1
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Rehman S, Antonovic AK, McIntire IE, Zheng H, Cleaver L, Baczynska M, Adams CO, Portlock T, Richardson K, Shaw R, Oregioni A, Mastroianni G, Whittaker SBM, Kelly G, Lorenz CD, Fornili A, Cianciotto NP, Garnett JA. The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycans. Nat Commun 2024; 15:4912. [PMID: 38851738 PMCID: PMC11162425 DOI: 10.1038/s41467-024-49255-4] [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: 09/16/2023] [Accepted: 05/30/2024] [Indexed: 06/10/2024] Open
Abstract
Bacterial adhesion is a fundamental process which enables colonisation of niche environments and is key for infection. However, in Legionella pneumophila, the causative agent of Legionnaires' disease, these processes are not well understood. The Legionella collagen-like protein (Lcl) is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. Here we report the crystal structure of the Lcl C-terminal domain (Lcl-CTD) and present a model for intact Lcl. Our data reveal that Lcl-CTD forms an unusual trimer arrangement with a positively charged external surface and negatively charged solvent exposed internal cavity. Through molecular dynamics simulations, we show how the glycosaminoglycan chondroitin-4-sulphate associates with the Lcl-CTD surface via distinct binding modes. Our findings show that Lcl homologs are present across both the Pseudomonadota and Fibrobacterota-Chlorobiota-Bacteroidota phyla and suggest that Lcl may represent a versatile carbohydrate-binding mechanism.
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Affiliation(s)
- Saima Rehman
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Anna Katarina Antonovic
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ian E McIntire
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Huaixin Zheng
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Maria Baczynska
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
- Biological Physics & Soft Matter Research Group, Department of Physics, King's College London, London, UK
| | - Carlton O Adams
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Theo Portlock
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Katherine Richardson
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rosie Shaw
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Alain Oregioni
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Giulia Mastroianni
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Sara B-M Whittaker
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Christian D Lorenz
- Biological Physics & Soft Matter Research Group, Department of Physics, King's College London, London, UK
| | - Arianna Fornili
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, UK.
| | - Nicholas P Cianciotto
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
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2
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Martin P, Kurth EA, Budean D, Momplaisir N, Qu E, Simien JM, Orellana GE, Brautigam CA, Smrcka AV, Haglund E. Biophysical characterization of the CXC chemokine receptor 2 ligands. PLoS One 2024; 19:e0298418. [PMID: 38625857 PMCID: PMC11020491 DOI: 10.1371/journal.pone.0298418] [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: 10/09/2023] [Accepted: 01/24/2024] [Indexed: 04/18/2024] Open
Abstract
The chemokines of the immune system act as first responders by operating as chemoattractants, directing immune cells to specific locations of inflamed tissues. This promiscuous network is comprised of 50 ligands and 18 receptors where the ligands may interact with the receptors in various oligomeric states i.e., monomers, homodimers, and heterodimers. Chemokine receptors are G-protein coupled receptors (GPCRs) present in the membrane of immune cells. The migration of immune cells occurs in response to a concentration gradient of the ligands. Chemotaxis of neutrophils is directed by CXC-ligand (CXCL) activation of the membrane bound CXC chemokine receptor 2 (CXCR2). CXCR2 plays an important role in human health and is linked to disorders such as autoimmune disorders, inflammation, and cancer. Yet, despite their important role, little is known about the biophysical characteristics controlling ligand:ligand and ligand:receptor interaction essential for biological activity. In this work, we study the homodimers of three of the CXCR2 cognate ligands, CXCL1, CXCL5, and CXCL8. The ligands share high structural integrity but a low sequence identity. We show that the sequence diversity has evolved different binding affinities and stabilities for the CXC-ligands resulting in diverse agonist/antagonist behavior. Furthermore, CXC-ligands fold through a three-state mechanism, populating a folded monomeric state before associating into an active dimer.
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Affiliation(s)
- Patrick Martin
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Emily A. Kurth
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - David Budean
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Nathalie Momplaisir
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Elaine Qu
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jennifer M. Simien
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Grace E. Orellana
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Chad A. Brautigam
- Department of Biophysics and the Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Alan V. Smrcka
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Ellinor Haglund
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
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3
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León-Vega II, Vadillo E, Vargas-Robles H, Rajarathnam K, Schnoor M. Cxcl1 monomer-dimer equilibrium controls neutrophil extravasation. J Leukoc Biol 2024; 115:565-572. [PMID: 38128116 DOI: 10.1093/jleuko/qiad159] [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: 04/20/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
The chemokine Cxcl1 plays a crucial role in recruiting neutrophils in response to infection. The early events in chemokine-mediated neutrophil extravasation involve a sequence of highly orchestrated steps including rolling, adhesion, arrest, and diapedesis. Cxcl1 function is determined by its properties of reversible monomer-dimer equilibrium and binding to Cxcr2 and glycosaminoglycans. Here, we characterized how these properties orchestrate extravasation using intravital microscopy of the cremaster. Compared to WT Cxcl1, which exists as both a monomer and a dimer, the trapped dimer caused faster rolling, less adhesion, and less extravasation. Whole-mount immunofluorescence of the cremaster and arrest assays confirmed these data. Moreover, the Cxcl1 dimer showed impaired LFA-1-mediated neutrophil arrest that could be attributed to impaired Cxcr2-mediated ERK signaling. We conclude that Cxcl1 monomer-dimer equilibrium and potent Cxcr2 activity of the monomer together coordinate the early events in neutrophil recruitment.
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Affiliation(s)
- Iliana I León-Vega
- Department for Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute, Avenida IPN 2508, San Pedro Zacatenco, 07300 Mexico City, Mexico
| | - Eduardo Vadillo
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security (IMSS), Avenida Cuauhtémoc 330, Doctores, 06720 Mexico City, Mexico
| | - Hilda Vargas-Robles
- Department for Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute, Avenida IPN 2508, San Pedro Zacatenco, 07300 Mexico City, Mexico
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, 5.142 Medical Research Building, Institute for Human Infections and Immunity, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, United States
| | - Michael Schnoor
- Department for Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute, Avenida IPN 2508, San Pedro Zacatenco, 07300 Mexico City, Mexico
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4
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Rehman S, Antonovic AK, McIntire IE, Zheng H, Cleaver L, Adams CO, Portlock T, Richardson K, Shaw R, Oregioni A, Mastroianni G, Whittaker SBM, Kelly G, Fornili A, Cianciotto NP, Garnett JA. The Legionella collagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570962. [PMID: 38106198 PMCID: PMC10723406 DOI: 10.1101/2023.12.10.570962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Bacterial adhesion is a fundamental process which enables colonisation of niche environments and is key for infection. However, in Legionella pneumophila, the causative agent of Legionnaires' disease, these processes are not well understood. The Legionella collagen-like protein (Lcl) is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans (GAGs) on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. Here we report the crystal structure of the Lcl C-terminal domain (Lcl-CTD) and present a model for intact Lcl. Our data reveal that Lcl-CTD forms an unusual dynamic trimer arrangement with a positively charged external surface and a negatively charged solvent exposed internal cavity. Through Molecular Dynamics (MD) simulations, we show how the GAG chondroitin-4-sulphate associates with the Lcl-CTD surface via unique binding modes. Our findings show that Lcl homologs are present across both the Pseudomonadota and Fibrobacterota-Chlorobiota-Bacteroidota phyla and suggest that Lcl may represent a versatile carbohydrate binding mechanism.
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Affiliation(s)
- Saima Rehman
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Anna K. Antonovic
- School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ian E. McIntire
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Huaixin Zheng
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Carlton O. Adams
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Theo Portlock
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Katherine Richardson
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rosie Shaw
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Alain Oregioni
- The Medical Research Council Biomedical NMR Centre, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Giulia Mastroianni
- School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Sara B-M. Whittaker
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Arianna Fornili
- School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Nicholas P. Cianciotto
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - James A. Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
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5
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Sawant KV, Sepuru KM, Penaranda B, Lowry E, Garofalo RP, Rajarathnam K. Chemokine Cxcl1-Cxcl2 heterodimer is a potent neutrophil chemoattractant. J Leukoc Biol 2023; 114:666-671. [PMID: 37625009 PMCID: PMC10673714 DOI: 10.1093/jleuko/qiad097] [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: 04/12/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Microbial infection is characterized by release of multiple proinflammatory chemokines that direct neutrophils to the insult site. How collective function of these chemokines orchestrates neutrophil recruitment is not known. Here, we characterized the role for heterodimer and show that the Cxcl1-Cxcl2 heterodimer is a potent neutrophil chemoattractant in mice and can recruit more neutrophils than the individual chemokines. Chemokine-mediated neutrophil recruitment is determined by Cxcr2 receptor signaling, Cxcr2 endocytosis, and binding to glycosaminoglycans. We have now determined heterodimer's Cxcr2 activity using cellular assays and Cxcr2 density in blood and recruited neutrophils in heterodimer-treated mice. We have shown that the heterodimer binds glycosaminoglycans with higher affinity and more efficiently than Cxcl1 or Cxcl2. These data collectively indicate that optimal glycosaminoglycan interactions and dampened receptor activity acting in concert in a dynamic fashion promote heterodimer-mediated robust neutrophil recruitment. We propose that this could play a critical role in combating infection.
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Affiliation(s)
- Kirti V Sawant
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, United States
| | - Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, United States
| | - Brigith Penaranda
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, United States
| | - Emily Lowry
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, United States
| | - Roberto P Garofalo
- Department of Pediatrics, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, United States
- Institute for Human Infections and Immunity, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, United States
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, United States
- Institute for Human Infections and Immunity, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, United States
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, United States
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6
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Sankaranarayanan NV, Sistla S, Nagarajan B, Chittum JE, Lau JTY, Desai UR. Computational studies on glycosaminoglycan recognition of sialyl transferases. Glycobiology 2023; 33:579-590. [PMID: 37171590 PMCID: PMC10426320 DOI: 10.1093/glycob/cwad040] [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: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/11/2023] [Indexed: 05/13/2023] Open
Abstract
Despite decades of research, glycosaminoglycans (GAGs) have not been known to interact with sialyl transferases (STs). Using our in-house combinatorial virtual library screening (CVLS) technology, we studied seven human isoforms, including ST6GAL1, ST6GAL2, ST3GAL1, ST3GAL3, ST3GAL4, ST3GAL5, and ST3GAL6, and predicted that GAGs, especially heparan sulfate (HS), are likely to differentially bind to STs. Exhaustive CVLS and molecular dynamics studies suggested that the common hexasaccharide sequence of HS preferentially recognized ST6GAL1 in a site overlapping the binding site of the donor substrate CMP-Sia. Interestingly, CVLS did not ascribe any special role for the rare 3-O-sulfate modification of HS in ST6GAL1 recognition. The computational predictions were tested using spectrofluorimetric studies, which confirmed preferential recognition of HS over other GAGs. A classic chain length-dependent binding of GAGs to ST6GAL1 was observed with polymeric HS displaying a tight affinity of ~65 nM. Biophysical studies also confirmed a direct competition between CMP-Sia and an HS oligosaccharide and CS polysaccharide for binding to ST6GAL1. Overall, our novel observation that GAGs bind to ST6GAL1 with high affinity and compete with the donor substrate is likely to be important because modulation of sialylation of glycan substrates on cells has considerable physiological/pathological consequences. Our work also brings forth the possibility of developing GAG-based chemical probes of ST6GAL1.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry, Virginia Commonwealth University, Virginia 23298, Richmond, USA
- Drug Discovery and Development, Virginia Commonwealth University, Institute for Structural Biology, Virginia 23219, Richmond, USA
| | - Srinivas Sistla
- Department of Medicinal Chemistry, Virginia Commonwealth University, Virginia 23298, Richmond, USA
- Drug Discovery and Development, Virginia Commonwealth University, Institute for Structural Biology, Virginia 23219, Richmond, USA
| | - Balaji Nagarajan
- Department of Medicinal Chemistry, Virginia Commonwealth University, Virginia 23298, Richmond, USA
- Drug Discovery and Development, Virginia Commonwealth University, Institute for Structural Biology, Virginia 23219, Richmond, USA
| | - John E Chittum
- Department of Medicinal Chemistry, Virginia Commonwealth University, Virginia 23298, Richmond, USA
- Drug Discovery and Development, Virginia Commonwealth University, Institute for Structural Biology, Virginia 23219, Richmond, USA
| | - Joseph T Y Lau
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo 14263, NY, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry, Virginia Commonwealth University, Virginia 23298, Richmond, USA
- Drug Discovery and Development, Virginia Commonwealth University, Institute for Structural Biology, Virginia 23219, Richmond, USA
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7
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Marcisz M, Samsonov SA. Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans. J Chem Inf Model 2023; 63:2147-2157. [PMID: 36989082 PMCID: PMC10091405 DOI: 10.1021/acs.jcim.2c01472] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
In computational studies of glycosaminoglycans (GAGs), a group of anionic, periodic linear polysaccharides, so far there has been very little discussion about the role of solvent models in the molecular dynamics simulations of these molecules. Predominantly, the TIP3P water model is commonly used as one of the most popular explicit water models in general. However, there are numerous alternative explicit and implicit water models that are neglected in the computational research of GAGs. Since solvent-mediated interactions are particularly important for GAG dynamic and structural properties, it would be of great interest for the GAG community to establish the solvent model that is suited the best in terms of the quality of theoretically obtained GAG parameters and, at the same time, would be reasonably demanding in terms of computational resources required. In this study, heparin (HP) was simulated using five implicit and six explicit solvent models with the aim to find out how different solvent models influence HP's molecular descriptors in the molecular dynamics simulations. Here, we initiate the search for the most appropriate solvent representation for GAG systems and we hope to encourage other groups to contribute to this highly relevant subject.
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Affiliation(s)
- Mateusz Marcisz
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
- Intercollegiate Faculty of Biotechnology of UG and MUG, ul. Abrahama 58, 80-307 Gdańsk, Poland
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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8
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Hogwood J, Mulloy B, Lever R, Gray E, Page CP. Pharmacology of Heparin and Related Drugs: An Update. Pharmacol Rev 2023; 75:328-379. [PMID: 36792365 DOI: 10.1124/pharmrev.122.000684] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 02/17/2023] Open
Abstract
Heparin has been used extensively as an antithrombotic and anticoagulant for close to 100 years. This anticoagulant activity is attributed mainly to the pentasaccharide sequence, which potentiates the inhibitory action of antithrombin, a major inhibitor of the coagulation cascade. More recently it has been elucidated that heparin exhibits anti-inflammatory effect via interference of the formation of neutrophil extracellular traps and this may also contribute to heparin's antithrombotic activity. This illustrates that heparin interacts with a broad range of biomolecules, exerting both anticoagulant and nonanticoagulant actions. Since our previous review, there has been an increased interest in these nonanticoagulant effects of heparin, with the beneficial role in patients infected with SARS2-coronavirus a highly topical example. This article provides an update on our previous review with more recent developments and observations made for these novel uses of heparin and an overview of the development status of heparin-based drugs. SIGNIFICANCE STATEMENT: This state-of-the-art review covers recent developments in the use of heparin and heparin-like materials as anticoagulant, now including immunothrombosis observations, and as nonanticoagulant including a role in the treatment of SARS-coronavirus and inflammatory conditions.
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Affiliation(s)
- John Hogwood
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Barbara Mulloy
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Rebeca Lever
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Elaine Gray
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Clive P Page
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
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9
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Pomin VH, Rajarathnam K. NMR Methods for Characterization of Glycosaminoglycan-Chemokine Interactions. Methods Mol Biol 2023; 2597:143-157. [PMID: 36374420 DOI: 10.1007/978-1-0716-2835-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Humans express around 50 chemokines that play crucial roles in human pathophysiology from combating infection to immune surveillance by directing and trafficking leukocytes to the target tissue. Glycosaminoglycans (GAGs) regulate chemokine function by tuning monomer/dimer levels, chemotactic/haptotactic gradients, and how they are presented to their receptors. Knowledge of the structural features of the chemokine-GAG complexes and GAG properties that define chemokine interactions is essential not only to understand chemokine function, but also for developing drugs that disrupt chemokine-GAG crosstalk and thereby impart protection against dysregulated host defense. Nuclear magnetic resonance (NMR) spectroscopy has proven to be quite useful for providing residue-specific interactions, binding geometry and models, specificity, and affinity. Multiple NMR methods have been used including (1) chemical shift perturbation (CSP), (2) saturation transfer difference (STD), and (3) paramagnetic relaxation enhancement (PRE) techniques. In this chapter, we describe how NMR CSP, STD, and PRE can be best used for characterizing chemokine-GAG interactions.
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Affiliation(s)
- Vitor H Pomin
- Department of BioMolecular Sciences and Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, USA.
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, Department of Microbiology and Immunology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
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10
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Sun L, Chopra P, Boons G. Chemoenzymatic Synthesis of Heparan Sulfate Oligosaccharides having a Domain Structure. Angew Chem Int Ed Engl 2022; 61:e202211112. [PMID: 36148891 PMCID: PMC9828060 DOI: 10.1002/anie.202211112] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Indexed: 01/12/2023]
Abstract
Heparan sulfate (HS) has a domain structure in which regions that are modified by epimerization and sulfonation (NS domains) are interspersed by unmodified fragments (NA domains). There is data to support that domain organization of HS can regulate binding of proteins, however, such model has been difficult to probe. Here, we report a chemoenzymatic methodology that can provide HS oligosaccharides composed of two or more NS domains separated by NA domains of different length. It is based on the chemical synthesis of a HS oligosaccharide that enzymatically was extended by various GlcA-GlcNAc units and terminated in GlcNAc having an azido moiety at C-6 position. HS oligosaccharides having an azide and alkyne moiety could be assembled by copper catalyzed alkyne-azide cycloaddition to give compounds having various NS domains separated by unsulfonated regions. Competition binding studies showed that the length of an NA domain modulates the binding of the chemokines CCL5 and CXCL8.
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Affiliation(s)
- Lifeng Sun
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht University3584 CGUtrecht (TheNetherlands
| | - Pradeep Chopra
- Complex Carbohydrate Research CenterUniversity of GeorgiaAthensGA-30602USA
| | - Geert‐Jan Boons
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht University3584 CGUtrecht (TheNetherlands,Complex Carbohydrate Research CenterUniversity of GeorgiaAthensGA-30602USA,Bijvoet Center for Biomolecular ResearchUtrecht UniversityUtrecht (TheNetherlands,Chemistry DepartmentUniversity of GeorgiaAthensGA-30602USA
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11
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Deng J, Jiang R, Meng E, Wu H. CXCL5: A coachman to drive cancer progression. Front Oncol 2022; 12:944494. [PMID: 35978824 PMCID: PMC9376318 DOI: 10.3389/fonc.2022.944494] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Chemokines are a class of pro-inflammatory cytokines that can recruit and activate chemotactic cells. C‐X‐C motif chemokine ligand 5 (CXCL5) is a member of the chemokine family binding CXCR2 (C-X-C Motif Chemokine Receptor 2), a G-protein coupled receptor. Accumulated evidence has shown that dysregulated CXCL5 participates in tumor metastasis and angiogenesis in human malignant tumors. In this review, we summarized the advances in research on CXCL5, including its dysregulation in different tumors and the mechanism associated with tumor behavior (formation of the immunosuppressive microenvironment, promotion of tumor angiogenesis, and metastasis). We also summarized and discussed the perspective about the potential application of CXCL5 in tumor therapy targeting the tumor inflammatory microenvironment.
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12
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Marcisz M, Gaardløs M, Bojarski KK, Siebenmorgen T, Zacharias M, Samsonov SA. Explicit solvent repulsive scaling replica exchange molecular dynamics (RS-REMD) in molecular modeling of protein-glycosaminoglycan complexes. J Comput Chem 2022; 43:1633-1640. [PMID: 35796487 DOI: 10.1002/jcc.26965] [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: 05/12/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022]
Abstract
Glycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes of biomolecules. Therefore, there is a lack of modeling tools designed specifically for docking GAGs. One has to rely on existing docking software developed mostly for small drug molecules substantially differing from GAGs in their basic physico-chemical properties. In this study, we present an updated protocol for docking GAGs based on the Repulsive Scaling Replica Exchange Molecular Dynamics (RS-REMD) that includes explicit solvent description. The use of this water model improved docking performance both in terms of its accuracy and speed. This method represents a significant computational progress in GAG-related research.
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Affiliation(s)
- Mateusz Marcisz
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.,Intercollegiate Faculty of Biotechnology, Universuty of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | | | - Krzysztof K Bojarski
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.,Department of Physical Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Till Siebenmorgen
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Zacharias
- Physics Department, Technical University of Munich, Garching, Germany
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13
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Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states. Curr Opin Struct Biol 2022; 74:102356. [DOI: 10.1016/j.sbi.2022.102356] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/08/2022] [Accepted: 02/13/2022] [Indexed: 11/18/2022]
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14
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Nagarajan B, Desai U. Aqueous Molecular Dynamics for Understanding Glycosaminoglycan Recognition by Proteins. Methods Mol Biol 2022; 2303:49-62. [PMID: 34626369 DOI: 10.1007/978-1-0716-1398-6_5] [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: 06/13/2023]
Abstract
Glycosaminoglycans (GAGs) are biopolymers that exist in most organisms. GAGs are known to bind to hundreds of proteins and partake in multiple biological processes such as growth, morphogenesis, inflammation, infection, and others. Their intrinsic structural heterogeneity and conformational variability introduce major challenges in experimental studies. On the other hand, recent advances in force field development and computational technology have yielded phenomenal opportunity to study thousands of GAG sequences simultaneously to understand recognition of target protein(s). Here, we describe experimental setup for conventional molecular dynamics simulations of GAGs to position an experimental biologist favorably in performance, analysis and interpretation of stability, specificity, and conformational properties of GAGs, while also elucidating their interactions with amino acid residues of a protein at an atomistic level in presence of water.
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Affiliation(s)
- Balaji Nagarajan
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA.
| | - Umesh Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
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15
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Dutta AK, Sepuru KM, Rösgen J, Rajarathnam K. Characterizing Thermodynamics of Protein-Glycosaminoglycan Interactions Using Isothermal Titration Calorimetry. Methods Mol Biol 2022; 2303:307-317. [PMID: 34626389 DOI: 10.1007/978-1-0716-1398-6_25] [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: 06/13/2023]
Abstract
It has now become increasingly clear that a complete atomic description of how biomacromolecules recognize each other requires knowledge not only of the structures of the complexes but also of how kinetics and thermodynamics drive the binding process. In particular, such knowledge is lacking for protein-glycosaminoglycan (GAG) complexes. Isothermal titration calorimetry (ITC) is the only technique that can provide all of the thermodynamic parameters-enthalpy, entropy, free energy (binding constant), and stoichiometry-from a single experiment. Here we describe different factors that must be taken into consideration in carrying out ITC titrations to obtain meaningful thermodynamic data of protein-GAG interactions.
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Affiliation(s)
- Amit K Dutta
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Jörg Rösgen
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, USA.
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16
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Joseph PRB, Sepuru KM, Poluri KM, Rajarathnam K. Solution NMR Spectroscopy for Characterizing Protein-Glycosaminoglycan Interactions. Methods Mol Biol 2022; 2303:13-23. [PMID: 34626366 DOI: 10.1007/978-1-0716-1398-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Solution nuclear magnetic resonance (NMR) spectroscopy and, in particular, chemical shift perturbation (CSP) titration experiments are ideally suited for mapping and characterizing the binding interface of macromolecular complexes. 1H-15N-HSQC-based CSP studies have become the method of choice due to their simplicity, short-time requirements, and minimal working knowledge of NMR. CSP studies for characterizing protein-glycosaminoglycan (GAG) interactions can be challenging due to binding-induced aggregation/precipitation and/or poor quality data. In this chapter, we discuss how optimizing experimental conditions such as protein concentration, choice of buffer pH, ionic strength, and GAG size, as well as sensitivity of NMR instrumentation can overcome these roadblocks to obtain meaningful structural insights into protein-GAG interactions.
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Affiliation(s)
- Prem Raj B Joseph
- Departments of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, USA
| | - Krishna Mohan Sepuru
- Departments of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, USA
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Krishna Rajarathnam
- Departments of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, USA.
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17
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De Zutter A, Van Damme J, Struyf S. The Role of Post-Translational Modifications of Chemokines by CD26 in Cancer. Cancers (Basel) 2021; 13:cancers13174247. [PMID: 34503058 PMCID: PMC8428238 DOI: 10.3390/cancers13174247] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/04/2021] [Accepted: 08/10/2021] [Indexed: 02/06/2023] Open
Abstract
Chemokines are a large family of small chemotactic cytokines that fulfill a central function in cancer. Both tumor-promoting and -impeding roles have been ascribed to chemokines, which they exert in a direct or indirect manner. An important post-translational modification that regulates chemokine activity is the NH2-terminal truncation by peptidases. CD26 is a dipeptidyl peptidase (DPPIV), which typically clips a NH2-terminal dipeptide from the chemokine. With a certain degree of selectivity in terms of chemokine substrate, CD26 only recognizes chemokines with a penultimate proline or alanine. Chemokines can be protected against CD26 recognition by specific amino acid residues within the chemokine structure, by oligomerization or by binding to cellular glycosaminoglycans (GAGs). Upon truncation, the binding affinity for receptors and GAGs is altered, which influences chemokine function. The consequences of CD26-mediated clipping vary, as unchanged, enhanced, and reduced activities are reported. In tumors, CD26 most likely has the most profound effect on CXCL12 and the interferon (IFN)-inducible CXCR3 ligands, which are converted into receptor antagonists upon truncation. Depending on the tumor type, expression of CD26 is upregulated or downregulated and often results in the preferential generation of the chemokine isoform most favorable for tumor progression. Considering the tight relationship between chemokine sequence and chemokine binding specificity, molecules with the appropriate characteristics can be chemically engineered to provide innovative therapeutic strategies in a cancer setting.
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18
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Sankaranarayanan NV, Nagarajan B, Desai UR. Combinatorial Virtual Library Screening Study of Transforming Growth Factor-β2-Chondroitin Sulfate System. Int J Mol Sci 2021; 22:7542. [PMID: 34299163 PMCID: PMC8305211 DOI: 10.3390/ijms22147542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022] Open
Abstract
Transforming growth factor-beta (TGF-β), a member of the TGF-β cytokine superfamily, is known to bind to sulfated glycosaminoglycans (GAGs), but the nature of this interaction remains unclear. In a recent study, we found that preterm human milk TGF-β2 is sequestered by chondroitin sulfate (CS) in its proteoglycan form. To understand the molecular basis of the TGF-β2-CS interaction, we utilized the computational combinatorial virtual library screening (CVLS) approach in tandem with molecular dynamics (MD) simulations. All possible CS oligosaccharides were generated in a combinatorial manner to give 24 di- (CS02), 192 tetra- (CS04), and 1536 hexa- (CS06) saccharides. This library of 1752 CS oligosaccharides was first screened against TGF-β2 using the dual filter CVLS algorithm in which the GOLDScore and root-mean-square-difference (RMSD) between the best bound poses were used as surrogate markers for in silico affinity and in silico specificity. CVLS predicted that both the chain length and level of sulfation are critical for the high affinity and high specificity recognition of TGF-β2. Interestingly, CVLS led to identification of two distinct sites of GAG binding on TGF-β2. CVLS also deduced the preferred composition of the high specificity hexasaccharides, which were further assessed in all-atom explicit solvent MD simulations. The MD results confirmed that both sites of binding form stable GAG-protein complexes. More specifically, the highly selective CS chains were found to engage the TGF-β2 monomer with high affinity. Overall, this work present key principles of recognition with regard to the TGF-β2-CS system. In the process, it led to the generation of the in silico library of all possible CS oligosaccharides, which can be used for advanced studies on other protein-CS systems. Finally, the study led to the identification of unique CS sequences that are predicted to selectively recognize TGF-β2 and may out-compete common natural CS biopolymers.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; (N.V.S.); (B.N.)
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; (N.V.S.); (B.N.)
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; (N.V.S.); (B.N.)
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
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19
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Latest update on chemokine receptors as therapeutic targets. Biochem Soc Trans 2021; 49:1385-1395. [PMID: 34060588 PMCID: PMC8286821 DOI: 10.1042/bst20201114] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/19/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022]
Abstract
The chemokine system plays a fundamental role in a diverse range of physiological processes, such as homeostasis and immune responses. Dysregulation in the chemokine system has been linked to inflammatory diseases and cancer, which renders chemokine receptors to be considered as therapeutic targets. In the past two decades, around 45 drugs targeting chemokine receptors have been developed, yet only three are clinically approved. The challenging factors include the limited understanding of aberrant chemokine signalling in malignant diseases, high redundancy of the chemokine system, differences between cell types and non-specific binding of the chemokine receptor antagonists due to the broad ligand-binding pockets. In recent years, emerging studies attempt to characterise the chemokine ligand–receptor interactions and the downstream signalling protein–protein interactions, aiming to fine tuning to the promiscuous interplay of the chemokine system for the development of precision medicine. This review will outline the updates on the mechanistic insights in the chemokine system and propose some potential strategies in the future development of targeted therapy.
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20
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Sawant KV, Sepuru KM, Lowry E, Penaranda B, Frevert CW, Garofalo RP, Rajarathnam K. Neutrophil recruitment by chemokines Cxcl1/KC and Cxcl2/MIP2: Role of Cxcr2 activation and glycosaminoglycan interactions. J Leukoc Biol 2021; 109:777-791. [PMID: 32881070 PMCID: PMC8296306 DOI: 10.1002/jlb.3a0820-207r] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/03/2020] [Accepted: 08/07/2020] [Indexed: 12/11/2022] Open
Abstract
Chemokines play a crucial role in combating microbial infection by recruiting blood neutrophils to infected tissue. In mice, the chemokines Cxcl1/KC and Cxcl2/MIP2 fulfill this role. Cxcl1 and Cxcl2 exist as monomers and dimers, and exert their function by activating the Cxcr2 receptor and binding glycosaminoglycans (GAGs). Here, we characterized Cxcr2 G protein and β-arrestin activities, and GAG heparan sulfate (HS) interactions of Cxcl1 and Cxcl2 and of the trapped dimeric variants. To understand how Cxcr2 and GAG interactions impact in vivo function, we characterized their neutrophil recruitment activity to the peritoneum, Cxcr2 and CD11b levels on peritoneal and blood neutrophils, and transport profiles out of the peritoneum. Cxcl2 variants compared with Cxcl1 variants were more potent for Cxcr2 activity. Native Cxcl1 compared with native Cxcl2 and dimers compared with native proteins bound HS with higher affinity. Interestingly, recruitment activity between native Cxcl1 and Cxcl2, between dimers, and between the native protein and the dimer could be similar or very different depending on the dose or the time point. These data indicate that peritoneal neutrophil recruitment cannot be solely attributed to Cxcr2 or GAG interactions, and that the relationship between recruited neutrophils, Cxcr2 activation, GAG interactions, and chemokine levels is complex and highly context dependent. We propose that the ability of Cxcl1 and Cxcl2 to reversibly exist as monomers and dimers and differences in their Cxcr2 activity and GAG interactions coordinate neutrophil recruitment and activation, which play a critical role for successful resolution of inflammation.
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Affiliation(s)
- Kirti V. Sawant
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Emily Lowry
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Brigith Penaranda
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Charles W. Frevert
- Department of Comparative Medicine and Center for Lung Biology, University of Washington, Seattle, WA, USA
| | - Roberto P. Garofalo
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, Texas, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas, USA
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21
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Grönloh MLB, Arts JJG, van Buul JD. Neutrophil transendothelial migration hotspots - mechanisms and implications. J Cell Sci 2021; 134:134/7/jcs255653. [PMID: 33795378 DOI: 10.1242/jcs.255653] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
During inflammation, leukocytes circulating in the blood stream exit the vasculature in a process called leukocyte transendothelial migration (TEM). The current paradigm of this process comprises several well-established steps, including rolling, adhesion, crawling, diapedesis and sub-endothelial crawling. Nowadays, the role of the endothelium in transmigration is increasingly appreciated. It has been established that leukocyte exit sites on the endothelium and in the pericyte layer are in fact not random but instead may be specifically recognized by migrating leukocytes. Here, we review the concept of transmigration hotspots, specific sites in the endothelial and pericyte layer where most transmigration events take place. Chemokine cues, adhesion molecules and membrane protrusions as well as physical factors, such as endothelial junction stability, substrate stiffness, the presence of pericytes and basement membrane composition, may all contribute to local hotspot formation to facilitate leukocytes exiting the vasculature. In this Review, we discuss the biological relevance of such hotspots and put forward multiple mechanisms and factors that determine a functional TEM hotspot.
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Affiliation(s)
- Max L B Grönloh
- Molecular Cell Biology Lab, Dept. Plasma proteins, Molecular and Cellular Homeostasis, Sanquin Research and Landsteiner Laboratory, University of Amsterdam, Amsterdam 1066CX, The Netherlands.,Leeuwenhoek Centre for Advanced Microscopy (LCAM), Molecular Cytology section at Swammerdam Institute for Life Sciences (SILS) at University of Amsterdam, Amsterdam 1066CX, The Netherlands
| | - Janine J G Arts
- Molecular Cell Biology Lab, Dept. Plasma proteins, Molecular and Cellular Homeostasis, Sanquin Research and Landsteiner Laboratory, University of Amsterdam, Amsterdam 1066CX, The Netherlands.,Leeuwenhoek Centre for Advanced Microscopy (LCAM), Molecular Cytology section at Swammerdam Institute for Life Sciences (SILS) at University of Amsterdam, Amsterdam 1066CX, The Netherlands
| | - Jaap D van Buul
- Molecular Cell Biology Lab, Dept. Plasma proteins, Molecular and Cellular Homeostasis, Sanquin Research and Landsteiner Laboratory, University of Amsterdam, Amsterdam 1066CX, The Netherlands .,Leeuwenhoek Centre for Advanced Microscopy (LCAM), Molecular Cytology section at Swammerdam Institute for Life Sciences (SILS) at University of Amsterdam, Amsterdam 1066CX, The Netherlands
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22
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Bu C, Jin L. NMR Characterization of the Interactions Between Glycosaminoglycans and Proteins. Front Mol Biosci 2021; 8:646808. [PMID: 33796549 PMCID: PMC8007983 DOI: 10.3389/fmolb.2021.646808] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/24/2021] [Indexed: 12/16/2022] Open
Abstract
Glycosaminoglycans (GAGs) constitute a considerable fraction of the glycoconjugates found on cellular membranes and in the extracellular matrix of virtually all mammalian tissues. The essential role of GAG-protein interactions in the regulation of physiological processes has been recognized for decades. However, the underlying molecular basis of these interactions has only emerged since 1990s. The binding specificity of GAGs is encoded in their primary structures, but ultimately depends on how their functional groups are presented to a protein in the three-dimensional space. This review focuses on the application of NMR spectroscopy on the characterization of the GAG-protein interactions. Examples of interpretation of the complex mechanism and characterization of structural motifs involved in the GAG-protein interactions are given. Selected families of GAG-binding proteins investigated using NMR are also described.
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Affiliation(s)
- Changkai Bu
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Lan Jin
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
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23
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Structural basis of a chemokine heterodimer binding to glycosaminoglycans. Biochem J 2021; 478:1009-1021. [PMID: 33463672 DOI: 10.1042/bcj20200927] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 11/17/2022]
Abstract
Chemokines Cxcl1/KC and Cxcl2/MIP2 play a crucial role in coordinating neutrophil migration to the insult site. Chemokines' recruitment activity is regulated by monomer-dimer equilibrium and binding to glycosaminoglycans (GAGs). GAG chains exist as covalently linked to core proteins of proteoglycans (PGs) and also as free chains due to cleavage by heparanases during the inflammatory response. Compared with free GAGs, binding to GAGs in a PG is influenced by their fixed directionality due to covalent linkage and restricted mobility. GAG interactions impact chemokine monomer/dimer levels, chemotactic and haptotactic gradients, life time, and presentation for receptor binding. Here, we show that Cxcl1 and Cxcl2 also form heterodimers. Using a disulfide-trapped Cxcl1-Cxcl2 heterodimer, we characterized its binding to free heparin using nuclear magnetic resonance and isothermal titration calorimetry, and to immobilized heparin and heparan sulfate using surface plasmon resonance. These data, in conjunction with molecular docking, indicate that the binding characteristics such as geometry and stoichiometry of the heterodimer are different between free and immobilized GAGs and are also distinctly different from those of the homodimers. We propose that the intrinsic asymmetry of the heterodimer structure, along with differences in its binding to PG GAGs and free GAGs, regulate chemokine function.
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24
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Shanthamurthy CD, Leviatan Ben-Arye S, Kumar NV, Yehuda S, Amon R, Woods RJ, Padler-Karavani V, Kikkeri R. Heparan Sulfate Mimetics Differentially Affect Homologous Chemokines and Attenuate Cancer Development. J Med Chem 2021; 64:3367-3380. [PMID: 33683903 DOI: 10.1021/acs.jmedchem.0c01800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Achieving selective inhibition of chemokine activity by structurally well-defined heparan sulfate (HS) or HS mimetic molecules can provide important insights into their roles in individual physiological and pathological cellular processes. Here, we report a novel tailor-made HS mimetic, which furnishes an exclusive iduronic acid (IdoA) scaffold with different sulfation patterns and oligosaccharide chain lengths as potential ligands to target chemokines. Notably, highly sulfated-IdoA tetrasaccharide (I-45) exhibited strong binding to CCL2 chemokine thereby blocking CCL2/CCR2-mediated in vitro cancer cell invasion and metastasis. Taken together, IdoA-based HS mimetics offer an alternative HS substrate to generate selective and efficient inhibitors for chemokines and pave the way to a wide range of new therapeutic applications in cancer biology and immunology.
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Affiliation(s)
- Chethan D Shanthamurthy
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
| | - Shani Leviatan Ben-Arye
- Department of Cell Research and Immunology, the Shmunis School of Biomedicine and Cancer Research, the George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | | | - Sharon Yehuda
- Department of Cell Research and Immunology, the Shmunis School of Biomedicine and Cancer Research, the George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ron Amon
- Department of Cell Research and Immunology, the Shmunis School of Biomedicine and Cancer Research, the George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens 306062 Georgia, United States
| | - Vered Padler-Karavani
- Department of Cell Research and Immunology, the Shmunis School of Biomedicine and Cancer Research, the George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Raghavendra Kikkeri
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
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25
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Nagarajan B, Sankaranarayanan NV, Desai UR. Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools. Glycobiology 2020; 30:516-527. [PMID: 32080710 PMCID: PMC8179626 DOI: 10.1093/glycob/cwaa015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 11/15/2022] Open
Abstract
Heparin/heparan sulfates (H/HS) are ubiquitous biopolymers that interact with many proteins to induce a range of biological functions. Unfortunately, how these biopolymers recognize their preferred protein targets remain poorly understood. It is suggested that computational simulations offer attractive avenues but a number of challenges, e.g., difficulty of selecting a comprehensive force field, few simple tools to interpret data, among others, remain. This work addresses several such challenges so as to help ease the implementation and analysis of computational experiments. First, this work presents a rigorous comparison of two different recent force fields, CHARMM36 and GLYCAM06, for H/HS studies. Second, it introduces two new straightforward parameters, i.e., end-to-end distance and minimum volume enclosing ellipsoid, to understand the myriad conformational forms of oligosaccharides that evolve over time in water. Third, it presents an application to elucidate the number and nature of inter and intramolecular, nondirect bridging water molecules, which help stabilize unique forms of H/HS. The results show that nonspecialists can use either CHARMM36 or GLYCAM06 force fields because both gave comparable results, albeit with small differences. The comparative study shows that the HS hexasaccharide samples a range of conformations with nearly equivalent energies, which could be the reason for its recognition by different proteins. Finally, analysis of the nondirect water bridges across the dynamics trajectory shows their importance in stabilization of certain conformational forms, which may become important for protein recognition. Overall, the work aids nonspecialists employ computational studies for understanding the solution behavior of H/HS.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Umesh R Desai
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
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Rajarathnam K, Desai UR. Structural Insights Into How Proteoglycans Determine Chemokine-CXCR1/CXCR2 Interactions: Progress and Challenges. Front Immunol 2020; 11:660. [PMID: 32391006 PMCID: PMC7193095 DOI: 10.3389/fimmu.2020.00660] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/23/2020] [Indexed: 01/01/2023] Open
Abstract
Proteoglycans (PGs), present in diverse environments, such as the cell membrane surface, extracellular milieu, and intracellular granules, are fundamental to life. Sulfated glycosaminoglycans (GAGs) are covalently attached to the core protein of proteoglycans. PGs are complex structures, and are diverse in terms of amino acid sequence, size, shape, and in the nature and number of attached GAG chains, and this diversity is further compounded by the phenomenal diversity in GAG structures. Chemokines play vital roles in human pathophysiology, from combating infection and cancer to leukocyte trafficking, immune surveillance, and neurobiology. Chemokines mediate their function by activating receptors that belong to the GPCR class, and receptor interactions are regulated by how, when, and where chemokines bind GAGs. GAGs fine-tune chemokine function by regulating monomer/dimer levels and chemotactic/haptotactic gradients, which are also coupled to how they are presented to their receptors. Despite their small size and similar structures, chemokines show a range of GAG-binding geometries, affinities, and specificities, indicating that chemokines have evolved to exploit the repertoire of chemical and structural features of GAGs. In this review, we summarize the current status of research on how GAG interactions regulate ELR-chemokine activation of CXCR1 and CXCR2 receptors, and discuss knowledge gaps that must be overcome to establish causal relationships governing the impact of GAG interactions on chemokine function in human health and disease.
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Affiliation(s)
- Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States.,Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch at Galveston, Galveston, TX, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Umesh R Desai
- Department of Medicinal Chemistry, Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
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Crijns H, Vanheule V, Proost P. Targeting Chemokine-Glycosaminoglycan Interactions to Inhibit Inflammation. Front Immunol 2020; 11:483. [PMID: 32296423 PMCID: PMC7138053 DOI: 10.3389/fimmu.2020.00483] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Leukocyte migration into tissues depends on the activity of chemokines that form concentration gradients to guide leukocytes to a specific site. Interaction of chemokines with their specific G protein-coupled receptors (GPCRs) on leukocytes induces leukocyte adhesion to the endothelial cells, followed by extravasation of the leukocytes and subsequent directed migration along the chemotactic gradient. Interaction of chemokines with glycosaminoglycans (GAGs) is crucial for extravasation in vivo. Chemokines need to interact with GAGs on endothelial cells and in the extracellular matrix in tissues in order to be presented on the endothelium of blood vessels and to create a concentration gradient. Local chemokine retention establishes a chemokine gradient and prevents diffusion and degradation. During the last two decades, research aiming at reducing chemokine activity mainly focused on the identification of inhibitors of the interaction between chemokines and their cognate GPCRs. This approach only resulted in limited success. However, an alternative strategy, targeting chemokine-GAG interactions, may be a promising approach to inhibit chemokine activity and inflammation. On this line, proteins derived from viruses and parasites that bind chemokines or GAGs may have the potential to interfere with chemokine-GAG interactions. Alternatively, chemokine mimetics, including truncated chemokines and mutant chemokines, can compete with chemokines for binding to GAGs. Such truncated or mutated chemokines are characterized by a strong binding affinity for GAGs and abrogated binding to their chemokine receptors. Finally, Spiegelmers that mask the GAG-binding site on chemokines, thereby preventing chemokine-GAG interactions, were developed. In this review, the importance of GAGs for chemokine activity in vivo and strategies that could be employed to target chemokine-GAG interactions will be discussed in the context of inflammation.
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Affiliation(s)
- Helena Crijns
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Vincent Vanheule
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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28
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Shu M, Long S, Huang Y, Li D, Li H, Li X. High strength and antibacterial polyelectrolyte complex CS/HS hydrogel films for wound healing. SOFT MATTER 2019; 15:7686-7694. [PMID: 31498364 DOI: 10.1039/c9sm01380f] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report a simple and facile self-assembly approach to fabricate polyelectrolyte complex (PEC) hydrogel films with positively charged chitosan (CS) and negatively charged heparin sodium (HS) by combining hydrogen bonding and electrostatic interactions. The CS/HS hydrogel films exhibited excellent tensile strength and toughness, good self-recovery ability, superior water absorbency, and pH-dependent surface charge characteristics. The gelation mechanism was investigated by zeta potential measurements. The CS/HS hydrogel films exhibited high antibacterial efficacy against E. coli at selected pHs or when coordinated with various metal ions and a significant effect on accelerating wound healing. The self-assembly approach presented in this work may serve as a generic strategy for the fabrication of novel multi-functional PEC hydrogels for broad biomedical applications.
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Affiliation(s)
- Mengmeng Shu
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Hubei University of Technology, Wuhan 430068, China.
| | - Shijun Long
- Collaborative Innovation Centre of Green Light-weight Materials and Processing, Hubei University of Technology, Wuhan 430068, China
| | - Yiwan Huang
- Collaborative Innovation Centre of Green Light-weight Materials and Processing, Hubei University of Technology, Wuhan 430068, China
| | - Dapeng Li
- Bioengineering Department, College of Engineering, University of Massachusetts Dartmouth, North Dartmouth, MA 02747-2300, USA
| | - Haiyan Li
- Med-X Research Institute, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xuefeng Li
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Hubei University of Technology, Wuhan 430068, China. and Collaborative Innovation Centre of Green Light-weight Materials and Processing, Hubei University of Technology, Wuhan 430068, China
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29
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Sepuru KM, Rajarathnam K. Structural basis of chemokine interactions with heparan sulfate, chondroitin sulfate, and dermatan sulfate. J Biol Chem 2019; 294:15650-15661. [PMID: 31455633 DOI: 10.1074/jbc.ra119.009879] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/23/2019] [Indexed: 11/06/2022] Open
Abstract
Chemokines play diverse roles in human pathophysiology, ranging from trafficking leukocytes and immunosurveillance to the regulation of metabolism and neural function. Chemokine function is intimately coupled to binding tissue glycosaminoglycans (GAGs), heparan sulfate (HS), chondroitin sulfate (CS), and dermatan sulfate (DS). Currently, very little is known about how the structural features and sequences of a given chemokine, the structure and sulfation pattern of a given GAG, and structural differences among GAGs and among chemokines impact binding interactions. In this study, we used solution NMR spectroscopy to characterize the binding interactions of two related neutrophil-activating chemokines, CXCL1 and CXCL5, with HS, CS, and DS. For both chemokines, the dimer bound all three GAGs with higher affinity than did the monomer, and affinities of the chemokines for CS and DS were lower than for HS. NMR-based structural models reveal diverse binding geometries and show that the binding surfaces for each of the three GAGs were different between the two chemokines. However, a given chemokine had similar binding interactions with CS and DS that were different from HS. Considering the fact that CXCL1 and CXCL5 activate the same CXCR2 receptor, we conclude that GAG interactions play a role in determining the nature of chemokine gradients, levels of free chemokine available for receptor activation, how chemokines bind their receptors, and that differences in these interactions determine chemokine-specific function.
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Affiliation(s)
- Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555-1055.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1055
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555-1055 .,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1055.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555-1055
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30
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Graham GJ, Handel TM, Proudfoot AE. Leukocyte Adhesion: Reconceptualizing Chemokine Presentation by Glycosaminoglycans. Trends Immunol 2019; 40:472-481. [DOI: 10.1016/j.it.2019.03.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 12/30/2022]
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Nagarajan B, Sankaranarayanan NV, Desai UR. Perspective on computational simulations of glycosaminoglycans. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2019; 9:e1388. [PMID: 31080520 PMCID: PMC6504973 DOI: 10.1002/wcms.1388] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/07/2018] [Indexed: 01/06/2023]
Abstract
Glycosaminoglycans (GAGs) represent a formidable frontier for chemists, biochemists, biologists, medicinal chemists and drug delivery specialists because of massive structural complexity. GAGs are arguably the most complex, natural linear biopolymers with theoretical diversity orders of magnitude higher than proteins and nucleic acids. Yet, this diversity remains generally untapped. Computational approaches offer major routes to understand GAG structure and dynamics so as to enable novel applications of these biopolymers. In fact, computational algorithms, softwares, online tools and techniques have reached a level of sophistication that help understand atomistic details of conformational variation and protein recognition of individual GAG sequences. This review describes current approaches and challenges in computational study of GAGs. It presents a history of major findings since the earliest mention of GAGs (the 1960s), the development of parameters and force fields specific for GAGs, and the application of these tools in understanding GAG structure-function relationship. This review also presents a section on how to perform simulation of GAGs, which is directed toward researchers interested in entering this promising field with potential to impact therapy.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
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Rajarathnam K, Schnoor M, Richardson RM, Rajagopal S. How do chemokines navigate neutrophils to the target site: Dissecting the structural mechanisms and signaling pathways. Cell Signal 2019; 54:69-80. [PMID: 30465827 PMCID: PMC6664297 DOI: 10.1016/j.cellsig.2018.11.004] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 12/12/2022]
Abstract
Chemokines play crucial roles in combating microbial infection and initiating tissue repair by recruiting neutrophils in a timely and coordinated manner. In humans, no less than seven chemokines (CXCL1, CXCL2, CXCL3, CXCL5, CXCL6, CXCL7, and CXCL8) and two receptors (CXCR1 and CXCR2) mediate neutrophil functions but in a context dependent manner. Neutrophil-activating chemokines reversibly exist as monomers and dimers, and their receptor binding triggers conformational changes that are coupled to G-protein and β-arrestin signaling pathways. G-protein signaling activates a variety of effectors including Ca2+ channels and phospholipase C. β-arrestin serves as a multifunctional adaptor and is coupled to several signaling hubs including MAP kinase and tyrosine kinase pathways. Both G-protein and β-arrestin signaling pathways play important non-overlapping roles in neutrophil trafficking and activation. Functional studies have established many similarities but distinct differences for a given chemokine and between chemokines at the level of monomer vs. dimer, CXCR1 vs. CXCR2 activation, and G-protein vs. β-arrestin pathways. We propose that two forms of the ligand binding two receptors and activating two signaling pathways enables fine-tuned neutrophil function compared to a single form, a single receptor, or a single pathway. We summarize the current knowledge on the molecular mechanisms by which chemokine monomers/dimers activate CXCR1/CXCR2 and how these interactions trigger G-protein/β-arrestin-coupled signaling pathways. We also discuss current challenges and knowledge gaps, and likely advances in the near future that will lead to a better understanding of the relationship between the chemokine-CXCR1/CXCR2-G-protein/β-arrestin axis and neutrophil function.
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Affiliation(s)
- Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, Department of Microbiology and Immunology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
| | - Michael Schnoor
- Department for Molecular Biomedicine, Cinvestav-IPN, 07360 Mexico City, Mexico
| | - Ricardo M Richardson
- Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, Durham, NC 27707, USA
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Sepuru KM, Nagarajan B, Desai UR, Rajarathnam K. Structural basis, stoichiometry, and thermodynamics of binding of the chemokines KC and MIP2 to the glycosaminoglycan heparin. J Biol Chem 2018; 293:17817-17828. [PMID: 30257866 DOI: 10.1074/jbc.ra118.004866] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/10/2018] [Indexed: 01/21/2023] Open
Abstract
Keratinocyte-derived chemokine (KC or mCXCL1) and macrophage inflammatory protein 2 (MIP2 or mCXCL2) play nonredundant roles in trafficking blood neutrophils to sites of infection and injury. The functional responses of KC and MIP2 are intimately coupled to their interactions with glycosaminoglycans (GAGs). GAG interactions orchestrate chemokine concentration gradients and modulate receptor activity, which together regulate neutrophil trafficking. Here, using NMR, molecular dynamics (MD) simulations, and isothermal titration calorimetry (ITC), we characterized the molecular basis of KC and MIP2 binding to the GAG heparin. Both chemokines reversibly exist as monomers and dimers, and the NMR analysis indicates that the dimer binds heparin with higher affinity. The ITC experiments indicate a stoichiometry of two GAGs per KC or MIP2 dimer and that the enthalpic and entropic contributions vary significantly between the two chemokine-heparin complexes. NMR-based structural models of heparin-KC and heparin-MIP2 complexes reveal that different combinations of residues from the N-loop, 40s turn, β3-strand, and C-terminal helix form a binding surface within a monomer and that both conserved residues and residues unique to a particular chemokine mediate the binding interactions. MD simulations indicate significant residue-specific differences in their contribution to binding and affinity for a given chemokine and between chemokines. On the basis of our observations that KC and MIP2 bind to GAG via distinct molecular interactions, we propose that the differences in these GAG interactions lead to differences in neutrophil recruitment and play nonoverlapping roles in resolution of inflammation.
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Affiliation(s)
- Krishna Mohan Sepuru
- From the Departments of Biochemistry and Molecular Biology; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555
| | - Balaji Nagarajan
- Department of Medicinal Chemistry and Institute for Structural Biology, and Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Umesh R Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, and Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Krishna Rajarathnam
- From the Departments of Biochemistry and Molecular Biology; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555; Microbiology and Immunology.
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Glycosaminoglycan-Protein Interactions by Nuclear Magnetic Resonance (NMR) Spectroscopy. Molecules 2018; 23:molecules23092314. [PMID: 30208595 PMCID: PMC6225283 DOI: 10.3390/molecules23092314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 08/29/2018] [Accepted: 09/05/2018] [Indexed: 02/07/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most utilized and informative analytical techniques for investigating glycosaminoglycan (GAG)-protein complexes. NMR methods that are commonly applied to GAG-protein systems include chemical shift perturbation, saturation transfer difference, and transferred nuclear Overhauser effect. Although these NMR methods have revealed valuable insight into the protein-GAG complexes, elucidating high-resolution structural and dynamic information of these often transient interactions remains challenging. In addition, preparation of structurally homogeneous and isotopically enriched GAG ligands for structural investigations continues to be laborious. As a result, understanding of the structure-activity relationship of GAGs is still primitive. To overcome these deficiencies, several innovative NMR techniques have been developed lately. Here, we review some of the commonly used techniques along with more novel methods such as waterLOGSY and experiments to examine structure and dynamic of lysine and arginine side chains to identify GAG-binding sites. We will also present the latest technology that is used to produce isotopically enriched as well as paramagnetically tagged GAG ligands. Recent results that were obtained from solid-state NMR of amyloid’s interaction with GAG are also presented together with a brief discussion on computer assisted modeling of GAG-protein complexes using sparse experimental data.
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Lysines and Arginines play non-redundant roles in mediating chemokine-glycosaminoglycan interactions. Sci Rep 2018; 8:12289. [PMID: 30115951 PMCID: PMC6095893 DOI: 10.1038/s41598-018-30697-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/02/2018] [Indexed: 12/26/2022] Open
Abstract
Glycosaminoglycans (GAGs) bind a large array of proteins and mediate fundamental and diverse roles in human physiology. Ion pair interactions between protein lysines/arginines and GAG sulfates/carboxylates mediate binding. Neutrophil-activating chemokines (NAC) are GAG-binding proteins, and their sequences reveal high selectivity for lysines over arginines indicating they are functionally not equivalent. NAC binding to GAGs impacts gradient formation, receptor functions, and endothelial activation, which together regulate different components of neutrophil migration. We characterized the consequence of mutating lysine to arginine in NAC CXCL8, a well-characterized GAG-binding protein. We chose three lysines — two highly conserved lysines (K20 and K64) and a CXCL8-specific lysine (K67). Interestingly, the double K64R/K20R and K64R/K67R mutants are highly impaired in recruiting neutrophils in a mouse model. Further, both the mutants bind GAG heparin with higher affinity but show similar receptor activity. NMR and MD studies indicate that the structures are essentially identical to the WT, but the mutations alter the network of intramolecular ion pair interactions. These observations collectively indicate that the reduced in vivo recruitment is due to altered GAG interactions, higher GAG binding affinity can be detrimental, and specificity of lysines fine-tunes in vivo GAG interactions and function.
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Joseph PRB, Sawant KV, Rajarathnam K. Heparin-bound chemokine CXCL8 monomer and dimer are impaired for CXCR1 and CXCR2 activation: implications for gradients and neutrophil trafficking. Open Biol 2018; 7:rsob.170168. [PMID: 29118271 PMCID: PMC5717344 DOI: 10.1098/rsob.170168] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/04/2017] [Indexed: 12/20/2022] Open
Abstract
Chemokine CXCL8 plays a pivotal role in host immune response by recruiting neutrophils to the infection site. CXCL8 exists as monomers and dimers, and mediates recruitment by interacting with glycosaminoglycans (GAGs) and activating CXCR1 and CXCR2 receptors. How CXCL8 monomer and dimer interactions with both receptors and GAGs mediate trafficking is poorly understood. In particular, both haptotactic (mediated by GAG-bound chemokine) and chemotactic (mediated by soluble chemokine) gradients have been implicated, and whether it is the free or the GAG-bound CXCL8 monomer and/or dimer that activates the receptor remains unknown. Using solution NMR spectroscopy, we have now characterized the binding of heparin-bound CXCL8 monomer and dimer to CXCR1 and CXCR2 receptor N-domains. Our data provide compelling evidence that heparin-bound monomers and dimers are unable to bind either of the receptors. Cellular assays also indicate that heparin-bound CXCL8 is impaired for receptor activity. Considering dimer binds GAGs with higher affinity, dimers will exist predominantly in the GAG-bound form and the monomer in the free form. We conclude that GAG interactions determine the levels of free CXCL8, and that it is the free, and not GAG-bound, CXCL8 that activates the receptors and mediates recruitment of blood neutrophils to the infected tissue.
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Affiliation(s)
- Prem Raj B Joseph
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Kirti V Sawant
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA .,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
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Sankaranarayanan NV, Nagarajan B, Desai UR. So you think computational approaches to understanding glycosaminoglycan-protein interactions are too dry and too rigid? Think again! Curr Opin Struct Biol 2018; 50:91-100. [PMID: 29328962 PMCID: PMC6037615 DOI: 10.1016/j.sbi.2017.12.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/17/2017] [Accepted: 12/15/2017] [Indexed: 12/20/2022]
Abstract
Glycosaminoglycans (GAGs) play key roles in virtually all biologic responses through their interaction with proteins. A major challenge in understanding these roles is their massive structural complexity. Computational approaches are extremely useful in navigating this bottleneck and, in some cases, the only avenue to gain comprehensive insight. We discuss the state-of-the-art on computational approaches and present a flowchart to help answer most basic, and some advanced, questions on GAG-protein interactions. For example, firstly, does my protein bind to GAGs?; secondly, where does the GAG bind?; thirdly, does my protein preferentially recognize a particular GAG type?; fourthly, what is the most optimal GAG chain length?; fifthly, what is the structure of the most favored GAG sequence?; and finally, is my GAG-protein system 'specific', 'non-specific', or a combination of both? Recent advances show the field is now poised to enable a non-computational researcher perform advanced experiments through the availability of various tools and online servers.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Balaji Nagarajan
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA.
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38
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Rajarathnam K, Sepuru KM, Joseph PRB, Sawant KV, Brown AJ. Glycosaminoglycan Interactions Fine-Tune Chemokine-Mediated Neutrophil Trafficking: Structural Insights and Molecular Mechanisms. J Histochem Cytochem 2018; 66:229-239. [PMID: 29290145 PMCID: PMC5958375 DOI: 10.1369/0022155417739864] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/10/2017] [Indexed: 01/01/2023] Open
Abstract
Circulating neutrophils, rapidly recruited in response to microbial infection, form the first line in host defense. Humans express ~50 chemokines, of which a subset of seven chemokines, characterized by the conserved "Glu-Leu-Arg" motif, mediate neutrophil recruitment. Neutrophil-activating chemokines (NACs) share similar structures, exist as monomers and dimers, activate the CXCR2 receptor on neutrophils, and interact with tissue glycosaminoglycans (GAGs). Considering cellular assays have shown that NACs have similar CXCR2 activity, the question has been and remains, why do humans express so many NACs? In this review, we make the case that NACs are not redundant and that distinct GAG interactions determine chemokine-specific in vivo functions. Structural studies have shown that the GAG-binding interactions of NACs are distinctly different, and that conserved and specific residues in the context of structure determine geometries that could not have been predicted from sequences alone. Animal studies indicate recruitment profiles of monomers and dimers are distinctly different, monomer-dimer equilibrium regulates recruitment, and that recruitment profiles vary between chemokines and between tissues, providing evidence that GAG interactions orchestrate neutrophil recruitment. We propose in vivo GAG interactions impact several chemokine properties including gradients and lifetime, and that these interactions fine-tune and define the functional response of each chemokine that can vary between different cell and tissue types for successful resolution of inflammation.
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Affiliation(s)
- Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas
| | - Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Prem Raj B Joseph
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Kirti V Sawant
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Aaron J Brown
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
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Procházka V, Jurčíková J, Vítková K, Pavliska L, Porubová L, Lassák O, Buszman P, Fernandez CA, Jalůvka F, Špačková I, Lochman I, Procházka M, Janíková M, Tauber Z, Franková J, Lachnit M, Hiles MC, Johnstone BH. The Role of miR-126 in Critical Limb Ischemia Treatment Using Adipose-Derived Stem Cell Therapeutic Factor Concentrate and Extracellular Matrix Microparticles. Med Sci Monit 2018; 24:511-522. [PMID: 29371587 PMCID: PMC5795917 DOI: 10.12659/msm.905442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Paracrine factors secreted by adipose-derived stem cells can be captured, fractionated, and concentrated to produce therapeutic factor concentrate (TFC). The present study examined whether TFC effects could be enhanced by combining TFC with a biological matrix to provide sustained release of factors in the target region. MATERIAL AND METHODS Unilateral hind limb ischemia was induced in rabbits. Ischemic limbs were injected with either placebo control, TFC, micronized small intestinal submucosa tissue (SIS), or TFC absorbed to SIS. Blood flow in both limbs was assessed with laser Doppler perfusion imaging. Tissues harvested at Day 48 were assessed immunohistochemically for vessel density; in situ hybridization and quantitative real-time PCR were employed to determine miR-126 expression. RESULTS LDP ratios were significantly elevated, compared to placebo control, on day 28 in all treatment groups (p=0.0816, p=0.0543, p=0.0639, for groups 2-4, respectively) and on day 36 in the TFC group (p=0.0866). This effect correlated with capillary density in the SIS and TFC+SIS groups (p=0.0093 and p=0.0054, respectively, compared to placebo). A correlation was observed between miR-126 levels and LDP levels at 48 days in SIS and TFC+SIS groups. CONCLUSIONS A single bolus administration of TFC and SIS had early, transient effects on reperfusion and promotion of ischemia repair. The effects were not additive. We also discovered that TFC modulated miR-126 levels that were expressed in cell types other than endothelial cells. These data suggested that TFC, alone or in combination with SIS, may be a potent therapy for patients with CLI that are at risk of amputation.
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Affiliation(s)
- Václav Procházka
- Radiodiagnostic Institute, University Hospital Ostrava, Ostrava, Czech Republic
| | - Jana Jurčíková
- Department of Deputy Director of Science and Research, University Hospital Ostrava, Ostrava, Czech Republic
| | - Kateřina Vítková
- Department of Deputy Director of Science and Research, University Hospital Ostrava, Ostrava, Czech Republic
| | - Lubomír Pavliska
- Department of Deputy Director of Science and Research, University Hospital Ostrava, Ostrava, Czech Republic
| | | | | | | | | | - František Jalůvka
- Department of Surgery, University Hospital Ostrava, Ostrava, Czech Republic
| | | | | | - Martin Procházka
- Department of Medical Genetics, University Hospital Olomouc and Palacky University Olomouc, Olomouc, Czech Republic
| | - Mária Janíková
- Department of Medical Genetics, University Hospital Olomouc and Palacky University Olomouc, Olomouc, Czech Republic.,Department of Clinical and Molecular Pathology, Palacky University Olomouc and University Hospital Olomouc, Olomouc, Czech Republic
| | - Zdeněk Tauber
- Department of Histology and Embryology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Jana Franková
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Martin Lachnit
- Department of Deputy Director of Science and Research, University Hospital Ostrava, Ostrava, Czech Republic
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Sepuru KM, Iwahara J, Rajarathnam K. Direct detection of lysine side chain NH 3+ in protein-heparin complexes using NMR spectroscopy. Analyst 2018; 143:635-638. [PMID: 29292440 DOI: 10.1039/c7an01406f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two NMR observables, the NζH3+ peak in the HISQC spectrum and Nζ chemical shift difference between the free and heparin-bound forms, can identify binding-interface lysines in protein-heparin complexes. Unlike backbone chemical shifts, these direct probes are stringent and are less prone to either false positives or false negatives.
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Affiliation(s)
- Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA. and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA. and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA. and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
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Samsonov SA. Computational Analysis of Solvent Inclusion in Docking Studies of Protein-Glycosaminoglycan Systems. Methods Mol Biol 2018; 1762:445-454. [PMID: 29594785 DOI: 10.1007/978-1-4939-7756-7_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Glycosaminoglycans (GAGs) are a class of anionic linear periodic polysaccharides, which play a key role in many cell signaling related processes via interactions with their protein targets. In silico analysis and, in particular, application of molecular docking approaches to these systems still experience many challenges including the need of proper treatment of solvent, which is crucial for protein-GAG interactions. Here, we describe two methods which we developed, to include solvent in the docking studies of protein-GAG systems: the first one allows to de novo predict favorable positions of water molecules as a part of a rigid receptor to be used for further molecular docking; the second one utilizes targeted molecular dynamics in explicit solvent for molecular docking.
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Affiliation(s)
- Sergey A Samsonov
- Laboratory of Molecular Modeling, Department of Theoretical Chemistry, Faculty of Chemistry , University of Gdańsk, Gdansk, Poland.
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42
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Brown AJ, Sepuru KM, Sawant KV, Rajarathnam K. Platelet-Derived Chemokine CXCL7 Dimer Preferentially Exists in the Glycosaminoglycan-Bound Form: Implications for Neutrophil-Platelet Crosstalk. Front Immunol 2017; 8:1248. [PMID: 29038657 PMCID: PMC5630695 DOI: 10.3389/fimmu.2017.01248] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 09/20/2017] [Indexed: 11/25/2022] Open
Abstract
Platelet-derived chemokine CXCL7 (also known as NAP-2) plays a crucial role in orchestrating neutrophil recruitment in response to vascular injury. CXCL7 exerts its function by activating the CXC chemokine receptor 2 (CXCR2) receptor and binding sulfated glycosaminoglycans (GAGs) that regulate receptor activity. CXCL7 exists as monomers, dimers, and tetramers, and previous studies have shown that the monomer dominates at lower and the tetramer at higher concentrations. These observations then raise the question: what, if any, is the role of the dimer? In this study, we make a compelling observation that the dimer is actually the favored form in the GAG-bound state. Further, we successfully characterized the structural basis of dimer binding to GAG heparin using solution nuclear magnetic resonance (NMR) spectroscopy. The chemical shift assignments were obtained by exploiting heparin binding-induced NMR spectral changes in the WT monomer and dimer and also using a disulfide-linked obligate dimer. We observe that the receptor interactions of the dimer are similar to the monomer and that heparin-bound dimer is occluded from receptor interactions. Cellular assays also show that the heparin-bound CXCL7 is impaired for CXCR2 activity. We conclude that the dimer–GAG interactions play an important role in neutrophil–platelet crosstalk, and that these interactions regulate gradient formation and the availability of the free monomer for CXCR2 activation and intrathrombus neutrophil migration to the injury site.
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Affiliation(s)
- Aaron J Brown
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - Kirti V Sawant
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
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43
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Moussouras NA, Getschman AE, Lackner ER, Veldkamp CT, Dwinell MB, Volkman BF. Differences in Sulfotyrosine Binding amongst CXCR1 and CXCR2 Chemokine Ligands. Int J Mol Sci 2017; 18:ijms18091894. [PMID: 28869519 PMCID: PMC5618543 DOI: 10.3390/ijms18091894] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 08/29/2017] [Accepted: 09/01/2017] [Indexed: 12/29/2022] Open
Abstract
Tyrosine sulfation, a post-translational modification found on many chemokine receptors, typically increases receptor affinity for the chemokine ligand. A previous bioinformatics analysis suggested that a sulfotyrosine (sY)-binding site on the surface of the chemokine CXCL12 may be conserved throughout the chemokine family. However, the extent to which receptor tyrosine sulfation contributes to chemokine binding has been examined in only a few instances. Computational solvent mapping correctly identified the conserved sulfotyrosine-binding sites on CXCL12 and CCL21 detected by nuclear magnetic resonance (NMR) spectroscopy, demonstrating its utility for hot spot analysis in the chemokine family. In this study, we analyzed five chemokines that bind to CXCR2, a subset of which also bind to CXCR1, to identify hot spots that could participate in receptor binding. A cleft containing the predicted sulfotyrosine-binding pocket was identified as a principal hot spot for ligand binding on the structures of CXCL1, CXCL2, CXCL7, and CXCL8, but not CXCL5. Sulfotyrosine titrations monitored via NMR spectroscopy showed specific binding to CXCL8, but not to CXCL5, which is consistent with the predictions from the computational solvent mapping. The lack of CXCL5–sulfotyrosine interaction and the presence of CXCL8–sulfotyrosine binding suggests a role for receptor post-translational modifications regulating ligand selectivity.
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Affiliation(s)
- Natasha A Moussouras
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Anthony E Getschman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Emily R Lackner
- Department of Chemistry, University of Wisconsin-Whitewater, Whitewater, WI 53190, USA.
| | | | - Michael B Dwinell
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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44
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Glycosaminoglycan Interactions with Chemokines Add Complexity to a Complex System. Pharmaceuticals (Basel) 2017; 10:ph10030070. [PMID: 28792472 PMCID: PMC5620614 DOI: 10.3390/ph10030070] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 12/12/2022] Open
Abstract
Chemokines have two types of interactions that function cooperatively to control cell migration. Chemokine receptors on migrating cells integrate signals initiated upon chemokine binding to promote cell movement. Interactions with glycosaminoglycans (GAGs) localize chemokines on and near cell surfaces and the extracellular matrix to provide direction to the cell movement. The matrix of interacting chemokine–receptor partners has been known for some time, precise signaling and trafficking properties of many chemokine–receptor pairs have been characterized, and recent structural information has revealed atomic level detail on chemokine–receptor recognition and activation. However, precise knowledge of the interactions of chemokines with GAGs has lagged far behind such that a single paradigm of GAG presentation on surfaces is generally applied to all chemokines. This review summarizes accumulating evidence which suggests that there is a great deal of diversity and specificity in these interactions, that GAG interactions help fine-tune the function of chemokines, and that GAGs have other roles in chemokine biology beyond localization and surface presentation. This suggests that chemokine–GAG interactions add complexity to the already complex functions of the receptors and ligands.
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Thompson S, Martínez-Burgo B, Sepuru KM, Rajarathnam K, Kirby JA, Sheerin NS, Ali S. Regulation of Chemokine Function: The Roles of GAG-Binding and Post-Translational Nitration. Int J Mol Sci 2017; 18:ijms18081692. [PMID: 28771176 PMCID: PMC5578082 DOI: 10.3390/ijms18081692] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/28/2017] [Accepted: 07/30/2017] [Indexed: 12/12/2022] Open
Abstract
The primary function of chemokines is to direct the migration of leukocytes to the site of injury during inflammation. The effects of chemokines are modulated by several means, including binding to G-protein coupled receptors (GPCRs), binding to glycosaminoglycans (GAGs), and through post-translational modifications (PTMs). GAGs, present on cell surfaces, bind chemokines released in response to injury. Chemokines bind leukocytes via their GPCRs, which directs migration and contributes to local inflammation. Studies have shown that GAGs or GAG-binding peptides can be used to interfere with chemokine binding and reduce leukocyte recruitment. Post-translational modifications of chemokines, such as nitration, which occurs due to the production of reactive species during oxidative stress, can also alter their biological activity. This review describes the regulation of chemokine function by GAG-binding ability and by post-translational nitration. These are both aspects of chemokine biology that could be targeted if the therapeutic potential of chemokines, like CXCL8, to modulate inflammation is to be realised.
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Affiliation(s)
- Sarah Thompson
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
| | - Beatriz Martínez-Burgo
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
| | - Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.
| | - John A Kirby
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
| | - Neil S Sheerin
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
| | - Simi Ali
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
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Protein Array-Based Detection of Proteins in Kidney Tissues from Patients with Membranous Nephropathy. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7843584. [PMID: 28337458 PMCID: PMC5350302 DOI: 10.1155/2017/7843584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 01/25/2017] [Accepted: 01/29/2017] [Indexed: 11/26/2022]
Abstract
Membranous nephropathy (MN) is an autoimmune inflammatory disease in which proteins related with plenty of biological processes play an important role. However, the role of these proteins in the pathogenesis of MN is still unclear. This study aimed to screen differential proteins in kidney tissue samples from MN patients by using protein arrays and determine the pathways involved in the pathogenesis of MN. This study first tested a quantitative protein array (QAH-INF-3) and two semiquantitative protein arrays (L-493 and L-507) with normal renal tissue and identified L-493 as the most appropriate assay to compare protein levels between MN tissues and normal control tissues. The L-493 array identified 66 differentially expressed proteins (DEPs) that may be associated with MN. The gene oncology (GO) and protein-protein interaction (PPI) analyses revealed several processes potentially involved in MN, including extracellular matrix disassembly and organization, cell adhesion, cell-cell signaling, cellular protein metabolic process, and immune response (P < 0.05). We suggest that these different pathways work together via protein signaling and result in the pathogenesis and progression of MN.
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47
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Brown AJ, Sepuru KM, Rajarathnam K. Structural Basis of Native CXCL7 Monomer Binding to CXCR2 Receptor N-Domain and Glycosaminoglycan Heparin. Int J Mol Sci 2017; 18:ijms18030508. [PMID: 28245630 PMCID: PMC5372524 DOI: 10.3390/ijms18030508] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/14/2017] [Accepted: 02/21/2017] [Indexed: 11/23/2022] Open
Abstract
CXCL7, a chemokine highly expressed in platelets, orchestrates neutrophil recruitment during thrombosis and related pathophysiological processes by interacting with CXCR2 receptor and sulfated glycosaminoglycans (GAG). CXCL7 exists as monomers and dimers, and dimerization (~50 μM) and CXCR2 binding (~10 nM) constants indicate that CXCL7 is a potent agonist as a monomer. Currently, nothing is known regarding the structural basis by which receptor and GAG interactions mediate CXCL7 function. Using solution nuclear magnetic resonance (NMR) spectroscopy, we characterized the binding of CXCL7 monomer to the CXCR2 N-terminal domain (CXCR2Nd) that constitutes a critical docking site and to GAG heparin. We found that CXCR2Nd binds a hydrophobic groove and that ionic interactions also play a role in mediating binding. Heparin binds a set of contiguous basic residues indicating a prominent role for ionic interactions. Modeling studies reveal that the binding interface is dynamic and that GAG adopts different binding geometries. Most importantly, several residues involved in GAG binding are also involved in receptor interactions, suggesting that GAG-bound monomer cannot activate the receptor. Further, this is the first study that describes the structural basis of receptor and GAG interactions of a native monomer of the neutrophil-activating chemokine family.
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Affiliation(s)
- Aaron J Brown
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555, USA.
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