1
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Daniyan MO. pyGROMODS: a Python package for the generation of input files for molecular dynamic simulation with GROMACS. J Biomol Struct Dyn 2024; 42:7207-7220. [PMID: 37489036 DOI: 10.1080/07391102.2023.2239929] [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] [Received: 05/17/2023] [Accepted: 07/15/2023] [Indexed: 07/26/2023]
Abstract
The pyGROMODS, an easy-to-use cross-platform python-based package, with a graphical user interface, for the generation of molecular dynamic (MD) input files and running MD simulation (MDS) of proteins, peptides, and protein-ligand complex using GROMACS, is here presented. Four routes, with underlining Python scripts, are implemented in pyGROMODS for the generation of MD input files. They are 'RLmulti' for processing multi-ligand protein complex, 'RLmany' for processing multiple ligands against a single protein target, 'RLsingle' for processing multiple pairs of proteins and ligands, and 'PPmore' for processing peptides or proteins without ligands or non-standard residues. In addition, using the package, the generated input files or appropriate input files from other sources can be uploaded to run MDS with GROMACS. The pyGROMODS is implemented with a unique ability to search the host machine systems for the installation of the required software, update and/or install required Python packages, allow the user to pre-define working directory, and generate unique workflow organization with well-defined folders and files in a well-organized manner. The pyGROMODS, which is released under the MIT License, is freely available for download via the GitHub (https://github.com/Dankem/pyGROMODS) and Zenodo (https://doi.org/10.5281/zenodo.7912747) repositories. The precompiled executables can also be downloaded from Zenodo (https://doi.org/10.5281/zenodo.8087090), and a video tutorial can be downloaded from https://youtu.be/I4OKc6uVx1M.Communicated by Ramaswamy H. Sarma.
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2
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Nguyen H, Podolnikova NP, Ugarova TP, Wang X. α MI-domain of integrin Mac-1 binds the cytokine pleiotrophin using multiple mechanisms. Structure 2024; 32:1184-1196.e4. [PMID: 38729161 PMCID: PMC11316656 DOI: 10.1016/j.str.2024.04.013] [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: 01/24/2024] [Revised: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024]
Abstract
The integrin Mac-1 (αMβ2, CD11b/CD18, CR3) is an adhesion receptor expressed on macrophages and neutrophils. Mac-1 is also a promiscuous integrin that binds a diverse set of ligands through its αMI-domain. However, the binding mechanism of most ligands remains unclear. We have characterized the interaction of αMI-domain with the cytokine pleiotrophin (PTN), a protein known to bind αMI-domain and induce Mac-1-mediated cell adhesion and migration. Our data show that PTN's N-terminal domain binds a unique site near the N- and C-termini of the αMI-domain using a metal-independent mechanism. However, a stronger interaction is achieved when an acidic amino acid in a zwitterionic motif in PTN's C-terminal domain chelates the divalent cation in the metal ion-dependent adhesion site of active αMI-domain. These results indicate that αMI-domain can bind ligands using multiple mechanisms and that the active αMI-domain has a preference for motifs containing both positively and negatively charged amino acids.
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Affiliation(s)
- Hoa Nguyen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | | | - Tatiana P Ugarova
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Xu Wang
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA.
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3
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Thomas MA, Naik P, Wang H, Giles JT, Girgis AA, Kim SY, Johnson TP, Curran AM, Crawford JD, Jahanbani S, Bingham CO, Robinson WH, Na CH, Darrah E. The monocyte cell surface is a unique site of autoantigen generation in rheumatoid arthritis. Proc Natl Acad Sci U S A 2024; 121:e2304199121. [PMID: 38630712 PMCID: PMC11047081 DOI: 10.1073/pnas.2304199121] [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: 03/15/2023] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
Although anti-citrullinated protein autoantibodies (ACPAs) are a hallmark serological feature of rheumatoid arthritis (RA), the mechanisms and cellular sources behind the generation of the RA citrullinome remain incompletely defined. Peptidylarginine deiminase IV (PAD4), one of the key enzymatic drivers of citrullination in the RA joint, is expressed by granulocytes and monocytes; however, the subcellular localization and contribution of monocyte-derived PAD4 to the generation of citrullinated autoantigens remain underexplored. In this study, we demonstrate that PAD4 displays a widespread cellular distribution in monocytes, including expression on the cell surface. Surface PAD4 was enzymatically active and capable of citrullinating extracellular fibrinogen and endogenous surface proteins in a calcium dose-dependent manner. Fibrinogen citrullinated by monocyte-surface PAD4 could be specifically recognized over native fibrinogen by a panel of eight human monoclonal ACPAs. Several unique PAD4 substrates were identified on the monocyte surface via mass spectrometry, with citrullination of the CD11b and CD18 components of the Mac-1 integrin complex being the most abundant. Citrullinated Mac-1 was found to be a target of ACPAs in 25% of RA patients, and Mac-1 ACPAs were significantly associated with HLA-DRB1 shared epitope alleles, higher C-reactive protein and IL-6 levels, and more erosive joint damage. Our findings implicate the monocyte cell surface as a unique and consequential site of extracellular and cell surface autoantigen generation in RA.
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Affiliation(s)
- Mekha A. Thomas
- Division of Rheumatology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD21224
| | - Pooja Naik
- Division of Rheumatology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD21224
| | - Hong Wang
- Division of Rheumatology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD21224
| | - Jon T. Giles
- Division of Rheumatology, Columbia University, College of Physicians and Surgeons, New York, NY10032
| | - Alexander A. Girgis
- Division of Rheumatology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD21224
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD21224
| | - Seok-Young Kim
- Department of Neurology, Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD21205
| | - Tory P. Johnson
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD20892
| | - Ashley M. Curran
- Division of Rheumatology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD21224
| | - Jonathan D. Crawford
- Division of Rheumatology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD21224
| | - Shaghayegh Jahanbani
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA94304
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA94550
| | - Clifton O. Bingham
- Division of Rheumatology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD21224
| | - William H. Robinson
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA94304
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA94550
| | - Chan Hyun Na
- Department of Neurology, Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD21205
| | - Erika Darrah
- Division of Rheumatology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD21224
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4
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Nguyen H, Podolnikova NP, Ugarova TP, Wang X. α MI-domain of Integrin Mac-1 Binds the Cytokine Pleiotrophin Using Multiple Mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578455. [PMID: 38352421 PMCID: PMC10862807 DOI: 10.1101/2024.02.01.578455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
The integrin Mac-1 (αMβ2, CD11b/CD18, CR3) is an important adhesion receptor expressed on macrophages and neutrophils. Mac-1 is also the most promiscuous member of the integrin family that binds a diverse set of ligands through its αMI-domain. However, the binding mechanism of most ligands is not clear. We have determined the interaction of αMI-domain with the cytokine pleiotrophin (PTN), a cationic protein known to bind αMI-domain and induce Mac-1-mediated cell adhesion and migration. Our data show that PTN's N-terminal domain binds a unique site near the N- and C-termini of the αMI-domain using a metal-independent mechanism. However, stronger interaction is achieved when an acidic amino acid in a zwitterionic motif in PTN's C-terminal domain chelates the divalent cation in the metal ion-dependent adhesion site of the active αMI-domain. These results indicate that αMI-domain can bind ligands using multiple mechanisms, and suggest that active αMI-domain prefers acidic amino acids in zwitterionic motifs.
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Affiliation(s)
- Hoa Nguyen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | | | | | - Xu Wang
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
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5
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Platelet-Neutrophil Crosstalk in Thrombosis. Int J Mol Sci 2023; 24:ijms24021266. [PMID: 36674781 PMCID: PMC9861587 DOI: 10.3390/ijms24021266] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Platelets are essential for the formation of a haemostatic plug to prevent bleeding, while neutrophils are the guardians of our immune defences against invading pathogens. The interplay between platelets and innate immunity, and subsequent triggering of the activation of coagulation is part of the host system to prevent systemic spread of pathogen in the blood stream. Aberrant immunothrombosis and excessive inflammation can however, contribute to the thrombotic burden observed in many cardiovascular diseases. In this review, we highlight how platelets and neutrophils interact with each other and how their crosstalk is central to both arterial and venous thrombosis and in COVID-19. While targeting platelets and coagulation enables efficient antithrombotic treatments, they are often accompanied with a bleeding risk. We also discuss how novel approaches to reduce platelet-mediated recruitment of neutrophils could represent promising therapies to treat thrombosis without affecting haemostasis.
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YANG QQ, FANG MS, TU J, MA QX, SHEN LY, XU YY, CHEN J, CHEN ML. Guanxinning tablet inhibits the interaction between leukocyte integrin Mac-1 and platelet GPIbα for antithrombosis without increased bleeding risk. Chin J Nat Med 2022; 20:589-600. [DOI: 10.1016/s1875-5364(22)60183-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Indexed: 11/03/2022]
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7
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Villanueva V, Li X, Jimenez V, Faridi HM, Gupta V. CD11b agonists offer a novel approach for treating lupus nephritis. Transl Res 2022; 245:41-54. [PMID: 35288363 PMCID: PMC9167730 DOI: 10.1016/j.trsl.2022.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/20/2022]
Abstract
Lupus nephritis (LN) develops in more than a third of all systemic lupus erythematosus (SLE) patients and is the strongest predictor of morbidity and mortality. Increased circulating levels of type I interferon (IFN I) and anti-double stranded DNA (anti-dsDNA) and anti-RNA binding protein (anti-RNP) antibodies lead to increased glomerular injury via leukocyte activation and glomerular infiltration. Uncontrolled Toll-like receptor (TLR) signaling in leukocytes results in increased production of IFN I and anti-dsDNA antibodies. ITGAM gene codes for integrin CD11b, the α-chain of integrin heterodimer CD11b/CD18, that is highly expressed in leukocytes and modulates TLR-dependent pro-inflammatory signaling. Three nonsynonymous SNPs in the ITGAM gene strongly correlate with increased risk for SLE and LN and with IFN I levels. Here we review the literature on the role of CD11b on leukocytes in LN. We also incorporate conclusions from several recent studies that show that these ITGAM SNPs result in a CD11b protein that is less able to suppress TLR-dependent pro-inflammatory pathways in leukocytes, that activation of CD11b via novel small molecule agonists suppresses TLR-dependent pathways, including reductions in circulating levels of IFN I and anti-dsDNA antibodies, and that CD11b activation reduces LN in model systems. Recent data strongly suggest that integrin CD11b is an exciting new therapeutic target in SLE and LN and that allosteric activation of CD11b is a novel therapeutic paradigm for effectively treating such autoimmune diseases.
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Affiliation(s)
- Veronica Villanueva
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois
| | - Xiaobo Li
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois
| | - Viviana Jimenez
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois
| | - Hafeez M Faridi
- Department of Pharmaceutical Sciences, College of Pharmacy, Chicago State University, Chicago, Illinois
| | - Vineet Gupta
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois.
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8
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Jensen RK, Pedersen H, Lorentzen J, Laursen NS, Vorup-Jensen T, Andersen GR. Structural insights into the function-modulating effects of nanobody binding to the integrin receptor α Mβ 2. J Biol Chem 2022; 298:102168. [PMID: 35738398 PMCID: PMC9287160 DOI: 10.1016/j.jbc.2022.102168] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 01/12/2023] Open
Abstract
The integrin receptor αMβ2 mediates phagocytosis of complement-opsonized objects, adhesion to the extracellular matrix, and transendothelial migration of leukocytes. However, the mechanistic aspects of αMβ2 signaling upon ligand binding are unclear. Here, we present the first atomic structure of the human αMβ2 headpiece fragment in complex with the nanobody (Nb) hCD11bNb1 at a resolution of 3.2 Å. We show that the receptor headpiece adopts the closed conformation expected to exhibit low ligand affinity. The crystal structure indicates that in the R77H αM variant, associated with systemic lupus erythematosus, the modified allosteric relationship between ligand binding and integrin outside–inside signaling is due to subtle conformational effects transmitted over a distance of 40 Å. Furthermore, we found the Nb binds to the αI domain of the αM subunit in an Mg2+-independent manner with low nanomolar affinity. Biochemical and biophysical experiments with purified proteins demonstrated that the Nb acts as a competitive inhibitor through steric hindrance exerted on the thioester domain of complement component iC3b attempting to bind the αM subunit. Surprisingly, we show that the Nb stimulates the interaction of cell-bound αMβ2 with iC3b, suggesting that it may represent a novel high-affinity proteinaceous αMβ2-specific agonist. Taken together, our data suggest that the iC3b–αMβ2 complex may be more dynamic than predicted from the crystal structure of the core complex. We propose a model based on the conformational spectrum of the receptor to reconcile these observations regarding the functional consequences of hCD11bNb1 binding to αMβ2.
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Affiliation(s)
- Rasmus K Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Henrik Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Josefine Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
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9
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Type IV Pili of Streptococcus sanguinis Contribute to Pathogenesis in Experimental Infective Endocarditis. Microbiol Spectr 2021; 9:e0175221. [PMID: 34756087 PMCID: PMC8579931 DOI: 10.1128/spectrum.01752-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus sanguinis is a common cause of infective endocarditis (IE). Efforts by research groups are aimed at identifying and characterizing virulence factors that contribute to the ability of this organism to cause IE. This Gram-positive pathogen causes heart infection by gaining access to the bloodstream, adhering to host extracellular matrix protein and/or platelets, colonizing the aortic endothelium, and incorporating itself into the aortic vegetation. While many virulence factors have been reported to contribute to the ability of S. sanguinis to cause IE, it is noteworthy that type IV pili (T4P) have not been described to be a virulence factor in this organism, although S. sanguinis strains typically encode these pili. Type IV pili are molecular machines that are capable of mediating diverse virulence functions and surface motility. T4P have been shown to mediate twitching motility in some strains of S. sanguinis, although in most strains it has been difficult to detect twitching motility. While we found that T4P are dispensable for direct in vitro platelet binding and aggregation phenotypes, we show that they are critical to the development of platelet-dependent biofilms representative of the cardiac vegetation. We also observed that T4P are required for in vitro invasion of S. sanguinis into human aortic endothelial cells, which indicates that S. sanguinis may use T4P to take advantage of an intracellular niche during infection. Importantly, we show that T4P of S. sanguinis are critical to disease progression (vegetation development) in a native valve IE rabbit model. The results presented here expand our understanding of IE caused by S. sanguinis and identify T4P as an important virulence factor for this pathogen. IMPORTANCE This work provides evidence that type IV pili produced by Streptococcus sanguinis SK36 are critical to the ability of these bacteria to attach to and colonize the aortic heart valve (endocarditis). We found that an S. sanguinis type IV pili mutant strain was defective in causing platelet-dependent aggregation in a 24-h infection assay but not in a 1-h platelet aggregation assay, suggesting that the type IV pili act at later stages of vegetation development. In a rabbit model of disease, a T4P mutant strain does not develop mature vegetations that form on the heart, indicating that this virulence factor is critical to disease and could be a target for IE therapy.
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10
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Jensen RK, Bajic G, Sen M, Springer TA, Vorup-Jensen T, Andersen GR. Complement Receptor 3 Forms a Compact High-Affinity Complex with iC3b. THE JOURNAL OF IMMUNOLOGY 2021; 206:3032-3042. [PMID: 34117107 DOI: 10.4049/jimmunol.2001208] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/13/2021] [Indexed: 11/19/2022]
Abstract
Complement receptor 3 (CR3, also known as Mac-1, integrin αMβ2, or CD11b/CD18) is expressed on a subset of myeloid and certain activated lymphoid cells. CR3 is essential for the phagocytosis of complement-opsonized particles such as pathogens and apoptotic or necrotic cells opsonized with the complement fragment iC3b and, to a lesser extent, C3dg. Although the interaction between the iC3b thioester domain and the ligand binding CR3 αM I-domain is structurally and functionally well characterized, the nature of additional CR3-iC3b interactions required for phagocytosis of complement-opsonized objects remains obscure. In this study, we analyzed the interaction between iC3b and the 150-kDa headpiece fragment of the CR3 ectodomain. Surface plasmon resonance experiments demonstrated a 30 nM affinity of the CR3 headpiece for iC3b compared with 515 nM for the iC3b thioester domain, whereas experiments monitoring binding of iC3b to CR3-expressing cells suggested an affinity of 50 nM for the CR3-iC3b interaction. Small angle x-ray scattering analysis revealed that iC3b adopts an extended but preferred conformation in solution. Upon interaction with CR3, iC3b rearranges to form a compact receptor-ligand complex. Overall, the data suggest that the iC3b-CR3 interaction is of high affinity and relies on minor contacts formed between CR3 and regions outside the iC3b thioester domain. Our results rationalize the more efficient phagocytosis elicited by iC3b than by C3dg and pave the way for the development of specific therapeutics for the treatment of inflammatory and neurodegenerative diseases that do not interfere with the recognition of noncomplement CR3 ligands.
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Affiliation(s)
- Rasmus K Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Goran Bajic
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatrics, Harvard Medical School, Boston, MA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Mehmet Sen
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Timothy A Springer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA; and
| | | | - Gregers R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark;
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11
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Lamers C, Plüss CJ, Ricklin D. The Promiscuous Profile of Complement Receptor 3 in Ligand Binding, Immune Modulation, and Pathophysiology. Front Immunol 2021; 12:662164. [PMID: 33995387 PMCID: PMC8118671 DOI: 10.3389/fimmu.2021.662164] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/12/2021] [Indexed: 12/19/2022] Open
Abstract
The β2-integrin receptor family has a broad spectrum of physiological functions ranging from leukocyte adhesion, cell migration, activation, and communication to the phagocytic uptake of cells and particles. Among the members of this family, complement receptor 3 (CR3; CD11b/CD18, Mac-1, αMβ2) is particularly promiscuous in its functional profile and ligand selectivity. There are close to 100 reported structurally unrelated ligands for CR3, and while many ligands appear to cluster at the αMI domain, molecular details about binding modes remain largely elusive. The versatility of CR3 is reflected in its functional portfolio, which includes prominent roles in the removal of invaders and cell debris, induction of tolerance and synaptic pruning, and involvement in the pathogenesis of numerous autoimmune and chronic inflammatory pathologies. While CR3 is an interesting therapeutic target for immune modulation due to these known pathophysiological associations, drug development efforts are limited by concerns of potential interference with host defense functions and, most importantly, an insufficient molecular understanding of the interplay between ligand binding and functional impact. Here, we provide a systematic summary of the various interaction partners of CR3 with a focus on binding mechanisms and functional implications. We also discuss the roles of CR3 as an immune receptor in health and disease, as an activation marker in research and diagnostics, and as a therapeutic target.
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Affiliation(s)
- Christina Lamers
- Molecular Pharmacy Unit, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
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12
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Jiang X, Sun X, Lin J, Ling Y, Fang Y, Wu J. MD Simulations on a Well-Built Docking Model Reveal Fine Mechanical Stability and Force-Dependent Dissociation of Mac-1/GPIbα Complex. Front Mol Biosci 2021; 8:638396. [PMID: 33968982 PMCID: PMC8100526 DOI: 10.3389/fmolb.2021.638396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/12/2021] [Indexed: 12/20/2022] Open
Abstract
Interaction of leukocyte integrin macrophage-1 antigen (Mac-1) to platelet glycoprotein Ibα (GPIbα) is critical for platelet-leukocyte crosstalk in hemostasis and inflammatory responses to vessel injuries under hemodynamic environments. The mechano-regulation and its molecular basis for binding of Mac-1 to GPIbα remain unclear, mainly coming from the lack of crystal structure of the Mac-1/GPIbα complex. We herein built a Mac-1/GPIbα complex model through a novel computer strategy, which included a flexible molecular docking and system equilibrium followed by a "force-ramp + snapback" molecular dynamics (MD) simulation. With this model, a series of "ramp-clamp" steered molecular dynamics (SMD) simulations were performed to examine the GPIbα-Mac-1 interaction under various loads. The results demonstrated that the complex was mechano-stable for both the high rupture force (>250 pN) at a pulling velocity of 3 Å/ns and the conformational conservation under various constant tensile forces (≤75 pN); a catch-slip bond transition was predicted through the dissociation probability, examined with single molecular AFM measurements, reflected by the interaction energy and the interface H-bond number, and related to the force-induced allostery of the complex; besides the mutation-identified residues D222 and R218, the residues were also dominant in the binding of Mac-1 to GPIbα. This study recommended a valid computer strategy for building a likely wild-type docking model of a complex, provided a novel insight into the mechanical regulation mechanism and its molecular basis for the interaction of Mac-1 with GPIbα, and would be helpful for understanding the platelet-leukocyte interaction in hemostasis and inflammatory responses under mechano-microenvironments.
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Affiliation(s)
- Xiaoyan Jiang
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaoxi Sun
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jiangguo Lin
- Research Department of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yingchen Ling
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ying Fang
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jianhua Wu
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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13
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Fukuda K, Lu F, Qin J. Molecular basis for Ras suppressor-1 binding to PINCH-1 in focal adhesion assembly. J Biol Chem 2021; 296:100685. [PMID: 33891945 PMCID: PMC8141872 DOI: 10.1016/j.jbc.2021.100685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 10/29/2022] Open
Abstract
Ras suppressor-1 (Rsu-1) is a leucine-rich repeat (LRR)-containing protein that is crucial for regulating cell adhesion and is involved in such physiological and pathological processes as focal adhesion assembly and tumor metastasis. Rsu-1 interacts with zinc-finger type multi-LIM domain-containing adaptor protein PINCH-1, known to be involved in the integrin-mediated consensus adhesome, but not with its highly homologous family member PINCH-2. However, the structural basis for and regulatory mechanisms of this specific interaction remain unclear. Here, we determined the crystal structures of Rsu-1 and its complex with the PINCH-1 LIM4-5 domains. Rsu-1 displays an arc-shaped solenoid architecture, with eight LRRs shielded by N- and C-terminal capping modules. We showed that the conserved concave surface of the Rsu-1 LRR domain binds and stabilizes the PINCH-1 LIM5 domain via salt bridge and hydrophobic interactions, while the C-terminal non-LIM region of PINCH-2 sterically disfavors Rsu-1 binding. We also showed that Rsu-1 can be assembled, via PINCH-1-binding, into a heteropentamer complex comprising Rsu-1, PINCH-1, ILK, Parvin, and Kindlin-2, which constitute a major consensus integrin adhesome crucial for focal adhesion assembly. Our mutagenesis and cell biological data emphasize the significance of the Rsu-1/PINCH-1 interaction in focal adhesion assembly and cell spreading, providing crucial molecular insights into Rsu-1-mediated cell adhesion with implications for disease development.
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Affiliation(s)
- Koichi Fukuda
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Ohio, USA
| | - Fan Lu
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Ohio, USA; Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jun Qin
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Ohio, USA; Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.
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Feng W, Nguyen H, Shen D, Deng H, Jiang Z, Podolnikova N, Ugarova T, Wang X. Structural Characterization of the Interaction between the α MI-Domain of the Integrin Mac-1 (α Mβ 2) and the Cytokine Pleiotrophin. Biochemistry 2021; 60:182-193. [PMID: 33427449 DOI: 10.1021/acs.biochem.0c00700] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Integrin Mac-1 (αMβ2) is an adhesion receptor vital to many functions of myeloid leukocytes. It is also the most promiscuous member of the integrin family capable of recognizing a broad range of ligands. In particular, its ligand-binding αMI-domain is known to bind cationic proteins/peptides depleted in acidic residues. This contradicts the canonical ligand-binding mechanism of αI-domains, which requires an acidic amino acid in the ligand to coordinate the divalent cation within the metal ion-dependent adhesion site (MIDAS) of αI-domains. The lack of acidic amino acids in the αMI-domain-binding sequences suggests the existence of an as-yet uncharacterized interaction mechanism. In the present study, we analyzed interactions of the αMI-domain with a representative Mac-1 ligand, the cationic cytokine pleiotrophin (PTN). Through NMR chemical shift perturbation analysis, cross saturation, NOESY, and mutagenesis studies, we found the interaction between the αMI-domain and PTN is divalent cation-independent and mediated mostly by hydrophobic contacts between the N-terminal domain of PTN and residues in the α5-β5 loop of αMI-domain. The observation that increased ionic strength weakens the interaction between the proteins indicates electrostatic forces may also play a significant role in the binding. On the basis of the results from these experiments, we formulated a model of the interaction between the αMI-domain and PTN.
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