an improved realistic pocket distribution. However, while being superior to other homology models, the accuracy of generated model pockets was comparable to AlphaFold2 models. Furthermore, in a docking benchmark using small-molecule ligands with a higher molecular weight between 400 and 700 Da, a higher success rate in creating native-like binding poses was observed. In summary, RosettaGPCRPocketSize can generate GPCR models with realistic orthosteric pocket volumes, which are useful for structure-based drug discovery applications.
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Affiliation(s)
- Fabian Liessmann
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
| | - Georg Künze
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
| | - Jens Meiler
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Center for Scalable Data Analytics and Artificial Intelligence, Leipzig University, 04105 Leipzig, Germany
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10
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Dumas L, Marfoglia M, Yang B, Hijazi M, Larabi AN, Lau K, Pojer F, Nash MA, Barth P. Uncovering and engineering the mechanical properties of the adhesion GPCR ADGRG1 GAIN domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535724. [PMID: 37066252 PMCID: PMC10104041 DOI: 10.1101/2023.04.05.535724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Key cellular functions depend on the transduction of extracellular mechanical signals by specialized membrane receptors including adhesion G-protein coupled receptors (aGPCRs). While recently solved structures support aGPCR activation through shedding of the extracellular GAIN domain, the molecular mechanisms underpinning receptor mechanosensing remain poorly understood. When probed using single-molecule atomic force spectroscopy and molecular simulations, ADGRG1 GAIN dissociated from its tethered agonist at forces significantly higher than other reported signaling mechanoreceptors. Strong mechanical resistance was achieved through specific structural deformations and force propagation pathways under mechanical load. ADGRG1 GAIN variants computationally designed to lock the alpha and beta subdomains and rewire mechanically-induced structural deformations were found to modulate the GPS-Stachel rupture forces. Our study provides unprecedented insights into the molecular underpinnings of GAIN mechanical stability and paves the way for engineering mechanosensors, better understanding aGPCR function, and informing drug-discovery efforts targeting this important receptor class.
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11
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Hewitt N, Ma N, Arang N, Martin SA, Prakash A, DiBerto JF, Knight KM, Ghosh S, Olsen RHJ, Roth BL, Gutkind JS, Vaidehi N, Campbell SL, Dohlman HG. Catalytic site mutations confer multiple states of G protein activation. Sci Signal 2023; 16:eabq7842. [PMID: 36787384 PMCID: PMC10021883 DOI: 10.1126/scisignal.abq7842] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 01/31/2023] [Indexed: 02/16/2023]
Abstract
Heterotrimeric guanine nucleotide-binding proteins (G proteins) that function as molecular switches for cellular growth and metabolism are activated by GTP and inactivated by GTP hydrolysis. In uveal melanoma, a conserved glutamine residue critical for GTP hydrolysis in the G protein α subunit is often mutated in Gαq or Gα11 to either leucine or proline. In contrast, other glutamine mutations or mutations in other Gα subtypes are rare. To uncover the mechanism of the genetic selection and the functional role of this glutamine residue, we analyzed all possible substitutions of this residue in multiple Gα isoforms. Through cell-based measurements of activity, we showed that some mutants were further activated and inactivated by G protein-coupled receptors. Through biochemical, molecular dynamics, and nuclear magnetic resonance-based structural studies, we showed that the Gα mutants were functionally distinct and conformationally diverse, despite their shared inability to hydrolyze GTP. Thus, the catalytic glutamine residue contributes to functions beyond GTP hydrolysis, and these functions include subtype-specific, allosteric modulation of receptor-mediated subunit dissociation. We conclude that G proteins do not function as simple on-off switches. Rather, signaling emerges from an ensemble of active states, a subset of which are favored in disease and may be uniquely responsive to receptor-directed ligands.
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Affiliation(s)
- Natalie Hewitt
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Nadia Arang
- Department of Pharmacology, University of California San Diego, San Diego, CA, 92093, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Sarah A. Martin
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ajit Prakash
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffrey F. DiBerto
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kevin M. Knight
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Soumadwip Ghosh
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Current address: Illumina Inc, 5200 Illumina Way, San Diego, CA 92037, USA
| | - Reid H. J. Olsen
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Current address: GPCR Pharmacology, Discovery Biology, Exscientia Ai, Oxford, UK OX4 4GE
| | - Bryan L. Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J. Silvio Gutkind
- Department of Pharmacology, University of California San Diego, San Diego, CA, 92093, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Sharon L. Campbell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Henrik G. Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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12
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Erman B. Mutual information analysis of mutation, nonlinearity, and triple interactions in proteins. Proteins 2023; 91:121-133. [PMID: 36000344 DOI: 10.1002/prot.26415] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 12/15/2022]
Abstract
Mutations are the cause of several diseases as well as the underlying force of evolution. A thorough understanding of their biophysical consequences is essential. We present a computational framework for evaluating different levels of mutual information (MI) and its dependence on mutation. We used molecular dynamics trajectories of the third PDZ domain and its different mutations. Nonlinear MI between all residue pairs are calculated by tensor Hermite polynomials up to the fifth order and compared with results from multivariate Gaussian distribution of joint probabilities. We show that MI is written as the sum of a Gaussian and a nonlinear component. Results for the PDZ domain show that the Gaussian term gives a sufficiently accurate representation of MI when compared with nonlinear terms up to the fifth order. Changes in MI between residue pairs show the characteristic patterns resulting from specific mutations. Emergence of new peaks in the MI versus residue index plots of mutated PDZ shows how mutation may change allosteric pathways. Triple correlations are characterized by evaluating MI between triplets of residues. We observed that certain triplets are strongly affected by mutation. Susceptibility of residues to perturbation is obtained by MI and discussed in terms of linear response theory.
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Affiliation(s)
- Burak Erman
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
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13
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Caniceiro AB, Bueschbell B, Schiedel AC, Moreira IS. Class A and C GPCR Dimers in Neurodegenerative Diseases. Curr Neuropharmacol 2022; 20:2081-2141. [PMID: 35339177 PMCID: PMC9886835 DOI: 10.2174/1570159x20666220327221830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/21/2022] [Accepted: 03/23/2022] [Indexed: 11/22/2022] Open
Abstract
Neurodegenerative diseases affect over 30 million people worldwide with an ascending trend. Most individuals suffering from these irreversible brain damages belong to the elderly population, with onset between 50 and 60 years. Although the pathophysiology of such diseases is partially known, it remains unclear upon which point a disease turns degenerative. Moreover, current therapeutics can treat some of the symptoms but often have severe side effects and become less effective in long-term treatment. For many neurodegenerative diseases, the involvement of G proteincoupled receptors (GPCRs), which are key players of neuronal transmission and plasticity, has become clearer and holds great promise in elucidating their biological mechanism. With this review, we introduce and summarize class A and class C GPCRs, known to form heterodimers or oligomers to increase their signalling repertoire. Additionally, the examples discussed here were shown to display relevant alterations in brain signalling and had already been associated with the pathophysiology of certain neurodegenerative diseases. Lastly, we classified the heterodimers into two categories of crosstalk, positive or negative, for which there is known evidence.
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Affiliation(s)
- Ana B. Caniceiro
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; ,These authors contributed equally to this work.
| | - Beatriz Bueschbell
- PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Casa Costa Alemão, 3030-789 Coimbra, Portugal; ,These authors contributed equally to this work.
| | - Anke C. Schiedel
- Department of Pharmaceutical & Medicinal Chemistry, Pharmaceutical Institute, University of Bonn, D-53121 Bonn, Germany;
| | - Irina S. Moreira
- University of Coimbra, Department of Life Sciences, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; ,Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, 3004-504 Coimbra, Portugal,Address correspondence to this author at the Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, 3004-504 Coimbra, Portugal; E-mail:
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14
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Wakefield AE, Bajusz D, Kozakov D, Keserű GM, Vajda S. Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors. J Chem Inf Model 2022; 62:4937-4954. [PMID: 36195573 PMCID: PMC9847135 DOI: 10.1021/acs.jcim.2c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Despite the growing number of G protein-coupled receptor (GPCR) structures, only 39 structures have been cocrystallized with allosteric inhibitors. These structures have been studied by protein mapping using the FTMap server, which determines the clustering of small organic probe molecules distributed on the protein surface. The method has found druggable sites overlapping with the cocrystallized allosteric ligands in 21 GPCR structures. Mapping of Alphafold2 generated models of these proteins confirms that the same sites can be identified without the presence of bound ligands. We then mapped the 394 GPCR X-ray structures available at the time of the analysis (September 2020). Results show that for each of the 21 structures with bound ligands there exist many other GPCRs that have a strong binding hot spot at the same location, suggesting potential allosteric sites in a large variety of GPCRs. These sites cluster at nine distinct locations, and each can be found in many different proteins. However, ligands binding at the same location generally show little or no similarity, and the amino acid residues interacting with these ligands also differ. Results confirm the possibility of specifically targeting these sites across GPCRs for allosteric modulation and help to identify the most likely binding sites among the limited number of potential locations. The FTMap server is available free of charge for academic and governmental use at https://ftmap.bu.edu/.
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Affiliation(s)
- Amanda E. Wakefield
- Department of Chemistry, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, H-1117 Budapest, Hungary
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook NY 11794
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, H-1117 Budapest, Hungary
| | - Sandor Vajda
- Department of Chemistry, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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15
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Tang WW, Naga Prasad SV. Autoantibodies and Cardiomyopathy: Focus on Beta-1 Adrenergic Receptor Autoantibodies. J Cardiovasc Pharmacol 2022; 80:354-363. [PMID: 35323150 PMCID: PMC9452444 DOI: 10.1097/fjc.0000000000001264] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/16/2022] [Indexed: 02/07/2023]
Abstract
ABSTRACT Antibody response to self-antigens leads to autoimmune response that plays a determinant role in cardiovascular disease outcomes including dilated cardiomyopathy (DCM). Although the origins of the self-reactive endogenous autoantibodies are not well-characterized, it is believed to be triggered by tissue injury or dysregulated humoral response. Autoantibodies that recognize G protein-coupled receptors are considered consequential because they act as modulators of downstream receptor signaling displaying a wide range of unique pharmacological properties. These wide range of pharmacological properties exhibited by autoantibodies has cellular consequences that is associated with progression of disease including DCM. Increase in autoantibodies recognizing beta-1 adrenergic receptor (β1AR), a G protein-coupled receptor critical for cardiac function, is observed in patients with DCM. Cellular and animal model studies have indicated pathological roles for the β1AR autoantibodies but less is understood about the molecular basis of their modulatory effects. Despite the recognition that β1AR autoantibodies could mediate deleterious outcomes, emerging evidence suggests that not all β1AR autoantibodies are deleterious. Recent clinical studies show that β1AR autoantibodies belonging to the IgG3 subclass is associated with beneficial cardiac outcomes in patients. This suggests that our understanding on the roles the β1AR autoantibodies play in mediating outcomes is not well-understood. Technological advances including structural determinants of antibody binding could provide insights on the modulatory capabilities of β1AR autoantibodies in turn, reflecting their diversity in mediating β1AR signaling response. In this study, we discuss the significance of the diversity in signaling and its implications in pathology.
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Affiliation(s)
- W.H. Wilson Tang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH
- Department of Cardiovascular Medicine, Heart, Vascular & Thoracic Institute, Cleveland Clinic, Cleveland, OH
| | - Sathyamangla V. Naga Prasad
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH
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16
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In Silico Study of Allosteric Communication Networks in GPCR Signaling Bias. Int J Mol Sci 2022; 23:ijms23147809. [PMID: 35887157 PMCID: PMC9315799 DOI: 10.3390/ijms23147809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
Signaling bias is a promising characteristic of G protein-coupled receptors (GPCRs) as it provides the opportunity to develop more efficacious and safer drugs. This is because biased ligands can avoid the activation of pathways linked to side effects whilst still producing the desired therapeutic effect. In this respect, a deeper understanding of receptor dynamics and implicated allosteric communication networks in signaling bias can accelerate the research on novel biased drug candidates. In this review, we aim to provide an overview of computational methods and techniques for studying allosteric communication and signaling bias in GPCRs. This includes (i) the detection of allosteric communication networks and (ii) the application of network theory for extracting relevant information pipelines and highly communicated sites in GPCRs. We focus on the most recent research and highlight structural insights obtained based on the framework of allosteric communication networks and network theory for GPCR signaling bias.
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17
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Haliloglu T, Hacisuleyman A, Erman B. Prediction of Allosteric Communication Pathways in Proteins. Bioinformatics 2022; 38:3590-3599. [PMID: 35674396 DOI: 10.1093/bioinformatics/btac380] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/12/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Allostery in proteins is an essential phenomenon in biological processes. In this paper, we present a computational model to predict paths of maximum information transfer between active and allosteric sites. In this information theoretic study, we use mutual information as the measure of information transfer, where transition probability of information from one residue to its contacting neighbors is proportional to the magnitude of mutual information between the two residues. Starting from a given residue and using a Hidden Markov Model, we successively determine the neighboring residues that eventually lead to a path of optimum information transfer. The Gaussian approximation of mutual information between residue pairs is adopted. The limits of validity of this approximation are discussed in terms of a nonlinear theory of mutual information and its reduction to the Gaussian form. RESULTS Predictions of the model are tested on six widely studied cases, CheY Bacterial Chemotaxis, B-cell Lymphoma extra-large Bcl-xL, Human proline isomerase cyclophilin A (CypA), Dihydrofolate reductase DHFR, HRas GTPase, and Caspase-1. The communication transmission rendering the propagation of local fluctuations from the active sites throughout the structure in multiple paths correlate well with the known experimental data. Distinct paths originating from the active site may likely represent a multi functionality such as involving more than one allosteric site and/or preexistence of some other functional states. Our model is computationally fast and simple, and can give allosteric communication pathways, which are crucial for the understanding and control of protein functionality. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Turkan Haliloglu
- Polymer Research Center and Chemical Engineering Department, Bogazici University, 34342, Turkey
| | - Aysima Hacisuleyman
- Institute of Bioengineering, Swiss Federal Institute of Technology (EPFL), 1015, Switzerland
| | - Burak Erman
- Chemical and Biological Engineering, Koc University, 34450, Turkey
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18
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Casadó-Anguera V, Casadó V. Unmasking allosteric binding sites: Novel targets for GPCR drug discovery. Expert Opin Drug Discov 2022; 17:897-923. [PMID: 35649692 DOI: 10.1080/17460441.2022.2085684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Unexpected non-apparent and hidden allosteric binding sites are non-classical and non-apparent allosteric centers in 3-D X-ray protein structures until orthosteric or allosteric ligands bind to them. The orthosteric center of one protomer that modulates binding centers of the other protomers within an oligomer is also an unexpected allosteric site. Furthermore, another partner protein can also produce these effects, acting as an unexpected allosteric modulator. AREAS COVERED This review summarizes both classical and non-classical allosterism. The authors focus on G protein-coupled receptor (GPCR) oligomers as a paradigm of allosteric molecules. Moreover, they show several examples of unexpected allosteric sites such as hidden allosteric sites in a protomer that appear after the interaction with other molecules and the allosterism exerted between orthosteric sites within GPCR oligomer, emphasizing on the allosteric modulations that can occur between binding sites. EXPERT OPINION The study of these new non-classical allosteric sites will expand the diversity of allosteric control on the function of orthosteric sites within proteins, whether GPCRs or other receptors, enzymes or transporters. Moreover, the design of new drugs targeting these hidden allosteric sites or already known orthosteric sites acting as allosteric sites in protein homo- or hetero-oligomers will increase the therapeutic potential of allosterism.
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Affiliation(s)
- Verònica Casadó-Anguera
- Laboratory of Molecular Neuropharmacology, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, and Institute of Biomedicine of the Universitat de Barcelona, Barcelona, Spain.,Laboratory of Neuropharmacology-Neurophar, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Vicent Casadó
- Laboratory of Molecular Neuropharmacology, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, and Institute of Biomedicine of the Universitat de Barcelona, Barcelona, Spain
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19
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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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20
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Shukla AK. Emerging paradigms in activation, signaling, and regulation of G protein-coupled receptors. FEBS J 2021; 288:2458-2460. [PMID: 33818907 PMCID: PMC7614522 DOI: 10.1111/febs.15839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022]
Abstract
This Special Issue of The FEBS Journal brings together a set of review articles focused on recent developments in the field of GPCR biology, with particular emphasis on novel paradigms of their activation, signaling, and regulation. These articles cover a broad repertoire of cellular, physiological, and structural aspects ranging from the interaction of GPCRs with their signal transducers, allosteric modulation of these receptors with therapeutic implications, and emerging technologies aimed to probe critical aspects of receptor signaling and regulation.
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Affiliation(s)
- Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
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