1
|
Sonawani A, Kharche S, Dasgupta D, Sengupta D. Insights into the dynamic interactions at chemokine-receptor interfaces and mechanistic models of chemokine binding. J Struct Biol 2022; 214:107877. [PMID: 35750237 DOI: 10.1016/j.jsb.2022.107877] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/20/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022]
Abstract
Chemokine receptors are the central signaling hubs of several processes such as cell migration, chemotaxis and cell positioning. In this graphical review, we provide an overview of the structural and mechanistic principles governing chemokine recognition that are currently emerging. Structural models of chemokine-receptor co-complexes with endogenous chemokines, viral chemokines and therapeutics have been resolved that highlight multiple interaction sites, termed as CRS1, CRS1.5 etc. The first site of interaction has been shown to be the N-terminal domain of the receptors (CRS1 site). A large structural flexibility of the N-terminal domain has been reported that was supported by both experimental and simulation studies. Upon chemokine binding, the N-terminal domain appears to show constricted dynamics and opens up to interact with the chemokine via a large interface. The subsequent sites such as CRS1.5 and CRS2 sites have been structurally well resolved although differences arise such as the localization of the N-terminus of the ligand to a major or minor pocket of the orthosteric binding site. Several computational studies have highlighted the dynamic protein-protein interface at the CRS1 site that seemingly appears to resolve the differences in NMR and mutagenesis studies. Interestingly, the differential dynamics at the CRS1 site suggests a mixed model of binding with complex signatures of both conformational selection and induced fit models. Integrative experimental and computational approaches could help unravel the structural basis of promiscuity and specificity in chemokine-receptor binding and open up new avenues of therapeutic design.
Collapse
Affiliation(s)
- Archana Sonawani
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, CBD Belapur, Navi Mumbai 400614, India
| | - Shalmali Kharche
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | - Debjani Dasgupta
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, CBD Belapur, Navi Mumbai 400614, India
| | - Durba Sengupta
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
| |
Collapse
|
2
|
Allosteric modulation of the chemokine receptor-chemokine CXCR4-CXCL12 complex by tyrosine sulfation. Int J Biol Macromol 2022; 206:812-822. [PMID: 35306016 DOI: 10.1016/j.ijbiomac.2022.03.078] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/03/2022] [Accepted: 03/13/2022] [Indexed: 11/21/2022]
Abstract
The chemokine receptor CXCR4 and its cognate ligand CXCL12 mediate pathways that lead to cell migration and chemotaxis. Although the structural details of related receptor-ligand complexes have been resolved, the roles of the N-terminal domain of the receptor and post-translational sulfation that are determinants of ligand selectivity and affinity remain unclear. Here, we analyze the structural dynamics induced by receptor sulfation by combining molecular dynamics, docking and network analysis. The sulfotyrosine residues, 7YsN-term, 12YsN-term and 21YsN-term allow the N-terminal domain of the apo-sulfated receptor to adopt an "open" conformation that appears to facilitate ligand binding. The overall topology of the CXCR4-CXCL12 complex is independent of the sulfation state, but an extensive network of protein-protein interactions characterizes the sulfated receptor, in line with its increased ligand affinity. The altered interactions of sulfotyrosine residues, such as 21YsN-term-47RCXCL12 replacing the 21YN-term-13FCXCL12 interaction, propagate via allosteric pathways towards the receptor lumen. In particular, our results suggest that the experimentally-reported receptor-ligand interactions 262D6.58-8RCXCL12 and 277E7.28-12RCXCL12 could be dependent on the sulfation state of the receptor and need to be carefully analyzed. Our work is an important step in understanding chemokine-receptor interactions and how post-translational modifications could modulate receptor-ligand complexes.
Collapse
|
3
|
Kharche S, Joshi M, Chattopadhyay A, Sengupta D. Conformational plasticity and dynamic interactions of the N-terminal domain of the chemokine receptor CXCR1. PLoS Comput Biol 2021; 17:e1008593. [PMID: 34014914 PMCID: PMC8172051 DOI: 10.1371/journal.pcbi.1008593] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 06/02/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
The dynamic interactions between G protein-coupled receptors (GPCRs) and their cognate protein partners are central to several cell signaling pathways. For example, the association of CXC chemokine receptor 1 (CXCR1) with its cognate chemokine, interleukin-8 (IL8 or CXCL8) initiates pathways leading to neutrophil-mediated immune responses. The N-terminal domain of chemokine receptors confers ligand selectivity, but unfortunately the conformational dynamics of this intrinsically disordered region remains unresolved. In this work, we have explored the interaction of CXCR1 with IL8 by microsecond time scale coarse-grain simulations, complemented by atomistic models and NMR chemical shift predictions. We show that the conformational plasticity of the apo-receptor N-terminal domain is restricted upon ligand binding, driving it to an open C-shaped conformation. Importantly, we corroborated the dynamic complex sampled in our simulations against chemical shift perturbations reported by previous NMR studies and show that the trends are similar. Our results indicate that chemical shift perturbation is often not a reporter of residue contacts in such dynamic associations. We believe our results represent a step forward in devising a strategy to understand intrinsically disordered regions in GPCRs and how they acquire functionally important conformational ensembles in dynamic protein-protein interfaces.
Collapse
Affiliation(s)
- Shalmali Kharche
- CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Manali Joshi
- Bioinformatics Centre, S. P. Pune University, Pune, India
| | | | - Durba Sengupta
- CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
4
|
Bous J, Orcel H, Floquet N, Leyrat C, Lai-Kee-Him J, Gaibelet G, Ancelin A, Saint-Paul J, Trapani S, Louet M, Sounier R, Déméné H, Granier S, Bron P, Mouillac B. Cryo-electron microscopy structure of the antidiuretic hormone arginine-vasopressin V2 receptor signaling complex. SCIENCE ADVANCES 2021; 7:7/21/eabg5628. [PMID: 34020960 PMCID: PMC8139594 DOI: 10.1126/sciadv.abg5628] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/01/2021] [Indexed: 05/08/2023]
Abstract
The antidiuretic hormone arginine-vasopressin (AVP) forms a signaling complex with the V2 receptor (V2R) and the Gs protein, promoting kidney water reabsorption. Molecular mechanisms underlying activation of this critical G protein-coupled receptor (GPCR) signaling system are still unknown. To fill this gap of knowledge, we report here the cryo-electron microscopy structure of the AVP-V2R-Gs complex. Single-particle analysis revealed the presence of three different states. The two best maps were combined with computational and nuclear magnetic resonance spectroscopy constraints to reconstruct two structures of the ternary complex. These structures differ in AVP and Gs binding modes. They reveal an original receptor-Gs interface in which the Gαs subunit penetrates deep into the active V2R. The structures help to explain how V2R R137H or R137L/C variants can lead to two severe genetic diseases. Our study provides important structural insights into the function of this clinically relevant GPCR signaling complex.
Collapse
Affiliation(s)
- Julien Bous
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Hélène Orcel
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Nicolas Floquet
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34093 Montpellier cedex 5, France
| | - Cédric Leyrat
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Joséphine Lai-Kee-Him
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Gérald Gaibelet
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Aurélie Ancelin
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Julie Saint-Paul
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Stefano Trapani
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Maxime Louet
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34093 Montpellier cedex 5, France
| | - Rémy Sounier
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Hélène Déméné
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Sébastien Granier
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France.
| | - Patrick Bron
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France.
| | - Bernard Mouillac
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France.
| |
Collapse
|
5
|
Souza PCT, Limongelli V, Wu S, Marrink SJ, Monticelli L. Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations. Front Mol Biosci 2021; 8:657222. [PMID: 33855050 PMCID: PMC8039319 DOI: 10.3389/fmolb.2021.657222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/05/2021] [Indexed: 01/12/2023] Open
Abstract
Molecular docking is central to rational drug design. Current docking techniques suffer, however, from limitations in protein flexibility and solvation models and by the use of simplified scoring functions. All-atom molecular dynamics simulations, on the other hand, feature a realistic representation of protein flexibility and solvent, but require knowledge of the binding site. Recently we showed that coarse-grained molecular dynamics simulations, based on the most recent version of the Martini force field, can be used to predict protein/ligand binding sites and pathways, without requiring any a priori information, and offer a level of accuracy approaching all-atom simulations. Given the excellent computational efficiency of Martini, this opens the way to high-throughput drug screening based on dynamic docking pipelines. In this opinion article, we sketch the roadmap to achieve this goal.
Collapse
Affiliation(s)
- Paulo C. T. Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
- PharmCADD, Busan, South Korea
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Institute of Computational Science, Università della Svizzera Italiana (USI), Lugano, Switzerland
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| | - Sangwook Wu
- PharmCADD, Busan, South Korea
- Department of Physics, Pukyong National University, Busan, South Korea
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France
| |
Collapse
|
7
|
Structure and dynamics of G protein-coupled receptor-bound ghrelin reveal the critical role of the octanoyl chain. Proc Natl Acad Sci U S A 2019; 116:17525-17530. [PMID: 31416915 DOI: 10.1073/pnas.1905105116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Ghrelin plays a central role in controlling major biological processes. As for other G protein-coupled receptor (GPCR) peptide agonists, the structure and dynamics of ghrelin bound to its receptor remain obscure. Using a combination of solution-state NMR and molecular modeling, we demonstrate that binding to the growth hormone secretagogue receptor is accompanied by a conformational change in ghrelin that structures its central region, involving the formation of a well-defined hydrophobic core. By comparing its acylated and nonacylated forms, we conclude that the ghrelin octanoyl chain is essential to form the hydrophobic core and promote access of ghrelin to the receptor ligand-binding pocket. The combination of coarse-grained molecular dynamics studies and NMR should prove useful in improving our mechanistic understanding of the complex conformational space explored by a natural peptide agonist when binding to its GPCR. Such information should also facilitate the design of new ghrelin receptor-selective drugs.
Collapse
|
8
|
Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications. Int J Mol Sci 2019; 20:ijms20153774. [PMID: 31375023 PMCID: PMC6696403 DOI: 10.3390/ijms20153774] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/28/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to capture the conformational dynamics and local motions. In addition, recent developments in coarse-grained models have opened the way to study the macromolecular complexes for time scales up to milliseconds. In this review, we have discussed the principle, applicability and recent development in coarse-grained models for biological systems. The potential of coarse-grained simulation has been reviewed through state-of-the-art examples of protein folding and structure prediction, self-assembly of complexes, membrane systems and carbohydrates fiber models. The multiscale simulation approaches have also been discussed in the context of their emerging role in unravelling hierarchical level information of biosystems. We conclude this review with the future scope of coarse-grained simulations as a constantly evolving tool to capture the dynamics of biosystems.
Collapse
|
9
|
Wang L, Yuan Y, Chen X, Chen J, Guo Y, Li M, Li C, Pu X. Probing the cooperative mechanism of the μ–δ opioid receptor heterodimer by multiscale simulation. Phys Chem Chem Phys 2018; 20:29969-29982. [DOI: 10.1039/c8cp06652c] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The activation-cooperativity of the μ–δ opioid receptor heterodimer was probed by multiscale simulation coupled with a protein structure network.
Collapse
Affiliation(s)
- Longrong Wang
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yuan Yuan
- College of Management
- Southwest University for Nationalities
- Chengdu 610041
- P. R. China
| | - Xin Chen
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Jiangfan Chen
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yanzhi Guo
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Menglong Li
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Chuan Li
- College of Computer Science
- Sichuan University
- Chengdu
- P. R. China
| | - Xuemei Pu
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| |
Collapse
|