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Yao G, Tian Y, Ke W, Fang J, Ma S, Li T, Cheng X, Xia B, Wen L, Gao Z. Direct Identification of Complex Glycans via a Highly Sensitive Engineered Nanopore. J Am Chem Soc 2024; 146:13356-13366. [PMID: 38602480 DOI: 10.1021/jacs.4c02081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The crucial roles that glycans play in biological systems are determined by their structures. However, the analysis of glycan structures still has numerous bottlenecks due to their inherent complexities. The nanopore technology has emerged as a powerful sensor for DNA sequencing and peptide detection. This has a significant impact on the development of a related research area. Currently, nanopores are beginning to be applied for the detection of simple glycans, but the analysis of complex glycans by this technology is still challenging. Here, we designed an engineered α-hemolysin nanopore M113R/T115A to achieve the sensing of complex glycans at micromolar concentrations and under label-free conditions. By extracting characteristic features to depict a three-dimensional (3D) scatter plot, glycans with different numbers of functional groups, various chain lengths ranging from disaccharide to decasaccharide, and distinct glycosidic linkages could be distinguished. Molecular dynamics (MD) simulations show different behaviors of glycans with β1,3- or β1,4-glycosidic bonds in nanopores. More importantly, the designed nanopore system permitted the discrimination of each glycan isomer with different lengths in a mixture with a separation ratio of over 0.9. This work represents a proof-of-concept demonstration that complex glycans can be analyzed using nanopore sequencing technology.
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Affiliation(s)
- Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Lingang Laboratory, Shanghai 200031, China
| | - Yinping Tian
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenjun Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Fang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shengzhou Ma
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tiehai Li
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 330106, China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
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Holmes SG, Desai UR. Assessing Genetic Algorithm-Based Docking Protocols for Prediction of Heparin Oligosaccharide Binding Geometries onto Proteins. Biomolecules 2023; 13:1633. [PMID: 38002315 PMCID: PMC10669598 DOI: 10.3390/biom13111633] [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: 10/12/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Although molecular docking has evolved dramatically over the years, its application to glycosaminoglycans (GAGs) has remained challenging because of their intrinsic flexibility, highly anionic character and rather ill-defined site of binding on proteins. GAGs have been treated as either fully "rigid" or fully "flexible" in molecular docking. We reasoned that an intermediate semi-rigid docking (SRD) protocol may be better for the recapitulation of native heparin/heparan sulfate (Hp/HS) topologies. Herein, we study 18 Hp/HS-protein co-complexes containing chains from disaccharide to decasaccharide using genetic algorithm-based docking with rigid, semi-rigid, and flexible docking protocols. Our work reveals that rigid and semi-rigid protocols recapitulate native poses for longer chains (5→10 mers) significantly better than the flexible protocol, while 2→4-mer poses are better predicted using the semi-rigid approach. More importantly, the semi-rigid docking protocol is likely to perform better when no crystal structure information is available. We also present a new parameter for parsing selective versus non-selective GAG-protein systems, which relies on two computational parameters including consistency of binding (i.e., RMSD) and docking score (i.e., GOLD Score). The new semi-rigid protocol in combination with the new computational parameter is expected to be particularly useful in high-throughput screening of GAG sequences for identifying promising druggable targets as well as drug-like Hp/HS sequences.
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Affiliation(s)
- Samuel G. Holmes
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA;
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
| | - Umesh R. Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA;
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
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Marcisz M, Samsonov SA. Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans. J Chem Inf Model 2023; 63:2147-2157. [PMID: 36989082 PMCID: PMC10091405 DOI: 10.1021/acs.jcim.2c01472] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
In computational studies of glycosaminoglycans (GAGs), a group of anionic, periodic linear polysaccharides, so far there has been very little discussion about the role of solvent models in the molecular dynamics simulations of these molecules. Predominantly, the TIP3P water model is commonly used as one of the most popular explicit water models in general. However, there are numerous alternative explicit and implicit water models that are neglected in the computational research of GAGs. Since solvent-mediated interactions are particularly important for GAG dynamic and structural properties, it would be of great interest for the GAG community to establish the solvent model that is suited the best in terms of the quality of theoretically obtained GAG parameters and, at the same time, would be reasonably demanding in terms of computational resources required. In this study, heparin (HP) was simulated using five implicit and six explicit solvent models with the aim to find out how different solvent models influence HP's molecular descriptors in the molecular dynamics simulations. Here, we initiate the search for the most appropriate solvent representation for GAG systems and we hope to encourage other groups to contribute to this highly relevant subject.
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Affiliation(s)
- Mateusz Marcisz
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
- Intercollegiate Faculty of Biotechnology of UG and MUG, ul. Abrahama 58, 80-307 Gdańsk, Poland
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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Heide F, Koch M, Stetefeld J. Heparin Mimetics and Their Impact on Extracellular Matrix Protein Assemblies. Pharmaceuticals (Basel) 2023; 16:ph16030471. [PMID: 36986571 PMCID: PMC10059586 DOI: 10.3390/ph16030471] [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: 02/06/2023] [Revised: 03/08/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Heparan sulfate is a crucial extracellular matrix component that organizes structural features and functional protein processes. This occurs through the formation of protein-heparan sulfate assemblies around cell surfaces, which allow for the deliberate local and temporal control of cellular signaling. As such, heparin-mimicking drugs can directly affect these processes by competing with naturally occurring heparan sulfate and heparin chains that then disturb protein assemblies and decrease regulatory capacities. The high number of heparan-sulfate-binding proteins that are present in the extracellular matrix can cause obscure pathological effects that should be considered and examined in more detail, especially when developing novel mimetics for clinical use. The objective of this article is to investigate recent studies that present heparan-sulfate-mediated protein assemblies and the impact of heparin mimetics on the assembly and function of these protein complexes.
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Affiliation(s)
- Fabian Heide
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Manuel Koch
- Institute for Experimental Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Liao YE, Liu J, Arnold K. Heparan sulfates and heparan sulfate binding proteins in sepsis. Front Mol Biosci 2023; 10:1146685. [PMID: 36865384 PMCID: PMC9971734 DOI: 10.3389/fmolb.2023.1146685] [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: 01/17/2023] [Accepted: 01/31/2023] [Indexed: 02/16/2023] Open
Abstract
Heparan sulfates (HSs) are the main components in the glycocalyx which covers endothelial cells and modulates vascular homeostasis through interactions with multiple Heparan sulfate binding proteins (HSBPs). During sepsis, heparanase increases and induces HS shedding. The process causes glycocalyx degradation, exacerbating inflammation and coagulation in sepsis. The circulating heparan sulfate fragments may serve as a host defense system by neutralizing dysregulated Heparan sulfate binding proteins or pro-inflammatory molecules in certain circumstances. Understanding heparan sulfates and heparan sulfate binding proteins in health and sepsis is critical to decipher the dysregulated host response in sepsis and advance drug development. In this review, we will overview the current understanding of HS in glycocalyx under septic condition and the dysfunctional heparan sulfate binding proteins as potential drug targets, particularly, high mobility group box 1 (HMGB1) and histones. Moreover, several drug candidates based on heparan sulfates or related to heparan sulfates, such as heparanase inhibitors or heparin-binding protein (HBP), will be discussed regarding their recent advances. By applying chemical or chemoenzymatic approaches, the structure-function relationship between heparan sulfates and heparan sulfate binding proteins is recently revealed with structurally defined heparan sulfates. Such homogenous heparan sulfates may further facilitate the investigation of the role of heparan sulfates in sepsis and the development of carbohydrate-based therapy.
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Affiliation(s)
- Yi-En Liao
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
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Quaranta DV, Weaver RR, Baumann KK, Fujimoto T, Williams LM, Kim HC, Logsdon AF, Omer M, Reed MJ, Banks WA, Erickson MA. Transport of the Proinflammatory Chemokines C-C Motif Chemokine Ligand 2 (MCP-1) and C-C Motif Chemokine Ligand 5 (RANTES) across the Intact Mouse Blood-Brain Barrier Is Inhibited by Heparin and Eprodisate and Increased with Systemic Inflammation. J Pharmacol Exp Ther 2023; 384:205-223. [PMID: 36310035 PMCID: PMC9827507 DOI: 10.1124/jpet.122.001380] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/26/2022] [Accepted: 10/17/2022] [Indexed: 01/12/2023] Open
Abstract
One important function of the vascular blood-brain barrier (BBB) is to facilitate neuroimmune communication. The BBB fulfills this function, in part, through its ability to transport cytokines and chemokines. C-C motif chemokine receptor 2 (CCL2) (MCP-1) and C-C motif chemokine receptor 5 (CCL5) (RANTES) are proinflammatory chemokines that mediate neuroimmune responses to acute insults and aspects of brain injury and neurodegenerative diseases; however, a blood-to-brain transport system has not been evaluated for either chemokine in vivo. Therefore, we determined whether CCL2 and CCL5 in blood can cross the intact BBB and enter the brain. Using CD-1 mice, we found that 125I-labeled CCL2 and CCL5 crossed the BBB and entered the brain parenchyma. We next aimed to identify the mechanisms of 125I-CCL2 and 125I-CCL5 transport in an in situ brain perfusion model. We found that both heparin and eprodisate inhibited brain uptake of 125I-CCL2 and 125I-CCL5 in situ, whereas antagonists of their receptors, CCR2 or CCR5, respectively, did not, suggesting that heparan sulfates at the endothelial surface mediate BBB transport. Finally, we showed that CCL2 and CCL5 transport across the BBB increased following a single injection of 0.3 mg/kg lipopolysaccharide. These data demonstrate that CCL2 and CCL5 in the brain can derive, in part, from the circulation, especially during systemic inflammation. Further, binding to the BBB-associated heparan sulfate is a mechanism by which both chemokines can cross the intact BBB, highlighting a novel therapeutic target for treating neuroinflammation. SIGNIFICANCE STATEMENT: Our work demonstrates that C-C motif chemokine ligand 2 (CCL2) and C-C motif chemokine ligand 5 (CCL5) can cross the intact blood-brain barrier and that transport is robustly increased during inflammation. These data suggest that circulating CCL2 and CCL5 can contribute to brain levels of each chemokine. We further show that the transport of both chemokines is inhibited by heparin and eprodisate, suggesting that CCL2/CCL5-heparan sulfate interactions could be therapeutically targeted to limit accumulation of these chemokines in the brain.
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Affiliation(s)
- Daniel V Quaranta
- Geriatric Research Education and Clinical Center, VA Puget Sound Healthcare System, Seattle, Washington (D.V.Q., R.R.W., K.K.B., T.F., L.M.W., H.C.K., A.F.L., M.O., M.J.R., W.A.B., M.A.E.); Department of Neurosurgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (T.F.); and Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington (H.C.K., A.F.L., M.J.R., W.A.B., M.A.E.)
| | - Riley R Weaver
- Geriatric Research Education and Clinical Center, VA Puget Sound Healthcare System, Seattle, Washington (D.V.Q., R.R.W., K.K.B., T.F., L.M.W., H.C.K., A.F.L., M.O., M.J.R., W.A.B., M.A.E.); Department of Neurosurgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (T.F.); and Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington (H.C.K., A.F.L., M.J.R., W.A.B., M.A.E.)
| | - Kristen K Baumann
- Geriatric Research Education and Clinical Center, VA Puget Sound Healthcare System, Seattle, Washington (D.V.Q., R.R.W., K.K.B., T.F., L.M.W., H.C.K., A.F.L., M.O., M.J.R., W.A.B., M.A.E.); Department of Neurosurgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (T.F.); and Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington (H.C.K., A.F.L., M.J.R., W.A.B., M.A.E.)
| | - Takashi Fujimoto
- Geriatric Research Education and Clinical Center, VA Puget Sound Healthcare System, Seattle, Washington (D.V.Q., R.R.W., K.K.B., T.F., L.M.W., H.C.K., A.F.L., M.O., M.J.R., W.A.B., M.A.E.); Department of Neurosurgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (T.F.); and Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington (H.C.K., A.F.L., M.J.R., W.A.B., M.A.E.)
| | - Lindsey M Williams
- Geriatric Research Education and Clinical Center, VA Puget Sound Healthcare System, Seattle, Washington (D.V.Q., R.R.W., K.K.B., T.F., L.M.W., H.C.K., A.F.L., M.O., M.J.R., W.A.B., M.A.E.); Department of Neurosurgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (T.F.); and Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington (H.C.K., A.F.L., M.J.R., W.A.B., M.A.E.)
| | - Hyung Chan Kim
- Geriatric Research Education and Clinical Center, VA Puget Sound Healthcare System, Seattle, Washington (D.V.Q., R.R.W., K.K.B., T.F., L.M.W., H.C.K., A.F.L., M.O., M.J.R., W.A.B., M.A.E.); Department of Neurosurgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (T.F.); and Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington (H.C.K., A.F.L., M.J.R., W.A.B., M.A.E.)
| | - Aric F Logsdon
- Geriatric Research Education and Clinical Center, VA Puget Sound Healthcare System, Seattle, Washington (D.V.Q., R.R.W., K.K.B., T.F., L.M.W., H.C.K., A.F.L., M.O., M.J.R., W.A.B., M.A.E.); Department of Neurosurgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (T.F.); and Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington (H.C.K., A.F.L., M.J.R., W.A.B., M.A.E.)
| | - Mohamed Omer
- Geriatric Research Education and Clinical Center, VA Puget Sound Healthcare System, Seattle, Washington (D.V.Q., R.R.W., K.K.B., T.F., L.M.W., H.C.K., A.F.L., M.O., M.J.R., W.A.B., M.A.E.); Department of Neurosurgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (T.F.); and Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington (H.C.K., A.F.L., M.J.R., W.A.B., M.A.E.)
| | - May J Reed
- Geriatric Research Education and Clinical Center, VA Puget Sound Healthcare System, Seattle, Washington (D.V.Q., R.R.W., K.K.B., T.F., L.M.W., H.C.K., A.F.L., M.O., M.J.R., W.A.B., M.A.E.); Department of Neurosurgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (T.F.); and Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington (H.C.K., A.F.L., M.J.R., W.A.B., M.A.E.)
| | - William A Banks
- Geriatric Research Education and Clinical Center, VA Puget Sound Healthcare System, Seattle, Washington (D.V.Q., R.R.W., K.K.B., T.F., L.M.W., H.C.K., A.F.L., M.O., M.J.R., W.A.B., M.A.E.); Department of Neurosurgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (T.F.); and Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington (H.C.K., A.F.L., M.J.R., W.A.B., M.A.E.)
| | - Michelle A Erickson
- Geriatric Research Education and Clinical Center, VA Puget Sound Healthcare System, Seattle, Washington (D.V.Q., R.R.W., K.K.B., T.F., L.M.W., H.C.K., A.F.L., M.O., M.J.R., W.A.B., M.A.E.); Department of Neurosurgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (T.F.); and Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington (H.C.K., A.F.L., M.J.R., W.A.B., M.A.E.)
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7
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Muronetz VI, Pozdyshev DV, Semenyuk PI. Polyelectrolytes for Enzyme Immobilization and the Regulation of Their Properties. Polymers (Basel) 2022; 14:polym14194204. [PMID: 36236151 PMCID: PMC9571273 DOI: 10.3390/polym14194204] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
In this review, we considered aspects related to the application of polyelectrolytes, primarily synthetic polyanions and polycations, to immobilize enzymes and regulate their properties. We mainly focused on the description of works in which polyelectrolytes were used to create complex and unusual systems (self-regulated enzyme-polyelectrolyte complexes, artificial chaperones, polyelectrolyte brushes, layer-by-layer immobilization and others). These works represent the field of "smart polymers", whilst the trivial use of charged polymers as carriers for adsorption or covalent immobilization of proteins is beyond the scope of this short review. In addition, we have included a section on the molecular modeling of interactions between proteins and polyelectrolytes, as modeling the binding of proteins with a strictly defined, and already known, spatial structure, to disordered polymeric molecules has its own unique characteristics.
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Affiliation(s)
- Vladimir I. Muronetz
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld 40, 119992 Moscow, Russia
- Butlerov Chemical Institute, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
- Correspondence: ; Tel.: +7-(495)939-14-56
| | - Denis V. Pozdyshev
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld 40, 119992 Moscow, Russia
| | - Pavel I. Semenyuk
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld 40, 119992 Moscow, Russia
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Marcisz M, Gaardløs M, Bojarski KK, Siebenmorgen T, Zacharias M, Samsonov SA. Explicit solvent repulsive scaling replica exchange molecular dynamics (RS-REMD) in molecular modeling of protein-glycosaminoglycan complexes. J Comput Chem 2022; 43:1633-1640. [PMID: 35796487 DOI: 10.1002/jcc.26965] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022]
Abstract
Glycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes of biomolecules. Therefore, there is a lack of modeling tools designed specifically for docking GAGs. One has to rely on existing docking software developed mostly for small drug molecules substantially differing from GAGs in their basic physico-chemical properties. In this study, we present an updated protocol for docking GAGs based on the Repulsive Scaling Replica Exchange Molecular Dynamics (RS-REMD) that includes explicit solvent description. The use of this water model improved docking performance both in terms of its accuracy and speed. This method represents a significant computational progress in GAG-related research.
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Affiliation(s)
- Mateusz Marcisz
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.,Intercollegiate Faculty of Biotechnology, Universuty of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | | | - Krzysztof K Bojarski
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.,Department of Physical Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Till Siebenmorgen
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Zacharias
- Physics Department, Technical University of Munich, Garching, Germany
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9
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Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states. Curr Opin Struct Biol 2022; 74:102356. [DOI: 10.1016/j.sbi.2022.102356] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/08/2022] [Accepted: 02/13/2022] [Indexed: 11/18/2022]
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10
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Ray B, Ali I, Jana S, Mukherjee S, Pal S, Ray S, Schütz M, Marschall M. Antiviral Strategies Using Natural Source-Derived Sulfated Polysaccharides in the Light of the COVID-19 Pandemic and Major Human Pathogenic Viruses. Viruses 2021; 14:35. [PMID: 35062238 PMCID: PMC8781365 DOI: 10.3390/v14010035] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/14/2022] Open
Abstract
Only a mere fraction of the huge variety of human pathogenic viruses can be targeted by the currently available spectrum of antiviral drugs. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak has highlighted the urgent need for molecules that can be deployed quickly to treat novel, developing or re-emerging viral infections. Sulfated polysaccharides are found on the surfaces of both the susceptible host cells and the majority of human viruses, and thus can play an important role during viral infection. Such polysaccharides widely occurring in natural sources, specifically those converted into sulfated varieties, have already proved to possess a high level and sometimes also broad-spectrum antiviral activity. This antiviral potency can be determined through multifold molecular pathways, which in many cases have low profiles of cytotoxicity. Consequently, several new polysaccharide-derived drugs are currently being investigated in clinical settings. We reviewed the present status of research on sulfated polysaccharide-based antiviral agents, their structural characteristics, structure-activity relationships, and the potential of clinical application. Furthermore, the molecular mechanisms of sulfated polysaccharides involved in viral infection or in antiviral activity, respectively, are discussed, together with a focus on the emerging methodology contributing to polysaccharide-based drug development.
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Affiliation(s)
- Bimalendu Ray
- Department of Chemistry, The University of Burdwan, Burdwan 713104, West Bengal, India; (I.A.); (S.J.); (S.M.); (S.P.)
| | - Imran Ali
- Department of Chemistry, The University of Burdwan, Burdwan 713104, West Bengal, India; (I.A.); (S.J.); (S.M.); (S.P.)
| | - Subrata Jana
- Department of Chemistry, The University of Burdwan, Burdwan 713104, West Bengal, India; (I.A.); (S.J.); (S.M.); (S.P.)
| | - Shuvam Mukherjee
- Department of Chemistry, The University of Burdwan, Burdwan 713104, West Bengal, India; (I.A.); (S.J.); (S.M.); (S.P.)
| | - Saikat Pal
- Department of Chemistry, The University of Burdwan, Burdwan 713104, West Bengal, India; (I.A.); (S.J.); (S.M.); (S.P.)
| | - Sayani Ray
- Department of Chemistry, The University of Burdwan, Burdwan 713104, West Bengal, India; (I.A.); (S.J.); (S.M.); (S.P.)
| | - Martin Schütz
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University (FAU) of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University (FAU) of Erlangen-Nürnberg, 91054 Erlangen, Germany
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11
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Harvey DJ. ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016. MASS SPECTROMETRY REVIEWS 2021; 40:408-565. [PMID: 33725404 DOI: 10.1002/mas.21651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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12
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Chhabra M, Doherty GG, See NW, Gandhi NS, Ferro V. From Cancer to COVID-19: A Perspective on Targeting Heparan Sulfate-Protein Interactions. CHEM REC 2021; 21:3087-3101. [PMID: 34145723 PMCID: PMC8441866 DOI: 10.1002/tcr.202100125] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/01/2021] [Indexed: 12/16/2022]
Abstract
Heparan sulfate (HS) is a complex, polyanionic polysaccharide ubiquitously expressed on cell surfaces and in the extracellular matrix. HS interacts with numerous proteins to mediate a vast array of biological and pathological processes. Inhibition of HS‐protein interactions is thus an attractive approach for new therapeutic development for cancer and infectious diseases, including COVID‐19; however, synthesis of well‐defined native HS oligosaccharides remains challenging. This has aroused significant interest in the development of HS mimetics which are more synthetically tractable and have fewer side effects, such as undesired anticoagulant activity. This account provides a perspective on the design and synthesis of different classes of HS mimetics with useful properties, and the development of various assays and molecular modelling tools to progress our understanding of their interactions with HS‐binding proteins.
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Affiliation(s)
- Mohit Chhabra
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, QLD, Australia
| | - Gareth G Doherty
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, QLD, Australia
| | - Nicholas W See
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, QLD, Australia
| | - Neha S Gandhi
- School of Chemistry and Physics, Queensland University of Technology, 4000, Brisbane, QLD, Australia
| | - Vito Ferro
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, QLD, Australia
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13
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Künze G, Huster D, Samsonov SA. Investigation of the structure of regulatory proteins interacting with glycosaminoglycans by combining NMR spectroscopy and molecular modeling - the beginning of a wonderful friendship. Biol Chem 2021; 402:1337-1355. [PMID: 33882203 DOI: 10.1515/hsz-2021-0119] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/09/2021] [Indexed: 11/15/2022]
Abstract
The interaction of regulatory proteins with extracellular matrix or cell surface-anchored glycosaminoglycans (GAGs) plays important roles in molecular recognition, wound healing, growth, inflammation and many other processes. In spite of their high biological relevance, protein-GAG complexes are significantly underrepresented in structural databases because standard tools for structure determination experience difficulties in studying these complexes. Co-crystallization with subsequent X-ray analysis is hampered by the high flexibility of GAGs. NMR spectroscopy experiences difficulties related to the periodic nature of the GAGs and the sparse proton network between protein and GAG with distances that typically exceed the detection limit of nuclear Overhauser enhancement spectroscopy. In contrast, computer modeling tools have advanced over the last years delivering specific protein-GAG docking approaches successfully complemented with molecular dynamics (MD)-based analysis. Especially the combination of NMR spectroscopy in solution providing sparse structural constraints with molecular docking and MD simulations represents a useful synergy of forces to describe the structure of protein-GAG complexes. Here we review recent methodological progress in this field and bring up examples where the combination of new NMR methods along with cutting-edge modeling has yielded detailed structural information on complexes of highly relevant cytokines with GAGs.
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Affiliation(s)
- Georg Künze
- Center for Structural Biology, Vanderbilt University, 465 21st Ave S, 5140 MRB3, Nashville, TN37240, USA.,Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN37235, USA.,Institute for Drug Discovery, University of Leipzig, Brüderstr. 34, D-04103Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107Leipzig, Germany
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Ul. Wita Stwosza 63, 80-308Gdańsk, Poland
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14
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Jain P, Shanthamurthy CD, Leviatan Ben-Arye S, Woods RJ, Kikkeri R, Padler-Karavani V. Discovery of rare sulfated N-unsubstituted glucosamine based heparan sulfate analogs selectively activating chemokines. Chem Sci 2021; 12:3674-3681. [PMID: 33889380 PMCID: PMC8025211 DOI: 10.1039/d0sc05862a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 01/15/2021] [Indexed: 12/24/2022] Open
Abstract
Achieving selective inhibition of chemokines with structurally well-defined heparan sulfate (HS) oligosaccharides can provide important insights into cancer cell migration and metastasis. However, HS is highly heterogeneous in chemical composition, which limits its therapeutic use. Here, we report the rational design and synthesis of N-unsubstituted (NU) and N-acetylated (NA) heparan sulfate tetrasaccharides that selectively inhibit structurally homologous chemokines. HS analogs were produced by divergent synthesis, where fully protected HS tetrasaccharide precursor was subjected to selective deprotection and regioselectively O-sulfated, and O-phosphorylated to obtain 13 novel HS tetrasaccharides. HS microarray and SPR analysis with a wide range of chemokines revealed the structural significance of sulfation patterns and NU domain in chemokine activities for the first time. Particularly, HT-3,6S-NH revealed selective recognition by CCL2 chemokine. Further systematic interrogation of the role of HT-3,6S-NH in cancer demonstrated an effective blockade of CCL2 and its receptor CCR2 interactions, thereby impairing cancer cell proliferation, migration and invasion, a step towards designing novel drug molecules.
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Affiliation(s)
- Prashant Jain
- Department of Chemistry , Indian Institute of Science Education and Research , Pune-411008 , India .
| | - Chethan D Shanthamurthy
- Department of Chemistry , Indian Institute of Science Education and Research , Pune-411008 , India .
| | - Shani Leviatan Ben-Arye
- Department of Cell Research and Immunology , The Shmunis School of Biomedicine and Cancer Research , The George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , 69978 , Israel .
| | - Robert J Woods
- Complex Carbohydrate Research Center , University of Georgia , Athens 30606 , GA , USA
| | - Raghavendra Kikkeri
- Department of Chemistry , Indian Institute of Science Education and Research , Pune-411008 , India .
| | - Vered Padler-Karavani
- Department of Cell Research and Immunology , The Shmunis School of Biomedicine and Cancer Research , The George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , 69978 , Israel .
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15
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Shanthamurthy CD, Leviatan Ben-Arye S, Kumar NV, Yehuda S, Amon R, Woods RJ, Padler-Karavani V, Kikkeri R. Heparan Sulfate Mimetics Differentially Affect Homologous Chemokines and Attenuate Cancer Development. J Med Chem 2021; 64:3367-3380. [PMID: 33683903 DOI: 10.1021/acs.jmedchem.0c01800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Achieving selective inhibition of chemokine activity by structurally well-defined heparan sulfate (HS) or HS mimetic molecules can provide important insights into their roles in individual physiological and pathological cellular processes. Here, we report a novel tailor-made HS mimetic, which furnishes an exclusive iduronic acid (IdoA) scaffold with different sulfation patterns and oligosaccharide chain lengths as potential ligands to target chemokines. Notably, highly sulfated-IdoA tetrasaccharide (I-45) exhibited strong binding to CCL2 chemokine thereby blocking CCL2/CCR2-mediated in vitro cancer cell invasion and metastasis. Taken together, IdoA-based HS mimetics offer an alternative HS substrate to generate selective and efficient inhibitors for chemokines and pave the way to a wide range of new therapeutic applications in cancer biology and immunology.
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Affiliation(s)
- Chethan D Shanthamurthy
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
| | - Shani Leviatan Ben-Arye
- Department of Cell Research and Immunology, the Shmunis School of Biomedicine and Cancer Research, the George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | | | - Sharon Yehuda
- Department of Cell Research and Immunology, the Shmunis School of Biomedicine and Cancer Research, the George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ron Amon
- Department of Cell Research and Immunology, the Shmunis School of Biomedicine and Cancer Research, the George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens 306062 Georgia, United States
| | - Vered Padler-Karavani
- Department of Cell Research and Immunology, the Shmunis School of Biomedicine and Cancer Research, the George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Raghavendra Kikkeri
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
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16
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Vignovich WP, Pomin VH. Saturation Transfer Difference in Characterization of Glycosaminoglycan-Protein Interactions. SLAS Technol 2020; 25:307-319. [PMID: 32452261 DOI: 10.1177/2472630320921130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Novel methods in nuclear magnetic resonance (NMR) spectroscopy have recently been developed to investigate the binding properties of intermolecular complexes endowed with biomedical functions. Among these methods is the saturation transfer difference (STD), which enables the mapping of specific binding motifs of functional ligands. STD can efficiently uncover the specific and preferential binding sites of these ligands in their intermolecular complexes. This is particularly useful in the case of glycosaminoglycans (GAGs), a group of sulfated polysaccharides that play pivotal roles in various biological and pathological processes. The activity of GAGs is ultimately mediated through molecular interactions with key functional proteins, namely, GAG-binding proteins (GBPs). The quality of the GAG-GBP interactions depends on sulfation patterns, oligosaccharide length, and the composing monosaccharides of GAGs. Through STD NMR, information about the atoms of the GAG ligands involved in the complexes is provided. Here we highlight the latest achievements of the literature using STD NMR on GAG oligosaccharide-GBP complexes. Interestingly, most of the GBPs studied so far by STD NMR belong to one of the three major classes: coagulation factors, growth factors, or chemokine/cytokines. Unveiling the structural requirements of GAG ligands in bindings with their protein partners is a crucial step to understand the biochemical and medical actions of GAGs. This process is also a requirement in GAG-based drug discovery and development.
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Affiliation(s)
- William P Vignovich
- BioMolecular Sciences Department, School of Pharmacy, the University of Mississippi, Oxford, MS, USA
| | - Vitor H Pomin
- BioMolecular Sciences Department, School of Pharmacy, the University of Mississippi, Oxford, MS, USA.,Research Institute of Pharmaceutical Sciences, School of Pharmacy, the University of Mississippi, Oxford, MS, USA
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17
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Li JY, Chen YC, Lee YZ, Huang CH, Sue SC. N-terminal Backbone Pairing Shifts in CCL5- 12AAA 14 Dimer Interface: Structural Significance of the FAY Sequence. Int J Mol Sci 2020; 21:ijms21051689. [PMID: 32121575 PMCID: PMC7084690 DOI: 10.3390/ijms21051689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 01/13/2023] Open
Abstract
CC-type chemokine ligand 5 (CCL5) has been known to regulate immune responses by mediating the chemotaxis of leukocytes. Depending on the environment, CCL5 forms different orders of oligomers to interact with targets and create functional diversity. A recent CCL5 trimer structure revealed that the N-terminal conversed F12-A13-Y14 (12FAY14) sequence is involved in CCL5 aggregation. The CCL5-12AAA14 mutant with two mutations had a deficiency in the formation of high-order oligomers. In the study, we clarify the respective roles of F12 and Y14 through NMR analysis and structural determination of the CCL5-12AAA14 mutant where F12 is involved in the dimer assembly and Y14 is involved in aggregation. The CCL5-12AAA14 structure contains a unique dimer packing. The backbone pairing shifts for one-residue in the N-terminal interface, when compared to the native CCL5 dimer. This difference creates a new structural orientation and leads to the conclusion that F12 confines the native CCL5 dimer configuration. Without F12 anchoring in the position, the interfacial backbone pairing is permitted to slide. Structural plasticity occurs in the N-terminal interaction. This is the first case to report this structural rearrangement through mutagenesis. The study provides a new idea for chemokine engineering and complements the understanding of CCL5 oligomerization and the role of the 12FAY14 sequence.
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Affiliation(s)
- Jin-Ye Li
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan; (J.-Y.L.); (Y.-C.C.); (Y.-Z.L.)
| | - Yi-Chen Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan; (J.-Y.L.); (Y.-C.C.); (Y.-Z.L.)
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan; (J.-Y.L.); (Y.-C.C.); (Y.-Z.L.)
- Instrument Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chun-Hsiang Huang
- Protein Diffraction Group, Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan;
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan; (J.-Y.L.); (Y.-C.C.); (Y.-Z.L.)
- Department of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan
- Correspondence: ; Tel.: +886-3-5742025; Fax: +886-3-5715934
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18
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Basa S, Nampally M, Honorato T, Das SN, Podile AR, El Gueddari NE, Moerschbacher BM. The Pattern of Acetylation Defines the Priming Activity of Chitosan Tetramers. J Am Chem Soc 2020; 142:1975-1986. [PMID: 31895979 DOI: 10.1021/jacs.9b11466] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The biological activity of chitosans depends on their degree of polymerization (DP) and degree of acetylation (DA). However, information could also be carried by the pattern of acetylation (PA): the sequence of β-1,4-linked glucosamine (deacetylated/D) and N-acetylglucosamine (acetylated/A) units. To address this hypothesis, we prepared partially acetylated chitosan oligosaccharides from a chitosan polymer (DA = 35%, DPw = 905) using recombinant chitosan hydrolases with distinct substrate and cleavage specificities. The mixtures were separated into fractions DP4-DP12, which were tested for elicitor and priming activities in rice cells. We confirmed that both activities were influenced by DP, but also observed apparent DA-dependent priming activity, with the ADDD+DADD fraction proving remarkably effective. We then compared all four monoacetylated tetramers prepared using different chitin deacetylases and observed significant differences in priming activity. This demonstrates for the first time that PA influences the biological activity of chitosans, which can now be recognized as bona fide information-carrying molecules.
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Affiliation(s)
- Sven Basa
- University of Münster , Institute for Biology and Biotechnology of Plants , Schlossplatz 8 , 48143 Münster , Germany
| | - Malathi Nampally
- University of Münster , Institute for Biology and Biotechnology of Plants , Schlossplatz 8 , 48143 Münster , Germany
| | - Talita Honorato
- University of Münster , Institute for Biology and Biotechnology of Plants , Schlossplatz 8 , 48143 Münster , Germany
| | - Subha N Das
- University of Münster , Institute for Biology and Biotechnology of Plants , Schlossplatz 8 , 48143 Münster , Germany.,University of Hyderabad , Department of Plant Sciences, School of Life Sciences , Hyderabad , India
| | - Appa R Podile
- University of Hyderabad , Department of Plant Sciences, School of Life Sciences , Hyderabad , India
| | - Nour E El Gueddari
- University of Münster , Institute for Biology and Biotechnology of Plants , Schlossplatz 8 , 48143 Münster , Germany
| | - Bruno M Moerschbacher
- University of Münster , Institute for Biology and Biotechnology of Plants , Schlossplatz 8 , 48143 Münster , Germany
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19
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Chen YC, Chen SP, Li JY, Chen PC, Lee YZ, Li KM, Zarivach R, Sun YJ, Sue SC. Integrative Model to Coordinate the Oligomerization and Aggregation Mechanisms of CCL5. J Mol Biol 2020; 432:1143-1157. [PMID: 31931012 DOI: 10.1016/j.jmb.2019.12.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 11/25/2022]
Abstract
CC-type chemokine ligand 5 (CCL5) is involved in the pathogenesis of many inflammatory conditions. Under physiological conditions, CCL5 oligomerization and aggregation are considered to be responsible for its inflammatory properties. The structural basis of CCL5 oligomerization remains controversial because the current oligomer models contain no consensus interactions. In this study, NMR and biophysical analyses proposed evidence that the CC-type CCL5 dimer acts as the basic unit to constitute the oligomer and that CCL5 oligomerizes alternatively through E66-K25 and E66-R44/K45 interactions. In addition, a newly determined trimer structure, constituted by CCL5 and the E66S mutant, reported an interfacial interaction through the N-terminal 12FAY14 sequence. The interaction contributes to CCL5 aggregation and precipitation but not to oligomerization. In accordance with the observations, an integrative model explains the CCL5 oligomerization and aggregation mechanism in which CCL5 assembly consists of two types of dimer-dimer interactions and one aggregation mechanism. For full-length CCL5, the molecular accumulation triggers oligomerization through the E66-K25 and E66-R44/K45 interactions, and the 12FAY14 interaction acts as a secondary effect to derive aggregation and precipitation. In contrast, the E66-R44/K45 interaction might dominate in CCL5 N-terminal truncations, and the interaction would lead to the filament-like formation in solution.
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Affiliation(s)
- Yi-Chen Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Siou-Pei Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Jin-Ye Li
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Pei-Chun Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan; Instrument Center, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Kun-Mou Li
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Raz Zarivach
- Department of Life Sciences, The National Institute for Biotechnology in the Negev and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yuh-Ju Sun
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Life Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Life Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
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20
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Stickney M, Sanderson P, Leach FE, Zhang F, Linhardt RJ, Amster IJ. Online Capillary Zone Electrophoresis Negative Electron Transfer Dissociation Tandem Mass Spectrometry of Glycosaminoglycan Mixtures. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2019; 445:116209. [PMID: 32641905 PMCID: PMC7343235 DOI: 10.1016/j.ijms.2019.116209] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Glycosaminoglycans (GAGs) are important biological molecules that are highly anionic and occur in nature as complex mixtures. A platform that combines capillary zone electrophoresis (CZE) separations with mass spectrometry (MS) and gas-phase sequencing by using negative electron transfer dissociation (NETD) is shown to be efficacious for the structural analysis of GAG mixtures. CZE is a separation method well suited to the highly negatively charged nature of GAGs. NETD is an electron-based ion activation method that enables the generation of informative fragments with retention of the labile sulfate half-ester modification that determine specific GAG function. Here we combine for the first time NETD and CZE for assigning the structures of GAG oligomers present in mixtures. The speed of ion activation by NETD is found to couple well with the narrow peaks resulting from CZE migration. The platform was optimized with mixtures of GAG tetrasaccharide standards. The potential of the platform is demonstrated by the analysis of enoxaparin, a complex mixture of low molecular weight heparins, which was separated by CZE within 30 minutes and characterized by NETD MS/MS in one online experiment. 37 unique molecular compositions have been identified in enoxaparin using CZE-MS and 9 structures have been assigned with CZE-NETD-MS/MS.
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Affiliation(s)
- Morgan Stickney
- Department of Chemistry, University of Georgia, Athens, GA 30602
| | | | - Franklin E. Leach
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602
| | - Fuming Zhang
- Center for Biotechnology & Interdisciplinary Studies, Departments of Chemistry and Chemical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Robert J. Linhardt
- Center for Biotechnology & Interdisciplinary Studies, Departments of Chemistry and Chemical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
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21
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Eustace AD, McNaughton EF, King S, Kehoe O, Kungl A, Mattey D, Nobbs AH, Williams N, Middleton J. Soluble syndecan-3 binds chemokines, reduces leukocyte migration in vitro and ameliorates disease severity in models of rheumatoid arthritis. Arthritis Res Ther 2019; 21:172. [PMID: 31300004 PMCID: PMC6625118 DOI: 10.1186/s13075-019-1939-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/10/2019] [Indexed: 01/04/2023] Open
Abstract
Background Syndecans are heparan sulfate proteoglycans that occur in membrane-bound or soluble forms. Syndecan-3, the least well-characterised of the syndecan family, is highly expressed on synovial endothelial cells in rheumatoid arthritis patients. Here, it binds pro-inflammatory chemokines with evidence for a role in chemokine presentation and leukocyte trafficking into the joint, promoting the inflammatory response. In this study, we explored the role of soluble syndecan-3 as a binder of chemokines and as an anti-inflammatory and therapeutic molecule. Methods A human monocytic cell line and CD14+ PBMCs were utilised in both Boyden chamber and trans-endothelial migration assays. Soluble syndecan-3 was tested in antigen-induced and collagen-induced in vivo arthritis models in mice. ELISA and isothermal fluorescence titration assays assessed the binding affinities. Syndecan-3 expression was identified by flow cytometry and PCR, and levels of shedding by ELISA. Results Using in vitro and in vivo models, soluble syndecan-3 inhibited leukocyte migration in vitro in response to CCL7 and its administration in murine models of rheumatoid arthritis reduced histological disease severity. Using isothermal fluorescence titration, the binding affinity of soluble syndecan-3 to inflammatory chemokines CCL2, CCL7 and CXCL8 was determined, revealing little difference, with Kds in the low nM range. TNFα increased cell surface expression and shedding of syndecan-3 from cultured human endothelial cells. Furthermore, soluble syndecan-3 occurred naturally in the sera of patients with rheumatoid arthritis and periodontitis, and its levels correlated with syndecan-1. Conclusions This study shows that the addition of soluble syndecan-3 may represent an alternative therapeutic approach in inflammatory disease. Electronic supplementary material The online version of this article (10.1186/s13075-019-1939-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew D Eustace
- Bristol Dental School, University of Bristol, Lower Maudlin Street, BS1 2LY, Bristol, UK
| | - Emily F McNaughton
- Bristol Dental School, University of Bristol, Lower Maudlin Street, BS1 2LY, Bristol, UK
| | - Sophie King
- Bristol Dental School, University of Bristol, Lower Maudlin Street, BS1 2LY, Bristol, UK
| | - Oksana Kehoe
- Leopold Muller Arthritis Research Centre, Medical School, RJAH Orthopaedic Hospital, ISTM, Keele University, Oswestry, UK
| | - Andreas Kungl
- Institute of Pharmaceutical Sciences, Karl-Franzens-University Graz, Humboldtstrasse 46, A-8010, Graz, Austria
| | - Derek Mattey
- Staffordshire Rheumatology Centre, Haywood Hospital, Stoke-on-Trent, UK
| | - Angela H Nobbs
- Bristol Dental School, University of Bristol, Lower Maudlin Street, BS1 2LY, Bristol, UK.
| | - Neil Williams
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, BS8 1TD, Bristol, UK
| | - Jim Middleton
- Bristol Dental School, University of Bristol, Lower Maudlin Street, BS1 2LY, Bristol, UK
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22
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Nurcombe V, Ling L, Hondermarck H, Cool SM, Smith RAA. Bringing Heparan Sulfate Glycomics Together with Proteomics for the Design of Novel Therapeutics: A Historical Perspective. Proteomics 2019; 19:e1800466. [PMID: 31197945 DOI: 10.1002/pmic.201800466] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/31/2019] [Indexed: 01/29/2023]
Abstract
Increasing knowledge of how peptides bind saccharides, and of how saccharides bind peptides, is starting to revolutionize understanding of cell-extracellular matrix relationships. Here, a historical perspective is taken of the relationship between heparan sulfate glycosaminoglycans and how they interact with peptide growth factors in order to both drive and modulate signaling through the appropriate cognate receptors. Such knowledge is guiding the preparation of targeted sugar mimetics that will impact the treatment of many different kinds of diseases, including cancer.
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Affiliation(s)
- Victor Nurcombe
- Institute of Medical Biology, Glycotherapeutics Group, A*STAR, 138648, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technology University-Imperial College London, 636921, Singapore
| | - Ling Ling
- Institute of Medical Biology, Glycotherapeutics Group, A*STAR, 138648, Singapore
| | - Hubert Hondermarck
- School of Biomedical Sciences and Pharmacy, University of Newcastle, NSW, 2308, Australia
| | - Simon M Cool
- Institute of Medical Biology, Glycotherapeutics Group, A*STAR, 138648, Singapore.,Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, 119228, Singapore
| | - Raymond A A Smith
- Institute of Medical Biology, Glycotherapeutics Group, A*STAR, 138648, Singapore
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23
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Uciechowska-Kaczmarzyk U, Chauvot de Beauchene I, Samsonov SA. Docking software performance in protein-glycosaminoglycan systems. J Mol Graph Model 2019; 90:42-50. [PMID: 30959268 DOI: 10.1016/j.jmgm.2019.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 01/09/2023]
Abstract
We present a benchmarking study for protein-glycosaminoglycan systems with eight docking programs: Dock, rDock, ClusPro, PLANTS, HADDOCK, Hex, SwissDock and ATTRACT. We used a non-redundant representative dataset of 28 protein-glycosaminoglycan complexes with experimentally available structures, where a glycosaminoglycan ligand was longer than a trimer. Overall, the ligand binding poses could be correctly predicted in many cases by the tested docking programs, however the ranks of the docking poses are often poorly assigned. Our results suggest that Dock program performs best in terms of the pose placement, has the most suitable scoring function, and its performance did not depend on the ligand size. This suggests that the implementation of the electrostatics as well as the shape complementarity procedure in Dock are the most suitable for docking glycosaminoglycan ligands. We also analyzed how free energy patterns of the benchmarking complexes affect the performance of the evaluated docking software.
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Affiliation(s)
- Urszula Uciechowska-Kaczmarzyk
- Laboratory of Molecular Modeling, Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | | | - Sergey A Samsonov
- Laboratory of Molecular Modeling, Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
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24
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Semenyuk P, Muronetz V. Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications. Int J Mol Sci 2019; 20:E1252. [PMID: 30871103 PMCID: PMC6429204 DOI: 10.3390/ijms20051252] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/18/2022] Open
Abstract
Interaction of proteins with charged macromolecules is involved in many processes in cells. Firstly, there are many naturally occurred charged polymers such as DNA and RNA, polyphosphates, sulfated glycosaminoglycans, etc., as well as pronouncedly charged proteins such as histones or actin. Electrostatic interactions are also important for "generic" proteins, which are not generally considered as polyanions or polycations. Finally, protein behavior can be altered due to post-translational modifications such as phosphorylation, sulfation, and glycation, which change a local charge of the protein region. Herein we review molecular modeling for the investigation of such interactions, from model polyanions and polycations to unfolded proteins. We will show that electrostatic interactions are ubiquitous, and molecular dynamics simulations provide an outstanding opportunity to look inside binding and reveal the contribution of electrostatic interactions. Since a molecular dynamics simulation is only a model, we will comprehensively consider its relationship with the experimental data.
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Affiliation(s)
- Pavel Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
| | - Vladimir Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia.
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25
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Cross-Species Analysis of Glycosaminoglycan Binding Proteins Reveals Some Animal Models Are "More Equal" than Others. Molecules 2019; 24:molecules24050924. [PMID: 30845788 PMCID: PMC6429508 DOI: 10.3390/molecules24050924] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/01/2019] [Accepted: 03/03/2019] [Indexed: 12/22/2022] Open
Abstract
Glycosaminoglycan (GAG) mimetics are synthetic or semi-synthetic analogues of heparin or heparan sulfate, which are designed to interact with GAG binding sites on proteins. The preclinical stages of drug development rely on efficacy and toxicity assessment in animals and aim to apply these findings to clinical studies. However, such data may not always reflect the human situation possibly because the GAG binding site on the protein ligand in animals and humans could differ. Possible inter-species differences in the GAG-binding sites on antithrombin III, heparanase, and chemokines of the CCL and CXCL families were examined by sequence alignments, molecular modelling and assessment of surface electrostatic potentials to determine if one species of laboratory animal is likely to result in more clinically relevant data than another. For each protein, current understanding of GAG binding is reviewed from a protein structure and function perspective. This combinatorial analysis shows chemokine dimers and oligomers can present different GAG binding surfaces for the same target protein, whereas a cleft-like GAG binding site will differently influence the types of GAG structures that bind and the species preferable for preclinical work. Such analyses will allow an informed choice of animal(s) for preclinical studies of GAG mimetic drugs.
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26
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Stickney M, Xia Q, Amster IJ. Investigation of electrospray for a capillary electrophoresis-mass spectrometry interface in reverse polarity and negative ion mode. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:157-163. [PMID: 30773923 PMCID: PMC6558982 DOI: 10.1177/1469066719828192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Capillary zone electrophoresis (CZE) paired with mass spectrometry (MS) is a powerful analytical technique for examining mixtures of ionic analytes such as glycosaminoglycans. This study examines the mechanics of the electrospray process for a sheath flow CZE-MS interface under reverse polarity negative ionization conditions. Liquid flow in a sheath flow nano-electrospray CZE-MS interface is driven by two mechanisms, electroosmotic flow and electrospray nebulization. The contribution of these two processes to the overall flow of solution to the electrospray tip is influenced by the surface coatings of the sheath flow emitter tip and by the solvent composition. We have investigated the application of this interface to the reverse polarity separation of glycosaminoglycans and find that the role of electroosmotic flow is far less than has been reported previously, and the electrospray process itself is the largest contributor to the flow of the sheath liquid.
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Affiliation(s)
| | - Qiangwei Xia
- 760 Parkside Avenue, STE 211, CMP Scientific, Corp, Brooklyn, NY, 11226
| | - I. Jonathan Amster
- 140 Cedar Street, University of Georgia, Athens, GA 30602
- Address for correspondence: Department of Chemistry, University of Georgia, Athens, GA 30602, Phone: 706-542-2726, FAX: 706-542-9454,
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27
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Bojarski KK, Sieradzan AK, Samsonov SA. Molecular dynamics insights into protein‐glycosaminoglycan systems from microsecond‐scale simulations. Biopolymers 2019; 110:e23252. [DOI: 10.1002/bip.23252] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/26/2018] [Accepted: 12/21/2018] [Indexed: 12/30/2022]
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28
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Duan J, Jonathan Amster I. An Automated, High-Throughput Method for Interpreting the Tandem Mass Spectra of Glycosaminoglycans. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1802-1811. [PMID: 29790112 PMCID: PMC6087482 DOI: 10.1007/s13361-018-1969-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/06/2018] [Accepted: 04/14/2018] [Indexed: 05/03/2023]
Abstract
The biological interactions between glycosaminoglycans (GAGs) and other biomolecules are heavily influenced by structural features of the glycan. The structure of GAGs can be assigned using tandem mass spectrometry (MS2), but analysis of these data, to date, requires manually interpretation, a slow process that presents a bottleneck to the broader deployment of this approach to solving biologically relevant problems. Automated interpretation remains a challenge, as GAG biosynthesis is not template-driven, and therefore, one cannot predict structures from genomic data, as is done with proteins. The lack of a structure database, a consequence of the non-template biosynthesis, requires a de novo approach to interpretation of the mass spectral data. We propose a model for rapid, high-throughput GAG analysis by using an approach in which candidate structures are scored for the likelihood that they would produce the features observed in the mass spectrum. To make this approach tractable, a genetic algorithm is used to greatly reduce the search-space of isomeric structures that are considered. The time required for analysis is significantly reduced compared to an approach in which every possible isomer is considered and scored. The model is coded in a software package using the MATLAB environment. This approach was tested on tandem mass spectrometry data for long-chain, moderately sulfated chondroitin sulfate oligomers that were derived from the proteoglycan bikunin. The bikunin data was previously interpreted manually. Our approach examines glycosidic fragments to localize SO3 modifications to specific residues and yields the same structures reported in literature, only much more quickly. Graphical Abstract ᅟ.
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Affiliation(s)
- Jiana Duan
- Department of Chemistry, University of Georgia, Athens, GA, 30606, USA
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, GA, 30606, USA.
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29
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Abstract
Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.
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Affiliation(s)
- Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
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30
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Thieker DF, Xu Y, Chapla D, Nora C, Qiu H, Felix T, Wang L, Moremen KW, Liu J, Esko JD, Woods RJ. Downstream Products are Potent Inhibitors of the Heparan Sulfate 2-O-Sulfotransferase. Sci Rep 2018; 8:11832. [PMID: 30087361 PMCID: PMC6081452 DOI: 10.1038/s41598-018-29602-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/09/2018] [Indexed: 12/31/2022] Open
Abstract
Heparan Sulfate (HS) is a cell signaling molecule linked to pathological processes ranging from cancer to viral entry, yet fundamental aspects of its biosynthesis remain incompletely understood. Here, the binding preferences of the uronyl 2-O-sulfotransferase (HS2ST) are examined with variably-sulfated hexasaccharides. Surprisingly, heavily sulfated oligosaccharides formed by later-acting sulfotransferases bind more tightly to HS2ST than those corresponding to its natural substrate or product. Inhibition assays also indicate that the IC50 values correlate simply with degree of oligosaccharide sulfation. Structural analysis predicts a mode of inhibition in which 6-O-sulfate groups located on glucosamine residues present in highly-sulfated oligosaccharides occupy the canonical binding site of the nucleotide cofactor. The unexpected finding that oligosaccharides associated with later stages in HS biosynthesis inhibit HS2ST indicates that the enzyme must be separated temporally and/or spatially from downstream products during biosynthesis in vivo, and highlights a challenge for the enzymatic synthesis of lengthy HS chains in vitro.
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Affiliation(s)
- David F Thieker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Rm 1044, Genetic Medicine Building, Chapel Hill, USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Chelsea Nora
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Hong Qiu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Thomas Felix
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Lianchun Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Rm 1044, Genetic Medicine Building, Chapel Hill, USA
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Robert J Woods
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
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31
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Brzyska A, Płaziński W, Woliński K. Force-induced structural changes in non-sulfated carrageenan based oligosaccharides - a theoretical study. SOFT MATTER 2018; 14:6264-6277. [PMID: 30004100 DOI: 10.1039/c8sm00319j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this work we use the Enforced Geometry Optimization (EGO) approach to simulate force-induced structural changes in the monomer, and di- up to pentameric oligomers of neutral and non-sulfated carrageenan based oligosaccharides. Our results indicate that the monosaccharide unit sequence in the oligomeric structure determines: (i) the type(s) of the enforced conformational transition(s), and (ii) the mechanical resistance to external forces. It is a direct consequence of the different glycosidic bonding types in the examined carregeenan based oligosaccharides.
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Affiliation(s)
- A Brzyska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland.
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32
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Sankaranarayanan NV, Nagarajan B, Desai UR. So you think computational approaches to understanding glycosaminoglycan-protein interactions are too dry and too rigid? Think again! Curr Opin Struct Biol 2018; 50:91-100. [PMID: 29328962 PMCID: PMC6037615 DOI: 10.1016/j.sbi.2017.12.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/17/2017] [Accepted: 12/15/2017] [Indexed: 12/20/2022]
Abstract
Glycosaminoglycans (GAGs) play key roles in virtually all biologic responses through their interaction with proteins. A major challenge in understanding these roles is their massive structural complexity. Computational approaches are extremely useful in navigating this bottleneck and, in some cases, the only avenue to gain comprehensive insight. We discuss the state-of-the-art on computational approaches and present a flowchart to help answer most basic, and some advanced, questions on GAG-protein interactions. For example, firstly, does my protein bind to GAGs?; secondly, where does the GAG bind?; thirdly, does my protein preferentially recognize a particular GAG type?; fourthly, what is the most optimal GAG chain length?; fifthly, what is the structure of the most favored GAG sequence?; and finally, is my GAG-protein system 'specific', 'non-specific', or a combination of both? Recent advances show the field is now poised to enable a non-computational researcher perform advanced experiments through the availability of various tools and online servers.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Balaji Nagarajan
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA.
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33
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Uciechowska-Kaczmarzyk U, Babik S, Zsila F, Bojarski KK, Beke-Somfai T, Samsonov SA. Molecular dynamics-based model of VEGF-A and its heparin interactions. J Mol Graph Model 2018; 82:157-166. [DOI: 10.1016/j.jmgm.2018.04.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 11/28/2022]
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34
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Sanderson P, Stickney M, Leach FE, Xia Q, Yu Y, Zhang F, Linhardt RJ, Amster IJ. Heparin/heparan sulfate analysis by covalently modified reverse polarity capillary zone electrophoresis-mass spectrometry. J Chromatogr A 2018; 1545:75-83. [PMID: 29501428 PMCID: PMC5862776 DOI: 10.1016/j.chroma.2018.02.052] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/17/2018] [Accepted: 02/24/2018] [Indexed: 12/21/2022]
Abstract
Reverse polarity capillary zone electrophoresis coupled to negative ion mode mass spectrometry (CZE-MS) is shown to be an effective and sensitive tool for the analysis of glycosaminoglycan mixtures. Covalent modification of the inner wall of the separation capillary with neutral or cationic reagents produces a stable and durable surface that provides reproducible separations. By combining CZE-MS with a cation-coated capillary and a sheath flow interface, a rapid and reliable method has been developed for the analysis of sulfated oligosaccharides from dp4 to dp12. Several different mixtures have been separated and detected by mass spectrometry. The mixtures were selected to test the capability of this approach to resolve subtle differences in structure, such as sulfation position and epimeric variation of the uronic acid. The system was applied to a complex mixture of heparin/heparan sulfate oligosaccharides varying in chain length from dp3 to dp12 and more than 80 molecular compositions were identified by accurate mass measurement.
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Affiliation(s)
- Patience Sanderson
- Department of Chemistry, University of Georgia, Athens, GA 30602, United States
| | - Morgan Stickney
- Department of Chemistry, University of Georgia, Athens, GA 30602, United States
| | - Franklin E Leach
- Department of Chemistry, University of Georgia, Athens, GA 30602, United States
| | - Qiangwei Xia
- 760 Parkside Avenue, STE 211, CMP Scientific, Corp., Brooklyn, NY, 11226, United States
| | - Yanlei Yu
- Biotech 4005, 110 8th Street, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - Fuming Zhang
- Biotech 4005, 110 8th Street, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - Robert J Linhardt
- Biotech 4005, 110 8th Street, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, GA 30602, United States.
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35
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Lord MS, Tang F, Rnjak-Kovacina J, Smith JGW, Melrose J, Whitelock JM. The multifaceted roles of perlecan in fibrosis. Matrix Biol 2018; 68-69:150-166. [PMID: 29475023 DOI: 10.1016/j.matbio.2018.02.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 12/11/2022]
Abstract
Perlecan, or heparan sulfate proteoglycan 2 (HSPG2), is a ubiquitous heparan sulfate proteoglycan that has major roles in tissue and organ development and wound healing by orchestrating the binding and signaling of mitogens and morphogens to cells in a temporal and dynamic fashion. In this review, its roles in fibrosis are reviewed by drawing upon evidence from tissue and organ systems that undergo fibrosis as a result of an uncontrolled response to either inflammation or traumatic cellular injury leading to an over production of a collagen-rich extracellular matrix. This review focuses on examples of fibrosis that occurs in lung, liver, kidney, skin, kidney, neural tissues and blood vessels and its link to the expression of perlecan in that particular organ system.
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Affiliation(s)
- Megan S Lord
- Graduate School of Biomedical Engineering, UNSW Sydney, NSW 2052, Australia.
| | - Fengying Tang
- Graduate School of Biomedical Engineering, UNSW Sydney, NSW 2052, Australia
| | | | - James G W Smith
- University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - James Melrose
- Graduate School of Biomedical Engineering, UNSW Sydney, NSW 2052, Australia; Raymond Purves Bone and Joint Research Laboratory, Kolling Institute Northern Sydney Local Health District, St. Leonards, NSW 2065, Australia; Sydney Medical School, Northern, The University of Sydney, Royal North Shore Hospital, St. Leonards, NSW 2065, Australia
| | - John M Whitelock
- Graduate School of Biomedical Engineering, UNSW Sydney, NSW 2052, Australia
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36
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Kang I, Chang MY, Wight TN, Frevert CW. Proteoglycans as Immunomodulators of the Innate Immune Response to Lung Infection. J Histochem Cytochem 2018; 66:241-259. [PMID: 29328866 DOI: 10.1369/0022155417751880] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Proteoglycans (PGs) are complex, multifaceted molecules that participate in diverse interactions vital for physiological and pathological processes. As structural components, they provide a scaffold for cells and structural organization that helps define tissue architecture. Through interactions with water, PGs enable molecular and cellular movement through tissues. Through selective ionic interactions with growth factors, chemokines, cytokines, and proteases, PGs facilitate the ability of these soluble ligands to regulate intracellular signaling events and to influence the inflammatory response. In addition, recent findings now demonstrate that PGs can activate danger-associated molecular patterns (DAMPs) and other signaling pathways to influence production of many of these soluble ligands, indicating a more direct role for PGs in influencing the immune response and tissue inflammation. This review will focus on PGs that are selectively expressed during lung inflammation and will examine the novel emerging concept of PGs as immunomodulatory regulators of the innate immune responses in lungs.
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Affiliation(s)
- Inkyung Kang
- Matrix Biology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington
| | - Mary Y Chang
- Comparative Pathology Program, Department of Comparative Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Thomas N Wight
- Matrix Biology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington
| | - Charles W Frevert
- Center for Lung Biology, Division of Pulmonary/Critical Care Medicine, University of Washington School of Medicine, Seattle, Washington
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37
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Farrugia BL, Lord MS, Melrose J, Whitelock JM. The Role of Heparan Sulfate in Inflammation, and the Development of Biomimetics as Anti-Inflammatory Strategies. J Histochem Cytochem 2018; 66:321-336. [PMID: 29290153 DOI: 10.1369/0022155417740881] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Key events that occur during inflammation include the recruitment, adhesion, and transmigration of leukocytes from the circulation to the site of inflammation. These events are modulated by chemokines, integrins, and selectins and the interaction of these molecules with glycosaminoglycans, predominantly heparan sulfate (HS). The development of HS/heparin mimetics that interfere or inhibit the interactions that occur between glycosaminoglycans and modulators of inflammation holds great potential for use as anti-inflammatory therapeutics. This review will detail the role of HS in the events that occur during inflammation, their interaction and modulation of inflammatory mediators, and the current advances in the development of HS/heparin mimetics as anti-inflammatory biotherapeutics.
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Affiliation(s)
- Brooke L Farrugia
- Graduate School of Biomedical Engineering, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Megan S Lord
- Graduate School of Biomedical Engineering, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - James Melrose
- Graduate School of Biomedical Engineering, University of New South Wales Sydney, Sydney, New South Wales, Australia.,Raymond Purves Bone and Joint Research Laboratory, Kolling Institute, Northern Sydney Local Health District, St. Leonards, New South Wales, Australia.,Sydney Medical School-Northern, Royal North Shore Hospital, The University of Sydney, St. Leonards, New South Wales, Australia
| | - John M Whitelock
- Graduate School of Biomedical Engineering, University of New South Wales Sydney, Sydney, New South Wales, Australia
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38
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Yang J, Chi L. Characterization of structural motifs for interactions between glycosaminoglycans and proteins. Carbohydr Res 2017; 452:54-63. [PMID: 29065343 DOI: 10.1016/j.carres.2017.10.008] [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: 08/22/2017] [Revised: 10/02/2017] [Accepted: 10/16/2017] [Indexed: 11/24/2022]
Abstract
Glycosaminoglycans (GAGs) are a family of linear and anionic polysaccharides that play essential roles in many biological and physiological processes. Interactions between GAGs and proteins regulate function in many proteins and are related to many human diseases and disorders. The structural motifs and mechanisms for interactions between GAGs and proteins are not fully understood. Specific bindings, including minor but unique sequences sporadically distributed along the GAG chains or variably sulfated domains interspersed by undersulfated regions, may be specifically recognized by defined domains of a variety of proteins. Understanding the molecular basis of these interactions will provide a template for developing novel glycotherapeutic agents. The present article reviews recent methodologies and progress on the characterization of structural motifs in both GAGs and proteins involved in GAG-protein interactions. The analytical approaches are categorized into three groups: affinity-based methods; molecular docking, nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography; and mass spectrometry (MS) techniques. The advantages and limitations of each category of methods are discussed and are based on examples of using these techniques to investigate binding between GAGs and proteins.
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Affiliation(s)
- Jiyuan Yang
- National Glycoengineering Research Center, Shandong University, Jinan 250100, China
| | - Lianli Chi
- National Glycoengineering Research Center, Shandong University, Jinan 250100, China.
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39
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Heparin Mimetics: Their Therapeutic Potential. Pharmaceuticals (Basel) 2017; 10:ph10040078. [PMID: 28974047 PMCID: PMC5748635 DOI: 10.3390/ph10040078] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/21/2017] [Accepted: 09/22/2017] [Indexed: 01/04/2023] Open
Abstract
Heparin mimetics are synthetic and semi-synthetic compounds that are highly sulfated, structurally distinct analogues of glycosaminoglycans. These mimetics are often rationally designed to increase potency and binding selectivity towards specific proteins involved in disease manifestations. Some of the major therapeutic arenas towards which heparin mimetics are targeted include: coagulation and thrombosis, cancers, and inflammatory diseases. Although Fondaparinux, a rationally designed heparin mimetic, is now approved for prophylaxis and treatment of venous thromboembolism, the search for novel anticoagulant heparin mimetics with increased affinity and fewer side effects remains a subject of research. However, increasingly, research is focusing on the non-anticoagulant activities of these molecules. Heparin mimetics have potential as anti-cancer agents due to their ability to: (1) inhibit heparanase, an endoglycosidase which facilitates the spread of tumor cells; and (2) inhibit angiogenesis by binding to growth factors. The heparin mimetic, PI-88 is in clinical trials for post-surgical hepatocellular carcinoma and advanced melanoma. The anti-inflammatory properties of heparin mimetics have primarily been attributed to their ability to interact with: complement system proteins, selectins and chemokines; each of which function differently to facilitate inflammation. The efficacy of low/non-anticoagulant heparin mimetics in animal models of different inflammatory diseases has been demonstrated. These findings, plus clinical data that indicates heparin has anti-inflammatory activity, will raise the momentum for developing heparin mimetics as a new class of therapeutic agent for inflammatory diseases.
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Thompson S, Martínez-Burgo B, Sepuru KM, Rajarathnam K, Kirby JA, Sheerin NS, Ali S. Regulation of Chemokine Function: The Roles of GAG-Binding and Post-Translational Nitration. Int J Mol Sci 2017; 18:ijms18081692. [PMID: 28771176 PMCID: PMC5578082 DOI: 10.3390/ijms18081692] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/28/2017] [Accepted: 07/30/2017] [Indexed: 12/12/2022] Open
Abstract
The primary function of chemokines is to direct the migration of leukocytes to the site of injury during inflammation. The effects of chemokines are modulated by several means, including binding to G-protein coupled receptors (GPCRs), binding to glycosaminoglycans (GAGs), and through post-translational modifications (PTMs). GAGs, present on cell surfaces, bind chemokines released in response to injury. Chemokines bind leukocytes via their GPCRs, which directs migration and contributes to local inflammation. Studies have shown that GAGs or GAG-binding peptides can be used to interfere with chemokine binding and reduce leukocyte recruitment. Post-translational modifications of chemokines, such as nitration, which occurs due to the production of reactive species during oxidative stress, can also alter their biological activity. This review describes the regulation of chemokine function by GAG-binding ability and by post-translational nitration. These are both aspects of chemokine biology that could be targeted if the therapeutic potential of chemokines, like CXCL8, to modulate inflammation is to be realised.
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Affiliation(s)
- Sarah Thompson
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
| | - Beatriz Martínez-Burgo
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
| | - Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.
| | - John A Kirby
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
| | - Neil S Sheerin
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
| | - Simi Ali
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
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Babik S, Samsonov SA, Pisabarro MT. Computational drill down on FGF1-heparin interactions through methodological evaluation. Glycoconj J 2017; 34:427-440. [PMID: 27858202 PMCID: PMC5487771 DOI: 10.1007/s10719-016-9745-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 01/22/2023]
Abstract
Glycosaminoglycans (GAGs) exhibit a key role in cellular communication processes through interactions with target proteins of the extracellular matrix (ECM). The sandwich-like interaction established between Fibroblast growth factor (FGF) and heparin (HE) represents quite a peculiar protein-GAG-protein system, which has been both structurally and functionally intensively studied. The molecular recognition characteristics of this system have been exploited in various computational studies in order to deepen understanding of GAG-protein interactions. Here, we drill down on the interactions established in this peculiar macromolecular complex by analyzing the applicability of docking techniques and molecular dynamics (MD)-based approaches, and we dissect the molecular recognition properties exhibited by FGF towards a series of HE derivatives. We examine the sensitivity of MM-GBSA free energy calculations in terms of receptor conformational space sampling and changes in the ligand structures. Furthermore, we investigate its predictive power in combination with other computational methods, namely the well-established Autodock3 (AD3) and dynamic molecular docking (DMD), a targeted MD-based docking method specifically developed to account for flexibility and solvent in computer simulations of protein-GAG systems. Our results show that a site-mapping approach can be effectively combined with AD3 and DMD calculations to accurately reproduce available experimental data and, furthermore, to determine specific GAG recognition patterns. This study deepens our understanding of the applicability of available theoretical approaches to the investigation of molecular recognition in protein-GAG systems.
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Affiliation(s)
- Sándor Babik
- Structural Bioinformatics, BIOTEC TU Dresden, Dresden, 01307, Germany
| | - Sergey A Samsonov
- Structural Bioinformatics, BIOTEC TU Dresden, Dresden, 01307, Germany
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Inflammation-induced brain endothelial activation leads to uptake of electrostatically stabilized iron oxide nanoparticles via sulfated glycosaminoglycans. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2017; 13:1411-1421. [DOI: 10.1016/j.nano.2017.01.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/20/2016] [Accepted: 01/12/2017] [Indexed: 12/17/2022]
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Wight TN, Frevert CW, Debley JS, Reeves SR, Parks WC, Ziegler SF. Interplay of extracellular matrix and leukocytes in lung inflammation. Cell Immunol 2017; 312:1-14. [PMID: 28077237 PMCID: PMC5290208 DOI: 10.1016/j.cellimm.2016.12.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 12/13/2022]
Abstract
During inflammation, leukocytes influx into lung compartments and interact with extracellular matrix (ECM). Two ECM components, versican and hyaluronan, increase in a range of lung diseases. The interaction of leukocytes with these ECM components controls leukocyte retention and accumulation, proliferation, migration, differentiation, and activation as part of the inflammatory phase of lung disease. In addition, bronchial epithelial cells from asthmatic children co-cultured with human lung fibroblasts generate an ECM that is adherent for monocytes/macrophages. Macrophages are present in both early and late lung inflammation. Matrix metalloproteinase 10 (MMP10) is induced in alveolar macrophages with injury and infection and modulates macrophage phenotype and their ability to degrade collagenous ECM components. Collectively, studies outlined in this review highlight the importance of specific ECM components in the regulation of inflammatory events in lung disease. The widespread involvement of these ECM components in the pathogenesis of lung inflammation make them attractive candidates for therapeutic intervention.
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Affiliation(s)
- Thomas N Wight
- Matrix Biology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA.
| | - Charles W Frevert
- Department of Comparative Medicine, University of Washington, Seattle, WA, USA
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, and Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Stephen R Reeves
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, and Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - William C Parks
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Steven F Ziegler
- Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
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Singh A, Tessier MB, Pederson K, Wang X, Venot AP, Boons GJ, Prestegard JH, Woods RJ. Extension and validation of the GLYCAM force field parameters for modeling glycosaminoglycans. CAN J CHEM 2016; 94:927-935. [PMID: 28603292 PMCID: PMC5464424 DOI: 10.1139/cjc-2015-0606] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Glycosaminoglycans (GAGs) are an important class of carbohydrates that serve critical roles in blood clotting, tissue repair, cell migration and adhesion, and lubrication. The variable sulfation pattern and iduronate ring conformations in GAGs influence their polymeric structure and nature of interaction. This study characterizes several heparin-like GAG disaccharides and tetrasaccharides using NMR and molecular dynamics simulations to assist in the development of parameters for GAGs within the GLYCAM06 force field. The force field additions include parameters and charges for a transferable sulfate group for O- and N-sulfation, neutral (COOH) forms of iduronic and glucuronic acid, and Δ4,5-unsaturated uronate (ΔUA) residues. ΔUA residues frequently arise from the enzymatic digestion of heparin and heparin sulfate. Simulations of disaccharides containing ΔUA reveal that the presence of sulfation on this residue alters the relative populations of 1H2 and 2H1 ring conformations. Simulations of heparin tetrasaccharides containing N-sulfation in place of N-acetylation on glucosamine residues influence the ring conformations of adjacent iduronate residues.
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Affiliation(s)
- Arunima Singh
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Matthew B Tessier
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Kari Pederson
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Andre P Venot
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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Samsonov SA, Pisabarro MT. Computational analysis of interactions in structurally available protein-glycosaminoglycan complexes. Glycobiology 2016; 26:850-861. [PMID: 27496767 DOI: 10.1093/glycob/cww055] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 04/26/2016] [Indexed: 01/01/2023] Open
Abstract
Glycosaminoglycans represent a class of linear anionic periodic polysaccharides, which play a key role in a variety of biological processes in the extracellular matrix via interactions with their protein targets. Computationally, glycosaminoglycans are very challenging due to their high flexibility, periodicity and electrostatics-driven nature of the interactions with their protein counterparts. In this work, we carry out a detailed computational characterization of the interactions in protein-glycosaminoglycan complexes from the Protein Data Bank (PDB), which are split into two subsets accounting for their intrinsic nature: non-enzymatic-protein-glycosaminoglycan and enzyme-glycosaminoglycan complexes. We apply molecular dynamics to analyze the differences in these two subsets in terms of flexibility, retainment of the native interactions in the simulations, free energy components of binding and contributions of protein residue types to glycosaminoglycan binding. Furthermore, we systematically demonstrate that protein electrostatic potential calculations, previously found to be successful for glycosaminoglycan binding sites prediction for individual systems, are in general very useful for proposing protein surface regions as putative glycosaminoglycan binding sites, which can be further used for local docking calculations with these particular polysaccharides. Finally, the performance of six different docking programs (Autodock 3, Autodock Vina, MOE, eHiTS, FlexX and Glide), some of which proved to perform well for particular protein-glycosaminoglycan complexes in previous work, is evaluated on the complete protein-glycosaminoglycan data set from the PDB. This work contributes to widen our knowledge of protein-glycosaminoglycan molecular recognition and could be useful to steer a choice of the strategies to be applied in theoretical studies of these systems.
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Affiliation(s)
- Sergey A Samsonov
- Structural Bioinformatics, BIOTEC TU Dresden, Dresden 01307, Germany
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Li JP, Kusche-Gullberg M. Heparan Sulfate: Biosynthesis, Structure, and Function. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 325:215-73. [PMID: 27241222 DOI: 10.1016/bs.ircmb.2016.02.009] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Heparan sulfate (HS) proteoglycans (PGs) are ubiquitously expressed on cell surfaces and in the extracellular matrix of most animal tissues, having essential functions in development and homeostasis, as well as playing various roles in disease processes. The functions of HSPGs are mainly dependent on interactions between the HS-side chains with a variety of proteins including cytokines, growth factors, and their receptors. In a given HS polysaccharide, negatively charged sulfate and carboxylate groups are arranged in various types of domains, generated through strictly regulated biosynthetic reactions and with enormous potential for structural variability. The mode of HS-protein interactions is assessed through binding experiments using saccharides of defined composition in vitro, signaling assays in cell models where HS structures are manipulated, and targeted disruption of genes for biosynthetic enzymes in animals (mouse, zebrafish, Drosophila, and Caenorhabditis elegans) followed by phenotype analysis. Whereas some protein ligands appear to require strictly defined HS structure, others bind to variable saccharide domains without apparent dependence on distinct saccharide sequence. These findings raise intriguing questions concerning the functional significance of regulation in HS biosynthesis and the potential for development of therapeutics targeting HS-protein interactions.
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Affiliation(s)
- J-P Li
- Department of Medical Biochemistry and Microbiology, University of Uppsala, Uppsala, Sweden; SciLifeLab, University of Uppsala, Uppsala, Sweden.
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Pugh RJ, Slee JB, Farwell SLN, Li Y, Barthol T, Patton WA, Lowe-Krentz LJ. Transmembrane Protein 184A Is a Receptor Required for Vascular Smooth Muscle Cell Responses to Heparin. J Biol Chem 2016; 291:5326-41. [PMID: 26769966 DOI: 10.1074/jbc.m115.681122] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 11/06/2022] Open
Abstract
Vascular cell responses to exogenous heparin have been documented to include decreased vascular smooth muscle cell proliferation following decreased ERK pathway signaling. However, the molecular mechanism(s) by which heparin interacts with cells to induce those responses has remained unclear. Previously characterized monoclonal antibodies that block heparin binding to vascular cells have been found to mimic heparin effects. In this study, those antibodies were employed to isolate a heparin binding protein. MALDI mass spectrometry data provide evidence that the protein isolated is transmembrane protein 184A (TMEM184A). Commercial antibodies against three separate regions of the TMEM184A human protein were used to identify the TMEM184A protein in vascular smooth muscle cells and endothelial cells. A GFP-TMEM184A construct was employed to determine colocalization with heparin after endocytosis. Knockdown of TMEM184A eliminated the physiological responses to heparin, including effects on ERK pathway activity and BrdU incorporation. Isolated GFP-TMEM184A binds heparin, and overexpression results in additional heparin uptake. Together, these data support the identification of TMEM184A as a heparin receptor in vascular cells.
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Affiliation(s)
- Raymond J Pugh
- Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015
| | - Joshua B Slee
- From the Departments of Biological Sciences and the Department of Natural Sciences, DeSales University, Center Valley, Pennsylvania 18034
| | | | - Yaqiu Li
- From the Departments of Biological Sciences and
| | | | - Walter A Patton
- the Department of Chemistry, Lebanon Valley College, Annville, Pennsylvania 17003, and
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Monneau Y, Arenzana-Seisdedos F, Lortat-Jacob H. The sweet spot: how GAGs help chemokines guide migrating cells. J Leukoc Biol 2015; 99:935-53. [DOI: 10.1189/jlb.3mr0915-440r] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 11/24/2015] [Indexed: 12/19/2022] Open
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