1
|
Kaffashi K, Dréau D, Nesmelova IV. Heterodimers Are an Integral Component of Chemokine Signaling Repertoire. Int J Mol Sci 2023; 24:11639. [PMID: 37511398 PMCID: PMC10380872 DOI: 10.3390/ijms241411639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Chemokines are a family of signaling proteins that play a crucial role in cell-cell communication, cell migration, and cell trafficking, particularly leukocytes, under both normal and pathological conditions. The oligomerization state of chemokines influences their biological activity. The heterooligomerization occurs when multiple chemokines spatially and temporally co-localize, and it can significantly affect cellular responses. Recently, obligate heterodimers have emerged as tools to investigate the activities and molecular mechanisms of chemokine heterodimers, providing valuable insights into their functional roles. This review focuses on the latest progress in understanding the roles of chemokine heterodimers and their contribution to the functioning of the chemokine network.
Collapse
Affiliation(s)
- Kimia Kaffashi
- Department of Biological Sciences, University of North Carolina, Charlotte, NC 28223, USA
- Department of Physics and Optical Sciences, University of North Carolina, Charlotte, NC 28223, USA
| | - Didier Dréau
- Department of Biological Sciences, University of North Carolina, Charlotte, NC 28223, USA
| | - Irina V Nesmelova
- Department of Physics and Optical Sciences, University of North Carolina, Charlotte, NC 28223, USA
- School of Data Science, University of North Carolina, Charlotte, NC 28223, USA
| |
Collapse
|
2
|
Aydin Y, Coin I. Biochemical insights into structure and function of arrestins. FEBS J 2021; 288:2529-2549. [DOI: 10.1111/febs.15811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 12/13/2022]
Affiliation(s)
- Yasmin Aydin
- Institute of Biochemistry Faculty of Life Sciences University of Leipzig Germany
| | - Irene Coin
- Institute of Biochemistry Faculty of Life Sciences University of Leipzig Germany
| |
Collapse
|
3
|
Capturing Peptide-GPCR Interactions and Their Dynamics. Molecules 2020; 25:molecules25204724. [PMID: 33076289 PMCID: PMC7587574 DOI: 10.3390/molecules25204724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
Many biological functions of peptides are mediated through G protein-coupled receptors (GPCRs). Upon ligand binding, GPCRs undergo conformational changes that facilitate the binding and activation of multiple effectors. GPCRs regulate nearly all physiological processes and are a favorite pharmacological target. In particular, drugs are sought after that elicit the recruitment of selected effectors only (biased ligands). Understanding how ligands bind to GPCRs and which conformational changes they induce is a fundamental step toward the development of more efficient and specific drugs. Moreover, it is emerging that the dynamic of the ligand–receptor interaction contributes to the specificity of both ligand recognition and effector recruitment, an aspect that is missing in structural snapshots from crystallography. We describe here biochemical and biophysical techniques to address ligand–receptor interactions in their structural and dynamic aspects, which include mutagenesis, crosslinking, spectroscopic techniques, and mass-spectrometry profiling. With a main focus on peptide receptors, we present methods to unveil the ligand–receptor contact interface and methods that address conformational changes both in the ligand and the GPCR. The presented studies highlight a wide structural heterogeneity among peptide receptors, reveal distinct structural changes occurring during ligand binding and a surprisingly high dynamics of the ligand–GPCR complexes.
Collapse
|
4
|
Clements JL, Pohl F, Muthupandi P, Rogers SC, Mao J, Doctor A, Birman VB, Held JM. A clickable probe for versatile characterization of S-nitrosothiols. Redox Biol 2020; 37:101707. [PMID: 32916549 PMCID: PMC7490559 DOI: 10.1016/j.redox.2020.101707] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 08/12/2020] [Accepted: 08/27/2020] [Indexed: 12/23/2022] Open
Abstract
S-nitrosation of cysteine thiols (SNOs), commonly referred to as S-nitrosylation, is a cysteine oxoform that plays an important role in cellular signaling and impacts protein function and stability. Direct labeling of SNOs in cells with the flexibility to perform a wide range of cellular and biochemical assays remains a bottleneck as all SNO-targeted probes to date employ a single analytical modality such as biotin or a specific fluorophore. We therefore developed a clickable, alkyne-containing SNO probe 'PBZyn' based on the o-phosphino-benzoyl group warhead that enables multi-modal analysis via click conjugation. We demonstrate the utility of PBZyn to assay SNOs using in situ cellular imaging, protein blotting and affinity purification, as well as mass spectrometry. The flexible PBZyn probe will greatly facilitate investigation into the regulation of SNOs.
Collapse
Affiliation(s)
- Jenna L Clements
- Department of Medicine, Washington University Medical School, St. Louis, MO, 63110, USA
| | - Franziska Pohl
- Department of Medicine, Washington University Medical School, St. Louis, MO, 63110, USA
| | - Pandi Muthupandi
- Department of Chemistry, Washington University in Saint Louis, St. Louis, MO, 63110, USA
| | - Stephen C Rogers
- Department of Pediatrics and Center for Blood Oxygen Transport and Hemostasis, University of Maryland, School of Medicine, Baltimore, MD, 21201, USA
| | - Jack Mao
- Department of Medicine, Washington University Medical School, St. Louis, MO, 63110, USA
| | - Allan Doctor
- Department of Pediatrics and Center for Blood Oxygen Transport and Hemostasis, University of Maryland, School of Medicine, Baltimore, MD, 21201, USA
| | - Vladimir B Birman
- Department of Chemistry, Washington University in Saint Louis, St. Louis, MO, 63110, USA
| | - Jason M Held
- Department of Medicine, Washington University Medical School, St. Louis, MO, 63110, USA; Siteman Cancer Center, Washington University Medical School, St. Louis, MO, 63110, USA; Department of Anesthesiology, Washington University Medical School, St. Louis, MO, 63110, USA.
| |
Collapse
|
5
|
Ngo T, Stephens BS, Gustavsson M, Holden LG, Abagyan R, Handel TM, Kufareva I. Crosslinking-guided geometry of a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity. PLoS Biol 2020; 18:e3000656. [PMID: 32271748 PMCID: PMC7173943 DOI: 10.1371/journal.pbio.3000656] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 04/21/2020] [Accepted: 03/02/2020] [Indexed: 12/15/2022] Open
Abstract
Chemokines and their receptors are orchestrators of cell migration in humans. Because dysregulation of the receptor-chemokine system leads to inflammation and cancer, both chemokines and receptors are highly sought therapeutic targets. Yet one of the barriers for their therapeutic targeting is the limited understanding of the structural principles behind receptor-chemokine recognition and selectivity. The existing structures do not include CXC subfamily complexes and lack information about the receptor distal N-termini, despite the importance of the latter in signaling, regulation, and bias. Here, we report the discovery of the geometry of the complex between full-length CXCR4, a prototypical CXC receptor and driver of cancer metastasis, and its endogenous ligand CXCL12. By comprehensive disulfide cross-linking, we establish the existence and the structure of a novel interface between the CXCR4 distal N-terminus and CXCL12 β1-strand, while also recapitulating earlier findings from nuclear magnetic resonance, modeling and crystallography of homologous receptors. A cross-linking-informed high-resolution model of the CXCR4-CXCL12 complex pinpoints the interaction determinants and reveals the occupancy of the receptor major subpocket by the CXCL12 proximal N terminus. This newly found positioning of the chemokine proximal N-terminus provides a structural explanation of CXC receptor-chemokine selectivity against other subfamilies. Our findings challenge the traditional two-site understanding of receptor-chemokine recognition, suggest the possibility of new affinity and signaling determinants, and fill a critical void on the structural map of an important class of therapeutic targets. These results will aid the rational design of selective chemokine-receptor targeting small molecules and biologics with novel pharmacology.
Collapse
Affiliation(s)
- Tony Ngo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Bryan S. Stephens
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Lauren G. Holden
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Tracy M. Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| |
Collapse
|
6
|
Gustavsson M. New insights into the structure and function of chemokine receptor:chemokine complexes from an experimental perspective. J Leukoc Biol 2020; 107:1115-1122. [DOI: 10.1002/jlb.2mr1219-288r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022] Open
Affiliation(s)
- Martin Gustavsson
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| |
Collapse
|
7
|
Arimont M, Hoffmann C, de Graaf C, Leurs R. Chemokine Receptor Crystal Structures: What Can Be Learned from Them? Mol Pharmacol 2019; 96:765-777. [PMID: 31266800 DOI: 10.1124/mol.119.117168] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 06/21/2019] [Indexed: 12/18/2022] Open
Abstract
Chemokine receptors belong to the class A of G protein-coupled receptors (GPCRs) and are implicated in a wide variety of physiologic functions, mostly related to the homeostasis of the immune system. Chemokine receptors are also involved in multiple pathologic processes, including immune and autoimmune diseases, as well as cancer. Hence, several members of this GPCR subfamily are considered to be very relevant therapeutic targets. Since drug discovery efforts can be significantly reinforced by the availability of crystal structures, substantial efforts in the area of chemokine receptor structural biology could dramatically increase the outcome of drug discovery campaigns. This short review summarizes the available data on chemokine receptor crystal structures, discusses the numerous applications from chemokine receptor structures that can enhance the daily work of molecular pharmacologists, and describes the challenges and pitfalls to consider when relying on crystal structures for further research applications. SIGNIFICANCE STATEMENT: This short review summarizes the available data on chemokine receptor crystal structures, discusses the numerous applications from chemokine receptor structures that can enhance the daily work of molecular pharmacologists, and describes the challenges and pitfalls to consider when relying on crystal structures for further research applications.
Collapse
Affiliation(s)
- Marta Arimont
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (M.A., R.L.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University, Jena, Germany (C.H.); and Sosei Heptares, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Carsten Hoffmann
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (M.A., R.L.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University, Jena, Germany (C.H.); and Sosei Heptares, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Chris de Graaf
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (M.A., R.L.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University, Jena, Germany (C.H.); and Sosei Heptares, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Rob Leurs
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (M.A., R.L.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University, Jena, Germany (C.H.); and Sosei Heptares, Great Abington, Cambridge, United Kingdom (C.d.G.)
| |
Collapse
|
8
|
Ming Q, Gonzalez-Perez D, Luca VC. Molecular engineering strategies for visualizing low-affinity protein complexes. Exp Biol Med (Maywood) 2019; 244:1559-1567. [PMID: 31184923 DOI: 10.1177/1535370219855401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The growing availability of complex structures in the Protein Data Bank has provided key insight into the molecular architecture of protein–protein interfaces. The remarkable diversity observed in protein binding modes is paralleled by a tremendous variation in binding affinities, with interaction half-lives ranging from days to milliseconds. Within the protein interactome, low-affinity binding events have been particularly difficult to visualize by traditional structural methods, which has spurred the development of innovative strategies for reconstituting these short-lived yet biologically essential assemblies. An important takeaway from structural studies of low-affinity systems is that there is no universal solution for stabilizing protein complexes, and approaches such as single-chain fusions, biochemical linkages, and affinity-maturation have each been successful in certain contexts. In this article, we review how advances in molecular engineering have been used to capture weakly associated complexes for structure determination, and we provide perspectives on how the continued application of these methods can shed new light on the “hidden world” of low-affinity interactions. Impact statement Low-affinity protein interactions, while biologically essential, have been difficult to visualize by traditional methods in structural biology. In this review, we describe a series of innovative molecular engineering strategies that have been used to stabilize weakly bound protein complexes for structure determination. By highlighting several examples from the literature along with potential advantages and disadvantages of the individual approaches, we hope to provide an introductory resource for structural biologists studying low-affinity systems.
Collapse
Affiliation(s)
- Qianqian Ming
- Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - David Gonzalez-Perez
- Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Vincent C Luca
- Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| |
Collapse
|
9
|
Seidel L, Zarzycka B, Katritch V, Coin I. Exploring Pairwise Chemical Crosslinking To Study Peptide-Receptor Interactions. Chembiochem 2019; 20:683-692. [PMID: 30565820 DOI: 10.1002/cbic.201800582] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Indexed: 01/29/2023]
Abstract
Pairwise crosslinking is a powerful technique to characterize interactions between G protein coupled receptors and their ligands in the live cell. In this work, the "thiol trapping" method, which exploits the proximity-enhanced reaction between haloacetamides and cysteine, is examined to identify intermolecular pairs of vicinal positions. By incorporating cysteine into the corticotropin-releasing factor receptor and either α-chloro- or α-bromoacetamide groups into its ligands, it is shown that thiol trapping provides highly reproducible signals and a low background, and represents a valid alternative to classical "disulfide trapping". The method is advantageous if reducing agents are required during sample analysis. Moreover, it can provide partially distinct spatial constraints, thus giving access to a wider dataset for molecular modeling. Finally, by applying recombinant mini-Gs, GTPγS, and Gαs-depleted HEK293 cells to modulate Gs coupling, it is shown that yields of crosslinking increase in the presence of elevated levels of Gs.
Collapse
Affiliation(s)
- Lisa Seidel
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Bruederstrasse 34, 04103, Leipzig, Germany
| | - Barbara Zarzycka
- Department of Biological Sciences, Bridge Institute, University of Southern California, 1002 Childs Way, MCB 317, Los Angeles, CA, 90089-3502, USA
| | - Vsevolod Katritch
- Department of Biological Sciences, Bridge Institute, University of Southern California, 1002 Childs Way, MCB 317, Los Angeles, CA, 90089-3502, USA.,Department of Chemistry, Bridge Institute, University of Southern California, 1002 Childs Way, MCB 317, Los Angeles, CA, 90089-3502, USA
| | - Irene Coin
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Bruederstrasse 34, 04103, Leipzig, Germany
| |
Collapse
|
10
|
Miller MC, Mayo KH. Chemokines from a Structural Perspective. Int J Mol Sci 2017; 18:ijms18102088. [PMID: 28974038 PMCID: PMC5666770 DOI: 10.3390/ijms18102088] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 08/30/2017] [Accepted: 09/26/2017] [Indexed: 01/04/2023] Open
Abstract
Chemokines are a family of small, highly conserved cytokines that mediate various biological processes, including chemotaxis, hematopoiesis, and angiogenesis, and that function by interacting with cell surface G-Protein Coupled Receptors (GPCRs). Because of their significant involvement in various biological functions and pathologies, chemokines and their receptors have been the focus of therapeutic discovery for clinical intervention. There are several sub-families of chemokines (e.g., CXC, CC, C, and CX3C) defined by the positions of sequentially conserved cysteine residues. Even though all chemokines also have a highly conserved, three-stranded β-sheet/α-helix tertiary structural fold, their quarternary structures vary significantly with their sub-family. Moreover, their conserved tertiary structures allow for subunit swapping within and between sub-family members, thus promoting the concept of a “chemokine interactome”. This review is focused on structural aspects of CXC and CC chemokines, their functional synergy and ability to form heterodimers within the chemokine interactome, and some recent developments in structure-based chemokine-targeted drug discovery.
Collapse
Affiliation(s)
- Michelle C Miller
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Kevin H Mayo
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| |
Collapse
|
11
|
Friedhoff P, Manelyte L, Giron-Monzon L, Winkler I, Groothuizen FS, Sixma TK. Use of Single-Cysteine Variants for Trapping Transient States in DNA Mismatch Repair. Methods Enzymol 2017; 592:77-101. [PMID: 28668131 DOI: 10.1016/bs.mie.2017.03.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
DNA mismatch repair (MMR) is necessary to prevent incorporation of polymerase errors into the newly synthesized DNA strand, as they would be mutagenic. In humans, errors in MMR cause a predisposition to cancer, called Lynch syndrome. The MMR process is performed by a set of ATPases that transmit, validate, and couple information to identify which DNA strand requires repair. To understand the individual steps in the repair process, it is useful to be able to study these large molecular machines structurally and functionally. However, the steps and states are highly transient; therefore, the methods to capture and enrich them are essential. Here, we describe how single-cysteine variants can be used for specific cross-linking and labeling approaches that allow trapping of relevant transient states. Analysis of these defined states in functional and structural studies is instrumental to elucidate the molecular mechanism of this important DNA MMR process.
Collapse
Affiliation(s)
- Peter Friedhoff
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany.
| | - Laura Manelyte
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
| | - Luis Giron-Monzon
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
| | - Ines Winkler
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
| | | | - Titia K Sixma
- Netherlands Cancer Institute, Amsterdam, The Netherlands.
| |
Collapse
|
12
|
Arimont M, Sun SL, Leurs R, Smit M, de Esch IJP, de Graaf C. Structural Analysis of Chemokine Receptor-Ligand Interactions. J Med Chem 2017; 60:4735-4779. [PMID: 28165741 PMCID: PMC5483895 DOI: 10.1021/acs.jmedchem.6b01309] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
This
review focuses on the construction and application of structural chemokine
receptor models for the elucidation of molecular determinants of chemokine
receptor modulation and the structure-based discovery and design of
chemokine receptor ligands. A comparative analysis of ligand binding
pockets in chemokine receptors is presented, including a detailed
description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures,
and their implication for modeling molecular interactions of chemokine
receptors with small-molecule ligands, peptide ligands, and large
antibodies and chemokines. These studies demonstrate how the integration
of new structural information on chemokine receptors with extensive
structure–activity relationship and site-directed mutagenesis
data facilitates the prediction of the structure of chemokine receptor–ligand
complexes that have not been crystallized. Finally, a review of structure-based
ligand discovery and design studies based on chemokine receptor crystal
structures and homology models illustrates the possibilities and challenges
to find novel ligands for chemokine receptors.
Collapse
Affiliation(s)
- Marta Arimont
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Shan-Liang Sun
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Rob Leurs
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Martine Smit
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Chris de Graaf
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| |
Collapse
|
13
|
Gustavsson M, Wang L, van Gils N, Stephens BS, Zhang P, Schall TJ, Yang S, Abagyan R, Chance MR, Kufareva I, Handel TM. Structural basis of ligand interaction with atypical chemokine receptor 3. Nat Commun 2017; 8:14135. [PMID: 28098154 PMCID: PMC5253664 DOI: 10.1038/ncomms14135] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/02/2016] [Indexed: 12/21/2022] Open
Abstract
Chemokines drive cell migration through their interactions with seven-transmembrane (7TM) chemokine receptors on cell surfaces. The atypical chemokine receptor 3 (ACKR3) binds chemokines CXCL11 and CXCL12 and signals exclusively through β-arrestin-mediated pathways, without activating canonical G-protein signalling. This receptor is upregulated in numerous cancers making it a potential drug target. Here we collected over 100 distinct structural probes from radiolytic footprinting, disulfide trapping, and mutagenesis to map the structures of ACKR3:CXCL12 and ACKR3:small-molecule complexes, including dynamic regions that proved unresolvable by X-ray crystallography in homologous receptors. The data are integrated with molecular modelling to produce complete and cohesive experimentally driven models that confirm and expand on the existing knowledge of the architecture of receptor:chemokine and receptor:small-molecule complexes. Additionally, we detected and characterized ligand-induced conformational changes in the transmembrane and intracellular regions of ACKR3 that elucidate fundamental structural elements of agonism in this atypical receptor.
Collapse
Affiliation(s)
- Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, MC 0684, La Jolla, California, 92093, USA
| | - Liwen Wang
- Center for Proteomics and Bioinformatics and Department of Nutrition, Case Western Reserve University School of Medicine, 10009 Euclid Avenue, Cleveland, Ohio 44109, USA
| | - Noortje van Gils
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, MC 0684, La Jolla, California, 92093, USA
| | - Bryan S Stephens
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, MC 0684, La Jolla, California, 92093, USA
| | - Penglie Zhang
- ChemoCentryx Inc., 850 W Maude Avenue, Mountain View, California 94043, USA
| | - Thomas J Schall
- ChemoCentryx Inc., 850 W Maude Avenue, Mountain View, California 94043, USA
| | - Sichun Yang
- Center for Proteomics and Bioinformatics and Department of Nutrition, Case Western Reserve University School of Medicine, 10009 Euclid Avenue, Cleveland, Ohio 44109, USA
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, MC 0684, La Jolla, California, 92093, USA
| | - Mark R Chance
- Center for Proteomics and Bioinformatics and Department of Nutrition, Case Western Reserve University School of Medicine, 10009 Euclid Avenue, Cleveland, Ohio 44109, USA
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, MC 0684, La Jolla, California, 92093, USA
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, MC 0684, La Jolla, California, 92093, USA
| |
Collapse
|
14
|
Kufareva I. Chemokines and their receptors: insights from molecular modeling and crystallography. Curr Opin Pharmacol 2016; 30:27-37. [PMID: 27459124 PMCID: PMC5071139 DOI: 10.1016/j.coph.2016.07.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/07/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
Chemokines are small secreted proteins that direct cell migration in development, immunity, inflammation, and cancer. They do so by binding and activating specific G protein coupled receptors on the surface of migrating cells. Despite the importance of receptor:chemokine interactions, their structural basis remained unclear for a long time. In 2015, the first atomic resolution insights were obtained with the publication of X-ray structures for two distantly related receptors bound to chemokines. In conjunction with experiment-guided molecular modeling, the structures suggest a conserved receptor:chemokine complex architecture, while highlighting the diverse details and functional roles of individual interaction epitopes. Novel findings promote the development and detailed structural interpretation of the canonical two-site hypothesis of receptor:chemokine recognition, and suggest new avenues for pharmacological modulation of chemokine receptors.
Collapse
Affiliation(s)
- Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| |
Collapse
|