1
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Damen LAA, Bui TP, van Wessel T, Li Y, Straten BF, Pampiermole R, Daamen WF, Fernig DG, van Kuppevelt TH. Identification of heparin-binding amino acid residues in antibody HS4C3 with the potential to design antibodies against heparan sulfate domains. Glycobiology 2024; 34:cwae046. [PMID: 38963938 PMCID: PMC11231949 DOI: 10.1093/glycob/cwae046] [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: 01/02/2024] [Revised: 06/06/2024] [Indexed: 07/06/2024] Open
Abstract
Heparan sulfate (HS) is a linear polysaccharide with high structural and functional diversity. Detection and localization of HS in tissues can be performed using single chain variable fragment (scFv) antibodies. Although several anti-HS antibodies recognizing different sulfation motifs have been identified, little is known about their interaction with HS. In this study the interaction between the scFv antibody HS4C3 and heparin was investigated. Heparin-binding lysine and arginine residues were identified using a protect and label methodology. Site-directed mutagenesis was applied to further identify critical heparin-binding lysine/arginine residues using immunohistochemical and biochemical assays. In addition, computational docking of a heparin tetrasaccharide towards a 3-D homology model of HS4C3 was applied to identify potential heparin-binding sites. Of the 12 lysine and 15 arginine residues within the HS4C3 antibody, 6 and 9, respectively, were identified as heparin-binding. Most of these residues are located within one of the complementarity determining regions (CDR) or in their proximity. All basic amino acid residues in the CDR3 region of the heavy chain were involved in binding. Computational docking showed a heparin tetrasaccharide close to these regions. Mutagenesis of heparin-binding residues reduced or altered reactivity towards HS and heparin. Identification of heparin-binding arginine and lysine residues in HS4C3 allows for better understanding of the interaction with HS and creates a framework to rationally design antibodies targeting specific HS motifs.
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Affiliation(s)
- Lars A A Damen
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, Radboud University Medical Center, PO Box 9101, Nijmegen 6500 HB, the Netherlands
| | - Thao P Bui
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrated Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Thierry van Wessel
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, Radboud University Medical Center, PO Box 9101, Nijmegen 6500 HB, the Netherlands
| | - Yong Li
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrated Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Bart F Straten
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, Radboud University Medical Center, PO Box 9101, Nijmegen 6500 HB, the Netherlands
| | - Robin Pampiermole
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, Radboud University Medical Center, PO Box 9101, Nijmegen 6500 HB, the Netherlands
| | - Willeke F Daamen
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, Radboud University Medical Center, PO Box 9101, Nijmegen 6500 HB, the Netherlands
| | - David G Fernig
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrated Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Toin H van Kuppevelt
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, Radboud University Medical Center, PO Box 9101, Nijmegen 6500 HB, the Netherlands
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2
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Alotaibi FS, Alsadun MMR, Alsaiari SA, Ramakrishnan K, Yates EA, Fernig DG. Interactions of proteins with heparan sulfate. Essays Biochem 2024:EBC20230093. [PMID: 38646914 DOI: 10.1042/ebc20230093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/22/2024] [Accepted: 04/02/2024] [Indexed: 04/23/2024]
Abstract
Heparan sulfate (HS) is a glycosaminoglycan, polysaccharides that are considered to have arisen in the last common unicellular ancestor of multicellular animals. In this light, the large interactome of HS and its myriad functions in relation to the regulation of cell communication are not surprising. The binding of proteins to HS determines their localisation and diffusion, essential for embryonic development and homeostasis. Following the biosynthesis of the initial heparosan polymer, the subsequent modifications comprise an established canonical pathway and a minor pathway. The more frequent former starts with N-deacetylation and N-sulfation of GlcNAc residues, the latter with C-5 epimerisation of a GlcA residue adjacent to a GlcNAc. The binding of proteins to HS is driven by ionic interactions. The multivalent effect arising from the many individual ionic bonds between a single protein and a polysaccharide chain results in a far stronger interaction than would be expected from an ion-exchange process. In many instances, upon binding, both parties undergo substantial conformational change, the resulting hydrogen and van der Waal bonds contributing significant free energy to the binding reaction. Nevertheless, ionic bonds dominate the protein-polysaccharide interaction kinetically. Together with the multivalent effect, this provides an explanation for the observed trapping of HS-binding proteins in extracellular matrix. Importantly, individual ionic bonds have been observed to be dynamic; breaking and reforming, while the protein remains bound to the polysaccharide. These considerations lead to a model for 1D diffusion of proteins in extracellular matrix on HS, involving mechanisms such as sliding, chain switching and rolling.
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Affiliation(s)
- Faizah S Alotaibi
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Marim M R Alsadun
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
- Department of Biology, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Sarah A Alsaiari
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah 21589, Saudi Arabia
| | - Krithika Ramakrishnan
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Edwin A Yates
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - David G Fernig
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
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3
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Grismer TS, Karundasa SS, Shrestha R, Byun D, Ni W, Reyes AV, Xu SL. Workflow enhancement of TurboID-mediated proximity labeling for SPY signaling network mapping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.17.580820. [PMID: 38405906 PMCID: PMC10888891 DOI: 10.1101/2024.02.17.580820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
TurboID-based proximity labeling coupled to mass spectrometry (PL-MS) has emerged as a powerful tool for mapping protein-protein interactions in both plant and animal systems. Despite advances in sensitivity, PL-MS studies can still suffer from false negatives, especially when dealing with low abundance bait proteins and their transient interactors. Protein-level enrichment for biotinylated proteins is well developed and popular, but direct detection of biotinylated proteins by peptide-level enrichment and the difference in results between direct and indirect detection remain underexplored. To address this gap, we compared and improved enrichment and data analysis methods using TurboID fused to SPY, a low-abundance O-fucose transferase, using an AAL-enriched SPY target library for cross-referencing. Our results showed that MyOne and M280 streptavidin beads significantly outperformed antibody beads for peptide-level enrichment, with M280 performing best. In addition, while a biotin concentration ≤ 50 μM is recommended for protein-level enrichment in plants, higher biotin concentrations can be used for peptide-level enrichment, allowing us to improve detection and data quality. FragPipe's MSFragger protein identification and quantification software outperformed Maxquant and Protein Prospector for SPY interactome enrichment due to its superior detection of biotinylated peptides. Our improved washing protocols for protein-level enrichment mitigated bead collapse issues, improving data quality, and reducing experimental time. We found that the two enrichment methods provided complementary results and identified a total of 160 SPY-TurboID-enriched interactors, including 60 previously identified in the AAL-enriched SPY target list and 100 additional novel interactors. SILIA quantitative proteomics comparing WT and spy-4 mutants showed that SPY affects the protein levels of some of the identified interactors, such as nucleoporin proteins. We expect that our improvement will extend beyond TurboID to benefit other PL systems and hold promise for broader applications in biological research.
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Affiliation(s)
- TaraBryn S Grismer
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Sumudu S Karundasa
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
| | - Ruben Shrestha
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
| | - Danbi Byun
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
| | - Weimin Ni
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
| | - Andres V Reyes
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Shou-Ling Xu
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
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4
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The New General Biological Property of Stem-like Tumor Cells (Part II: Surface Molecules, Which Belongs to Distinctive Groups with Particular Functions, Form a Unique Pattern Characteristic of a Certain Type of Tumor Stem-like Cells). Int J Mol Sci 2022; 23:ijms232415800. [PMID: 36555446 PMCID: PMC9785054 DOI: 10.3390/ijms232415800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/16/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
An ability of poorly differentiated cells of different genesis, including tumor stem-like cells (TSCs), to internalize extracellular double-stranded DNA (dsDNA) fragments was revealed in our studies. Using the models of Krebs-2 murine ascites carcinoma and EBV-induced human B-cell lymphoma culture, we demonstrated that dsDNA internalization into the cell consists of several mechanistically distinct phases. The primary contact with cell membrane factors is determined by electrostatic interactions. Firm contacts with cell envelope proteins are then formed, followed by internalization into the cell of the complex formed between the factor and the dsDNA probe bound to it. The key binding sites were found to be the heparin-binding domains, which are constituents of various cell surface proteins of TSCs-either the C1q domain, the collagen-binding domain, or domains of positively charged amino acids. These results imply that the interaction between extracellular dsDNA fragments and the cell, as well as their internalization, took place with the involvement of glycocalyx components (proteoglycans/glycoproteins (PGs/GPs) and glycosylphosphatidylinositol-anchored proteins (GPI-APs)) and the system of scavenger receptors (SRs), which are characteristic of TSCs and form functional clusters of cell surface proteins in TSCs. The key provisions of the concept characterizing the principle of organization of the "group-specific" cell surface factors of TSCs of various geneses were formulated. These factors belong to three protein clusters: GPs/PGs, GIP-APs, and SRs. For TSCs of different tumors, these clusters were found to be represented by different members with homotypic functions corresponding to the general function of the cluster to which they belong.
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5
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Moreau T, Gautron J, Hincke MT, Monget P, Réhault-Godbert S, Guyot N. Antimicrobial Proteins and Peptides in Avian Eggshell: Structural Diversity and Potential Roles in Biomineralization. Front Immunol 2022; 13:946428. [PMID: 35967448 PMCID: PMC9363672 DOI: 10.3389/fimmu.2022.946428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/22/2022] [Indexed: 11/21/2022] Open
Abstract
The calcitic avian eggshell provides physical protection for the embryo during its development, but also regulates water and gaseous exchange, and is a calcium source for bone mineralization. The calcified eggshell has been extensively investigated in the chicken. It is characterized by an inventory of more than 900 matrix proteins. In addition to proteins involved in shell mineralization and regulation of its microstructure, the shell also contains numerous antimicrobial proteins and peptides (AMPPs) including lectin-like proteins, Bacterial Permeability Increasing/Lipopolysaccharide Binding Protein/PLUNC family proteins, defensins, antiproteases, and chelators, which contribute to the innate immune protection of the egg. In parallel, some of these proteins are thought to be crucial determinants of the eggshell texture and its resulting mechanical properties. During the progressive solubilization of the inner mineralized eggshell during embryonic development (to provide calcium to the embryo), some antimicrobials may be released simultaneously to reinforce egg defense and protect the egg from contamination by external pathogens, through a weakened eggshell. This review provides a comprehensive overview of the diversity of avian eggshell AMPPs, their three-dimensional structures and their mechanism of antimicrobial activity. The published chicken eggshell proteome databases are integrated for a comprehensive inventory of its AMPPs. Their biochemical features, potential dual function as antimicrobials and as regulators of eggshell biomineralization, and their phylogenetic evolution will be described and discussed with regard to their three-dimensional structural characteristics. Finally, the repertoire of chicken eggshell AMPPs are compared to orthologs identified in other avian and non-avian eggshells. This approach sheds light on the similarities and differences exhibited by AMPPs, depending on bird species, and leads to a better understanding of their sequential or dual role in biomineralization and innate immunity.
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Affiliation(s)
- Thierry Moreau
- INRAE, Université de Tours, BOA, Nouzilly, France
- *Correspondence: Nicolas Guyot, ; Thierry Moreau,
| | - Joël Gautron
- INRAE, Université de Tours, BOA, Nouzilly, France
| | - Maxwell T. Hincke
- Department of Innovation in Medical Education, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Philippe Monget
- INRAE, CNRS, IFCE, Université de Tours, PRC, Nouzilly, France
| | | | - Nicolas Guyot
- INRAE, Université de Tours, BOA, Nouzilly, France
- *Correspondence: Nicolas Guyot, ; Thierry Moreau,
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6
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Stage II of Chronic Kidney Disease—A Tipping Point in Disease Progression? Biomedicines 2022; 10:biomedicines10071522. [PMID: 35884827 PMCID: PMC9313233 DOI: 10.3390/biomedicines10071522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/20/2022] [Accepted: 06/25/2022] [Indexed: 11/17/2022] Open
Abstract
Chronic kidney disease (CKD) is the progressive loss of renal function. Although advances have been made in understanding the progression of CKD, key molecular events in complex pathophysiological mechanisms that mark each stage of renal failure remain largely unknown. Changes in plasma protein profiles in different disease stages are important for identification of early diagnostic markers and potential therapeutic targets. The goal of this study was to determine the molecular profile of each CKD stage (from 1 to 5), aiming to specifically point out markedly expressed or downregulated proteins. We performed a cross-sectional shotgun-proteomic study of pooled plasma across CKD stages and compared them to healthy controls. After sample pooling and heparin-column purification we analysed proteomes from healthy to CKD stage 1 through 5 participants’ plasma by liquid-chromatography/mass-spectrometry. We identified 453 proteins across all study groups. Our results indicate that key events, which may later affect the course of disease progression and the overall pathophysiological background, are most pronounced in CKD stage 2, with an emphasis on inflammation, lipoprotein metabolism, angiogenesis and tissue regeneration. We hypothesize that CKD stage 2 is the tipping point in disease progression and a suitable point in disease course for the development of therapeutic solutions.
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7
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Ryan EO, Jiang Z, Nguyen H, Wang X. Interactions of Pleiotrophin with a Structurally Defined Heparin Hexasaccharide. Biomolecules 2021; 12:biom12010050. [PMID: 35053198 PMCID: PMC8773689 DOI: 10.3390/biom12010050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/21/2021] [Accepted: 12/27/2021] [Indexed: 11/21/2022] Open
Abstract
Pleiotrophin (PTN) is a potent cytokine that plays an important role in neural generation, angiogenesis, inflammation, and cancers. Its interactions with the polysaccharide glycosaminoglycan (GAG) are crucial to PTN’s biological activities. In this study, we investigated the interaction of selectively protonated PTN with the heparin hexasaccharide ΔUA2S-(GlcNS6S-IdoA2S)2-GlcNS6S using solution NMR. The use of a structurally defined oligosaccharide and selectively protonated PTN enabled us to obtain intermolecular contacts using unfiltered NOESY experiments, significantly increasing the amount of high-resolution structural information obtainable. Our data showed that PTN’s arginines, lysines, and tryptophans in the two structured domains have strong interactions with the 2-O-sulfated uronate protons in the heparin hexasaccharide. Consistent with the NMR data is the observation that 2-O-desulfation and N-desulfation/N-acetylation significantly decreased heparin hexasaccharides’ affinity for PTN, while 6-O-desulfation only modestly affected the interactions with PTN. These results allowed us to hypothesize that PTN has a preference for sulfate clusters centered on the GlcNS6S-IdoA2S disaccharide. Using these data and the fact that PTN domains mostly bind heparin hexasaccharides independently, models of the PTN-heparin complex were constructed.
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Affiliation(s)
| | | | | | - Xu Wang
- Correspondence: ; Tel.: +1-480-7278256
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8
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Xu Z, Chen S, Feng D, Liu Y, Wang Q, Gao T, Liu Z, Zhang Y, Chen J, Qiu L. Biological role of heparan sulfate in osteogenesis: A review. Carbohydr Polym 2021; 272:118490. [PMID: 34420746 DOI: 10.1016/j.carbpol.2021.118490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/14/2022]
Abstract
Heparan sulfate (HS) is extensively expressed in cells, for example, cell membrane and extracellular matrix of most mammalian cells and tissues, playing a key role in the growth and development of life by maintaining homeostasis and implicating in the etiology and diseases. Recent studies have revealed that HS is involved in osteogenesis via coordinating multiple signaling pathways. The potential effect of HS on osteogenesis is a complicated and delicate biological process, which involves the participation of osteocytes, chondrocytes, osteoblasts, osteoclasts and a variety of cytokines. In this review, we summarized the structural and functional characteristics of HS and highlighted the molecular mechanism of HS in bone metabolism to provide novel research perspectives for the further medical research.
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Affiliation(s)
- Zhujie Xu
- Department of Orthopedics, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, PR China
| | - Shayang Chen
- Department of Orthopedics, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, PR China
| | - Dehong Feng
- Department of Orthopedics, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, PR China
| | - Yi Liu
- Department of Orthopedics, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, PR China.
| | - Qiqi Wang
- Department of Orthopedics, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, PR China
| | - Tianshu Gao
- Department of Orthopedics, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, PR China
| | - Zhenwei Liu
- Department of Orthopedics, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, PR China
| | - Yan Zhang
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Jinghua Chen
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Lipeng Qiu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China.
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9
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Tahir R, Madugundu AK, Udainiya S, Cutler JA, Renuse S, Wang L, Pearson NA, Mitchell CJ, Mahajan N, Pandey A, Wu X. Proximity-Dependent Biotinylation to Elucidate the Interactome of TNK2 Nonreceptor Tyrosine Kinase. J Proteome Res 2021; 20:4566-4577. [PMID: 34428048 DOI: 10.1021/acs.jproteome.1c00551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonreceptor tyrosine kinases (NRTKs) represent an important class of signaling molecules driving diverse cellular pathways. Aberrant expression and hyperphosphorylation of TNK2, an NRTK, have been implicated in multiple cancers. However, the exact proteins and cellular events that mediate phenotypic changes downstream of TNK2 are unclear. Biological systems that employ proximity-dependent biotinylation methods, such as BioID, are being increasingly used to map protein-protein interactions, as they provide increased sensitivity in discovering interaction partners. In this study, we employed stable isotope labeling with amino acids in cell culture and BioID coupled to the biotinylation site identification technology (BioSITe) method that we recently developed to quantitatively explore the interactome of TNK2. By performing a controlled comparative analysis between full-length TNK2 and its truncated counterpart, we were able to not only identify site-level biotinylation of previously well-established TNK2 binders and substrates including NCK1, NCK2, CTTN, and STAT3, but also discover several novel TNK2 interacting partners. We also performed co-immunoprecipitation and immunofluorescence analysis to validate the interaction between TNK2 and CLINT1, a novel TNK2 interacting protein. Overall, this work reveals the power of the BioSITe method coupled to BioID and highlights several molecules that warrant further exploration to assess their functional significance in TNK2-mediated signaling.
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Affiliation(s)
- Raiha Tahir
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Ginkgo Bioworks, Boston, Massachusetts 02210, United States
| | - Anil K Madugundu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, Karnataka, India.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Savita Udainiya
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, Karnataka, India.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Jevon A Cutler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Pre-Doctoral Training Program in Human Genetics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Santosh Renuse
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Li Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Nicole A Pearson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | | | - Nupam Mahajan
- Siteman Cancer Center, Washington University, St. Louis, Missouri 63110, United States
| | - Akhilesh Pandey
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, Karnataka, India.,Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Xinyan Wu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.,Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, United States
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10
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Chemical Modification of Glycosaminoglycan Polysaccharides. Molecules 2021; 26:molecules26175211. [PMID: 34500644 PMCID: PMC8434129 DOI: 10.3390/molecules26175211] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/20/2021] [Accepted: 08/21/2021] [Indexed: 12/16/2022] Open
Abstract
The linear anionic class of polysaccharides, glycosaminoglycans (GAGs), are critical throughout the animal kingdom for developmental processes and the maintenance of healthy tissues. They are also of interest as a means of influencing biochemical processes. One member of the GAG family, heparin, is exploited globally as a major anticoagulant pharmaceutical and there is a growing interest in the potential of other GAGs for diverse applications ranging from skin care to the treatment of neurodegenerative conditions, and from the treatment and prevention of microbial infection to biotechnology. To realize the potential of GAGs, however, it is necessary to develop effective tools that are able to exploit the chemical manipulations to which GAGs are susceptible. Here, the current knowledge concerning the chemical modification of GAGs, one of the principal approaches for the study of the structure-function relationships in these molecules, is reviewed. Some additional methods that were applied successfully to the analysis and/or processing of other carbohydrates, but which could be suitable in GAG chemistry, are also discussed.
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11
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Sedlář A, Trávníčková M, Matějka R, Pražák Š, Mészáros Z, Bojarová P, Bačáková L, Křen V, Slámová K. Growth Factors VEGF-A 165 and FGF-2 as Multifunctional Biomolecules Governing Cell Adhesion and Proliferation. Int J Mol Sci 2021; 22:1843. [PMID: 33673317 PMCID: PMC7917819 DOI: 10.3390/ijms22041843] [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: 01/19/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/11/2022] Open
Abstract
Vascular endothelial growth factor-A165 (VEGF-A165) and fibroblast growth factor-2 (FGF-2) are currently used for the functionalization of biomaterials designed for tissue engineering. We have developed a new simple method for heterologous expression and purification of VEGF-A165 and FGF-2 in the yeast expression system of Pichia pastoris. The biological activity of the growth factors was assessed in cultures of human and porcine adipose tissue-derived stem cells (ADSCs) and human umbilical vein endothelial cells (HUVECs). When added into the culture medium, VEGF-A165 stimulated proliferation only in HUVECs, while FGF-2 stimulated the proliferation of both cell types. A similar effect was achieved when the growth factors were pre-adsorbed to polystyrene wells. The effect of our recombinant growth factors was slightly lower than that of commercially available factors, which was attributed to the presence of some impurities. The stimulatory effect of the VEGF-A165 on cell adhesion was rather weak, especially in ADSCs. FGF-2 was a potent stimulator of the adhesion of ADSCs but had no to negative effect on the adhesion of HUVECs. In sum, FGF-2 and VEGF-A165 have diverse effects on the behavior of different cell types, which maybe utilized in tissue engineering.
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Affiliation(s)
- Antonín Sedlář
- Laboratory of Biomaterials and Tissue Engineering, Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Praha 4, Czech Republic; (A.S.); (M.T.); or or (Š.P.)
- Department of Physiology, Faculty of Science, Charles University, Viničná 7, CZ 12844 Praha 2, Czech Republic
| | - Martina Trávníčková
- Laboratory of Biomaterials and Tissue Engineering, Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Praha 4, Czech Republic; (A.S.); (M.T.); or or (Š.P.)
| | - Roman Matějka
- Laboratory of Biomaterials and Tissue Engineering, Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Praha 4, Czech Republic; (A.S.); (M.T.); or or (Š.P.)
- Faculty of Biomedical Engineering, Czech Technical University in Prague, CZ 27201 Kladno, Czech Republic;
| | - Šimon Pražák
- Laboratory of Biomaterials and Tissue Engineering, Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Praha 4, Czech Republic; (A.S.); (M.T.); or or (Š.P.)
- Faculty of Biomedical Engineering, Czech Technical University in Prague, CZ 27201 Kladno, Czech Republic;
| | - Zuzana Mészáros
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Praha 4, Czech Republic; (Z.M.); (V.K.)
- Department of Biochemistry, University of Chemistry and Technology Prague, Technická 6, CZ 16628 Praha 6, Czech Republic
| | - Pavla Bojarová
- Faculty of Biomedical Engineering, Czech Technical University in Prague, CZ 27201 Kladno, Czech Republic;
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Praha 4, Czech Republic; (Z.M.); (V.K.)
| | - Lucie Bačáková
- Laboratory of Biomaterials and Tissue Engineering, Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Praha 4, Czech Republic; (A.S.); (M.T.); or or (Š.P.)
| | - Vladimír Křen
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Praha 4, Czech Republic; (Z.M.); (V.K.)
| | - Kristýna Slámová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Praha 4, Czech Republic; (Z.M.); (V.K.)
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12
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Ryan E, Shen D, Wang X. Pleiotrophin interacts with glycosaminoglycans in a highly flexible and adaptable manner. FEBS Lett 2021; 595:925-941. [PMID: 33529353 DOI: 10.1002/1873-3468.14052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/14/2022]
Abstract
Pleiotrophin (PTN) is a potent mitogenic cytokine whose activities are controlled by its interactions with glycosaminoglycan (GAG). We examined the specificity of PTN for several types of GAG oligosaccharides. Our data indicate that the interaction of PTN with GAGs is dependent on the sulfation density of GAGs. Surprisingly, an acidic peptide also had similar interactions with PTN as GAGs. This shows that the interaction of PTN with anionic polymers is flexible and adaptable and that the charge density is the main determinant of the interaction. In addition, we show that PTN can compensate for the loss of its termini in interactions with heparin oligosaccharides, allowing it to maintain its affinity for GAGs in the absence of the termini. Taken together, these data provide valuable insight into the interactions of PTN with its proteoglycan receptors.
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Affiliation(s)
- Eathen Ryan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Di Shen
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Xu Wang
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
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13
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Gómez Toledo A, Sorrentino JT, Sandoval DR, Malmström J, Lewis NE, Esko JD. A Systems View of the Heparan Sulfate Interactome. J Histochem Cytochem 2021; 69:105-119. [PMID: 33494649 PMCID: PMC7841697 DOI: 10.1369/0022155420988661] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 12/28/2022] Open
Abstract
Heparan sulfate proteoglycans consist of a small family of proteins decorated with one or more covalently attached heparan sulfate glycosaminoglycan chains. These chains have intricate structural patterns based on the position of sulfate groups and uronic acid epimers, which dictate their ability to engage a large repertoire of heparan sulfate-binding proteins, including extracellular matrix proteins, growth factors and morphogens, cytokines and chemokines, apolipoproteins and lipases, adhesion and growth factor receptors, and components of the complement and coagulation system. This review highlights recent progress in the characterization of the so-called "heparan sulfate interactome," with a major focus on systems-wide strategies as a tool for discovery and characterization of this subproteome. In addition, we compiled all heparan sulfate-binding proteins reported in the literature to date and grouped them into a few major functional classes by applying a networking approach.
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Affiliation(s)
- Alejandro Gómez Toledo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
- Department of Clinical Sciences, Lund, Division of Infection Medicine, Lund University, Lund, Sweden
| | - James T Sorrentino
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California
- Department of Bioengineering, University of California, San Diego, La Jolla, California
| | - Daniel R Sandoval
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
| | - Johan Malmström
- Department of Clinical Sciences, Lund, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego, La Jolla, California
- Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
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14
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Incorporation of FGF-2 into Pharmaceutical Grade Fucoidan/Chitosan Polyelectrolyte Multilayers. Mar Drugs 2020; 18:md18110531. [PMID: 33114688 PMCID: PMC7692699 DOI: 10.3390/md18110531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 12/24/2022] Open
Abstract
Biopolymer polyelectrolyte multilayers are a commonly studied soft matter system for wound healing applications due to the biocompatibility and beneficial properties of naturally occurring polyelectrolytes. In this work, a popular biopolymer, chitosan, was combined with the lesser known polysaccharide, fucoidan, to create a multilayer film capable of sequestering growth factor for later release. Fucoidan has been shown to act as a heparin-mimic due to similarities in the structure of the two molecules, however, the binding of fibroblast growth factor-2 to fucoidan has not been demonstrated in a multilayer system. This study assesses the ability of fucoidan to bind fibroblast growth factor-2 within a fucoidan/chitosan polyelectrolyte multilayer structure using attenuated total internal reflectance infrared spectroscopy and quartz crystal microbalance with dissipation monitoring. The fibroblast growth factor-2 was sequestered into the polyelectrolyte multilayer as a cationic layer in the uppermost layers of the film structure. In addition, the diffusion of fibroblast growth factor-2 into the multilayer has been assessed.
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15
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Vijaya Kumar A, Brézillon S, Untereiner V, Sockalingum GD, Kumar Katakam S, Mohamed HT, Kemper B, Greve B, Mohr B, Ibrahim SA, Goycoolea FM, Kiesel L, Pavão MSG, Motta JM, Götte M. HS2ST1-dependent signaling pathways determine breast cancer cell viability, matrix interactions, and invasive behavior. Cancer Sci 2020; 111:2907-2922. [PMID: 32573871 PMCID: PMC7419026 DOI: 10.1111/cas.14539] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/19/2022] Open
Abstract
Heparan sulfate proteoglycans (HSPGs) act as signaling co‐receptors by interaction of their sulfated glycosaminoglycan chains with numerous signaling molecules. In breast cancer, the function of heparan sulfate 2‐O‐sulfotransferase (HS2ST1), the enzyme mediating 2‐O‐sulfation of HS, is largely unknown. Hence, a comparative study on the functional consequences of HS2ST1 overexpression and siRNA knockdown was performed in the breast cancer cell lines MCF‐7 and MDA‐MB‐231. HS2ST1 overexpression inhibited Matrigel invasion, while its knockdown reversed the phenotype. Likewise, cell motility and adhesion to fibronectin and laminin were affected by altered HS2ST1 expression. Phosphokinase array screening revealed a general decrease in signaling via multiple pathways. Fluorescent ligand binding studies revealed altered binding of fibroblast growth factor 2 (FGF‐2) to HS2ST1‐expressing cells compared with control cells. HS2ST1‐overexpressing cells showed reduced MAPK signaling responses to FGF‐2, and altered expression of epidermal growth factor receptor (EGFR), E‐cadherin, Wnt‐7a, and Tcf4. The increased viability of HS2ST1‐depleted cells was reduced to control levels by pharmacological MAPK pathway inhibition. Moreover, MAPK inhibitors generated a phenocopy of the HS2ST1‐dependent delay in scratch wound repair. In conclusion, HS2ST1 modulation of breast cancer cell invasiveness is a compound effect of altered E‐cadherin and EGFR expression, leading to altered signaling via MAPK and additional pathways.
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Affiliation(s)
- Archana Vijaya Kumar
- Department of Gynecology and Obstetrics, Münster University Hospital, Münster, Germany
| | - Stéphane Brézillon
- CNRS, MEDyC UMR 7369, UFR de Médecine, Université de Reims Champagne-Ardenne, Reims, France
| | | | | | - Sampath Kumar Katakam
- Department of Gynecology and Obstetrics, Münster University Hospital, Münster, Germany
| | - Hossam Taha Mohamed
- CNRS, MEDyC UMR 7369, UFR de Médecine, Université de Reims Champagne-Ardenne, Reims, France.,Department of Zoology, Faculty of Science, Cairo University, Giza, Egypt.,Faculty of Biotechnology, October University for Modern Sciences and Arts, Giza, Egypt
| | - Björn Kemper
- Biomedical Technology Center of the Medical Faculty, University of Münster, Münster, Germany
| | - Burkhard Greve
- Department of Radiotherapy - Radiooncology, University Hospital Münster, Münster, Germany
| | - Benedikt Mohr
- Department of Gynecology and Obstetrics, Münster University Hospital, Münster, Germany
| | | | | | - Ludwig Kiesel
- Department of Gynecology and Obstetrics, Münster University Hospital, Münster, Germany
| | - Mauro S G Pavão
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana M Motta
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Martin Götte
- Department of Gynecology and Obstetrics, Münster University Hospital, Münster, Germany
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16
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Damen LAA, van de Westerlo EMA, Versteeg EMM, van Wessel T, Daamen WF, van Kuppevelt TH. Construction and evaluation of an antibody phage display library targeting heparan sulfate. Glycoconj J 2020; 37:445-455. [PMID: 32468289 PMCID: PMC7329785 DOI: 10.1007/s10719-020-09925-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/30/2020] [Accepted: 04/13/2020] [Indexed: 12/17/2022]
Abstract
Heparan sulfate (HS) is a linear polysaccharide with high structural diversity. Different HS epitopes have been detected and localized using single chain variable fragment (scFv) antibodies from a ‘single pot’ phage display library containing a randomized complementarity determining region of the heavy chain (CDR3). In this study, we created a new library containing anti-HS scFvs that all harbor a dp-38 heavy chain segment where the CDR3 region was engineered to contain the XBBXBX heparin binding consensus site (X = any amino acid, B = R, K or H). The library contained ~1.73 × 106 unique antibodies and was biopanned against HS from several sources. The selected antibodies were sequenced and chemically/immunohistologically characterized. A number of 67 anti-HS scFv antibodies were selected, of which 31 contained a XBBXBX CDR3 sequence. There was a clear preference for glycine at the first and proline at the fourth position of the CDR3. The sequence GZZP(R/K)X (Z = R, K or H, but may also contain N, S, or Q) was unusually overrepresented. Selected antibodies reacted with HS/heparin, but not with other glycosaminoglycans. Antibodies reacted differentially with respect to N-, 2-O, or 6-O-desulfated heparin preparations, and showed distinct topologies of HS epitopes in rat kidney sections. The library may be instrumental in the selection of a large pool of HS epitope-specific antibodies, and - since all antibodies differ only in their 6 amino acid CDR region - may be a tool for a rational design of antibodies recognizing specific HS sulfation patterns.
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Affiliation(s)
- Lars A A Damen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Els M A van de Westerlo
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Elly M M Versteeg
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Thierry van Wessel
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Willeke F Daamen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Toin H van Kuppevelt
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands.
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17
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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18
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The Challenge of Modulating Heparan Sulfate Turnover by Multitarget Heparin Derivatives. Molecules 2020; 25:molecules25020390. [PMID: 31963505 PMCID: PMC7024324 DOI: 10.3390/molecules25020390] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
This review comes as a part of the special issue "Emerging frontiers in GAGs and mimetics". Our interest is in the manipulation of heparan sulfate (HS) turnover by employing HS mimetics/heparin derivatives that exert pleiotropic effects and are interesting for interfering at multiple levels with pathways in which HS is implicated. Due to the important role of heparanase in HS post-biosynthetic modification and catabolism, we focus on the possibility to target heparanase, at both extracellular and intracellular levels, a strategy that can be applied to many conditions, from inflammation to cancer and neurodegeneration.
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19
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Hubka KM, Carson DD, Harrington DA, Farach-Carson MC. Perlecan domain I gradients establish stable biomimetic heparin binding growth factor gradients for cell migration in hydrogels. Acta Biomater 2019; 97:385-398. [PMID: 31351252 DOI: 10.1016/j.actbio.2019.07.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 07/13/2019] [Accepted: 07/23/2019] [Indexed: 12/12/2022]
Abstract
Growth factor gradients orchestrate many biological processes including organogenesis, wound healing, cancer invasion, and metastasis. Heparin-binding growth factor (HBGF) gradients are established in living systems by proteoglycans including the extracellular matrix heparan sulfate proteoglycan, perlecan/HSPG2. Three potential HBGF-binding glycosaminoglycan attachment sites occur in N-terminal domain I of perlecan's five domains. Our overarching goal was to form stable, biomimetic non-covalently bound HBGF gradients surrounding cells encapsulated in hyaluronate-based hydrogels by first establishing perlecan domain I (PlnD1) gradients. A versatile multichannel gradient maker device (MGMD) was designed and 3D printed, then used to create desired gradients of microparticles in hydrogels. Next, we used the device to covalently incorporate gradients of PEGylated PlnD1 in hydrogels with high-low-high or high-medium-low concentrations across the hydrogel width. Fluorescently-labeled fibroblast growth factor-2 was delivered to hydrogels in phosphate-buffered saline and allowed to electrostatically bind to the covalently pre-incorporated PlnD1, producing stable non-covalent HBGF gradients. To test cell viability after flow through the MGMD, delicate primary human salivary stem/progenitor cells were encapsulated in gradient hydrogels where they showed high viability and continued to grow. Next, to test migratory behavior in response to HBGF gradients, two cell types, preosteoblastic MC3T3-E1 cell line and breast cancer cell line MDA-MB-231 were encapsulated in or adjacent to PlnD1-modified hydrogels. Both cell lines migrated toward HBGFs bound to PlnD1. We conclude that establishing covalently-bound PlnD1 gradients in hydrogels provides a new means to establish physiologically-relevant gradients of HBGFs that are useful for a variety of applications in tissue engineering and cancer biology. STATEMENT OF SIGNIFICANCE: Gradients of heparin binding growth factors (HBGFs) direct cell behavior in living systems. HBGFs bind electrostatically to gradients of HS proteoglycans in the extracellular matrix creating HBGF gradients. We recreated HBGF gradients in physiological hyaluronate-based hydrogels using a 3D-printed multichannel gradient maker device (MGMD) that created gradients of HS proteoglycan-derived perlecan/HSPG2 domain I. We demonstrated the ability of a variety of cells, including primary salivary stem/progenitor cells, pre-osteoblastic cells and an invasive breast cancer cell line, to be co-encapsulated in gradient hydrogels by flowing them together through the MGMD. The versatile device and the ability to create HBGF gradients in hydrogels for a variety of applications is innovative and of broad utility in both cancer biology and tissue engineering applications.
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Affiliation(s)
- Kelsea M Hubka
- Department of Bioengineering, Rice University, MS-142, 6100 Main Street, Houston, TX 77005, USA; Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge Street Room 4401, Houston, TX 77054, USA.
| | - Daniel D Carson
- Department of Biosciences, Rice University, MS-140, P.O. Box 1892, Houston, TX 77251, USA; Department of Genetics, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
| | - Daniel A Harrington
- Department of Biosciences, Rice University, MS-140, P.O. Box 1892, Houston, TX 77251, USA; Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge Street Room 4401, Houston, TX 77054, USA.
| | - Mary C Farach-Carson
- Department of Bioengineering, Rice University, MS-142, 6100 Main Street, Houston, TX 77005, USA; Department of Biosciences, Rice University, MS-140, P.O. Box 1892, Houston, TX 77251, USA; Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge Street Room 4401, Houston, TX 77054, USA.
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20
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Sun C, Liu M, Sun P, Yang M, Yates EA, Guo Z, Fernig DG. Sulfated polysaccharides interact with fibroblast growth factors and protect from denaturation. FEBS Open Bio 2019; 9:1477-1487. [PMID: 31271519 PMCID: PMC6668377 DOI: 10.1002/2211-5463.12696] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 01/08/2023] Open
Abstract
Fibroblast growth factors (FGFs) regulate embryonic development and homeostasis, including tissue and organ repair and specific aspects of metabolism. The basic FGF and acidic FGF, now known as FGF2 and FGF1, are widely used protein drugs for tissue repair. However, they are susceptible to denaturation at ambient temperatures and during long-time storage, which will reduce their biological activity. The interaction of FGFs with the sulfated domains of heparan sulfate and heparin is essential for their cellular signaling and stability. Therefore, we analyzed the interactions of FGF1 and FGF2 with four sulfated polysaccharides: heparin, dextran sulfate (DXS), λ-carrageenan, and chondroitin sulfate. The results of thermal stability and cell proliferation assays demonstrate that heparin, DXS, and λ-carrageenan bound to both FGFs and protected them from denaturation. Our results suggest heparin, DXS, and λ-carrageenan are potential formulation materials that bind and stabilize FGFs, and which may also potentiate their activity and control their delivery.
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Affiliation(s)
- Changye Sun
- Henan Key Laboratory of Medical Tissue RegenerationXinxiang Medical UniversityChina
| | - Mengxin Liu
- Henan Key Laboratory of Medical Tissue RegenerationXinxiang Medical UniversityChina
| | - Panwen Sun
- Henan Key Laboratory of Medical Tissue RegenerationXinxiang Medical UniversityChina
| | - Mingming Yang
- Department of CardiologySchool of MedicineAffiliated Zhongda HospitalSoutheast UniversityNanjingChina
| | - Edwin A. Yates
- Department of BiochemistryInstitute of Integrative BiologyUniversity of LiverpoolUK
| | - Zhikun Guo
- Henan Key Laboratory of Medical Tissue RegenerationXinxiang Medical UniversityChina
| | - David G. Fernig
- Department of BiochemistryInstitute of Integrative BiologyUniversity of LiverpoolUK
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21
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Ghiselli G. Heparin Binding Proteins as Therapeutic Target: An Historical Account and Current Trends. MEDICINES (BASEL, SWITZERLAND) 2019; 6:E80. [PMID: 31362364 PMCID: PMC6789896 DOI: 10.3390/medicines6030080] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 12/16/2022]
Abstract
The polyanionic nature and the ability to interact with proteins with different affinities are properties of sulfated glycosaminoglycans (GAGs) that determine their biological function. In designing drugs affecting the interaction of proteins with GAGs the challenge has been to generate agents with high binding specificity. The example to emulated has been a heparin-derived pentasaccharide that binds to antithrombin-III with high affinity. However, the portability of this model to other biological situations is questioned on several accounts. Because of their structural flexibility, oligosaccharides with different sulfation and uronic acid conformation can display the same binding proficiency to different proteins and produce comparable biological effects. This circumstance represents a formidable obstacle to the design of drugs based on the heparin scaffold. The conceptual framework discussed in this article is that through a direct intervention on the heparin-binding functionality of proteins is possible to achieve a high degree of action specificity. This objective is currently pursued through two strategies. The first makes use of small molecules for which in the text we provide examples from past and present literature concerning angiogenic factors and enzymes. The second approach entails the mutagenesis of the GAG-binding site of proteins as a means to generate a new class of biologics of therapeutic interest.
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Affiliation(s)
- Giancarlo Ghiselli
- Independent Researcher, 1326 Spruce Street Suite 706, Philadephia, PA 19107, USA.
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22
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Taylor SL, Hogwood J, Guo W, Yates EA, Turnbull JE. By-Products of Heparin Production Provide a Diverse Source of Heparin-like and Heparan Sulfate Glycosaminoglycans. Sci Rep 2019; 9:2679. [PMID: 30804383 PMCID: PMC6389988 DOI: 10.1038/s41598-019-39093-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/14/2019] [Indexed: 11/09/2022] Open
Abstract
Global production of pharmaceutical heparin (Hp) is increasing, and the production process from raw mucosal material results in large amounts of waste by-products. These contain lower sulfated Hp-like and heparan sulfate (HS), as well as other glycosaminoglycans, which are bioactive entities with pharmaceutical potential. Here we describe the first purification, structural and functional characterisation of Hp-like and HS polysaccharides from the four major by-product fractions of standard heparin production. Analysis of the by-products by disaccharide composition analysis and NMR demonstrated a range of structural characteristics which differentiate them from Hp (particularly reduced sulfation and sulfated disaccharide content), and that they are each distinct. Functional properties of the purified by-products varied, each displaying distinct anticoagulant profiles in different assays, and all exhibiting significantly lower global and specific inhibition of the coagulation pathway than Hp. The by-products retained the ability to promote cell proliferation via fibroblast growth factor receptor signalling, with only minor differences between them. These collective analyses indicate that they represent an untapped and economical source of structurally-diverse Hp-like and HS polysaccharides with the potential for enhancing future structure-activity studies and uncovering new biomedical applications of these important natural products.
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Affiliation(s)
- Sarah L Taylor
- Centre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - John Hogwood
- National Institute for Biological Standards and Controls (NIBSC), Blanche Lane, South Mimms, EN6 3GQ, UK
| | - Wei Guo
- Suzhou Erye Pharmaceutical Co. Ltd, No. 2 Anmin Road, Dongqiao, Huangtai Town, Xiangcheng District, Suzhou, 215000, Jiangsu Province, P.R. China.,Jieyang Runda Casing Co. Ltd., East side No. 1 Street, Jieyang High-tech Industrial Development Zone, Jieyang City, 515500, Guangdong Province, P.R. China
| | - Edwin A Yates
- Centre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jeremy E Turnbull
- Centre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
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23
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Collins LE, Troeberg L. Heparan sulfate as a regulator of inflammation and immunity. J Leukoc Biol 2018; 105:81-92. [PMID: 30376187 DOI: 10.1002/jlb.3ru0618-246r] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/30/2018] [Accepted: 10/01/2018] [Indexed: 12/19/2022] Open
Abstract
Heparan sulfate is found on the surface of most cell types, as well as in basement membranes and extracellular matrices. Its strong anionic properties and highly variable structure enable this glycosaminoglycan to provide binding sites for numerous protein ligands, including many soluble mediators of the immune system, and may promote or inhibit their activity. The formation of ligand binding sites on heparan sulfate (HS) occurs in a tissue- and context-specific fashion through the action of several families of enzymes, most of which have multiple isoforms with subtly different specificities. Changes in the expression levels of these biosynthetic enzymes occur in response to inflammatory stimuli, resulting in structurally different HS and acquisition or loss of binding sites for immune mediators. In this review, we discuss the multiple roles for HS in regulating immune responses, and the evidence for inflammation-associated changes to HS structure.
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Affiliation(s)
- Laura E Collins
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Linda Troeberg
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
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24
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Karamanos NK, Piperigkou Z, Theocharis AD, Watanabe H, Franchi M, Baud S, Brézillon S, Götte M, Passi A, Vigetti D, Ricard-Blum S, Sanderson RD, Neill T, Iozzo RV. Proteoglycan Chemical Diversity Drives Multifunctional Cell Regulation and Therapeutics. Chem Rev 2018; 118:9152-9232. [DOI: 10.1021/acs.chemrev.8b00354] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Nikos K. Karamanos
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras 26110, Greece
- Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), Patras 26110, Greece
| | - Zoi Piperigkou
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras 26110, Greece
- Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), Patras 26110, Greece
| | - Achilleas D. Theocharis
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras 26110, Greece
| | - Hideto Watanabe
- Institute for Molecular Science of Medicine, Aichi Medical University, Aichi 480-1195, Japan
| | - Marco Franchi
- Department for Life Quality Studies, University of Bologna, Rimini 47100, Italy
| | - Stéphanie Baud
- Université de Reims Champagne-Ardenne, Laboratoire SiRMa, CNRS UMR MEDyC 7369, Faculté de Médecine, 51 rue Cognacq Jay, Reims 51100, France
| | - Stéphane Brézillon
- Université de Reims Champagne-Ardenne, Laboratoire de Biochimie Médicale et Biologie Moléculaire, CNRS UMR MEDyC 7369, Faculté de Médecine, 51 rue Cognacq Jay, Reims 51100, France
| | - Martin Götte
- Department of Gynecology and Obstetrics, Münster University Hospital, Münster 48149, Germany
| | - Alberto Passi
- Department of Medicine and Surgery, University of Insubria, Varese 21100, Italy
| | - Davide Vigetti
- Department of Medicine and Surgery, University of Insubria, Varese 21100, Italy
| | - Sylvie Ricard-Blum
- University Claude Bernard Lyon 1, CNRS, UMR 5246, Institute of Molecular and Supramolecular Chemistry and Biochemistry, Villeurbanne 69622, France
| | - Ralph D. Sanderson
- Department of Pathology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Thomas Neill
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 10107, United States
| | - Renato V. Iozzo
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 10107, United States
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25
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Muraoka A, Matsuura Y, Naitow H, Ihara M, Kunishima N. Availability of NHS-biotin labeling to identify free protein lysine revealed by experiment and MD simulation. Anal Biochem 2018; 557:46-58. [PMID: 30025973 DOI: 10.1016/j.ab.2018.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/04/2018] [Accepted: 07/13/2018] [Indexed: 11/27/2022]
Abstract
It is known that the crystallizability of protein molecules may be improved by replacing their surface lysine residues with other residue types. Here an experimental method to identify surface lysine residues by NHS-biotin chemical modification combined with MALDI-TOF MS was proposed and was evaluated using PH1033 protein from Pyrococcus horikoshii. Interestingly, the biotinylation experiment with a protein-reagent molar ratio of 1:1 revealed that only seven of twenty-two lysine residues in the protein comprising 144 residues were labeled. To investigate the result, we analyzed structures from a molecular-dynamics simulation mimicking the experiment. A logistic regression analysis revealed that the biotinylation was significantly correlated with four factors relevant to the local environment of lysine residues: the solvent accessibility, the electrostatic energy, the number of hydrogen bonds, and the estimated pKa value. This result is overall in agreement with that from the same analysis on the crystal structure. However, reflecting the flexibility of the protein molecule in solution state, the factors except for the electrostatic energy were highly variable in the MD structures depending upon the protonation state of Tyr87. The present procedure of biotin-labeling can avoid lysine residues with extensive intramolecular interactions that are incompatible with the rational design of protein crystals.
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Affiliation(s)
- Aiichiro Muraoka
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Matsuura
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hisashi Naitow
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Makoto Ihara
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara City, Nara 631-8505, Japan
| | - Naoki Kunishima
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; RIKEN RSC-Rigaku Collaboration Center, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
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26
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Katagiri Y, Morgan AA, Yu P, Bangayan NJ, Junka R, Geller HM. Identification of novel binding sites for heparin in receptor protein-tyrosine phosphatase (RPTPσ): Implications for proteoglycan signaling. J Biol Chem 2018; 293:11639-11647. [PMID: 29880643 DOI: 10.1074/jbc.ra118.003081] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/24/2018] [Indexed: 12/31/2022] Open
Abstract
Receptor protein-tyrosine phosphatase RPTPσ has important functions in modulating neural development and regeneration. Compelling evidence suggests that both heparan sulfate (HS) and chondroitin sulfate (CS) glycosaminoglycans (GAGs) bind to a series of Lys residues located in the first Ig domain of RPTPσ. However, HS promotes and CS inhibits axonal growth. Mutation of these Lys residues abolished binding and signal transduction of RPTPσ to CS, whereas HS binding was reduced, and signaling persisted. This activity was mediated through novel heparin-binding sites identified in the juxtamembrane region. Although different functional outcomes of HS and CS have been previously attributed to the differential oligomeric state of RPTPσ upon GAG binding, we found that RPTPσ was clustered by both heparin and CS GAG rich in 4,6-O-disulfated disaccharide units. We propose an additional mechanism by which RPTPσ distinguishes between HS and CS through these novel binding sites.
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Affiliation(s)
- Yasuhiro Katagiri
- Laboratory of Developmental Neurobiology, Cell Biology and Physiology Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20892.
| | - Ashlea A Morgan
- Laboratory of Developmental Neurobiology, Cell Biology and Physiology Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Panpan Yu
- Laboratory of Developmental Neurobiology, Cell Biology and Physiology Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Nathanael J Bangayan
- Laboratory of Developmental Neurobiology, Cell Biology and Physiology Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Radoslaw Junka
- Laboratory of Developmental Neurobiology, Cell Biology and Physiology Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Herbert M Geller
- Laboratory of Developmental Neurobiology, Cell Biology and Physiology Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
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27
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Kjellén L, Lindahl U. Specificity of glycosaminoglycan–protein interactions. Curr Opin Struct Biol 2018; 50:101-108. [DOI: 10.1016/j.sbi.2017.12.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/15/2017] [Accepted: 12/22/2017] [Indexed: 12/21/2022]
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28
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Rudd TR, Preston MD, Yates EA. The nature of the conserved basic amino acid sequences found among 437 heparin binding proteins determined by network analysis. MOLECULAR BIOSYSTEMS 2018; 13:852-865. [PMID: 28317949 DOI: 10.1039/c6mb00857g] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In multicellular organisms, a large number of proteins interact with the polyanionic polysaccharides heparan sulphate (HS) and heparin. These interactions are usually assumed to be dominated by charge-charge interactions between the anionic carboxylate and/or sulfate groups of the polysaccharide and cationic amino acids of the protein. A major question is whether there exist conserved amino acid sequences for HS/heparin binding among these diverse proteins. Potentially conserved HS/heparin binding sequences were sought amongst 437 HS/heparin binding proteins. Amino acid sequences were extracted and compared using a Levenshtein distance metric. The resultant similarity matrices were visualised as graphs, enabling extraction of strongly conserved sequences from highly variable primary sequences while excluding short, core regions. This approach did not reveal extensive, conserved HS/heparin binding sequences, rather a number of shorter, more widely spaced sequences that may work in unison to form heparin-binding sites on protein surfaces, arguing for convergent evolution. Thus, it is the three-dimensional arrangement of these conserved motifs on the protein surface, rather than the primary sequence per se, which are the evolutionary elements.
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Affiliation(s)
- Timothy R Rudd
- The National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK.
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29
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Mackmull MT, Klaus B, Heinze I, Chokkalingam M, Beyer A, Russell RB, Ori A, Beck M. Landscape of nuclear transport receptor cargo specificity. Mol Syst Biol 2017; 13:962. [PMID: 29254951 PMCID: PMC5740495 DOI: 10.15252/msb.20177608] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Nuclear transport receptors (NTRs) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore complexes (NPCs). About 30 different NTRs constitute different transport pathways in humans and bind to a multitude of different cargos. The exact cargo spectrum of the majority of NTRs, their specificity and even the extent to which active nucleocytoplasmic transport contributes to protein localization remains understudied because of the transient nature of these interactions and the wide dynamic range of cargo concentrations. To systematically map cargo-NTR relationships in situ, we used proximity ligation coupled to mass spectrometry (BioID). We systematically fused the engineered biotin ligase BirA* to 16 NTRs. We estimate that a considerable fraction of the human proteome is subject to active nuclear transport. We quantified the specificity and redundancy in NTR interactions and identified transport pathways for cargos. We extended the BioID method by the direct identification of biotinylation sites. This approach enabled us to identify interaction interfaces and to discriminate direct versus piggyback transport mechanisms. Data are available via ProteomeXchange with identifier PXD007976.
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Affiliation(s)
- Marie-Therese Mackmull
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Bernd Klaus
- Centre for Statistical Data Analysis, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ivonne Heinze
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Andreas Beyer
- Cellular Networks and Systems Biology, CECAD, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Robert B Russell
- Heidelberg University Biochemistry Centre & Bioquant, Heidelberg, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany .,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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30
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Shen D, Podolnikova NP, Yakubenko VP, Ardell CL, Balabiyev A, Ugarova TP, Wang X. Pleiotrophin, a multifunctional cytokine and growth factor, induces leukocyte responses through the integrin Mac-1. J Biol Chem 2017; 292:18848-18861. [PMID: 28939773 DOI: 10.1074/jbc.m116.773713] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 09/08/2017] [Indexed: 12/27/2022] Open
Abstract
Pleiotrophin (PTN) is a multifunctional, cationic, glycosaminoglycan-binding cytokine and growth factor involved in numerous physiological and pathological processes, including tissue repair and inflammation-related diseases. PTN has been shown to promote leukocyte responses by inducing their migration and expression of inflammatory cytokines. However, the mechanisms through which PTN mediates these responses remain unclear. Here, we identified the integrin Mac-1 (αMβ2, CD11b/CD18) as the receptor mediating macrophage adhesion and migration to PTN. We also found that expression of Mac-1 on the surface of human embryonic kidney (HEK) 293 cells induced their adhesion and migration to PTN. Accordingly, PTN promoted Mac-1-dependent cell spreading and initiated intracellular signaling manifested in phosphorylation of Erk1/2. While binding to PTN, Mac-1 on Mac-1-expressing HEK293 cells appears to cooperate with cell-surface proteoglycans because both anti-Mac-1 function-blocking mAb and heparin were required to block adhesion. Moreover, biolayer interferometry and NMR indicated a direct interaction between the αMI domain, the major ligand-binding region of Mac-1, and PTN. Using peptide libraries, we found that in PTN the αMI domain bound sequences enriched in basic and hydrophobic residues, indicating that PTN conforms to the general principle of ligand-recognition specificity of the αMI domain toward cationic proteins/peptides. Finally, using recombinant PTN-derived fragments, we show that PTN contains two distinct Mac-1-binding sites in each of its constitutive domains. Collectively, these results identify PTN as a ligand for the integrin Mac-1 on the surface of leukocytes and suggest that this interaction may play a role in inflammatory responses.
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Affiliation(s)
- Di Shen
- From the Schools of Molecular and
| | | | - Valentin P Yakubenko
- Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
| | - Christopher L Ardell
- Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
| | - Arnat Balabiyev
- Life Sciences, Arizona State University, Tempe, Arizona 85287 and
| | | | - Xu Wang
- From the Schools of Molecular and
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31
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Ayerst BI, Merry CLR, Day AJ. The Good the Bad and the Ugly of Glycosaminoglycans in Tissue Engineering Applications. Pharmaceuticals (Basel) 2017; 10:E54. [PMID: 28608822 PMCID: PMC5490411 DOI: 10.3390/ph10020054] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/05/2017] [Accepted: 06/05/2017] [Indexed: 12/14/2022] Open
Abstract
High sulfation, low cost, and the status of heparin as an already FDA- and EMA- approved product, mean that its inclusion in tissue engineering (TE) strategies is becoming increasingly popular. However, the use of heparin may represent a naïve approach. This is because tissue formation is a highly orchestrated process, involving the temporal expression of numerous growth factors and complex signaling networks. While heparin may enhance the retention and activity of certain growth factors under particular conditions, its binding 'promiscuity' means that it may also inhibit other factors that, for example, play an important role in tissue maintenance and repair. Within this review we focus on articular cartilage, highlighting the complexities and highly regulated processes that are involved in its formation, and the challenges that exist in trying to effectively engineer this tissue. Here we discuss the opportunities that glycosaminoglycans (GAGs) may provide in advancing this important area of regenerative medicine, placing emphasis on the need to move away from the common use of heparin, and instead focus research towards the utility of specific GAG preparations that are able to modulate the activity of growth factors in a more controlled and defined manner, with less off-target effects.
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Affiliation(s)
- Bethanie I Ayerst
- Wellcome Trust Centre for Cell-Matrix Research, Division of Cell-Matrix Biology & Regenerative Medicine, School of Biology, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK.
| | - Catherine L R Merry
- Stem Cell Glycobiology Group, Wolfson Centre for Stem Cells, Tissue Engineering & Modelling (STEM), Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Anthony J Day
- Wellcome Trust Centre for Cell-Matrix Research, Division of Cell-Matrix Biology & Regenerative Medicine, School of Biology, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK.
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32
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Nagarajan B, Sankaranarayanan NV, Patel BB, Desai UR. A molecular dynamics-based algorithm for evaluating the glycosaminoglycan mimicking potential of synthetic, homogenous, sulfated small molecules. PLoS One 2017; 12:e0171619. [PMID: 28182755 PMCID: PMC5300208 DOI: 10.1371/journal.pone.0171619] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/23/2017] [Indexed: 01/06/2023] Open
Abstract
Glycosaminoglycans (GAGs) are key natural biopolymers that exhibit a range of biological functions including growth and differentiation. Despite this multiplicity of function, natural GAG sequences have not yielded drugs because of problems of heterogeneity and synthesis. Recently, several homogenous non-saccharide glycosaminoglycan mimetics (NSGMs) have been reported as agents displaying major therapeutic promise. Yet, it remains unclear whether sulfated NSGMs structurally mimic sulfated GAGs. To address this, we developed a three-step molecular dynamics (MD)-based algorithm to compare sulfated NSGMs with GAGs. In the first step of this algorithm, parameters related to the range of conformations sampled by the two highly sulfated molecules as free entities in water were compared. The second step compared identity of binding site geometries and the final step evaluated comparable dynamics and interactions in the protein-bound state. Using a test case of interactions with fibroblast growth factor-related proteins, we show that this three-step algorithm effectively predicts the GAG structure mimicking property of NSGMs. Specifically, we show that two unique dimeric NSGMs mimic hexameric GAG sequences in the protein-bound state. In contrast, closely related monomeric and trimeric NSGMs do not mimic GAG in either the free or bound states. These results correspond well with the functional properties of NSGMs. The results show for the first time that appropriately designed sulfated NSGMs can be good structural mimetics of GAGs and the incorporation of a MD-based strategy at the NSGM library screening stage can identify promising mimetics of targeted GAG sequences.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Bhaumik B. Patel
- Hunter Holmes Muire VA Medical Center, Richmond, Virginia, United States of America
- Division of Hematology, Oncology, and Palliative Care, Department of Internal Medicine and Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
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33
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Li Y, Sun C, Yates EA, Jiang C, Wilkinson MC, Fernig DG. Heparin binding preference and structures in the fibroblast growth factor family parallel their evolutionary diversification. Open Biol 2016; 6:rsob.150275. [PMID: 27030175 PMCID: PMC4821243 DOI: 10.1098/rsob.150275] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The interaction of a large number of extracellular proteins with heparan sulfate (HS) regulates their transport and effector functions, but the degree of molecular specificity underlying protein–polysaccharide binding is still debated. The 15 paracrine fibroblast growth factors (FGFs) are one of the paradigms for this interaction. Here, we measure the binding preferences of six FGFs (FGF3, FGF4, FGF6, FGF10, FGF17, FGF20) for a library of modified heparins, representing structures in HS, and model glycosaminoglycans, using differential scanning fluorimetry. This is complemented by the identification of the lysine residues in the primary and secondary binding sites of the FGFs by a selective labelling approach. Pooling these data with previous sets provides good coverage of the FGF phylogenetic tree, deduced from amino acid sequence alignment. This demonstrates that the selectivity of the FGFs for binding structures in sulfated polysaccharides and the pattern of secondary binding sites on the surface of FGFs follow the phylogenetic relationship of the FGFs, and so are likely to be the result of the natural selection pressures that led to the expansion of the FGF family in the course of the evolution of more complex animal body plans.
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Affiliation(s)
- Yong Li
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Changye Sun
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Edwin A Yates
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Chao Jiang
- School of Pharmaceutical Science, Wenzhou Medical University, Chashan University Park, Wenzhou 325035, China
| | - Mark C Wilkinson
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - David G Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
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34
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Ulbricht D, Oertwig K, Arnsburg K, Saalbach A, Pippel J, Sträter N, Heiker JT. Basic Residues of β-Sheet A Contribute to Heparin Binding and Activation of Vaspin (Serpin A12). J Biol Chem 2016; 292:994-1004. [PMID: 27941022 DOI: 10.1074/jbc.m116.748020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/14/2016] [Indexed: 01/08/2023] Open
Abstract
Many members of the serine protease inhibitor (serpin) family are activated by glycosaminoglycans (GAGs). Visceral adipose tissue-derived serpin (vaspin), serpin A12 of the serpin family, and its target protease kallikrein 7 (KLK7) are heparin-binding proteins, and inhibition of KLK7 by vaspin is accelerated by heparin. However, the nature of GAG binding to vaspin is not known. Here, we measured vaspin binding of various glycosaminoglycans and low molecular weight heparins by microscale thermophoresis and analyzed acceleration of protease inhibition by these molecules. In addition, basic residues contributing to heparin binding and heparin activation were identified by a selective labeling approach. Together, these data show that vaspin binds heparin with high affinity (KD = 21 ± 2 nm) and that binding takes place at a basic patch on top of β-sheet A and is different from other heparin-binding serpins. Mutation of basic residues decreased heparin binding and activation of vaspin. Similarly, reactive center loop insertion into sheet A decreased heparin binding because it disturbs the basic cluster. Finally, using vaspin-overexpressing keratinocyte cells, we show that a significant part of secreted vaspin is bound in the extracellular matrix on the cell surface. Together, basic residues of central β-sheet A contribute to heparin binding and activation of vaspin. Thus, binding to GAGs in the extracellular matrix can direct and regulate vaspin interaction with target proteases or other proteins and may play an important role in the various beneficial functions of vaspin in different tissues.
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Affiliation(s)
- David Ulbricht
- From the Institute of Biochemistry, Faculty of Biosciences, Pharmacy, and Psychology
| | - Kathrin Oertwig
- From the Institute of Biochemistry, Faculty of Biosciences, Pharmacy, and Psychology
| | - Kristin Arnsburg
- From the Institute of Biochemistry, Faculty of Biosciences, Pharmacy, and Psychology
| | - Anja Saalbach
- the Department of Dermatology, Venerology, and Allergology, and
| | - Jan Pippel
- the Center for Biotechnology and Biomedicine, Institute of Bioanalytical Chemistry, University of Leipzig, 04103 Leipzig, Germany
| | - Norbert Sträter
- the Center for Biotechnology and Biomedicine, Institute of Bioanalytical Chemistry, University of Leipzig, 04103 Leipzig, Germany
| | - John T Heiker
- From the Institute of Biochemistry, Faculty of Biosciences, Pharmacy, and Psychology,
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35
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Ricard-Blum S, Lisacek F. Glycosaminoglycanomics: where we are. Glycoconj J 2016; 34:339-349. [PMID: 27900575 DOI: 10.1007/s10719-016-9747-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/28/2016] [Accepted: 11/01/2016] [Indexed: 01/21/2023]
Abstract
Glycosaminoglycans regulate numerous physiopathological processes such as development, angiogenesis, innate immunity, cancer and neurodegenerative diseases. Cell surface GAGs are involved in cell-cell and cell-matrix interactions, cell adhesion and signaling, and host-pathogen interactions. GAGs contribute to the assembly of the extracellular matrix and heparan sulfate chains are able to sequester growth factors in the ECM. Their biological activities are regulated by their interactions with proteins. The structural heterogeneity of GAGs, mostly due to chemical modifications occurring during and after their synthesis, makes the development of analytical techniques for their profiling in cells, tissues, and biological fluids, and of computational tools for mining GAG-protein interaction data very challenging. We give here an overview of the experimental approaches used in glycosaminoglycomics, of the major GAG-protein interactomes characterized so far, and of the computational tools and databases available to analyze and store GAG structures and interactions.
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Affiliation(s)
- Sylvie Ricard-Blum
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, UMR 5246 CNRS - Université Lyon 1, INSA Lyon, CPE Lyon, 69622, Villeurbanne Cedex, France.
| | - Frédérique Lisacek
- SIB Swiss Institute of Bioinformatics, 1 Rue Michel-Servet, 1211, Geneva, Switzerland.,Computer Science Department, University of Geneva, Geneva, Switzerland
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Miller RL, Guimond SE, Shivkumar M, Blocksidge J, Austin JA, Leary JA, Turnbull JE. Heparin Isomeric Oligosaccharide Separation Using Volatile Salt Strong Anion Exchange Chromatography. Anal Chem 2016; 88:11542-11550. [DOI: 10.1021/acs.analchem.6b02801] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Rebecca L. Miller
- Centre
for Glycobiology, Department of Biochemistry, Institute of Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
- Departments
of Molecular and Cellular Biology and Chemistry, University of California, 1 Shields Drive, Davis, California 95616, United States
| | - Scott E. Guimond
- Centre
for Glycobiology, Department of Biochemistry, Institute of Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Maitreyi Shivkumar
- Centre
for Glycobiology, Department of Biochemistry, Institute of Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Jemma Blocksidge
- Centre
for Glycobiology, Department of Biochemistry, Institute of Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - James A. Austin
- Centre
for Glycobiology, Department of Biochemistry, Institute of Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Julie A. Leary
- Departments
of Molecular and Cellular Biology and Chemistry, University of California, 1 Shields Drive, Davis, California 95616, United States
| | - Jeremy E. Turnbull
- Centre
for Glycobiology, Department of Biochemistry, Institute of Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
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37
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Leitner A. Cross-linking and other structural proteomics techniques: how chemistry is enabling mass spectrometry applications in structural biology. Chem Sci 2016; 7:4792-4803. [PMID: 30155128 PMCID: PMC6016523 DOI: 10.1039/c5sc04196a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 04/25/2016] [Indexed: 01/05/2023] Open
Abstract
The biological function of proteins is heavily influenced by their structures and their organization into assemblies such as protein complexes and regulatory networks. Mass spectrometry (MS) has been a key enabling technology for high-throughput and comprehensive protein identification and quantification on a proteome-wide scale. Besides these essential contributions, MS can also be used to study higher-order structures of biomacromolecules in a variety of ways. In one approach, intact proteins or protein complexes may be directly probed in the mass spectrometer. Alternatively, various forms of solution-phase chemistry are used to introduce modifications in intact proteins and localizing these modifications by MS analysis at the peptide level is used to derive structural information. Here, I will put a spotlight on the central role of chemistry in such mass spectrometry-based methods that bridge proteomics and structural biology, with a particular emphasis on chemical cross-linking of protein complexes.
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Affiliation(s)
- Alexander Leitner
- Department of Biology , Institute of Molecular Systems Biology , ETH Zurich , Auguste-Piccard-Hof 1 , 8093 Zurich , Switzerland .
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38
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Wijesinghe SJ, Ling L, Murali S, Qing YH, Hinkley SFR, Carnachan SM, Bell TJ, Swaminathan K, Hui JH, van Wijnen AJ, Nurcombe V, Cool SM. Affinity Selection of FGF2-Binding Heparan Sulfates for Ex Vivo Expansion of Human Mesenchymal Stem Cells. J Cell Physiol 2016; 232:566-575. [PMID: 27291835 DOI: 10.1002/jcp.25454] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 06/10/2016] [Indexed: 12/25/2022]
Abstract
The future of human mesenchymal stem cells (hMSCs) as a successful cell therapy relies on bioprocessing strategies to improve the scalability of these cells without compromising their therapeutic ability. The culture-expansion of hMSCs can be enhanced by supplementation with growth factors, particularly fibroblast growth factor 2 (FGF2). The biological activity of FGF2 is controlled through interactions with heparan sulfate (HS) that facilitates ligand-receptor complex formation. We previously reported on an FGF2-interacting HS variant (termed HS2) isolated from embryonic tissue by anionic exchange chromatography that increased the proliferation and potency of hMSCs. Here, we detail the isolation of an FGF2 affinity-purified HS variant (HS8) using a scalable platform technology previously employed to generate HS variants with increased affinity for BMP-2 or VEGF165 . This process used a peptide sequence derived from the heparin-binding domain of FGF2 as a substrate to affinity-isolate HS8 from a commercially available source of porcine mucosal HS. Our data show that HS8 binds to FGF2 with higher affinity than to FGF1, FGF7, BMP2, PDGF-BB, or VEGF165 . Also, HS8 protects FGF2 from thermal destabilization and increases FGF signaling and hMSC proliferation through FGF receptor 1. Long-term supplementation of cultures with HS8 increased both hMSC numbers and their colony-forming efficiency without adversely affecting the expression of hMSC-related cell surface antigens. This strategy further exemplifies the utility of affinity-purifying HS variants against particular ligands important to the stem cell microenvironment and advocates for their addition as adjuvants for the culture-expansion of hMSCs destined for cellular therapy. J. Cell. Physiol. 232: 566-575, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Ling Ling
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Sadasivam Murali
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yeong Hui Qing
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Simon F R Hinkley
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Susan M Carnachan
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Tracey J Bell
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | | | - James H Hui
- Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Andre J van Wijnen
- Department of Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Victor Nurcombe
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Simon M Cool
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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39
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Migliorini E, Thakar D, Kühnle J, Sadir R, Dyer DP, Li Y, Sun C, Volkman BF, Handel TM, Coche-Guerente L, Fernig DG, Lortat-Jacob H, Richter RP. Cytokines and growth factors cross-link heparan sulfate. Open Biol 2016; 5:rsob.150046. [PMID: 26269427 PMCID: PMC4554917 DOI: 10.1098/rsob.150046] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The glycosaminoglycan heparan sulfate (HS), present at the surface of most cells and ubiquitous in extracellular matrix, binds many soluble extracellular signalling molecules such as chemokines and growth factors, and regulates their transport and effector functions. It is, however, unknown whether upon binding HS these proteins can affect the long-range structure of HS. To test this idea, we interrogated a supramolecular model system, in which HS chains grafted to streptavidin-functionalized oligoethylene glycol monolayers or supported lipid bilayers mimic the HS-rich pericellular or extracellular matrix, with the biophysical techniques quartz crystal microbalance (QCM-D) and fluorescence recovery after photobleaching (FRAP). We were able to control and characterize the supramolecular presentation of HS chains—their local density, orientation, conformation and lateral mobility—and their interaction with proteins. The chemokine CXCL12α (or SDF-1α) rigidified the HS film, and this effect was due to protein-mediated cross-linking of HS chains. Complementary measurements with CXCL12α mutants and the CXCL12γ isoform provided insight into the molecular mechanism underlying cross-linking. Fibroblast growth factor 2 (FGF-2), which has three HS binding sites, was also found to cross-link HS, but FGF-9, which has just one binding site, did not. Based on these data, we propose that the ability to cross-link HS is a generic feature of many cytokines and growth factors, which depends on the architecture of their HS binding sites. The ability to change matrix organization and physico-chemical properties (e.g. permeability and rigidification) implies that the functions of cytokines and growth factors may not simply be confined to the activation of cognate cellular receptors.
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Affiliation(s)
- Elisa Migliorini
- Université Grenoble Alpes, Departement de Chimie Moléculaire (DCM), Grenoble, France CNRS, DCM, Grenoble, France CIC biomaGUNE, San Sebastian, Spain
| | - Dhruv Thakar
- Université Grenoble Alpes, Departement de Chimie Moléculaire (DCM), Grenoble, France CNRS, DCM, Grenoble, France
| | - Jens Kühnle
- Department of Biophysical Chemistry, University of Heidelberg, Heidelberg, Germany
| | - Rabia Sadir
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), Grenoble, France CNRS, IBS, Grenoble, France CEA, IBS, Grenoble, France
| | - Douglas P Dyer
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA
| | - Yong Li
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Changye Sun
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Tracy M Handel
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA
| | - Liliane Coche-Guerente
- Université Grenoble Alpes, Departement de Chimie Moléculaire (DCM), Grenoble, France CNRS, DCM, Grenoble, France
| | - David G Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Hugues Lortat-Jacob
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), Grenoble, France CNRS, IBS, Grenoble, France CEA, IBS, Grenoble, France
| | - Ralf P Richter
- Université Grenoble Alpes, Departement de Chimie Moléculaire (DCM), Grenoble, France CNRS, DCM, Grenoble, France CIC biomaGUNE, San Sebastian, Spain Max Planck Institute for Intelligent Systems, Stuttgart, Germany
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40
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Ryan E, Shen D, Wang X. Structural studies reveal an important role for the pleiotrophin C-terminus in mediating interactions with chondroitin sulfate. FEBS J 2016; 283:1488-503. [PMID: 26896299 DOI: 10.1111/febs.13686] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 12/30/2015] [Accepted: 02/15/2016] [Indexed: 12/26/2022]
Abstract
UNLABELLED Pleiotrophin (PTN) is a potent glycosaminoglycan-binding cytokine that is important in neural development, angiogenesis and tissue regeneration. Much of its activity is attributed to its interactions with the chondroitin sulfate (CS) proteoglycan, receptor type protein tyrosine phosphatase ζ (PTPRZ). However, there is little high resolution structural information on the interactions between PTN and CS, nor is it clear why the C-terminal tail of PTN is necessary for signaling through PTPRZ, even though it does not contribute to heparin binding. We determined the first structure of PTN and analyzed its interactions with CS. Our structure shows that PTN possesses large basic surfaces on both of its structured domains and also that residues in the hinge segment connecting the domains have significant contacts with the C-terminal domain. Our analysis of PTN-CS interactions showed that the C-terminal tail of PTN is essential for maintaining stable interactions with chondroitin sulfate A, the type of CS commonly found on PTPRZ. These results offer the first possible explanation of why truncated PTN missing the C-terminal tail is unable to signal through PTPRZ. NMR analysis of the interactions of PTN with CS revealed that the C-terminal domain and hinge of PTN make up the major CS-binding site in PTN, and that removal of the C-terminal tail weakened the affinity of the site for CSA but not for other high sulfation density CS. DATABASE Coordinates of the ensemble of ten PTN structures have been deposited in RCSB under accession number 2n6f. Chemical shifts assignments and structural constraints have been deposited in BMRB under accession number 25762.
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Affiliation(s)
- Eathen Ryan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Di Shen
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Xu Wang
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
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41
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Sun C, Marcello M, Li Y, Mason D, Lévy R, Fernig DG. Selectivity in glycosaminoglycan binding dictates the distribution and diffusion of fibroblast growth factors in the pericellular matrix. Open Biol 2016; 6:150277. [PMID: 27009190 PMCID: PMC4821244 DOI: 10.1098/rsob.150277] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/02/2016] [Indexed: 12/13/2022] Open
Abstract
The range of biological outcomes generated by many signalling proteins in development and homeostasis is increased by their interactions with glycosaminoglycans, particularly heparan sulfate (HS). This interaction controls the localization and movement of these signalling proteins, but whether such control depends on the specificity of the interactions is not known. We used five fibroblast growth factors with an N-terminal HaloTag (Halo-FGFs) for fluorescent labelling, with well-characterized and distinct HS-binding properties, and measured their binding and diffusion in pericellular matrix of fixed rat mammary 27 fibroblasts. Halo-FGF1, Halo-FGF2 and Halo-FGF6 bound to HS, whereas Halo-FGF10 also interacted with chondroitin sulfate/dermatan sulfate, and FGF20 did not bind detectably. The distribution of bound FGFs in the pericellular matrix was not homogeneous, and for FGF10 exhibited striking clusters. Fluorescence recovery after photobleaching showed that FGF2 and FGF6 diffused faster, whereas FGF1 diffused more slowly, and FGF10 was immobile. The results demonstrate that the specificity of the interactions of proteins with glycosaminoglycans controls their binding and diffusion. Moreover, cells regulate the spatial distribution of different protein-binding sites in glycosaminoglycans independently of each other, implying that the extracellular matrix has long-range structure.
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Affiliation(s)
- Changye Sun
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Marco Marcello
- Centre for Cell Imaging, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Yong Li
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - David Mason
- Centre for Cell Imaging, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Raphaël Lévy
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - David G Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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42
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Nunes QM, Li Y, Sun C, Kinnunen TK, Fernig DG. Fibroblast growth factors as tissue repair and regeneration therapeutics. PeerJ 2016; 4:e1535. [PMID: 26793421 PMCID: PMC4715458 DOI: 10.7717/peerj.1535] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/05/2015] [Indexed: 12/25/2022] Open
Abstract
Cell communication is central to the integration of cell function required for the development and homeostasis of multicellular animals. Proteins are an important currency of cell communication, acting locally (auto-, juxta-, or paracrine) or systemically (endocrine). The fibroblast growth factor (FGF) family contributes to the regulation of virtually all aspects of development and organogenesis, and after birth to tissue maintenance, as well as particular aspects of organism physiology. In the West, oncology has been the focus of translation of FGF research, whereas in China and to an extent Japan a major focus has been to use FGFs in repair and regeneration settings. These differences have their roots in research history and aims. The Chinese drive into biotechnology and the delivery of engineered clinical grade FGFs by a major Chinese research group were important enablers in this respect. The Chinese language clinical literature is not widely accessible. To put this into context, we provide the essential molecular and functional background to the FGF communication system covering FGF ligands, the heparan sulfate and Klotho co-receptors and FGF receptor (FGFR) tyrosine kinases. We then summarise a selection of clinical reports that demonstrate the efficacy of engineered recombinant FGF ligands in treating a wide range of conditions that require tissue repair/regeneration. Alongside, the functional reasons why application of exogenous FGF ligands does not lead to cancers are described. Together, this highlights that the FGF ligands represent a major opportunity for clinical translation that has been largely overlooked in the West.
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Affiliation(s)
- Quentin M. Nunes
- Department of Molecular and Clinical Cancer Medicine, NIHR Liverpool Pancreas Biomedical Research Unit, University of Liverpool, Liverpool, United Kingdom
| | - Yong Li
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Changye Sun
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Tarja K. Kinnunen
- Department of Biology, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - David G. Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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43
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Lee J, Wee S, Gunaratne J, Chua RJE, Smith RAA, Ling L, Fernig DG, Swaminathan K, Nurcombe V, Cool SM. Structural determinants of heparin-transforming growth factor-β1 interactions and their effects on signaling. Glycobiology 2015; 25:1491-504. [PMID: 26306634 DOI: 10.1093/glycob/cwv064] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/08/2015] [Indexed: 12/28/2022] Open
Abstract
Transforming growth factor-β1 (TGF-β1, Uniprot: P01137) is a heparin-binding protein that has been implicated in a number of physiological processes, including the initiation of chondrogenesis by human mesenchymal stem cells (hMSCs). Here, we identify the molecular features in the protein and in heparin required for binding and their effects on the potentiation of TGF-β1's activity on hMSCs. Using a proteomics "Protect and Label" approach, lysines K291, K304, K309, K315, K338, K373, K375 and K388 were identified as being directly involved in binding heparin (Data are available via ProteomeXchange with identifier PXD002772). Competition assays in an optical biosensor demonstrated that TGF-β1 does require N- and 6-O-sulfate groups for binding but that 2-O-sulfate groups are unlikely to underpin the interaction. Heparin-derived oligosaccharides as short as degree of polymerization (dp) 4 have a weak ability to compete for TGF-β1 binding to heparin, which increases with the length of the oligosaccharide to reach a maximum between dp18 and dp24. In cell-based assays, heparin, 2-O-, 6-O- and N-desulfated re-N-acetylated heparin and oligosaccharides 14-24 saccharides (dp14-24) in length all increased the phosphorylation of mothers against decapentaplegic homolog 2 (SMAD2) after 6 h of stimulation with TGF-β1. The results provide the structural basis for a model of heparin/heparan sulfate binding to TGF-β1 and demonstrate that the features in the polysaccharide required for binding are not identical to those required for sustaining the signaling by TGF-β1 in hMSCs.
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Affiliation(s)
- Jonathan Lee
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore 117456 Glycotherapeutics Group, Institute of Medical Biology, Agency for Science, Technology and Research, Singapore, Singapore 138648
| | - Sheena Wee
- Quantitative Proteomics Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore 138673
| | - Jayantha Gunaratne
- Quantitative Proteomics Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore 138673
| | - R J E Chua
- Glycotherapeutics Group, Institute of Medical Biology, Agency for Science, Technology and Research, Singapore, Singapore 138648
| | - Raymond A A Smith
- Glycotherapeutics Group, Institute of Medical Biology, Agency for Science, Technology and Research, Singapore, Singapore 138648
| | - Ling Ling
- Glycotherapeutics Group, Institute of Medical Biology, Agency for Science, Technology and Research, Singapore, Singapore 138648
| | - David G Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | | | - Victor Nurcombe
- Glycotherapeutics Group, Institute of Medical Biology, Agency for Science, Technology and Research, Singapore, Singapore 138648 Lee Kong Chian School of Medicine, Nanyang Technological University-Imperial College, Singapore, Singapore 639798
| | - Simon M Cool
- Glycotherapeutics Group, Institute of Medical Biology, Agency for Science, Technology and Research, Singapore, Singapore 138648 Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore 119228
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A novel chemical footprinting approach identifies critical lysine residues involved in the binding of receptor-associated protein to cluster II of LDL receptor-related protein. Biochem J 2015; 468:65-72. [PMID: 25728577 DOI: 10.1042/bj20140977] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Tandem mass tags (TMTs) were utilized in a novel chemical footprinting approach to identify lysine residues that mediate the interaction of receptor-associated protein (RAP) with cluster II of LDL (low-density lipoprotein) receptor (LDLR)-related protein (LRP). The isolated RAP D3 domain was modified with TMT-126 and the D3 domain-cluster II complex with TMT-127. Nano-LC-MS analysis revealed reduced modification with TMT-127 of peptides including Lys(256), Lys(270) and Lys(305)-Lys(306) suggesting that these residues contribute to cluster II binding. This agrees with previous findings that Lys(256) and Lys(270) are critical for binding cluster II sub-domains [Fisher, Beglova and Blacklow (2006) Mol. Cell 22, 277-283]. Cluster II-binding studies utilizing D3 domain variants K(256)A, K(305)A and K(306)A now showed that Lys(306) contributes to cluster II binding as well. For full-length RAP, we observed that peptides including Lys(60), Lys(191), Lys(256), Lys(270) and Lys(305)-Lys(306) exhibited reduced modification with TMT in the RAP-cluster II complex. Notably, Lys(60) has previously been implicated to mediate D1 domain interaction with cluster II. Our results suggest that also Lys(191) of the D2 domain contributes to cluster II binding. Binding studies employing the RAP variants K(191)A, K(256)A, K(305)A and K(306)A, however, revealed a modest reduction in cluster II binding for the K(256)A variant only. This suggests that the other lysine residues can compensate for the absence of a single lysine residue for effective complex assembly. Collectively, novel insight has been obtained into the contribution of lysine residues of RAP to cluster II binding. In addition, we propose that TMTs can be utilized to identify lysine residues critical for protein complex formation.
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45
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Heparin/Heparan sulfate proteoglycans glycomic interactome in angiogenesis: biological implications and therapeutical use. Molecules 2015; 20:6342-88. [PMID: 25867824 PMCID: PMC6272510 DOI: 10.3390/molecules20046342] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 12/20/2022] Open
Abstract
Angiogenesis, the process of formation of new blood vessel from pre-existing ones, is involved in various intertwined pathological processes including virus infection, inflammation and oncogenesis, making it a promising target for the development of novel strategies for various interventions. To induce angiogenesis, angiogenic growth factors (AGFs) must interact with pro-angiogenic receptors to induce proliferation, protease production and migration of endothelial cells (ECs). The action of AGFs is counteracted by antiangiogenic modulators whose main mechanism of action is to bind (thus sequestering or masking) AGFs or their receptors. Many sugars, either free or associated to proteins, are involved in these interactions, thus exerting a tight regulation of the neovascularization process. Heparin and heparan sulfate proteoglycans undoubtedly play a pivotal role in this context since they bind to almost all the known AGFs, to several pro-angiogenic receptors and even to angiogenic inhibitors, originating an intricate network of interaction, the so called "angiogenesis glycomic interactome". The decoding of the angiogenesis glycomic interactome, achievable by a systematic study of the interactions occurring among angiogenic modulators and sugars, may help to design novel antiangiogenic therapies with implications in the cure of angiogenesis-dependent diseases.
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Dos Santos C, Blanc C, Elahouel R, Prescott M, Carpentier G, Ori A, Courty J, Hamma-Kourbali Y, Fernig DG, Delbé J. Proliferation and migration activities of fibroblast growth factor-2 in endothelial cells are modulated by its direct interaction with heparin affin regulatory peptide. Biochimie 2014; 107 Pt B:350-7. [PMID: 25315978 DOI: 10.1016/j.biochi.2014.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 10/02/2014] [Indexed: 11/15/2022]
Abstract
Angiogenesis is the physiological process involving the growth of new blood vessels from pre-existing vessels. In normal or pathological angiogenesis, angiogenic growth factors activate cognate receptors on endothelial cells. Fibroblast growth factor-2 (FGF-2) and heparin affin regulatory peptide (HARP) are two heparin-binding growth factors and were described for their pro-angiogenic properties on human umbilical endothelial cells (HUVEC). We now show that HARP acts as a mediator of FGF-2's stimulatory effects, since it is able to inhibit the proliferation and migration of HUVEC induced by FGF-2. We demonstrate by ELISA and optical biosensor binding assay that HARP and FGF-2 interact through direct binding. We have adapted a previously developed structural proteomics method for the identification of residues involved in protein-protein interactions. Application of this method showed that two sequences in HARP were involved in binding FGF-2. One was in the C-thrombospondin type 1 repeat (C-TSR-1) domain and the other in the C-terminal domain of HARP. The identification of these regions as mediating the binding of FGF-2 was confirmed by ELISA using synthetic peptides, which are as well mediators of FGF-2-induced proliferation, migration and tubes formation on HUVEC in vitro. These results imply that besides a regulation of the proliferation, migration and angiogenesis of HUVEC by direct interaction of FGF-2 with its receptors, an alternative pathway exists involving its binding to growth factors such as HARP.
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Affiliation(s)
- Célia Dos Santos
- Laboratoire CRRET, CNRS, Université Paris Est, Avenue du Général de Gaulle, 94010 Créteil Cedex, France.
| | - Charly Blanc
- IMRB INSERM, U955, Equipe 07, Faculté de Médecine, 8 rue du Général Sarrail, 94010 Créteil, France
| | - Rania Elahouel
- Laboratoire CRRET, CNRS, Université Paris Est, Avenue du Général de Gaulle, 94010 Créteil Cedex, France
| | - Mark Prescott
- Department of Structural and Chemical Biology, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
| | - Gilles Carpentier
- Laboratoire CRRET, CNRS, Université Paris Est, Avenue du Général de Gaulle, 94010 Créteil Cedex, France
| | - Alessandro Ori
- Department of Structural and Chemical Biology, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
| | - José Courty
- Laboratoire CRRET, CNRS, Université Paris Est, Avenue du Général de Gaulle, 94010 Créteil Cedex, France
| | - Yamina Hamma-Kourbali
- Laboratoire CRRET, CNRS, Université Paris Est, Avenue du Général de Gaulle, 94010 Créteil Cedex, France
| | - David G Fernig
- Department of Structural and Chemical Biology, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jean Delbé
- Laboratoire CRRET, CNRS, Université Paris Est, Avenue du Général de Gaulle, 94010 Créteil Cedex, France
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NMR characterization of the electrostatic interaction of the basic residues in HDGF and FGF2 during heparin binding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1851-9. [DOI: 10.1016/j.bbapap.2014.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/25/2014] [Accepted: 08/05/2014] [Indexed: 11/19/2022]
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Uniewicz KA, Ori A, Ahmed YA, Yates EA, Fernig DG. Characterisation of the interaction of neuropilin-1 with heparin and a heparan sulfate mimetic library of heparin-derived sugars. PeerJ 2014; 2:e461. [PMID: 25024924 PMCID: PMC4089425 DOI: 10.7717/peerj.461] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/09/2014] [Indexed: 12/22/2022] Open
Abstract
Background. Neuropilin-1 (NRP-1) is a multidomain membrane protein with soluble isoforms interacting with a complex network of other membrane receptors, their respective ligands and heparan sulfate (HS). It is involved in the development of vasculature, neural patterning, immunological responses and pathological angiogenesis. Methods. We have characterised the binding of a Fc fusion of rat NRP-1 (Fc rNRP-1) and of a soluble isoform, corresponding to the first four extracellular domains of human NRP-1, shNRP-1, using optical biosensor-based binding assays with a library of heparin derivatives. Selective labelling of lysines protected upon heparin binding allowed their identification by mass spectrometry. Results. Fc rNRP-1 bound to heparin with high affinity (2.5 nM) and fast ka (9.8 × 10(6) M(-1)s(-1)). Unusually, NRP-1 bound both highly sulfated and completely desulfated stretches of heparin and exhibited a complex pattern of preferences for chemically modified heparins possessing one or two sulfate groups, e.g., it bound heparin with just a 6-O sulfate group better than heparin with any two of N-sulfate, 6-O sulfate and 2-O sulfate. Mass-spectrometry based mapping identified that, in addition to the expected the b1 domain, the a1, and c domains and the L2 linker were also involved in the interaction. In contrast, shNRP-1 bound heparin far more weakly. This could only be shown by affinity chromatography and by differential scanning fluorimetry. Discussion. The results suggest that the interaction of NRP-1 with HS is more complex than anticipated and involving a far greater extent of the protein than just the b1-b2 domains. NRP-1's preference for binding long saccharide structures suggests it has the potential to bind large segments of HS chains and so organise their local structure. In contrast, the four domain soluble isoform, shNRP-1 binds heparin weakly and so would be expected to diffuse away rapidly from the source cell.
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Affiliation(s)
- Katarzyna A Uniewicz
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom
| | - Alessandro Ori
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom
| | - Yassir A Ahmed
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom
| | - Edwin A Yates
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom
| | - David G Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom
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Gesslbauer B, Theuer M, Schweiger D, Adage T, Kungl AJ. New targets for glycosaminoglycans and glycosaminoglycans as novel targets. Expert Rev Proteomics 2013; 10:77-95. [PMID: 23414361 DOI: 10.1586/epr.12.75] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Biological functions of a variety of proteins are mediated via their interaction with glycosaminoglycans (GAGs). The structural diversity within the wide GAG landscape provides individual interaction sites for a multitude of proteins involved in several pathophysiological processes. This 'GAG angle' of such proteins as well as their specific GAG ligands give rise to novel therapeutic concepts for drug development. Current glycomic technologies to elucidate the glycan structure-function relationships, methods to investigate the selectivity and specificity of glycan-protein interactions and existing therapeutic approaches to interfere with GAG-protein interactions are discussed.
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Affiliation(s)
- Bernd Gesslbauer
- ProtAffin Biotechnologie AG, Reininghausstrasse 13a, 8020 Graz, Austria
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Xu R, Rudd TR, Hughes AJ, Siligardi G, Fernig DG, Yates EA. Analysis of the fibroblast growth factor receptor (FGFR) signalling network with heparin as coreceptor: evidence for the expansion of the core FGFR signalling network. FEBS J 2013; 280:2260-70. [DOI: 10.1111/febs.12201] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/06/2013] [Accepted: 02/18/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Ruoyan Xu
- Department of Structural and Chemical Biology, Institute of Integrative Biology; University of Liverpool; UK
| | | | | | | | - David G. Fernig
- Department of Structural and Chemical Biology, Institute of Integrative Biology; University of Liverpool; UK
| | - Edwin A. Yates
- Department of Structural and Chemical Biology, Institute of Integrative Biology; University of Liverpool; UK
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