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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.
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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
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Gutierrez JA, Japas ML, Silber JJ, Falcone RD, Correa NM. Is it Necessary for the Use of Fluorinated Compounds to Formulate Reverse Micelles in a Supercritical Fluid? Searching the Best Cosurfactant to Create "Green" AOT Reverse Micelle Media. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:445-453. [PMID: 33373249 DOI: 10.1021/acs.langmuir.0c03093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Herein, we report the effect of employing two different alcohols, such as n-pentanol and 2,2,3,3,4,4,5,5-octafluoro pentanol (from now on F-pentanol), into 1,4-bis-2-ethylhexylsulfosuccinate (AOT) reverse micelles (RMs), to determine the interfacial activity and establish the best candidate to act as a cosurfactant in supercritical RMs. Dynamic light scattering (DLS), Fourier transform infrared (FT-IR), and fluorescence emission spectroscopy allowed us to determine and understand the behavior of alkanols in RMs. As a result, we found interesting displacements of alkanol molecules within the RMs, suggesting that the electrostatic interaction between SO3- and Na+ weakens because of new interactions of n-pentanol with SO3- through H-bonds, changing the curvature of the micellar interface. According to FT-IR and DLS studies, F-pentanol forms a RM polar core interacting through intermolecular H-bonds, suggesting no perturbations of the AOT RM interface. Hence, n-pentanol was selected as a cosurfactant to form supercritical RMs, which is confirmed by red edge excitation shift studies, using C343 as a molecular probe. Herein, we were able to create RMs under supercritical conditions without the presence of modified surfactants, fluorinated or multitailed compounds, which, to the best of our knowledge, was not shown before.
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Affiliation(s)
- Jorge A Gutierrez
- Programa de Seguridad y Salud en el Trabajo, Universidad del Quindío, Carrera 15 Calle 12 Norte, C.P. 630004 Armenia, Colombia
| | - M Laura Japas
- Gerencia Química, Centro Atómico Constituyentes-CNEA, AV. Gral. Paz 1499, Pcia, de Buenos Aires B1650KNA, San Martín, Argentina
| | - Juana J Silber
- Instituto para el Desarrollo Agroindustrial y de la Salud, IDAS, (CONICET-UNRC), Departamento de Química, Universidad Nacional de Río Cuarto, Agencia Postal # 3. C.P. X5804BYA Río Cuarto, Argentina
| | - R Darío Falcone
- Instituto para el Desarrollo Agroindustrial y de la Salud, IDAS, (CONICET-UNRC), Departamento de Química, Universidad Nacional de Río Cuarto, Agencia Postal # 3. C.P. X5804BYA Río Cuarto, Argentina
| | - N Mariano Correa
- Instituto para el Desarrollo Agroindustrial y de la Salud, IDAS, (CONICET-UNRC), Departamento de Química, Universidad Nacional de Río Cuarto, Agencia Postal # 3. C.P. X5804BYA Río Cuarto, Argentina
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Pal S, Chattopadhyay A. Extramembranous Regions in G Protein-Coupled Receptors: Cinderella in Receptor Biology? J Membr Biol 2019; 252:483-497. [DOI: 10.1007/s00232-019-00092-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
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Sanchez J, E Huma Z, Lane JR, Liu X, Bridgford JL, Payne RJ, Canals M, Stone MJ. Evaluation and extension of the two-site, two-step model for binding and activation of the chemokine receptor CCR1. J Biol Chem 2018; 294:3464-3475. [PMID: 30567735 DOI: 10.1074/jbc.ra118.006535] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/07/2018] [Indexed: 11/06/2022] Open
Abstract
Interactions between secreted immune proteins called chemokines and their cognate G protein-coupled receptors regulate the trafficking of leukocytes in inflammatory responses. The two-site, two-step model describes these interactions. It involves initial binding of the chemokine N-loop/β3 region to the receptor's N-terminal region and subsequent insertion of the chemokine N-terminal region into the transmembrane helical bundle of the receptor concurrent with receptor activation. Here, we test aspects of this model with C-C motif chemokine receptor 1 (CCR1) and several chemokine ligands. First, we compared the chemokine-binding affinities of CCR1 with those of peptides corresponding to the CCR1 N-terminal region. Relatively low affinities of the peptides and poor correlations between CCR1 and peptide affinities indicated that other regions of the receptor may contribute to binding affinity. Second, we evaluated the contributions of the two CCR1-interacting regions of the cognate chemokine ligand CCL7 (formerly monocyte chemoattractant protein-3 (MCP-3)) using chimeras between CCL7 and the non-cognate ligand CCL2 (formerly MCP-1). The results revealed that the chemokine N-terminal region contributes significantly to binding affinity but that differences in binding affinity do not completely account for differences in receptor activation. On the basis of these observations, we propose an elaboration of the two-site, two-step model-the "three-step" model-in which initial interactions of the first site result in low-affinity, nonspecific binding; rate-limiting engagement of the second site enables high-affinity, specific binding; and subsequent conformational rearrangement gives rise to receptor activation.
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Affiliation(s)
- Julie Sanchez
- From the Infection and Immunity Program, Monash Biomedicine Discovery Institute, and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,the Drug Discovery Biology Program, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Zil E Huma
- From the Infection and Immunity Program, Monash Biomedicine Discovery Institute, and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,the Drug Discovery Biology Program, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - J Robert Lane
- the Drug Discovery Biology Program, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia.,the Centre for Membrane Proteins and Receptors, Nottingham University, Nottingham NG7 2UH, United Kingdom
| | - Xuyu Liu
- the School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia, and
| | - Jessica L Bridgford
- From the Infection and Immunity Program, Monash Biomedicine Discovery Institute, and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,the Drug Discovery Biology Program, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Richard J Payne
- the School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia, and
| | - Meritxell Canals
- the Drug Discovery Biology Program, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia, .,the Centre for Membrane Proteins and Receptors, Nottingham University, Nottingham NG7 2UH, United Kingdom
| | - Martin J Stone
- From the Infection and Immunity Program, Monash Biomedicine Discovery Institute, and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia,
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Kundu K, Singh AP, Panda S, Singh V, Gardas RL, Senapati S. Study on the Conformation of Entrapped Protein inside the Reverse Micellar Confinement Based on the Amino Acid Derived Ionic Liquid. ChemistrySelect 2018. [DOI: 10.1002/slct.201800918] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kaushik Kundu
- Department of Biotechnology; Bhupat and Jyoti Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 India
| | - Akhil Pratap Singh
- Department of Biotechnology; Bhupat and Jyoti Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 India
- Department of Chemistry; Indian Institute of Technology Madras; Chennai 600036 India
| | - Somenath Panda
- Department of Chemistry; Indian Institute of Technology Madras; Chennai 600036 India
| | - Vikram Singh
- Department of Chemistry; Indian Institute of Technology Madras; Chennai 600036 India
| | - Ramesh L. Gardas
- Department of Chemistry; Indian Institute of Technology Madras; Chennai 600036 India
| | - Sanjib Senapati
- Department of Biotechnology; Bhupat and Jyoti Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 India
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Berkamp S, Park SH, De Angelis AA, Marassi FM, Opella SJ. Structure of monomeric Interleukin-8 and its interactions with the N-terminal Binding Site-I of CXCR1 by solution NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2017; 69:111-121. [PMID: 29143165 PMCID: PMC5869024 DOI: 10.1007/s10858-017-0128-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
The structure of monomeric human chemokine IL-8 (residues 1-66) was determined in aqueous solution by NMR spectroscopy. The structure of the monomer is similar to that of each subunit in the dimeric full-length protein (residues 1-72), with the main differences being the location of the N-loop (residues 10-22) relative to the C-terminal α-helix and the position of the side chain of phenylalanine 65 near the truncated dimerization interface (residues 67-72). NMR was used to analyze the interactions of monomeric IL-8 (1-66) with ND-CXCR1 (residues 1-38), a soluble polypeptide corresponding to the N-terminal portion of the ligand binding site (Binding Site-I) of the chemokine receptor CXCR1 in aqueous solution, and with 1TM-CXCR1 (residues 1-72), a membrane-associated polypeptide that includes the same N-terminal portion of the binding site, the first trans-membrane helix, and the first intracellular loop of the receptor in nanodiscs. The presence of neither the first transmembrane helix of the receptor nor the lipid bilayer significantly affected the interactions of IL-8 with Binding Site-I of CXCR1.
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Affiliation(s)
- Sabrina Berkamp
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, San Diego, CA, 92093-0307, USA
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, San Diego, CA, 92093-0307, USA
| | - Anna A De Angelis
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, San Diego, CA, 92093-0307, USA
| | - Francesca M Marassi
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, San Diego, CA, 92037, USA
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, San Diego, CA, 92093-0307, USA.
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Kharche S, Joshi M, Sengupta D, Chattopadhyay A. Membrane-induced organization and dynamics of the N-terminal domain of chemokine receptor CXCR1: insights from atomistic simulations. Chem Phys Lipids 2017; 210:142-148. [PMID: 28939366 DOI: 10.1016/j.chemphyslip.2017.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 12/28/2022]
Abstract
The CXC chemokine receptor 1 (CXCR1) is an important member of the G protein-coupled receptor (GPCR) family in which the extracellular N-terminal domain has been implicated in ligand binding and selectivity. The structure of this domain has not yet been elucidated due to its inherent dynamics, but experimental evidence points toward membrane-dependent organization and dynamics. To gain molecular insight into the interaction of the N-terminal domain with the membrane bilayer, we performed a series of microsecond time scale atomistic simulations of the N-terminal domain of CXCR1 in the presence and absence of POPC bilayers. Our results show that the peptide displays a high propensity to adopt a β-sheet conformation in the presence of the membrane bilayer. The interaction of the peptide with the membrane bilayer was found to be transient in our simulations. Interestingly, a scrambled peptide, containing the same residues in a randomly varying sequence, did not exhibit membrane-modulated structural dynamics. These results suggest that sequence-dependent electrostatics, modulated by the membrane, could play an important role in folding of the N-terminal domain. We believe that our results reinforce the emerging paradigm that cellular membranes could be important modulators of function of G protein-coupled receptors such as CXCR1.
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Affiliation(s)
- Shalmali Kharche
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India; Academy of Scientific and Innovative Research, New Delhi, India
| | - Manali Joshi
- Bioinformatics Center, S.P. Pune University, Ganeshkhind Road, Pune 411 007, India
| | - Durba Sengupta
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India; Academy of Scientific and Innovative Research, New Delhi, India.
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