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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ge P, Luo Y, Zhang G, Chen H. The role of proteomics in acute pancreatitis: new and old knowledge. Expert Rev Proteomics 2024; 21:115-123. [PMID: 38372668 DOI: 10.1080/14789450.2024.2320810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/10/2024] [Indexed: 02/20/2024]
Abstract
INTRODUCTION Around 20% of individuals diagnosed with acute pancreatitis (AP) may develop severe acute pancreatitis (SAP), possibly resulting in a mortality rate ranging from 15% to 35%. There is an urgent need to thoroughly understand the molecular phenotypes of SAP resulting from diverse etiologies. The field of translational research on AP has seen the use of several innovative proteomic methodologies via the ongoing improvement of isolation, tagging, and quantification methods. AREAS COVERED This paper provides a comprehensive overview of differentially abundant proteins (DAPs) identified in AP by searching the PubMed/MEDLINE database (2003-2023) and adds significantly to the current theoretical framework. EXPERT OPINION DAPs for potentially diagnosing AP based on proteomic identification need to be confirmed by multi-center studies that include larger samples. The discovery of DAPs in various organs at different AP stages via proteomic technologies is essential better to understand the pathophysiology of AP-related multiple organ dysfunction syndrome. Regarding the translational research of AP, novel approaches like single-cell proteomics and imaging using mass spectrometry may be used as soon as they become available.
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Affiliation(s)
- Peng Ge
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yalan Luo
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Guixin Zhang
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Hailong Chen
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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3
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Farrugia BL, Melrose J. The Glycosaminoglycan Side Chains and Modular Core Proteins of Heparan Sulphate Proteoglycans and the Varied Ways They Provide Tissue Protection by Regulating Physiological Processes and Cellular Behaviour. Int J Mol Sci 2023; 24:14101. [PMID: 37762403 PMCID: PMC10531531 DOI: 10.3390/ijms241814101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
This review examines the roles of HS-proteoglycans (HS-PGs) in general, and, in particular, perlecan and syndecan as representative examples and their interactive ligands, which regulate physiological processes and cellular behavior in health and disease. HS-PGs are essential for the functional properties of tissues both in development and in the extracellular matrix (ECM) remodeling that occurs in response to trauma or disease. HS-PGs interact with a biodiverse range of chemokines, chemokine receptors, protease inhibitors, and growth factors in immune regulation, inflammation, ECM stabilization, and tissue protection. Some cell regulatory proteoglycan receptors are dually modified hybrid HS/CS proteoglycans (betaglycan, CD47). Neurexins provide synaptic stabilization, plasticity, and specificity of interaction, promoting neurotransduction, neurogenesis, and differentiation. Ternary complexes of glypican-1 and Robbo-Slit neuroregulatory proteins direct axonogenesis and neural network formation. Specific neurexin-neuroligin complexes stabilize synaptic interactions and neural activity. Disruption in these interactions leads to neurological deficits in disorders of functional cognitive decline. Interactions with HS-PGs also promote or inhibit tumor development. Thus, HS-PGs have complex and diverse regulatory roles in the physiological processes that regulate cellular behavior and the functional properties of normal and pathological tissues. Specialized HS-PGs, such as the neurexins, pikachurin, and Eyes-shut, provide synaptic stabilization and specificity of neural transduction and also stabilize the axenome primary cilium of phototoreceptors and ribbon synapse interactions with bipolar neurons of retinal neural networks, which are essential in ocular vision. Pikachurin and Eyes-Shut interactions with an α-dystroglycan stabilize the photoreceptor synapse. Novel regulatory roles for HS-PGs controlling cell behavior and tissue function are expected to continue to be uncovered in this fascinating class of proteoglycan.
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Affiliation(s)
- Brooke L. Farrugia
- Department of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Melbourne, Melbourne, VIC 3010, Australia;
| | - James Melrose
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Raymond Purves Laboratory of Bone and Joint Research, Kolling Institute of Medical Research, Northern Sydney Local Health District, Royal North Shore Hospital, St. Leonards, NSW 2065, Australia
- Sydney Medical School (Northern), University of Sydney at Royal North Shore Hospital, St. Leonards, NSW 2065, Australia
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Wang R, Wang Y, Tao Y, Hu L, Qiu Q, Pu Q, Yang J, Wang S, Huang Y, Chen X, Zhu P, Yang H, Xia Q, Du D. Temporal Proteomic and Lipidomic Profiles of Cerulein-Induced Acute Pancreatitis Reveal Novel Insights for Metabolic Alterations in the Disease Pathogenesis. ACS Omega 2023; 8:12310-12326. [PMID: 37033809 PMCID: PMC10077560 DOI: 10.1021/acsomega.3c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
The pathophysiological mechanisms of acute pancreatitis (AP) are complex and have remained a mystery to date, but metabolism is gradually recognized as an important driver of AP onset and development. We used a cerulein-induced AP mouse model to conduct liquid chromatography-mass spectrometry (LC-MS/MS)-based time-course proteomics and lipidomics in order to better understand the underlying metabolic alterations linked with AP. Results showed that a series of significant changes in proteins over time with a boost in expression were enriched in lipase activity, lipoprotein, and lipids absorption and transport regulation. Furthermore, 16 proteins associated with lipid metabolism and signaling pathways together with the whole lipid species changing profile led to the vital identification of changing law in glycerides, phosphoglycerides, and free fatty acids. In addition to lipid metabolism and regulation-associated proteins, several digestive enzymes and adaptive anti-trypsin, stress response, and energy metabolism-related proteins showed an increment in abundance. Notably, central carbon and branched chain amino acid metabolism were enhanced during 0-24 h from the first cerulein stimulation. Taken together, this integrated proteomics and lipidomics revealed a novel metabolic insight into metabolites transforming rules that might be relevant to their function and drug targets investigation. (Created with Biorender.com.).
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Affiliation(s)
- Rui Wang
- West
China Centre of Excellence for Pancreatitis, Institute of Integrated
Traditional Chinese and Western Medicine, Sichuan Provincial Pancreatitis
Centre and West China-Liverpool Biomedical Research Centre, West China
Hospital/West China Medical School, Sichuan
University, Chengdu 610041, China
- Advanced
Mass Spectrometry Center, Research Core Facility, Frontiers Science
Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yiqin Wang
- West
China Centre of Excellence for Pancreatitis, Institute of Integrated
Traditional Chinese and Western Medicine, Sichuan Provincial Pancreatitis
Centre and West China-Liverpool Biomedical Research Centre, West China
Hospital/West China Medical School, Sichuan
University, Chengdu 610041, China
| | - Yiran Tao
- West
China-California Research Center for Predictive Intervention Medicine,
West China Hospital, Sichuan University, Chengdu 610041, China
| | - Liqiang Hu
- Advanced
Mass Spectrometry Center, Research Core Facility, Frontiers Science
Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qi Qiu
- West
China Centre of Excellence for Pancreatitis, Institute of Integrated
Traditional Chinese and Western Medicine, Sichuan Provincial Pancreatitis
Centre and West China-Liverpool Biomedical Research Centre, West China
Hospital/West China Medical School, Sichuan
University, Chengdu 610041, China
| | - Qianlun Pu
- Advanced
Mass Spectrometry Center, Research Core Facility, Frontiers Science
Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Juqin Yang
- Biobank,
West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shisheng Wang
- Proteomics-Metabolomics
Platform of Core Facilities, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yan Huang
- West
China Centre of Excellence for Pancreatitis, Institute of Integrated
Traditional Chinese and Western Medicine, Sichuan Provincial Pancreatitis
Centre and West China-Liverpool Biomedical Research Centre, West China
Hospital/West China Medical School, Sichuan
University, Chengdu 610041, China
| | - Xiaoting Chen
- Animal Experimental
Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ping Zhu
- West
China Centre of Excellence for Pancreatitis, Institute of Integrated
Traditional Chinese and Western Medicine, Sichuan Provincial Pancreatitis
Centre and West China-Liverpool Biomedical Research Centre, West China
Hospital/West China Medical School, Sichuan
University, Chengdu 610041, China
| | - Hao Yang
- Proteomics-Metabolomics
Platform of Core Facilities, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qing Xia
- West
China Centre of Excellence for Pancreatitis, Institute of Integrated
Traditional Chinese and Western Medicine, Sichuan Provincial Pancreatitis
Centre and West China-Liverpool Biomedical Research Centre, West China
Hospital/West China Medical School, Sichuan
University, Chengdu 610041, China
| | - Dan Du
- West
China Centre of Excellence for Pancreatitis, Institute of Integrated
Traditional Chinese and Western Medicine, Sichuan Provincial Pancreatitis
Centre and West China-Liverpool Biomedical Research Centre, West China
Hospital/West China Medical School, Sichuan
University, Chengdu 610041, China
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Ganjoo R, Sharma S, Verma C, Quraishi MA, Kumar A. Heteropolysaccharides in sustainable corrosion inhibition: 4E (Energy, Economy, Ecology, and Effectivity) dimensions. Int J Biol Macromol 2023; 235:123571. [PMID: 36750168 DOI: 10.1016/j.ijbiomac.2023.123571] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 01/24/2023] [Accepted: 02/03/2023] [Indexed: 02/07/2023]
Abstract
Carbohydrate polymers (polysaccharides) and their derivatives are widely utilized in sustainable corrosion inhibition (SCI) because of their various fascinating properties including multiple adsorption sites, high solubility and high efficiency. Contrary to traditional synthetic polymer-based corrosion inhibitors, polysaccharides are related to the 4E dimension, which stands for Energy, Economy, Ecology, and Effectivity. Furthermore, they are relatively more environmentally benign, biodegradable, and non-bioaccumulative. The current review describes the SCI features of various heteropolysaccharides, including gum Arabic (GA), glycosaminoglycans (chondroitin-4-sulfate (CS), hyaluronic acid (HA), heparin, etc.), pectin, alginates, and agar for the first time. They demonstrate impressive anticorrosive activity for different metals and alloys in a variety of corrosive electrolytes. Through their adsorption at the metal/electrolyte interface, heteropolysaccharides function by producing a corrosion-protective film. In general, their adsorption follows the Langmuir isotherm model. In their molecular structures, heteropolysaccharides contain several polar functional groups like -OH, -NH2, -COCH3, -CH2OH, cyclic and bridging O, -CH2SO3H, -SO3OH, -COOH, -NHCOCH3, -OHOR, etc. that serve as adsorption centers when they bind to metallic surfaces.
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Affiliation(s)
- Richika Ganjoo
- Department of Chemistry, School of Chemical Engineering and Physical Sciences, Lovely Professional University, Punjab, India
| | - Shveta Sharma
- Department of Chemistry, School of Chemical Engineering and Physical Sciences, Lovely Professional University, Punjab, India
| | - Chandrabhan Verma
- Center of Research Excellence in Corrosion, Research Institute, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia.
| | - M A Quraishi
- Center of Research Excellence in Corrosion, Research Institute, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
| | - Ashish Kumar
- Department of Chemistry, School of Chemical Engineering and Physical Sciences, Lovely Professional University, Punjab, India; NCE, Department of Science and Technology, Government of Bihar, India.
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Hayes AJ, Melrose J. HS, an Ancient Molecular Recognition and Information Storage Glycosaminoglycan, Equips HS-Proteoglycans with Diverse Matrix and Cell-Interactive Properties Operative in Tissue Development and Tissue Function in Health and Disease. Int J Mol Sci 2023; 24. [PMID: 36674659 DOI: 10.3390/ijms24021148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
Heparan sulfate is a ubiquitous, variably sulfated interactive glycosaminoglycan that consists of repeating disaccharides of glucuronic acid and glucosamine that are subject to a number of modifications (acetylation, de-acetylation, epimerization, sulfation). Variable heparan sulfate chain lengths and sequences within the heparan sulfate chains provide structural diversity generating interactive oligosaccharide binding motifs with a diverse range of extracellular ligands and cellular receptors providing instructional cues over cellular behaviour and tissue homeostasis through the regulation of essential physiological processes in development, health, and disease. heparan sulfate and heparan sulfate-PGs are integral components of the specialized glycocalyx surrounding cells. Heparan sulfate is the most heterogeneous glycosaminoglycan, in terms of its sequence and biosynthetic modifications making it a difficult molecule to fully characterize, multiple ligands also make an elucidation of heparan sulfate functional properties complicated. Spatio-temporal presentation of heparan sulfate sulfate groups is an important functional determinant in tissue development and in cellular control of wound healing and extracellular remodelling in pathological tissues. The regulatory properties of heparan sulfate are mediated via interactions with chemokines, chemokine receptors, growth factors and morphogens in cell proliferation, differentiation, development, tissue remodelling, wound healing, immune regulation, inflammation, and tumour development. A greater understanding of these HS interactive processes will improve therapeutic procedures and prognoses. Advances in glycosaminoglycan synthesis and sequencing, computational analytical carbohydrate algorithms and advanced software for the evaluation of molecular docking of heparan sulfate with its molecular partners are now available. These advanced analytic techniques and artificial intelligence offer predictive capability in the elucidation of heparan sulfate conformational effects on heparan sulfate-ligand interactions significantly aiding heparan sulfate therapeutics development.
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Caputo D, Coppola A, Quagliarini E, Di Santo R, Capriotti AL, Cammarata R, Laganà A, Papi M, Digiacomo L, Coppola R, Pozzi D, Caracciolo G. Multiplexed Detection of Pancreatic Cancer by Combining a Nanoparticle-Enabled Blood Test and Plasma Levels of Acute-Phase Proteins. Cancers (Basel) 2022; 14:4658. [PMID: 36230585 PMCID: PMC9563576 DOI: 10.3390/cancers14194658] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary In this study, a multiplexed strategy based on the combination of a nanoparticle-enabled blood test and serum levels of acute-phase proteins proved to be able to distinguish pancreatic cancer patients from healthy controls with a good and sex-dependent prediction ability. This study suggests a possible role of acute-phase proteins as pancreatic cancer biomarkers and paves the way for the development of multiplexed technologies for early cancer detection. Abstract The development of new tools for the early detection of pancreatic ductal adenocarcinoma (PDAC) represents an area of intense research. Recently, the concept has emerged that multiplexed detection of different signatures from a single biospecimen (e.g., saliva, blood, etc.) may exhibit better diagnostic capability than single biomarkers. In this work, we develop a multiplexed strategy for detecting PDAC by combining characterization of the nanoparticle (NP)-protein corona, i.e., the protein layer that surrounds NPs upon exposure to biological fluids and circulating levels of plasma proteins belonging to the acute phase protein (APPs) family. As a first step, we developed a nanoparticle-enabled blood (NEB) test that employed 600 nm graphene oxide (GO) nanosheets and human plasma (HP) (5% vol/vol) to produce 75 personalized protein coronas (25 from healthy subjects and 50 from PDAC patients). Isolation and characterization of protein corona patterns by 1-dimensional (1D) SDS-PAGE identified significant differences in the abundance of low-molecular-weight corona proteins (20–30 kDa) between healthy subjects and PDAC patients. Coupling the outcomes of the NEB test with the circulating levels of alpha 2 globulins, we detected PDAC with a global capacity of 83.3%. Notably, a version of the multiplexed detection strategy run on sex-disaggregated data provided substantially better classification accuracy for men (93.1% vs. 77.8%). Nanoliquid chromatography tandem mass spectrometry (nano-LC MS/MS) experiments allowed to correlate PDAC with an altered enrichment of Apolipoprotein A-I, Apolipoprotein D, Complement factor D, Alpha-1-antichymotrypsin and Alpha-1-antitrypsin in the personalized protein corona. Moreover, other significant changes in the protein corona of PDAC patients were found. Overall, the developed multiplexed strategy is a valid tool for PDAC detection and paves the way for the identification of new potential PDAC biomarkers.
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Parafioriti M, Ni M, Petitou M, Mycroft-West CJ, Rudd TR, Gandhi NS, Ferro V, Turnbull JE, Lima MA, Skidmore MA, Fernig DG, Yates EA, Bisio A, Guerrini M, Elli S. Evidence for Multiple Binding Modes in the Initial Contact Between SARS-CoV-2 Spike S1 Protein and Cell Surface Glycans. Chemistry 2022; 29:e202202599. [PMID: 36134621 PMCID: PMC9537976 DOI: 10.1002/chem.202202599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Indexed: 01/05/2023]
Abstract
Infection of host cells by SARS-CoV-2 begins with recognition by the virus S (spike) protein of cell surface heparan sulfate (HS), tethering the virus to the extracellular matrix environment, and causing the subunit S1-RBD to undergo a conformational change into the 'open' conformation. These two events promote the binding of S1-RBD to the angiotensin converting enzyme 2 (ACE2) receptor, a preliminary step toward viral-cell membrane fusion. Combining ligand-based NMR spectroscopy with molecular dynamics, oligosaccharide analogues were used to explore the interactions between S1-RBD of SARS CoV-2 and HS, revealing several low-specificity binding modes and previously unidentified potential sites for the binding of extended HS polysaccharide chains. The evidence for multiple binding modes also suggest that highly specific inhibitors will not be optimal against protein S but, rather, diverse HS-based structures, characterized by high affinity and including multi-valent compounds, may be required.
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Affiliation(s)
- Michela Parafioriti
- Istituto di Ricerche Chimiche e Biochimiche 'G. Ronzoni'NMR and carbohydratesvia Giuseppe Colombo 8120133MilanoITALY
| | - Minghong Ni
- Istituto di Ricerche Chimiche e Biochimiche 'G. Ronzoni'Organic Chemistryvia Giuseppe Colombo 8120133MilanoITALY
| | - Maurice Petitou
- Istituto di Ricerche Chimiche e Biochimiche 'G Ronzoni'Organic chemistryvia Giuseppe Colombo 8120133MilanoITALY
| | | | - Timothy R. Rudd
- National Institute for Biological Standards and ControlAnalytical and Biological Sciences DivisionPotters Bar, Hertfordshire, United KingdomPotters Bar, HertfordshireUNITED KINGDOM
| | - Neha S. Gandhi
- Queensland University of Technology Institute of Health and Biomedical InnovationSchool of Chemistry and Physics2 George StBrisbaneAUSTRALIA
| | - Vito Ferro
- The University of Queensland School of Chemistry and Molecular BiosciencesSchool of Chemistry and Molecular BiosciencesBrisbaneAUSTRALIA
| | - Jeremy E. Turnbull
- University of Liverpool Institute of Integrative BiologyInstitute of Systems, Molecular and Integrative BiologyCrown StreetL69 7ZBLiverpoolUNITED KINGDOM
| | - Marcelo A. Lima
- Keele University School of Life SciencesCentre for GlycoscienceHuxley Building 203ST5 5BGNewcastle-Under-LymeUNITED KINGDOM
| | - Mark A. Skidmore
- Keele University School of Life SciencesCentre for GlycoscienceHuxley Building 174ST5 5BGNewcastle-Under-LymeUNITED KINGDOM
| | - David G. Fernig
- University of Liverpool Institute of Integrative BiologyInstitute of Systems, Molecular and Integrative BiologyCrown StreetL69 7BELiverpoolUNITED KINGDOM
| | - Edwin A. Yates
- University of Liverpool Institute of Integrative BiologyDepartment of Biochemistry and Systems BiologyCrown StreetL69 7ZBLiverpoolUNITED KINGDOM
| | - Antonella Bisio
- Istituto di Ricerche Chimiche e Biochimiche 'G. Ronzoni'Biochemistry and molecular biologyvia Giuseppe Colombo 8120133MilanoITALY
| | - Marco Guerrini
- Istituto di Ricerche Chimiche e Biochimiche 'G. Ronzoni'NMR and Carbohydratevia Giuseppe Colombo 8120133MilanoITALY
| | - Stefano Elli
- Istituto di ricerche chimiche e biochimiche G Ronzoni (Milano)NMR and Carbohydratesvia Giuseppe Colombo 8120133MilanoITALY
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Lima MA, Rudd TR, Fernig DG, Yates EA. Phosphorylation and sulfation share a common biosynthetic pathway, but extend biochemical and evolutionary diversity of biological macromolecules in distinct ways. J R Soc Interface 2022; 19:20220391. [PMID: 35919982 PMCID: PMC9346353 DOI: 10.1098/rsif.2022.0391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phosphate and sulfate groups are integral to energy metabolism and introduce negative charges into biological macromolecules. One purpose of such modifications is to elicit precise binding/activation of protein partners. The physico-chemical properties of the two groups, while superficially similar, differ in one important respect—the valency of the central (phosphorus or sulfur) atom. This dictates the distinct properties of their respective esters, di-esters and hence their charges, interactions with metal ions and their solubility. These, in turn, determine the contrasting roles for which each group has evolved in biological systems. Biosynthetic links exist between the two modifications; the sulfate donor 3′-phosphoadenosine-5′-phosphosulfate being formed from adenosine triphosphate (ATP) and adenosine phosphosulfate, while the latter is generated from sulfate anions and ATP. Furthermore, phosphorylation, by a xylosyl kinase (Fam20B, glycosaminoglycan xylosylkinase) of the xylose residue of the tetrasaccharide linker region that connects nascent glycosaminoglycan (GAG) chains to their parent proteoglycans, substantially accelerates their biosynthesis. Following observations that GAG chains can enter the cell nucleus, it is hypothesized that sulfated GAGs could influence events in the nucleus, which would complete a feedback loop uniting the complementary anionic modifications of phosphorylation and sulfation through complex, inter-connected signalling networks and warrants further exploration.
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Affiliation(s)
- M A Lima
- Centre for Glycosciences, Keele University, Keele ST5 5BG, UK.,School of Life Sciences, Keele University, Keele ST5 5BG, UK
| | - T R Rudd
- Analytical and Biological Science Department, National Institute of Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar EN6 3QG, UK.,Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
| | - D G Fernig
- Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
| | - E A Yates
- School of Life Sciences, Keele University, Keele ST5 5BG, UK.,Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
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10
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Ricard-blum S, Perez S. Glycosaminoglycan interaction networks and databases. Curr Opin Struct Biol 2022; 74:102355. [DOI: 10.1016/j.sbi.2022.102355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/14/2022]
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Abstract
Glycosaminoglycans (GAGs) are complex linear polysaccharides, which are covalently attached to core proteins (except for hyaluronan) to form proteoglycans. They play key roles in the organization of the extracellular matrix, and at the cell surface where they contribute to the regulation of cell signaling and of cell adhesion. To explore the mechanisms and pathways underlying their functions, we have generated an expanded dataset of 4290 interactions corresponding to 3464 unique GAG-binding proteins, four times more than the first version of the GAG interactome (Vallet and Ricard-Blum, 2021 J Histochem Cytochem 69:93-104). The increased size of the GAG network is mostly due to the addition of GAG-binding proteins captured from cell lysates and biological fluids by affinity chromatography and identified by mass spectrometry. We review here the interaction repertoire of natural GAGs and of synthetic sulfated hyaluronan, the specificity and molecular functions of GAG-binding proteins, and the biological processes and pathways they are involved in. This dataset is also used to investigate the differences between proteins binding to iduronic acid-containing GAGs (dermatan sulfate and heparin/heparan sulfate) and those interacting with GAGs lacking iduronic acid (chondroitin sulfate, hyaluronan, and keratan sulfate).
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12
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Su D, Li Y, Yates EA, Skidmore MA, Lima MA, Fernig DG. Analysis of protein-heparin interactions using a portable SPR instrument. PeerJ Analytical Chemistry 2022. [DOI: 10.7717/peerj-achem.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Optical biosensors such as those based on surface plasmon resonance (SPR) are a key analytical tool for understanding biomolecular interactions and function as well as the quantitative analysis of analytes in a wide variety of settings. The advent of portable SPR instruments enables analyses in the field. A critical step in method development is the passivation and functionalisation of the sensor surface. We describe the assembly of a surface of thiolated oleyl ethylene glycol/biotin oleyl ethylene glycol and its functionalisation with streptavidin and reducing end biotinylated heparin for a portable SPR instrument. Such surfaces can be batch prepared and stored. Two examples of the analysis of heparin-binding proteins are presented. The binding of fibroblast growth factor 2 and competition for the binding of a heparan sulfate sulfotransferase by a library of selectively modified heparins and suramin, which identify the selectivity of the enzyme for sulfated structures in the polysaccharide and demonstrate suramin as a competitor for the enzyme’s sugar acceptor site. Heparin functionalised surfaces should have a wide applicability, since this polysaccharide is a close structural analogue of the host cell surface polysaccharide, heparan sulfate, a receptor for many endogenous proteins and viruses.
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Affiliation(s)
- Dunhao Su
- Biochemistry, University of Liverpool, Liverpool, United Kingdom
| | - Yong Li
- Biochemistry, University of Liverpool, Liverpool, United Kingdom
| | - Edwin A. Yates
- Biochemistry, University of Liverpool, Liverpool, United Kingdom
| | - Mark A. Skidmore
- Molecular & Structural Biosciences, School of Life Sciences, University of Keele, Newcastle-Under-Lyme, United Kingdom
| | - Marcelo A. Lima
- Molecular & Structural Biosciences, School of Life Sciences, University of Keele, Newcastle-Under-Lyme, United Kingdom
| | - David G. Fernig
- Biochemistry, University of Liverpool, Liverpool, United Kingdom
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13
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Nakamura M, Sato A. Glycan-binding Properties of Basic Whey Protein Lactoferrin and Its Application in Nerve Regenerative Medicine. TRENDS GLYCOSCI GLYC 2022. [DOI: 10.4052/tigg.1957.1e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Masao Nakamura
- Department of Peptidomics, Sasaki Institute, Sasaki Foundation
| | - Atsushi Sato
- School of Bioscience and Biotechnology, Tokyo University of Technology
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14
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Nakamura M, Sato A. Glycan-binding Properties of Basic Whey Protein Lactoferrin and Its Application in Nerve Regenerative Medicine. TRENDS GLYCOSCI GLYC 2022. [DOI: 10.4052/tigg.1957.1j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Masao Nakamura
- Department of Peptidomics, Sasaki Institute, Sasaki Foundation
| | - Atsushi Sato
- School of Bioscience and Biotechnology, Tokyo University of Technology
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15
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Liu P, Li H, Liao C, Tang Y, Li M, Wang Z, Wu Q, Zhou Y. Identification of key genes and biological pathways in Chinese lung cancer population using bioinformatics analysis. PeerJ 2022; 10:e12731. [PMID: 35178291 PMCID: PMC8812315 DOI: 10.7717/peerj.12731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 12/11/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Identification of accurate prognostic biomarkers is still particularly urgent for improving the poor survival of lung cancer patients. In this study, we aimed to identity the potential biomarkers in Chinese lung cancer population via bioinformatics analysis. METHODS In this study, the differentially expressed genes (DEGs) in lung cancer were identified using six datasets from Gene Expression Omnibus (GEO) database. Subsequently, enrichment analysis was conducted to evaluate the underlying molecular mechanisms involved in progression of lung cancer. Protein-protein interaction (PPI) and CytoHubba analysis were performed to determine the hub genes. The GEPIA, Human Protein Atlas (HPA), Kaplan-Meier plotter, and TIMER databases were used to explore the hub genes. The receiver operating characteristic (ROC) analysis was performed to evaluate the diagnostic value of hub genes. Reverse transcription quantitative PCR (qRT-PCR) was used to validate the expression levels of hub genes in 10 pairs of lung cancer paired tissues. RESULTS A total of 499 overlapping DEGs (160 upregulated and 339 downregulated genes) were identified in the microarray datasets. DEGs were mainly associated with pathways in cancer, focal adhesion, and protein digestion and absorption. There were nine hub genes (CDKN3, MKI67, CEP55, SPAG5, AURKA, TOP2A, UBE2C, CHEK1 and BIRC5) identified by PPI and module analysis. In GEPIA database, the expression levels of these genes in lung cancer tissues were significantly upregulated compared with normal lung tissues. The results of prognostic analysis showed that relatively higher expression of hub genes was associated with poor prognosis of lung cancer. In HPA database, most hub genes were highly expressed in lung cancer tissues. The hub genes have good diagnostic efficiency in lung cancer and normal tissues. The expression of any hub gene was associated with the infiltration of at least two immune cells. qRT-PCR confirmed that the expression level of CDKN3, MKI67, CEP55, SPAG5, AURKA, TOP2A were highly expressed in lung cancer tissues. CONCLUSIONS The hub genes and functional pathways identified in this study may contribute to understand the molecular mechanisms of lung cancer. Our findings may provide new therapeutic targets for lung cancer patients.
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Affiliation(s)
- Ping Liu
- Department of Respiratory Medicine, The First Hospital of Changsha, Changsha, China
| | - Hui Li
- Department of Respiratory Medicine, The First Hospital of Changsha, Changsha, China
| | - Chunfeng Liao
- Department of Cardiology, The First Hospital of Changsha, Changsha, China
| | - Yuling Tang
- Department of Respiratory Medicine, The First Hospital of Changsha, Changsha, China
| | - Mengzhen Li
- MyGene Diagnostics Co., Ltd., Guangzhou, China
| | - Zhouyu Wang
- MyGene Diagnostics Co., Ltd., Guangzhou, China
| | - Qi Wu
- Department of Emergency, The First Hospital of Changsha, Changsha, China
| | - Yun Zhou
- Department of Spinal Surgery, The First Hospital of Changsha, Changsha, China
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16
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Zhou L, Chen J, Mu G, Lu Z, Li W, Deng Y. Heparin-binding protein (HBP) worsens the severity of pancreatic necrosis via up-regulated M1 macrophages activation in acute pancreatitis mouse models. Bioengineered 2021; 12:11978-11986. [PMID: 34895060 PMCID: PMC8810113 DOI: 10.1080/21655979.2021.2011018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022] Open
Abstract
Acute pancreatitis (AP) is one of the most widespread clinical emergencies. Macrophages are the most common immune cells in AP pancreatic tissue and are closely associated with pancreatic necrosis and recovery. The level of heparin-binding protein (HBP) is closely linked to inflammation. In this study, we assessed the effect of HBP on AP tissue necrosis severity and whether HBP is associated with M1 macrophages in pancreatic necrosis. We observed the dynamic changes of HBP levels in the pancreas during acute inflammation in the caerulein-induced AP mice model. We used hematoxylin-eosin staining to evaluate pancreatic edema and necrosis, and to detect infiltration of macrophages by immunohistochemistry. Moreover, expressions of the maker and cytokines of macrophages, including inducible nitric oxide synthase (iNOS), and arginase 1 (Arg-1), interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) mRNA, were detected by real-time polymerase-chain reaction (RT-PCR). High levels of HBP in the pancreas were detected at 48 h, and heparin inhibited HBP expression in AP pancreatic tissue. Inhibiting HBP expression by injecting heparin before AP can alleviate pancreatic necrosis and inhibit F4/80 labeled M1 macrophage infiltration and IL-6, TNF-α, and iNOS mRNA expression. Clodronate liposome (CLDL) intraperitoneally treated mice showed no change in pancreatic HBP levels, but pancreatic macrophage-specific antigen F4/80 and TNF-α, IL-1β, and IL-6 mRNA levels decreased after CLDL treatment. HBP is critical for pancreatic necrosis response in acute pancreatitis by increasing the infiltration of M1 macrophages and promoting the secretion of inflammatory factors, such as TNF-α, IL-6, IL-1β, which can be reduced by heparin.
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Affiliation(s)
- Liangliang Zhou
- Department of Intensive Care Medicine, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School/The First People’s Hospital of Yancheng, Yancheng, Jiangsu Province, China
| | - Jianjun Chen
- Department of Intensive Care Medicine, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School/The First People’s Hospital of Yancheng, Yancheng, Jiangsu Province, China
| | - Genhua Mu
- Department of Intensive Care Medicine, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School/The First People’s Hospital of Yancheng, Yancheng, Jiangsu Province, China
| | - Zhongqian Lu
- Department of Intensive Care Medicine, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School/The First People’s Hospital of Yancheng, Yancheng, Jiangsu Province, China
| | - Weiqin Li
- Department of Intensive Care Medicine, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School/The First People’s Hospital of Yancheng, Yancheng, Jiangsu Province, China
| | - Yijun Deng
- Department of Intensive Care Medicine, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School/The First People’s Hospital of Yancheng, Yancheng, Jiangsu Province, China
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17
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Shu W, Wan J, Yang X, Chen J, Yang Q, Liu F, Xia L. Heparin-Binding Protein Levels at Admission and Within 24 h Are Associated with Persistent Organ Failure in Acute Pancreatitis. Dig Dis Sci 2021; 66:3597-3603. [PMID: 33094452 DOI: 10.1007/s10620-020-06660-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Identification of patients at risk for persistent organ failure (POF) early in the course of acute pancreatitis (AP) is critical for early intervention. Heparin-binding protein (HBP) levels are closely related to inflammation. Therefore, we investigated the relationship between HBP levels and POF in patients with AP. METHODS This observational cohort study analyzed 66 patients with AP and 14 healthy volunteers between June 2019 and December 2019. Baseline characteristics, laboratory data, and severity scores of patients with different degrees of AP were compared. Levels of HBP were measured by ELISA. Serum HBP levels were analyzed using receiver operating characteristic curves to identify POF in AP. RESULTS Concentrations of serum HBP in healthy volunteers, MAP, MSAP, and SAP groups were 3.9 (range: 3.4-5) ng/ml, 5.2 (3.9-6.8) ng/ml, 5.9 (4.6-7.7) ng/ml, and 11 (8.0-13.8) ng/ml, respectively. The level of HBP in SAP patients was significantly elevated compared to the other groups (P < 0.01). HBP levels ≥ 7 ng/ml showed a specificity of 74%, a sensitivity of 90%, and an AUC of 0.82 for predicting POF. CONCLUSIONS HBP levels in patients with POF were significantly elevated. HBP is a useful marker for predicting severe AP.
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Affiliation(s)
- Wenqing Shu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Jianhua Wan
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Xiaoyu Yang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Jie Chen
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Qinyu Yang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Fen Liu
- Department of Intensive Care Unit, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Liang Xia
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi, People's Republic of China.
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18
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Oliveira T, Zhang M, Joo EJ, Abdel-Azim H, Chen CW, Yang L, Chou CH, Qin X, Chen J, Alagesan K, Almeida A, Jacob F, Packer NH, von Itzstein M, Heisterkamp N, Kolarich D. Glycoproteome remodeling in MLL-rearranged B-cell precursor acute lymphoblastic leukemia. Am J Cancer Res 2021; 11:9519-9537. [PMID: 34646384 PMCID: PMC8490503 DOI: 10.7150/thno.65398] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/03/2021] [Indexed: 01/13/2023] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) with mixed-lineage leukemia gene rearrangement (MLL-r) is a poor-prognosis subtype for which additional therapeutic targets are urgently needed. Currently no multi-omics data set for primary MLL r patient cells exists that integrates transcriptomics, proteomics and glycomics to gain an inclusive picture of theranostic targets. Methods: We have integrated transcriptomics, proteomics and glycomics to i) obtain the first inclusive picture of primary patient BCP-ALL cells and identify molecular signatures that distinguish leukemic from normal precursor B-cells and ii) better understand the benefits and limitations of the applied technologies to deliver deep molecular sequence data across major cellular biopolymers. Results: MLL-r cells feature an extensive remodeling of their glycocalyx, with increased levels of Core 2-type O-glycans and complex N-glycans as well as significant changes in sialylation and fucosylation. Notably, glycosaminoglycan remodeling from chondroitin sulfate to heparan sulfate was observed. A survival screen, to determine if glycan remodeling enzymes are redundant, identified MGAT1 and NGLY1, essential components of the N-glycosylation/degradation pathway, as highly relevant within this in vitro screening. OGT and OGA, unique enzymes that regulate intracellular O-GlcNAcylation, were also indispensable. Transcriptomics and proteomics further identified Fes and GALNT7-mediated glycosylation as possible therapeutic targets. While there is overall good correlation between transcriptomics and proteomics data, we demonstrate that a systematic combined multi-omics approach delivers important diagnostic information that is missed when applying a single omics technology. Conclusions: Apart from confirming well-known MLL-r BCP-ALL glycoprotein markers, our integrated multi-omics workflow discovered previously unidentified diagnostic/therapeutic protein targets.
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Affiliation(s)
- Tiago Oliveira
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia
| | - Mingfeng Zhang
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Eun Ji Joo
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Hisham Abdel-Azim
- Division of Hematology/Oncology and Bone Marrow Transplant, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Chih-Hsing Chou
- Division of Hematology/Oncology and Bone Marrow Transplant, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Xi Qin
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Kathirvel Alagesan
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia
| | - Andreia Almeida
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia
| | - Francis Jacob
- Glyco-Oncology, Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Nicolle H Packer
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia.,Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia.,ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia
| | - Nora Heisterkamp
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA.,✉ Corresponding authors: Equal contributions of Nora Heisterkamp, E-mail: ; and Daniel Kolarich, E-mail:
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia.,ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia.,✉ Corresponding authors: Equal contributions of Nora Heisterkamp, E-mail: ; and Daniel Kolarich, E-mail:
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19
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Hayes AJ, Melrose J. What Are the Potential Roles of Nuclear Perlecan and Other Heparan Sulphate Proteoglycans in the Normal and Malignant Phenotype. Int J Mol Sci 2021; 22:4415. [PMID: 33922532 DOI: 10.3390/ijms22094415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 12/27/2022] Open
Abstract
The recent discovery of nuclear and perinuclear perlecan in annulus fibrosus and nucleus pulposus cells and its known matrix stabilizing properties in tissues introduces the possibility that perlecan may also have intracellular stabilizing or regulatory roles through interactions with nuclear envelope or cytoskeletal proteins or roles in nucleosomal-chromatin organization that may regulate transcriptional factors and modulate gene expression. The nucleus is a mechano-sensor organelle, and sophisticated dynamic mechanoresponsive cytoskeletal and nuclear envelope components support and protect the nucleus, allowing it to perceive and respond to mechano-stimulation. This review speculates on the potential roles of perlecan in the nucleus based on what is already known about nuclear heparan sulphate proteoglycans. Perlecan is frequently found in the nuclei of tumour cells; however, its specific role in these diseased tissues is largely unknown. The aim of this review is to highlight probable roles for this intriguing interactive regulatory proteoglycan in the nucleus of normal and malignant cell types.
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20
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Meneghetti MCZ, Deboni P, Palomino CMV, Braga LP, Cavalheiro RP, Viana GM, Yates EA, Nader HB, Lima MA. ER-Golgi dynamics of HS-modifying enzymes via vesicular trafficking is a critical prerequisite for the delineation of HS biosynthesis. Carbohydr Polym 2021; 255:117477. [PMID: 33436240 DOI: 10.1016/j.carbpol.2020.117477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 10/22/2022]
Abstract
The cell surface and extracellular matrix polysaccharide, heparan sulfate (HS) conveys chemical information to control crucial biological processes. HS chains are synthesized in a non-template driven process mainly in the Golgi apparatus, involving a large number of enzymes capable of subtly modifying its substitution pattern, hence, its interactions and biological effects. Changes in the localization of HS-modifying enzymes throughout the Golgi were found to correlate with changes in the structure of HS, rather than protein expression levels. Following BFA treatment, the HS-modifying enzymes localized preferentially in COPII vesicles and at the trans-Golgi. Shortly after heparin treatment, the HS-modifying enzyme moved from cis to trans-Golgi, which coincided with increased HS sulfation. Finally, it was shown that COPI subunits and Sec24 gene expression changed. Collectively, these findings demonstrate that knowledge of the ER-Golgi dynamics of HS-modifying enzymes via vesicular trafficking is a critical prerequisite for the complete delineation of HS biosynthesis.
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Affiliation(s)
- Maria C Z Meneghetti
- Departamento de Bioquímica, Instituto de Farmacologia e Biologia Molecular, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio, 100, São Paulo, SP 04044-020, Brazil
| | - Paula Deboni
- Departamento de Bioquímica, Instituto de Farmacologia e Biologia Molecular, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio, 100, São Paulo, SP 04044-020, Brazil
| | - Carlos M V Palomino
- Departamento de Bioquímica, Instituto de Farmacologia e Biologia Molecular, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio, 100, São Paulo, SP 04044-020, Brazil
| | - Luiz P Braga
- Departamento de Bioquímica, Instituto de Farmacologia e Biologia Molecular, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio, 100, São Paulo, SP 04044-020, Brazil
| | - Renan P Cavalheiro
- Departamento de Bioquímica, Instituto de Farmacologia e Biologia Molecular, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio, 100, São Paulo, SP 04044-020, Brazil
| | - Gustavo M Viana
- Departamento de Bioquímica, Instituto de Farmacologia e Biologia Molecular, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio, 100, São Paulo, SP 04044-020, Brazil
| | - Edwin A Yates
- Departamento de Bioquímica, Instituto de Farmacologia e Biologia Molecular, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio, 100, São Paulo, SP 04044-020, Brazil; Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Helena B Nader
- Departamento de Bioquímica, Instituto de Farmacologia e Biologia Molecular, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio, 100, São Paulo, SP 04044-020, Brazil
| | - Marcelo A Lima
- Departamento de Bioquímica, Instituto de Farmacologia e Biologia Molecular, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio, 100, São Paulo, SP 04044-020, Brazil; Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK.
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21
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Mycroft-West CJ, Su D, Pagani I, Rudd TR, Elli S, Gandhi NS, Guimond SE, Miller GJ, Meneghetti MCZ, Nader HB, Li Y, Nunes QM, Procter P, Mancini N, Clementi M, Bisio A, Forsyth NR, Ferro V, Turnbull JE, Guerrini M, Fernig DG, Vicenzi E, Yates EA, Lima MA, Skidmore MA. Heparin Inhibits Cellular Invasion by SARS-CoV-2: Structural Dependence of the Interaction of the Spike S1 Receptor-Binding Domain with Heparin. Thromb Haemost 2020; 120:1700-1715. [PMID: 33368089 PMCID: PMC7869224 DOI: 10.1055/s-0040-1721319] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022]
Abstract
The dependence of development and homeostasis in animals on the interaction of hundreds of extracellular regulatory proteins with the peri- and extracellular glycosaminoglycan heparan sulfate (HS) is exploited by many microbial pathogens as a means of adherence and invasion. Heparin, a widely used anticoagulant drug, is structurally similar to HS and is a common experimental proxy. Exogenous heparin prevents infection by a range of viruses, including S-associated coronavirus isolate HSR1. Here, we show that heparin inhibits severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) invasion of Vero cells by up to 80% at doses achievable through prophylaxis and, particularly relevant, within the range deliverable by nebulisation. Surface plasmon resonance and circular dichroism spectroscopy demonstrate that heparin and enoxaparin, a low-molecular-weight heparin which is a clinical anticoagulant, bind and induce a conformational change in the spike (S1) protein receptor-binding domain (S1 RBD) of SARS-CoV-2. A library of heparin derivatives and size-defined fragments were used to probe the structural basis of this interaction. Binding to the RBD is more strongly dependent on the presence of 2-O or 6-O sulfate groups than on N-sulfation and a hexasaccharide is the minimum size required for secondary structural changes to be induced in the RBD. It is likely that inhibition of viral infection arises from an overlap between the binding sites of heparin/HS on S1 RBD and that of the angiotensin-converting enzyme 2. The results suggest a route for the rapid development of a first-line therapeutic by repurposing heparin and its derivatives as antiviral agents against SARS-CoV-2 and other members of the Coronaviridae.
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Affiliation(s)
- Courtney J. Mycroft-West
- Molecular and Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire, United Kingdom
| | - Dunhao Su
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Isabel Pagani
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Timothy R. Rudd
- Analytical and Biological Sciences Division, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom
| | - Stefano Elli
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Neha S. Gandhi
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, Australia
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Scott E. Guimond
- School of Medicine, Keele University, Newcastle-Under-Lyme, Staffordshire, United Kingdom
| | - Gavin J. Miller
- School of Chemical and Physical Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire, United Kingdom
| | - Maria C. Z. Meneghetti
- Biochemistry Department, Federal University of São Paulo (UNIFESP), São Paulo, SP Brazil
| | - Helena B. Nader
- Biochemistry Department, Federal University of São Paulo (UNIFESP), São Paulo, SP Brazil
| | - Yong Li
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Quentin M. Nunes
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Patricia Procter
- Molecular and Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire, United Kingdom
| | | | | | - Antonella Bisio
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Nicholas R. Forsyth
- Guy Hilton Research Centre, School of Pharmacy and Bioengineering, Keele University, Hartshill, Stoke-on-Trent, Staffordshire, United Kingdom
| | - Vito Ferro
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
| | - Jeremy E. Turnbull
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Marco Guerrini
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - David G. Fernig
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Edwin A. Yates
- Molecular and Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire, United Kingdom
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Marcelo A. Lima
- Molecular and Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire, United Kingdom
| | - Mark A. Skidmore
- Molecular and Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire, United Kingdom
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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22
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Mycroft-West CJ, Su D, Pagani I, Rudd TR, Elli S, Gandhi NS, Guimond SE, Miller GJ, Meneghetti MCZ, Nader HB, Li Y, Nunes QM, Procter P, Mancini N, Clementi M, Bisio A, Forsyth NR, Ferro V, Turnbull JE, Guerrini M, Fernig DG, Vicenzi E, Yates EA, Lima MA, Skidmore MA. Heparin Inhibits Cellular Invasion by SARS-CoV-2: Structural Dependence of the Interaction of the Spike S1 Receptor-Binding Domain with Heparin. Thromb Haemost 2020; 120:1700-1715. [PMID: 33368089 DOI: 10.1101/2020.04.28.066761] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The dependence of development and homeostasis in animals on the interaction of hundreds of extracellular regulatory proteins with the peri- and extracellular glycosaminoglycan heparan sulfate (HS) is exploited by many microbial pathogens as a means of adherence and invasion. Heparin, a widely used anticoagulant drug, is structurally similar to HS and is a common experimental proxy. Exogenous heparin prevents infection by a range of viruses, including S-associated coronavirus isolate HSR1. Here, we show that heparin inhibits severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) invasion of Vero cells by up to 80% at doses achievable through prophylaxis and, particularly relevant, within the range deliverable by nebulisation. Surface plasmon resonance and circular dichroism spectroscopy demonstrate that heparin and enoxaparin, a low-molecular-weight heparin which is a clinical anticoagulant, bind and induce a conformational change in the spike (S1) protein receptor-binding domain (S1 RBD) of SARS-CoV-2. A library of heparin derivatives and size-defined fragments were used to probe the structural basis of this interaction. Binding to the RBD is more strongly dependent on the presence of 2-O or 6-O sulfate groups than on N-sulfation and a hexasaccharide is the minimum size required for secondary structural changes to be induced in the RBD. It is likely that inhibition of viral infection arises from an overlap between the binding sites of heparin/HS on S1 RBD and that of the angiotensin-converting enzyme 2. The results suggest a route for the rapid development of a first-line therapeutic by repurposing heparin and its derivatives as antiviral agents against SARS-CoV-2 and other members of the Coronaviridae.
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Affiliation(s)
- Courtney J Mycroft-West
- Molecular and Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire, United Kingdom
| | - Dunhao Su
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Isabel Pagani
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Timothy R Rudd
- Analytical and Biological Sciences Division, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom
| | - Stefano Elli
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Neha S Gandhi
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, Australia
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Scott E Guimond
- School of Medicine, Keele University, Newcastle-Under-Lyme, Staffordshire, United Kingdom
| | - Gavin J Miller
- School of Chemical and Physical Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire, United Kingdom
| | - Maria C Z Meneghetti
- Biochemistry Department, Federal University of São Paulo (UNIFESP), São Paulo, SP Brazil
| | - Helena B Nader
- Biochemistry Department, Federal University of São Paulo (UNIFESP), São Paulo, SP Brazil
| | - Yong Li
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Quentin M Nunes
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Patricia Procter
- Molecular and Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire, United Kingdom
| | | | | | - Antonella Bisio
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Nicholas R Forsyth
- Guy Hilton Research Centre, School of Pharmacy and Bioengineering, Keele University, Hartshill, Stoke-on-Trent, Staffordshire, United Kingdom
| | - Vito Ferro
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
| | - Jeremy E Turnbull
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Marco Guerrini
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - David G Fernig
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Edwin A Yates
- Molecular and Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire, United Kingdom
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Marcelo A Lima
- Molecular and Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire, United Kingdom
| | - Mark A Skidmore
- Molecular and Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire, United Kingdom
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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23
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Nakamura M, Matsuzaki T, Iimori A, Sato A. Harnessing the chondroitin sulfate-binding characteristics of human lactoferrin to neutralize neurite outgrowth inhibition. Biochem Biophys Res Commun 2020; 534:1076-1082. [PMID: 33129446 DOI: 10.1016/j.bbrc.2020.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 10/06/2020] [Indexed: 11/30/2022]
Abstract
Human lactoferrin (hLF) is a glycosaminoglycan (GAG)-binding protein involved in various biological functions. It consists of two globular functional domains, referred to as the N- and C-lobes. Both heparin (HP) and heparan sulfate (HS) bind to the N-lobe domain of hLF. Although some biological functions of hLF such as neuroprotective effects and cancer growth inhibition are regulated by its binding to HS, the binding characteristics of hLF with other GAG subtypes, and their effects on biological activities are still poorly understood. Here, we report that hLF binds to chondroitin sulfate (CS)-E, a GAG subtype involved in various neurodegenerative diseases. The α-helical content of hLF, which is an indicator of changes in the secondary structure of hLF, increased in the presence of CS-C, CS-D, or CS-E, but not in the presence of HP, HS, CS-A, or CS-B. This structural change was also observed in the N-lobe, the N-terminal half region of the hLF. Additionally, the thermal stability of the N-lobe showed a dose-dependent improvement in the presence of CS-E, but not in the presence of HP. This indicates that the binding mode of hLF/N-lobe to CS-E may differ from that of HP. hLF was also found to neutralize CS-E-induced inhibition of neurite outgrowth and neuronal growth cone collapse, which are neurodegenerative responses to spinal cord injury, in cultured dorsal root ganglion neurons. Thus, hLF is a promising drug candidate for the treatment of CS-E-induced neurodegenerative diseases such as spinal cord injury.
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Affiliation(s)
- Masao Nakamura
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan; Department of Peptidomics, Sasaki Institute, Sasaki Foundation, 2-2 Kandasurugadai, Chiyoda-ku, Tokyo, 101-0062, Japan.
| | - Takumi Matsuzaki
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan
| | - Ami Iimori
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan
| | - Atsushi Sato
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan.
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24
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Niu C, Zhao Y, Bobst CE, Savinov SN, Kaltashov IA. Identification of Protein Recognition Elements within Heparin Chains Using Enzymatic Foot-Printing in Solution and Online SEC/MS. Anal Chem 2020; 92:7565-7573. [PMID: 32347711 DOI: 10.1021/acs.analchem.0c00115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding molecular mechanisms governing interactions of glycosaminoglycans (such as heparin) with proteins remains challenging due to their enormous structural heterogeneity. Commonly accepted approaches seek to reduce the structural complexity by searching for "binding epitopes" within the limited subsets of short heparin oligomers produced either enzymatically or synthetically. A top-down approach presented in this work seeks to preserve the chemical diversity displayed by heparin by allowing the longer and structurally diverse chains to interact with the client protein. Enzymatic lysis of the protein-bound heparin chains followed by the product analysis using size exclusion chromatography with online mass spectrometry detection (SEC/MS) reveals the oligomers that are protected from lysis due to their tight association with the protein, and enables their characterization (both the oligomer length, and the number of incorporated sulfate and acetyl groups). When applied to a paradigmatic heparin/antithrombin system, the new method generates a series of oligomers with surprisingly distinct sulfation levels. The extent of sulfation of the minimal-length binder (hexamer) is relatively modest yet persistent, consistent with the notion of six sulfate groups being both essential and sufficient for antithrombin binding. However, the masses of longer surviving chains indicate complete sulfation of disaccharides beyond the hexasaccharide core. Molecular dynamics simulations confirm the existence of favorable electrostatic interactions between the high charge-density saccharide residues flanking the "canonical" antithrombin-binding hexasaccharide and the positive patch on the surface of the overall negatively charged protein. Furthermore, electrostatics may rescue the heparin/protein interaction in the absence of the canonical binding element.
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Affiliation(s)
- Chendi Niu
- Chemistry Department, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Yunlong Zhao
- Chemistry Department, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Cedric E Bobst
- Chemistry Department, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Sergey N Savinov
- Biochemistry and Molecular Biology Department, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Igor A Kaltashov
- Chemistry Department, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
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25
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Sandoval DR, Gomez Toledo A, Painter CD, Tota EM, Sheikh MO, West AMV, Frank MM, Wells L, Xu D, Bicknell R, Corbett KD, Esko JD. Proteomics-based screening of the endothelial heparan sulfate interactome reveals that C-type lectin 14a (CLEC14A) is a heparin-binding protein. J Biol Chem 2020; 295:2804-2821. [PMID: 31964714 DOI: 10.1074/jbc.ra119.011639] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/10/2020] [Indexed: 12/21/2022] Open
Abstract
Animal cells express heparan sulfate proteoglycans that perform many important cellular functions by way of heparan sulfate-protein interactions. The identification of membrane heparan sulfate-binding proteins is challenging because of their low abundance and the need for extensive enrichment. Here, we report a proteomics workflow for the identification and characterization of membrane-anchored and extracellular proteins that bind heparan sulfate. The technique is based on limited proteolysis of live cells in the absence of denaturation and fixation, heparin-affinity chromatography, and high-resolution LC-MS/MS, and we designate it LPHAMS. Application of LPHAMS to U937 monocytic and primary murine and human endothelial cells identified 55 plasma membrane, extracellular matrix, and soluble secreted proteins, including many previously unidentified heparin-binding proteins. The method also facilitated the mapping of the heparin-binding domains, making it possible to predict the location of the heparin-binding site. To validate the discovery feature of LPHAMS, we characterized one of the newly-discovered heparin-binding proteins, C-type lectin 14a (CLEC14A), a member of the C-type lectin family that modulates angiogenesis. We found that the C-type lectin domain of CLEC14A binds one-to-one to heparin with nanomolar affinity, and using molecular modeling and mutagenesis, we mapped its heparin-binding site. CLEC14A physically interacted with other glycosaminoglycans, including endothelial heparan sulfate and chondroitin sulfate E, but not with neutral or sialylated oligosaccharides. The LPHAMS technique should be applicable to other cells and glycans and provides a way to expand the repertoire of glycan-binding proteins for further study.
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Affiliation(s)
- Daniel R Sandoval
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California 92093
| | - Alejandro Gomez Toledo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093
| | - Chelsea D Painter
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California 92093
| | - Ember M Tota
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093
| | - M Osman Sheikh
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Alan M V West
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California 92093
| | | | - Lance Wells
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Ding Xu
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, Buffalo, New York 14214
| | - Roy Bicknell
- College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093; Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California 92093.
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