1
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Piszczatowski RT, Bülow HE, Steidl U. Heparan sulfates and heparan sulfate proteoglycans in hematopoiesis. Blood 2024; 143:2571-2587. [PMID: 38639475 DOI: 10.1182/blood.2023022736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/20/2024] Open
Abstract
ABSTRACT From signaling mediators in stem cells to markers of differentiation and lineage commitment to facilitators for the entry of viruses, such as HIV-1, cell surface heparan sulfate (HS) glycans with distinct modification patterns play important roles in hematopoietic biology. In this review, we provide an overview of the importance of HS and the proteoglycans (HSPGs) to which they are attached within the major cellular subtypes of the hematopoietic system. We summarize the roles of HSPGs, HS, and HS modifications within each main hematopoietic cell lineage of both myeloid and lymphoid arms. Lastly, we discuss the biological advances in the detection of HS modifications and their potential to further discriminate cell types within hematopoietic tissue.
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Affiliation(s)
- Richard T Piszczatowski
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY
- Department of Pediatrics, Weill Cornell Medicine, New York Presbyterian Hospital, New York, NY
| | - Hannes E Bülow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine-Montefiore Health System, Bronx, NY
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine-Montefiore Health System, Bronx, NY
- Departments of Oncology, Albert Einstein College of Medicine-Montefiore Health System, Bronx, NY
- Blood Cancer Institute, Albert Einstein College of Medicine, Bronx, NY
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY
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2
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Nikovics K, Favier AL, Rocher M, Mayinga C, Gomez J, Dufour-Gaume F, Riccobono D. In Situ Identification of Both IL-4 and IL-10 Cytokine-Receptor Interactions during Tissue Regeneration. Cells 2023; 12:1522. [PMID: 37296643 PMCID: PMC10253026 DOI: 10.3390/cells12111522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/19/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Cytokines secreted by individual immune cells regulate tissue regeneration and allow communication between various cell types. Cytokines bind to cognate receptors and trigger the healing process. Determining the orchestration of cytokine interactions with their receptors on their cellular targets is essential to fully understanding the process of inflammation and tissue regeneration. To this end, we have investigated the interactions of Interleukin-4 cytokine (IL-4)/Interleukin-4 cytokine receptor (IL-4R) and Interleukin-10 cytokine (IL-10)/Interleukin-10 cytokine receptor (IL-10R) using in situ Proximity Ligation Assays in a regenerative model of skin, muscle and lung tissues in the mini-pig. The pattern of protein-protein interactions was distinct for the two cytokines. IL-4 bound predominantly to receptors on macrophages and endothelial cells around the blood vessels while the target cells of IL-10 were mainly receptors on muscle cells. Our results show that in situ studies of cytokine-receptor interactions can unravel the fine details of the mechanism of action of cytokines.
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Affiliation(s)
- Krisztina Nikovics
- Imagery Unit, Department of Platforms and Technology Research, French Armed Forces Biomedical Research Institute, 91223 Brétigny-sur-Orge, France; (A.-L.F.); (M.R.); (C.M.); (J.G.)
| | - Anne-Laure Favier
- Imagery Unit, Department of Platforms and Technology Research, French Armed Forces Biomedical Research Institute, 91223 Brétigny-sur-Orge, France; (A.-L.F.); (M.R.); (C.M.); (J.G.)
| | - Mathilde Rocher
- Imagery Unit, Department of Platforms and Technology Research, French Armed Forces Biomedical Research Institute, 91223 Brétigny-sur-Orge, France; (A.-L.F.); (M.R.); (C.M.); (J.G.)
| | - Céline Mayinga
- Imagery Unit, Department of Platforms and Technology Research, French Armed Forces Biomedical Research Institute, 91223 Brétigny-sur-Orge, France; (A.-L.F.); (M.R.); (C.M.); (J.G.)
| | - Johanna Gomez
- Imagery Unit, Department of Platforms and Technology Research, French Armed Forces Biomedical Research Institute, 91223 Brétigny-sur-Orge, France; (A.-L.F.); (M.R.); (C.M.); (J.G.)
| | - Frédérique Dufour-Gaume
- War Traumatology Unit, Department of NRBC Defense, French Armed Forces Biomedical Research Institute, 91223 Brétigny-sur-Orge, France;
| | - Diane Riccobono
- Department of Radiation Bioeffects, French Armed Forces Biomedical Research Institute, 1, Place du Général Valérie André, 91223 Brétigny-sur-Orge, France;
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3
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Guvench O. Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes. Molecules 2022; 27:7276. [PMID: 36364098 PMCID: PMC9658939 DOI: 10.3390/molecules27217276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/28/2023] Open
Abstract
This review summarizes the atomic-resolution structural biology of hyaluronan and its complexes available in the Protein Data Bank, as well as published studies of atomic-resolution explicit-solvent molecular dynamics simulations on these and other hyaluronan and hyaluronan-containing systems. Advances in accurate molecular mechanics force fields, simulation methods and software, and computer hardware have supported a recent flourish in such simulations, such that the simulation publications now outnumber the structural biology publications by an order of magnitude. In addition to supplementing the experimental structural biology with computed dynamic and thermodynamic information, the molecular dynamics studies provide a wealth of atomic-resolution information on hyaluronan-containing systems for which there is no atomic-resolution structural biology either available or possible. Examples of these summarized in this review include hyaluronan pairing with other hyaluronan molecules and glycosaminoglycans, with ions, with proteins and peptides, with lipids, and with drugs and drug-like molecules. Despite limitations imposed by present-day computing resources on system size and simulation timescale, atomic-resolution explicit-solvent molecular dynamics simulations have been able to contribute significant insight into hyaluronan's flexibility and capacity for intra- and intermolecular non-covalent interactions.
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Affiliation(s)
- Olgun Guvench
- Department of Pharmaceutical Sciences and Administration, School of Pharmacy, Westbrook College of Health Professions, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA
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4
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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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5
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Roy R, Jonniya NA, Kar P. Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study. J Phys Chem B 2022; 126:3852-3866. [PMID: 35594147 DOI: 10.1021/acs.jpcb.2c01807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Glycosaminoglycans (GAGs) are anionic biopolymers present on cell surfaces as a part of proteoglycans. The biological activities of GAGs depend on the sulfation pattern. In our study, we have considered three octadecasaccharide dermatan sulfate (DS) chains with increasing order of sulfation (dp6s, dp7s, and dp12s) to illuminate the role of sulfation on the GAG units and its chain conformation through 10 μs-long Gaussian accelerated molecular dynamics simulations. DS is composed of repeating disaccharide units of iduronic acid (IdoA) and N-acetylgalactosamine (N-GalNAc). Here, N-GalNAc is linked to IdoA via β(1-4), while IdoA is linked to N-GalNAc through α(1-3). With the increase in sulfation, the DS structure becomes more rigid and linear, as is evident from the distribution of root-mean-square deviations (RMSDs) and end-to-end distances. The tetrasaccharide linker region of the main chain shows a rigid conformation in terms of the glycosidic linkage. We have observed that upon sulfation (i.e., dp12s), the ring flip between two chair forms vanished for IdoA. The dynamic cross-correlation analysis reveals that the anticorrelation motions in dp12s are reduced significantly compared to dp6s or dp7s. An increase in sulfation generates relatively more stable hydrogen-bond networks, including water bridging with the neighboring monosaccharides. Despite the favorable linear structures of the GAG chains, our study also predicts few significant bendings related to the different puckering states, which may play a notable role in the function of the DS. The relation between the global conformation with the micro-level parameters such as puckering and water-mediated hydrogen bonds shapes the overall conformational space of GAGs. Overall, atomistic details of the DS chain provided in this study will help understand their functional and mechanical roles, besides developing new biomaterials.
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Affiliation(s)
- Rajarshi Roy
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore 453552, Madhya Pradesh, India
| | - Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore 453552, Madhya Pradesh, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore 453552, Madhya Pradesh, India
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6
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Cui JY, Lisi GP. Molecular Level Insights Into the Structural and Dynamic Factors Driving Cytokine Function. Front Mol Biosci 2021; 8:773252. [PMID: 34760929 PMCID: PMC8573031 DOI: 10.3389/fmolb.2021.773252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Cytokines are key mediators of cellular communication and regulators of biological advents. The timing, quantity and localization of cytokines are key features in producing specific biological outcomes, and thus have been thoroughly studied and reviewed while continuing to be a focus of the cytokine biology community. Due to the complexity of cellular signaling and multitude of factors that can affect signaling outcomes, systemic level studies of cytokines are ongoing. Despite their small size, cytokines can exhibit structurally promiscuous and dynamic behavior that plays an equally important role in biological activity. In this review using case studies, we highlight the recent insight gained from observing cytokines through a molecular lens and how this may complement a system-level understanding of cytokine biology, explain diversity of downstream signaling events, and inform therapeutic and experimental development.
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Affiliation(s)
- Jennifer Y Cui
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - George P Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
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7
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Marcisz M, Zacharias M, Samsonov SA. Modeling Protein-Glycosaminoglycan Complexes: Does the Size Matter? J Chem Inf Model 2021; 61:4475-4485. [PMID: 34494837 PMCID: PMC8479808 DOI: 10.1021/acs.jcim.1c00664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Docking glycosaminoglycans (GAGs) has been challenging because
of the complex nature of these long periodic linear and negatively
charged polysaccharides. Although standard docking tools like Autodock3
are successful when docking GAGs up to hexameric length, they experience
challenges to properly dock longer GAGs. Similar limitations concern
other docking approaches typically developed for docking ligands of
limited size to proteins. At the same time, most of more advanced
docking approaches are challenging for a user who is inexperienced
with complex in silico methodologies. In this work,
we evaluate the binding energies of complexes with different lengths
of GAGs using all-atom molecular dynamics simulations. Based on this
analysis, we propose a new docking protocol for long GAGs that consists
of conventional docking of short GAGs and further elongation with
the use of a coarse-grained representation of the GAG parts not being
in direct contact with its protein receptor. This method automated
by a simple script is straightforward to use within the Autodock3
framework but also useful in combination with other standard docking
tools. We believe that this method with some minor case-specific modifications
could also be used for docking other linear charged polymers.
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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
| | - Martin Zacharias
- Center of Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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8
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Zhang B, Chi L. Chondroitin Sulfate/Dermatan Sulfate-Protein Interactions and Their Biological Functions in Human Diseases: Implications and Analytical Tools. Front Cell Dev Biol 2021; 9:693563. [PMID: 34422817 PMCID: PMC8377502 DOI: 10.3389/fcell.2021.693563] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/20/2021] [Indexed: 01/12/2023] Open
Abstract
Chondroitin sulfate (CS) and dermatan sulfate (DS) are linear anionic polysaccharides that are widely present on the cell surface and in the cell matrix and connective tissue. CS and DS chains are usually attached to core proteins and are present in the form of proteoglycans (PGs). They not only are important structural substances but also bind to a variety of cytokines, growth factors, cell surface receptors, adhesion molecules, enzymes and fibrillary glycoproteins to execute series of important biological functions. CS and DS exhibit variable sulfation patterns and different sequence arrangements, and their molecular weights also vary within a large range, increasing the structural complexity and diversity of CS/DS. The structure-function relationship of CS/DS PGs directly and indirectly involves them in a variety of physiological and pathological processes. Accumulating evidence suggests that CS/DS serves as an important cofactor for many cell behaviors. Understanding the molecular basis of these interactions helps to elucidate the occurrence and development of various diseases and the development of new therapeutic approaches. The present article reviews the physiological and pathological processes in which CS and DS participate through their interactions with different proteins. Moreover, classic and emerging glycosaminoglycan (GAG)-protein interaction analysis tools and their applications in CS/DS-protein characterization are also discussed.
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Affiliation(s)
- Bin Zhang
- National Glycoengineering Research Center, Shandong University, Qingdao, China
| | - Lianli Chi
- National Glycoengineering Research Center, Shandong University, Qingdao, China
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9
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Höfurthner T, Mateos B, Konrat R. On-Cell NMR Contributions to Membrane Receptor Binding Characterization. Chempluschem 2021; 86:938-945. [PMID: 34160899 DOI: 10.1002/cplu.202100134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/28/2021] [Indexed: 12/21/2022]
Abstract
NMR spectroscopy has matured into a powerful tool to characterize interactions between biological molecules at atomic resolution, most importantly even under near to native (physiological) conditions. The field of in-cell NMR aims to study proteins and nucleic acids inside living cells. However, cells interrogate their environment and are continuously modulated by external stimuli. Cell signaling processes are often initialized by membrane receptors on the cell surface; therefore, characterizing their interactions at atomic resolution by NMR, hereafter referred as on-cell NMR, can provide valuable mechanistic information. This review aims to summarize recent on-cell NMR tools that give information about the binding site and the affinity of membrane receptors to their ligands together with potential applications to in vivo drug screening systems.
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Affiliation(s)
- Theresa Höfurthner
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Borja Mateos
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
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10
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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: 14] [Impact Index Per Article: 4.7] [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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11
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Bu C, Jin L. NMR Characterization of the Interactions Between Glycosaminoglycans and Proteins. Front Mol Biosci 2021; 8:646808. [PMID: 33796549 PMCID: PMC8007983 DOI: 10.3389/fmolb.2021.646808] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/24/2021] [Indexed: 12/16/2022] Open
Abstract
Glycosaminoglycans (GAGs) constitute a considerable fraction of the glycoconjugates found on cellular membranes and in the extracellular matrix of virtually all mammalian tissues. The essential role of GAG-protein interactions in the regulation of physiological processes has been recognized for decades. However, the underlying molecular basis of these interactions has only emerged since 1990s. The binding specificity of GAGs is encoded in their primary structures, but ultimately depends on how their functional groups are presented to a protein in the three-dimensional space. This review focuses on the application of NMR spectroscopy on the characterization of the GAG-protein interactions. Examples of interpretation of the complex mechanism and characterization of structural motifs involved in the GAG-protein interactions are given. Selected families of GAG-binding proteins investigated using NMR are also described.
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Affiliation(s)
- Changkai Bu
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Lan Jin
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
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12
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Marcisz M, Huard B, Lipska AG, Samsonov SA. Further analyses of APRIL/APRIL-Receptor/Glycosaminoglycan interactions by biochemical assays linked to computational studies. Glycobiology 2021; 31:772-786. [PMID: 33682874 DOI: 10.1093/glycob/cwab016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
A proliferation-inducing ligand (APRIL) is a member of the tumor necrosis factor superfamily. APRIL is quite unique in this superfamily for at least for two reasons: i) it binds to glycosaminoglycans (GAGs) via its positively charged N-terminus; ii) one of its signaling receptor, the transmembrane activator CAML interactor (TACI) was also reported to bind GAGs. Here, as provided by biochemical evidences with the use of an APRIL deletion mutant linked to computational studies, APRIL-GAG interaction involved other regions than the APRIL N-terminus. Preferential interaction of APRIL with heparin followed by chondroitin sulfate E were confirmed by in silico analysis. Both computational and experimental approaches did not reveal heparan sulfate binding to TACI. Together, computational results corroborated experiments contributing with atomistic details to the knowledge on this biologically relevant trimolecular system. Additionally, a high-throughput rigorous analysis of the free energy calculations data was performed to critically evaluate the applied computational methodologies.
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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
| | - Bertrand Huard
- TIMC-IMAG, university Grenoble-Alpes, CNRS UMR 5525, La Tronche, France
| | - Agnieszka G Lipska
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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13
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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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14
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Samsonov SA, Freza S, Zsila F. In silico analysis of heparin and chondroitin sulfate binding mechanisms of the antiprotozoal drug berenil and pentamidine. Carbohydr Res 2019; 482:107742. [DOI: 10.1016/j.carres.2019.107742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/18/2022]
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15
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Penk A, Baumann L, Huster D, Samsonov SA. NMR and molecular modeling reveal specificity of the interactions between CXCL14 and glycosaminoglycans. Glycobiology 2019; 29:715-725. [DOI: 10.1093/glycob/cwz047] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/25/2019] [Accepted: 06/25/2019] [Indexed: 12/13/2022] Open
Abstract
Abstract
CXCL14, chemokine (C-X-C motif) ligand 14, is a novel highly conserved chemokine with unique features. Despite exhibiting the typical chemokine fold, it has a very short N-terminus of just two amino acid residues responsible for chemokine receptor activation. CXCL14 actively participates in homeostatic immune surveillance of skin and mucosae, is linked to metabolic disorders and fibrotic lung diseases and possesses strong anti-angiogenic properties in early tumor development. In this work, we investigated the interaction of CXCL14 with various glycosaminoglycans (GAGs) by nuclear magnetic resonance spectroscopy, microscale thermophoresis, analytical heparin (HE) affinity chromatography and in silico approaches to understand the molecular basis of GAG-binding. We observed different GAG-binding modes specific for the GAG type used in the study. In particular, the CXCL14 epitope for HE suggests a binding pose distinguishable from the ones of the other GAGs investigated (hyaluronic acid, chondroitin sulfate-A/C, −D, dermatan sulfate). This observation is also supported by computational methods that included molecular docking, molecular dynamics and free energy calculations. Based on our results, we suggest that distinct GAG sulfation patterns confer specificity beyond simple electrostatic interactions usually considered to represent the driving forces in protein–GAG interactions. The CXCL14–GAG system represents a promising approach to investigate the specificity of GAG–protein interactions, which represents an important topic for developing the rational approaches to novel strategies in regenerative medicine.
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Affiliation(s)
- Anja Penk
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. Leipzig, Germany
| | - Lars Baumann
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. Leipzig, Germany
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, Poland
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16
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Pudełko A, Wisowski G, Olczyk K, Koźma EM. The dual role of the glycosaminoglycan chondroitin-6-sulfate in the development, progression and metastasis of cancer. FEBS J 2019; 286:1815-1837. [PMID: 30637950 PMCID: PMC6850286 DOI: 10.1111/febs.14748] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/14/2018] [Accepted: 01/10/2019] [Indexed: 12/16/2022]
Abstract
The remarkable structural heterogeneity of chondroitin sulfate (CS) and dermatan sulfate (DS) generates biological information that can be unique to each of these glycosaminoglycans (GAGs), and changes in their composition are translated into alterations in the binding profiles of these molecules. CS/DS can bind to various cytokines and growth factors, cell surface receptors, adhesion molecules, enzymes and fibrillar glycoproteins of the extracellular matrix, thereby influencing both cell behavior and the biomechanical and biochemical properties of the matrix. In this review, we summarize the current knowledge concerning CS/DS metabolism in the human cancer stroma. The remodeling of the GAG profile in the tumor niche is manifested as a substantial increase in the CS content and a gradual decrease in the proportion between DS and CS. Furthermore, the composition of CS and DS is also affected, which results in a substantial increase in the 6‐O‐sulfated and/or unsulfated disaccharide content, which is concomitant with a decrease in the 4‐O‐sulfation level. Here, we discuss the possible impact of alterations in the CS/DS sulfation pattern on the binding capacity and specificity of these GAGs. Moreover, we propose potential consequences of the stromal accumulation of chondroitin‐6‐sulfate for the progression and metastasis of cancer.
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Affiliation(s)
- Adam Pudełko
- Department of Clinical Chemistry and Laboratory Diagnostics, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Grzegorz Wisowski
- Department of Clinical Chemistry and Laboratory Diagnostics, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Krystyna Olczyk
- Department of Clinical Chemistry and Laboratory Diagnostics, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Ewa Maria Koźma
- Department of Clinical Chemistry and Laboratory Diagnostics, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
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17
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Glycosaminoglycan-Protein Interactions by Nuclear Magnetic Resonance (NMR) Spectroscopy. Molecules 2018; 23:molecules23092314. [PMID: 30208595 PMCID: PMC6225283 DOI: 10.3390/molecules23092314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 08/29/2018] [Accepted: 09/05/2018] [Indexed: 02/07/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most utilized and informative analytical techniques for investigating glycosaminoglycan (GAG)-protein complexes. NMR methods that are commonly applied to GAG-protein systems include chemical shift perturbation, saturation transfer difference, and transferred nuclear Overhauser effect. Although these NMR methods have revealed valuable insight into the protein-GAG complexes, elucidating high-resolution structural and dynamic information of these often transient interactions remains challenging. In addition, preparation of structurally homogeneous and isotopically enriched GAG ligands for structural investigations continues to be laborious. As a result, understanding of the structure-activity relationship of GAGs is still primitive. To overcome these deficiencies, several innovative NMR techniques have been developed lately. Here, we review some of the commonly used techniques along with more novel methods such as waterLOGSY and experiments to examine structure and dynamic of lysine and arginine side chains to identify GAG-binding sites. We will also present the latest technology that is used to produce isotopically enriched as well as paramagnetically tagged GAG ligands. Recent results that were obtained from solid-state NMR of amyloid’s interaction with GAG are also presented together with a brief discussion on computer assisted modeling of GAG-protein complexes using sparse experimental data.
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18
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Wang Y, Yang E, Wells MM, Bondarenko V, Woll K, Carnevale V, Granata D, Klein ML, Eckenhoff RG, Dailey WP, Covarrubias M, Tang P, Xu Y. Propofol inhibits the voltage-gated sodium channel NaChBac at multiple sites. J Gen Physiol 2018; 150:1317-1331. [PMID: 30018039 PMCID: PMC6122922 DOI: 10.1085/jgp.201811993] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 05/02/2018] [Accepted: 06/15/2018] [Indexed: 12/24/2022] Open
Abstract
Voltage-gated sodium (NaV) channels are important targets of general anesthetics, including the intravenous anesthetic propofol. Electrophysiology studies on the prokaryotic NaV channel NaChBac have demonstrated that propofol promotes channel activation and accelerates activation-coupled inactivation, but the molecular mechanisms of these effects are unclear. Here, guided by computational docking and molecular dynamics simulations, we predict several propofol-binding sites in NaChBac. We then strategically place small fluorinated probes at these putative binding sites and experimentally quantify the interaction strengths with a fluorinated propofol analogue, 4-fluoropropofol. In vitro and in vivo measurements show that 4-fluoropropofol and propofol have similar effects on NaChBac function and nearly identical anesthetizing effects on tadpole mobility. Using quantitative analysis by 19F-NMR saturation transfer difference spectroscopy, we reveal strong intermolecular cross-relaxation rate constants between 4-fluoropropofol and four different regions of NaChBac, including the activation gate and selectivity filter in the pore, the voltage sensing domain, and the S4-S5 linker. Unlike volatile anesthetics, 4-fluoropropofol does not bind to the extracellular interface of the pore domain. Collectively, our results show that propofol inhibits NaChBac at multiple sites, likely with distinct modes of action. This study provides a molecular basis for understanding the net inhibitory action of propofol on NaV channels.
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Affiliation(s)
- Yali Wang
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Elaine Yang
- Department of Neuroscience and Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College and Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA
| | - Marta M Wells
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Vasyl Bondarenko
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Kellie Woll
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, PA
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, College of Science and Technology, Temple University, Philadelphia, PA
| | - Daniele Granata
- Institute for Computational Molecular Science, College of Science and Technology, Temple University, Philadelphia, PA
| | - Michael L Klein
- Institute for Computational Molecular Science, College of Science and Technology, Temple University, Philadelphia, PA
| | - Roderic G Eckenhoff
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, PA
| | - William P Dailey
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA
| | - Manuel Covarrubias
- Department of Neuroscience and Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College and Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA
| | - Pei Tang
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Yan Xu
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA
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19
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Nordsieck K, Baumann L, Hintze V, Pisabarro MT, Schnabelrauch M, Beck-Sickinger AG, Samsonov SA. The effect of interleukin-8 truncations on its interactions with glycosaminoglycans. Biopolymers 2018; 109:e23103. [DOI: 10.1002/bip.23103] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/23/2017] [Accepted: 01/08/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Karoline Nordsieck
- Institute of Biochemistry, Universität Leipzig, Brüderstr. 34; Leipzig 04103 Germany
| | - Lars Baumann
- Institute of Biochemistry, Universität Leipzig, Brüderstr. 34; Leipzig 04103 Germany
- Institute for Medical Physics and Biophysics, Universität Leipzig, Härtelstr. 16-18; Leipzig 04107 Germany
| | - Vera Hintze
- Institute of Materials Science, Max Bergmann Center of Biomaterials, TU Dresden, Budapester Strasse 27; Dresden 01069 Germany
| | - M. Teresa Pisabarro
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg 47-49; Dresden 01307 Germany
| | | | | | - Sergey A. Samsonov
- Faculty of Chemistry; University of Gdańsk, ul. Wita Stwosza 63; Gdańsk 80-308 Poland
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20
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Gulati K, Meher MK, Poluri KM. Glycosaminoglycan-based resorbable polymer composites in tissue refurbishment. Regen Med 2017. [DOI: 10.2217/rme-2017-0012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Regeneration of tissue structure with the aid of bioactive polymer matrices/composites and scaffolds for respective applications is one of the emerging areas of biomedical engineering. Recent advances in conjugated glycosaminoglycan (GAG) hybrids using natural and synthetic polymers have opened new avenues for producing a wide variety of resorbable polymer matrices. These hybrid scaffolds are low-immunogenic, highly biocompatible and biodegradable with incredible mechanical and tensile properties. GAG-based resorbable polymeric matrices are being exploited in migration of stem cells, cartilage and bone replacement/regeneration and production of scaffolds for various tissue engineering applications. In the current review, we will discuss the role of GAG-based resorbable polymer matrices in the field of regenerative medicine.
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Affiliation(s)
- Khushboo Gulati
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Mukesh Kumar Meher
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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21
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Mulloy B, Hogwood J, Gray E, Lever R, Page CP. Pharmacology of Heparin and Related Drugs. Pharmacol Rev 2016; 68:76-141. [PMID: 26672027 DOI: 10.1124/pr.115.011247] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Heparin has been recognized as a valuable anticoagulant and antithrombotic for several decades and is still widely used in clinical practice for a variety of indications. The anticoagulant activity of heparin is mainly attributable to the action of a specific pentasaccharide sequence that acts in concert with antithrombin, a plasma coagulation factor inhibitor. This observation has led to the development of synthetic heparin mimetics for clinical use. However, it is increasingly recognized that heparin has many other pharmacological properties, including but not limited to antiviral, anti-inflammatory, and antimetastatic actions. Many of these activities are independent of its anticoagulant activity, although the mechanisms of these other activities are currently less well defined. Nonetheless, heparin is being exploited for clinical uses beyond anticoagulation and developed for a wide range of clinical disorders. This article provides a "state of the art" review of our current understanding of the pharmacology of heparin and related drugs and an overview of the status of development of such drugs.
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Affiliation(s)
- Barbara Mulloy
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - John Hogwood
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - Elaine Gray
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - Rebecca Lever
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - Clive P Page
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
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22
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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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23
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Köhling S, Künze G, Lemmnitzer K, Bermudez M, Wolber G, Schiller J, Huster D, Rademann J. Chemoenzymatic Synthesis of Nonasulfated Tetrahyaluronan with a Paramagnetic Tag for Studying Its Complex with Interleukin-10. Chemistry 2016; 22:5563-74. [DOI: 10.1002/chem.201504459] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Sebastian Köhling
- Institute of Pharmacy-Medicinal Chemistry; Freie Universität Berlin; Königin-Luise-Str. 2+4 14195 Berlin Germany
- Institute of Medical Physics and Biophysics; Universität Leipzig; Härtelstr. 16/18 04107 Leipzig Germany
| | - Georg Künze
- Institute of Medical Physics and Biophysics; Universität Leipzig; Härtelstr. 16/18 04107 Leipzig Germany
| | - Katharina Lemmnitzer
- Institute of Medical Physics and Biophysics; Universität Leipzig; Härtelstr. 16/18 04107 Leipzig Germany
| | - Marcel Bermudez
- Institute of Pharmacy-Medicinal Chemistry; Freie Universität Berlin; Königin-Luise-Str. 2+4 14195 Berlin Germany
| | - Gerhard Wolber
- Institute of Pharmacy-Medicinal Chemistry; Freie Universität Berlin; Königin-Luise-Str. 2+4 14195 Berlin Germany
| | - Jürgen Schiller
- Institute of Medical Physics and Biophysics; Universität Leipzig; Härtelstr. 16/18 04107 Leipzig Germany
| | - Daniel Huster
- Institute of Medical Physics and Biophysics; Universität Leipzig; Härtelstr. 16/18 04107 Leipzig Germany
| | - Jörg Rademann
- Institute of Pharmacy-Medicinal Chemistry; Freie Universität Berlin; Königin-Luise-Str. 2+4 14195 Berlin Germany
- Institute of Medical Physics and Biophysics; Universität Leipzig; Härtelstr. 16/18 04107 Leipzig Germany
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24
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Künze G, Köhling S, Vogel A, Rademann J, Huster D. Identification of the Glycosaminoglycan Binding Site of Interleukin-10 by NMR Spectroscopy. J Biol Chem 2016; 291:3100-13. [PMID: 26677224 PMCID: PMC4742770 DOI: 10.1074/jbc.m115.681759] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 12/10/2015] [Indexed: 11/06/2022] Open
Abstract
The biological function of interleukin-10 (IL-10), a pleiotropic cytokine with an essential role in inflammatory processes, is known to be affected by glycosaminoglycans (GAGs). GAGs are highly negatively charged polysaccharides and integral components of the extracellular matrix with important functions in the biology of many growth factors and cytokines. The molecular mechanism of the IL-10/GAG interaction is unclear. In particular, experimental evidence about IL-10/GAG binding sites is lacking, despite its importance for understanding the biological role of the interaction. Here, we report the experimental determination of a GAG binding site of IL-10. Although no co-crystal structure of the IL-10·GAG complex could be obtained, its structural characterization was possible by NMR spectroscopy. Chemical shift perturbations of IL-10 induced by GAG binding were used to narrow down the location of the binding site and to assess the affinity for different GAG molecules. Subsequent observation of NMR pseudocontact shifts of IL-10 and its heparin ligand, as induced by a protein-attached lanthanide spin label, provided structural restraints for the protein·ligand complex. Using these restraints, pseudocontact shift-based rigid body docking together with molecular dynamics simulations yielded a GAG binding model. The heparin binding site is located at the C-terminal end of helix D and the adjacent DE loop and coincides with a patch of positively charged residues involving arginines 102, 104, 106, and 107 and lysines 117 and 119. This study represents the first experimental characterization of the IL-10·GAG complex structure and provides the starting point for revealing the biological significance of the interaction of IL-10 with GAGs.
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Affiliation(s)
- Georg Künze
- From the Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstrasse 16/18, 04107 Leipzig, Germany and
| | - Sebastian Köhling
- From the Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstrasse 16/18, 04107 Leipzig, Germany and the Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany
| | - Alexander Vogel
- From the Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstrasse 16/18, 04107 Leipzig, Germany and
| | - Jörg Rademann
- From the Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstrasse 16/18, 04107 Leipzig, Germany and the Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany
| | - Daniel Huster
- From the Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstrasse 16/18, 04107 Leipzig, Germany and
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25
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Solera C, Macchione G, Maza S, Kayser MM, Corzana F, de Paz JL, Nieto PM. Chondroitin Sulfate Tetrasaccharides: Synthesis, Three-Dimensional Structure and Interaction with Midkine. Chemistry 2016; 22:2356-69. [DOI: 10.1002/chem.201504440] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Cristina Solera
- Glycosystems Laboratory; Instituto de Investigaciones Químicas (IIQ); cicCartuja, CSIC and Universidad de Sevilla; Americo Vespucio, 49 41092 Sevilla Spain
| | - Giuseppe Macchione
- Glycosystems Laboratory; Instituto de Investigaciones Químicas (IIQ); cicCartuja, CSIC and Universidad de Sevilla; Americo Vespucio, 49 41092 Sevilla Spain
| | - Susana Maza
- Glycosystems Laboratory; Instituto de Investigaciones Químicas (IIQ); cicCartuja, CSIC and Universidad de Sevilla; Americo Vespucio, 49 41092 Sevilla Spain
| | - M. Mar Kayser
- Glycosystems Laboratory; Instituto de Investigaciones Químicas (IIQ); cicCartuja, CSIC and Universidad de Sevilla; Americo Vespucio, 49 41092 Sevilla Spain
| | - Francisco Corzana
- Departamento de Química; Centro de Investigación en Síntesis Química; Universidad de La Rioja; Madre de Dios, 51 26006 Logroño Spain
| | - José L. de Paz
- Glycosystems Laboratory; Instituto de Investigaciones Químicas (IIQ); cicCartuja, CSIC and Universidad de Sevilla; Americo Vespucio, 49 41092 Sevilla Spain
| | - Pedro M. Nieto
- Glycosystems Laboratory; Instituto de Investigaciones Químicas (IIQ); cicCartuja, CSIC and Universidad de Sevilla; Americo Vespucio, 49 41092 Sevilla Spain
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26
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Mechanistic and therapeutic overview of glycosaminoglycans: the unsung heroes of biomolecular signaling. Glycoconj J 2015; 33:1-17. [DOI: 10.1007/s10719-015-9642-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 12/28/2022]
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27
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Gehrcke JP, Pisabarro MT. Identification and characterization of a glycosaminoglycan binding site on interleukin-10 via molecular simulation methods. J Mol Graph Model 2015; 62:97-104. [DOI: 10.1016/j.jmgm.2015.09.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/13/2015] [Accepted: 09/01/2015] [Indexed: 01/09/2023]
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28
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Pomin VH, Mulloy B. Current structural biology of the heparin interactome. Curr Opin Struct Biol 2015; 34:17-25. [PMID: 26038285 DOI: 10.1016/j.sbi.2015.05.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/03/2015] [Accepted: 05/12/2015] [Indexed: 10/23/2022]
Abstract
Heparin is the best known therapeutically active carbohydrate. It can bind and regulate multiple functional proteins such as coagulation cofactors, chemokines, and growth factors. This versatility has led to the recently developed concept of the heparin interactome--a group of proteins that, as the name implies, interact with heparin. The heparin interactome is structurally and functionally diverse. Though natural ligands of this class of proteins may be any of the glycosaminoglycans however, their structural biology is generally studied using heparin as a model compound. NMR spectroscopy contributes significantly to structural investigations of the resultant complexes in solution. This review aims therefore at discussing the current status in structural biology of the molecular complexes formed between heparin and its protein partners through the current concept of the heparin interactome.
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Affiliation(s)
- Vitor H Pomin
- Program of Glycobiology, Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-913, Brazil.
| | - Barbara Mulloy
- Glycosciences Laboratory, Imperial College, Department of Medicine, Burlington Danes Building, Du Cane Road, London W12 0NN, UK.
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