1
|
Schulze C, Danielsson A, Liwo A, Huster D, Samsonov SA, Penk A. Ligand binding of interleukin-8: a comparison of glycosaminoglycans and acidic peptides. Phys Chem Chem Phys 2023; 25:24930-24947. [PMID: 37694394 DOI: 10.1039/d3cp02457a] [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: 09/12/2023]
Abstract
Recognition and binding of regulatory proteins to glycosaminoglycans (GAGs) from the extracellular matrix is a process of high biological importance. The interaction between negatively charged sulfate or carboxyl groups of the GAGs and clusters of basic amino acids on the protein is crucial in this binding process and it is believed that electrostatics represent the key factor for this interaction. However, given the rather undirected nature of electrostatics, it is important to achieve a clear understanding of its role in protein-GAG interactions and how specificity and selectivity in these systems can be achieved, when the classical key-lock binding motif is not applicable. Here, we compare protein binding of a highly charged heparin (HP) hexasaccharide with four de novo designed decapeptides of varying negative net charge. The charge density of these peptides was comparable to typical GAGs of the extracellular matrix. We used the regulatory protein interleukin-8 (IL-8) because its interactions with GAGs are well described. All four peptide ligands bind to the same epitope of IL-8 but show much weaker binding affinity as revealed in 1H-15N HSQC NMR titration experiments. Complementary molecular docking and molecular dynamics simulations revealed further atomistic details of the interaction mode of GAG versus peptide ligands. Overall, similar contributions to the binding energy and hydrogen bond formation are determined for HP and the highly charged peptides, suggesting that the entropic loss of the peptides upon binding likely account for the remarkably different affinity of GAG versus peptide ligands to IL-8.
Collapse
Affiliation(s)
- Christian Schulze
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107 Leipzig, Germany.
| | - Annemarie Danielsson
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107 Leipzig, Germany.
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Anja Penk
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107 Leipzig, Germany.
| |
Collapse
|
2
|
Brunori F, Padhi DK, Alshanski I, Freyse J, Dürig JN, Penk A, Vaccaro L, Hurevich M, Rademann J, Yitzchaik S. Sulfation Pattern Dependent Iron(III) Mediated Interleukin-8 Glycan Binding. Chembiochem 2021; 23:e202100552. [PMID: 34851004 DOI: 10.1002/cbic.202100552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/01/2021] [Indexed: 12/30/2022]
Abstract
Cytokines such as interleukin-8 activate the immune system during infection and interact with sulfated glycosaminoglycans with specific sulfation patterns. In some cases, these interactions are mediated by metal ion binding which can be used to tune surface-based glycan-protein interactions. We evaluated the effect of both hyaluronan sulfation degree and Fe3+ on interleukin-8 binding by electrochemical impedance spectroscopy and surface characterizations. Our results show that sulfation degree and metal ion interactions have a synergistic effect in tuning the electrochemical response of the glycated surfaces to the cytokine.
Collapse
Affiliation(s)
- Francesco Brunori
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel.,Laboratory of Green Synthetic Organic Chemistry, Dipartimento di Chimica, Biologiae Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123, Perugia, Italy
| | - Deepak Kumar Padhi
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Israel Alshanski
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Joanna Freyse
- Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, Berlin, 14195, Germany
| | - Jan-Niklas Dürig
- Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, Berlin, 14195, Germany
| | - Anja Penk
- Institute of Medical Physics and Biophysics, Leipzig University, Medical Faculty, Härtelstraße 16/18, 04107, Leipzig, Germany
| | - Luigi Vaccaro
- Laboratory of Green Synthetic Organic Chemistry, Dipartimento di Chimica, Biologiae Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123, Perugia, Italy
| | - Mattan Hurevich
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Jörg Rademann
- Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, Berlin, 14195, Germany
| | - Shlomo Yitzchaik
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Maszota-Zieleniak M, Marcisz M, Kogut MM, Siebenmorgen T, Zacharias M, Samsonov SA. Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans. J Comput Chem 2021; 42:1040-1053. [PMID: 33768554 DOI: 10.1002/jcc.26496] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/19/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
Glycosaminoglycans (GAGs), long linear periodic anionic polysaccharides, are key molecules in the extracellular matrix (ECM). Therefore, deciphering their role in the biologically relevant context is important for fundamental understanding of the processes ongoing in ECM and for establishing new strategies in the regenerative medicine. Although GAGs represent a number of computational challenges, molecular docking is a powerful tool for analysis of their interactions. Despite the recent development of GAG-specific docking approaches, there is plenty of room for improvement. Here, replica exchange molecular dynamics with repulsive scaling (REMD-RS) recently proved to be a successful approach for protein-protein complexes, was applied to dock GAGs. In this method, effective pairwise radii are increased in different Hamiltonian replicas. REMD-RS is shown to be an attractive alternative to classical docking approaches for GAGs. This work contributes to setting up of GAG-specific computational protocols and provides new insights into the nature of these biological systems.
Collapse
Affiliation(s)
| | | | | | - Till Siebenmorgen
- Physics Department, Technical University of Munich, Garching, Germany
| | - Martin Zacharias
- Physics Department, Technical University of Munich, Garching, Germany
| | | |
Collapse
|
6
|
Crijns H, Vanheule V, Proost P. Targeting Chemokine-Glycosaminoglycan Interactions to Inhibit Inflammation. Front Immunol 2020; 11:483. [PMID: 32296423 PMCID: PMC7138053 DOI: 10.3389/fimmu.2020.00483] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Leukocyte migration into tissues depends on the activity of chemokines that form concentration gradients to guide leukocytes to a specific site. Interaction of chemokines with their specific G protein-coupled receptors (GPCRs) on leukocytes induces leukocyte adhesion to the endothelial cells, followed by extravasation of the leukocytes and subsequent directed migration along the chemotactic gradient. Interaction of chemokines with glycosaminoglycans (GAGs) is crucial for extravasation in vivo. Chemokines need to interact with GAGs on endothelial cells and in the extracellular matrix in tissues in order to be presented on the endothelium of blood vessels and to create a concentration gradient. Local chemokine retention establishes a chemokine gradient and prevents diffusion and degradation. During the last two decades, research aiming at reducing chemokine activity mainly focused on the identification of inhibitors of the interaction between chemokines and their cognate GPCRs. This approach only resulted in limited success. However, an alternative strategy, targeting chemokine-GAG interactions, may be a promising approach to inhibit chemokine activity and inflammation. On this line, proteins derived from viruses and parasites that bind chemokines or GAGs may have the potential to interfere with chemokine-GAG interactions. Alternatively, chemokine mimetics, including truncated chemokines and mutant chemokines, can compete with chemokines for binding to GAGs. Such truncated or mutated chemokines are characterized by a strong binding affinity for GAGs and abrogated binding to their chemokine receptors. Finally, Spiegelmers that mask the GAG-binding site on chemokines, thereby preventing chemokine-GAG interactions, were developed. In this review, the importance of GAGs for chemokine activity in vivo and strategies that could be employed to target chemokine-GAG interactions will be discussed in the context of inflammation.
Collapse
Affiliation(s)
- Helena Crijns
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Vincent Vanheule
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| |
Collapse
|
7
|
Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
Collapse
Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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
| |
Collapse
|
10
|
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.
Collapse
Affiliation(s)
- Sándor Babik
- Structural Bioinformatics, BIOTEC TU Dresden, Dresden, 01307, Germany
| | - Sergey A Samsonov
- Structural Bioinformatics, BIOTEC TU Dresden, Dresden, 01307, Germany
| | | |
Collapse
|
11
|
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.
Collapse
Affiliation(s)
- Sergey A Samsonov
- Structural Bioinformatics, BIOTEC TU Dresden, Dresden 01307, Germany
| | | |
Collapse
|
12
|
Structural analysis of the interleukin-8/glycosaminoglycan interactions by amide hydrogen/deuterium exchange mass spectrometry. Methods 2015; 89:45-53. [DOI: 10.1016/j.ymeth.2015.02.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/12/2015] [Accepted: 02/19/2015] [Indexed: 12/22/2022] Open
|
13
|
Solution NMR characterization of chemokine CXCL8/IL-8 monomer and dimer binding to glycosaminoglycans: structural plasticity mediates differential binding interactions. Biochem J 2015; 472:121-33. [PMID: 26371375 PMCID: PMC4692082 DOI: 10.1042/bj20150059] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 09/11/2015] [Indexed: 01/05/2023]
Abstract
Structural plasticity plays a major role in determining differential binding of CXCL8 monomer and dimer to glycosaminoglycans (GAGs) and that dimer is the high-affinity GAG ligand. We propose that these properties play important roles in orchestrating in vivo chemokine-mediated neutrophil function. Chemokine CXCL8/interleukin-8 (IL-8) plays a crucial role in directing neutrophils and oligodendrocytes to combat infection/injury and tumour cells in metastasis development. CXCL8 exists as monomers and dimers and interaction of both forms with glycosaminoglycans (GAGs) mediate these diverse cellular processes. However, very little is known regarding the structural basis underlying CXCL8–GAG interactions. There are conflicting reports on the affinities, geometry and whether the monomer or dimer is the high-affinity GAG ligand. To resolve these issues, we characterized the binding of a series of heparin-derived oligosaccharides [heparin disaccharide (dp2), heparin tetrasaccharide (dp4), heparin octasaccharide (dp8) and heparin 14-mer (dp14)] to the wild-type (WT) dimer and a designed monomer using solution NMR spectroscopy. The pattern and extent of binding-induced chemical shift perturbation (CSP) varied between dimer and monomer and between longer and shorter oligosaccharides. NMR-based structural models show that different interaction modes coexist and that the nature of interactions varied between monomer and dimer and oligosaccharide length. MD simulations indicate that the binding interface is structurally plastic and provided residue-specific details of the dynamic nature of the binding interface. Binding studies carried out under conditions at which WT CXCL8 exists as monomers and dimers provide unambiguous evidence that the dimer is the high-affinity GAG ligand. Together, our data indicate that a set of core residues function as the major recognition/binding site, a set of peripheral residues define the various binding geometries and that the structural plasticity of the binding interface allows multiplicity of binding interactions. We conclude that structural plasticity most probably regulates in vivo CXCL8 monomer/dimer–GAG interactions and function.
Collapse
|
14
|
Beck-Sickinger AG, Panitz N. Semi-synthesis of chemokines. Curr Opin Chem Biol 2014; 22:100-7. [DOI: 10.1016/j.cbpa.2014.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/19/2014] [Accepted: 09/19/2014] [Indexed: 01/04/2023]
|
15
|
Grant OC, Woods RJ. Recent advances in employing molecular modelling to determine the specificity of glycan-binding proteins. Curr Opin Struct Biol 2014; 28:47-55. [PMID: 25108191 DOI: 10.1016/j.sbi.2014.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 01/11/2023]
Abstract
Impressive improvements in docking performance can be achieved by applying energy bonuses to poses in which glycan hydroxyl groups occupy positions otherwise preferred by bound waters. In addition, inclusion of glycosidic conformational energies allows unlikely glycan conformations to be appropriately penalized. A method for predicting the binding specificity of glycan-binding proteins has been developed, which is based on grafting glycan branches onto a minimal binding determinant in the binding site. Grafting can be used either to screen virtual libraries of glycans, such as the known glycome, or to identify docked poses of minimal binding determinants that are consistent with specificity data. The reviewed advances allow accurate modelling of carbohydrate-protein 3D co-complexes, but challenges remain in ranking the affinity of congeners.
Collapse
Affiliation(s)
- Oliver C Grant
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, United States
| | - Robert J Woods
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, United States; School of Chemistry, University Road, National University of Ireland, Galway, Ireland.
| |
Collapse
|
16
|
Gerlza T, Hecher B, Jeremic D, Fuchs T, Gschwandtner M, Falsone A, Gesslbauer B, Kungl AJ. A combinatorial approach to biophysically characterise chemokine-glycan binding affinities for drug development. Molecules 2014; 19:10618-34. [PMID: 25054442 PMCID: PMC6271861 DOI: 10.3390/molecules190710618] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/07/2014] [Accepted: 07/16/2014] [Indexed: 01/06/2023] Open
Abstract
Chemokine binding to glycosaminoglycans (GAGs) is recognised to be an important step in inflammation and other pathological disorders like tumor growth and metastasis. Although different ways and strategies to interfere with these interactions are being pursued, no major breakthrough in the development of glycan-targeting drugs has been reported so far. We have engineered CXCL8 towards a dominant-negative form of this chemokine (dnCXCL8) which was shown to be highly active in various inflammatory animal models due to its inability to bind/activate the cognate CXCL8 GPC receptors on neutrophils in combination with its significantly increased GAG-binding affinity [1]. For the development of GAG-targeting chemokine-based biopharmaceuticals, we have established a repertoire of methods which allow the quantification of protein-GAG interactions. Isothermal fluorescence titration (IFT), surface plasmon resonance (SPR), isothermal titration calorimetry (ITC), and a novel ELISA-like competition assay (ELICO) have been used to determine Kd and IC50 values for CXCL8 and dnCXCL8 interacting with heparin and heparan sulfate (HS), the proto-typical members of the GAG family. Although the different methods gave different absolute affinities for the four protein-ligand pairs, the relative increase in GAG-binding affinity of dnCXCL8 compared to the wild type chemokine was found by all methods. In combination, these biophysical methods allow to discriminate between unspecific and specific protein-GAG interactions.
Collapse
Affiliation(s)
- Tanja Gerlza
- Institute of Pharmaceutical Sciences, Karl-Franzens-University Graz, Humboldtstrasse 46, A-8010 Graz, Austria
| | - Bianca Hecher
- Institute of Pharmaceutical Sciences, Karl-Franzens-University Graz, Humboldtstrasse 46, A-8010 Graz, Austria
| | - Dalibor Jeremic
- ProtAffin Biotechnologie AG, Reininghausstrasse 13a, A-802 Graz, Austria
| | - Thomas Fuchs
- ProtAffin Biotechnologie AG, Reininghausstrasse 13a, A-802 Graz, Austria
| | | | - Angelika Falsone
- ProtAffin Biotechnologie AG, Reininghausstrasse 13a, A-802 Graz, Austria
| | - Bernd Gesslbauer
- Institute of Pharmaceutical Sciences, Karl-Franzens-University Graz, Humboldtstrasse 46, A-8010 Graz, Austria
| | - Andreas J Kungl
- Institute of Pharmaceutical Sciences, Karl-Franzens-University Graz, Humboldtstrasse 46, A-8010 Graz, Austria.
| |
Collapse
|
17
|
Gimenez LE, Babilon S, Wanka L, Beck-Sickinger AG, Gurevich VV. Mutations in arrestin-3 differentially affect binding to neuropeptide Y receptor subtypes. Cell Signal 2014; 26:1523-31. [PMID: 24686081 PMCID: PMC4033671 DOI: 10.1016/j.cellsig.2014.03.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/16/2014] [Indexed: 12/21/2022]
Abstract
Based on the identification of residues that determine receptor selectivity in arrestins and the phylogenetic analysis of the arrestin (arr) family, we introduced fifteen mutations of receptor-discriminator residues in arr-3, which were identified previously using mutagenesis, in vitro binding, and BRET-based recruitment assay in intact cells. The effects of these mutations were tested using neuropeptide Y receptors Y1R and Y2R. NPY-elicited arr-3 recruitment to Y1R was not affected by these mutations, or even alanine substitution of all ten residues (arr-3-NCA), which prevented arr-3 binding to other receptors tested so far. However, NCA and two other mutations prevented agonist-independent arr-3 pre-docking to Y1R. In contrast, eight out of 15 mutations significantly reduced agonist-dependent arr-3 recruitment to Y2R. NCA eliminated arr-3 binding to active Y2R, whereas Tyr239Thr reduced it ~7-fold. Thus, manipulation of key residues on the receptor-binding surface generates arr-3 with high preference for Y1R over Y2R. Several mutations differentially affect arr-3 pre-docking and agonist-induced recruitment. Thus, arr-3 recruitment to the receptor involves several mechanistically distinct steps. Targeted mutagenesis can fine-tune arrestins directing them to specific receptors and particular activation states of the same receptor.
Collapse
Affiliation(s)
- Luis E Gimenez
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Stefanie Babilon
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany
| | - Lizzy Wanka
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany
| | - Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA.
| |
Collapse
|
18
|
Steinhagen M, Hoffmeister PG, Nordsieck K, Hötzel R, Baumann L, Hacker MC, Schulz-Siegmund M, Beck-Sickinger AG. Matrix metalloproteinase 9 (MMP-9) mediated release of MMP-9 resistant stromal cell-derived factor 1α (SDF-1α) from surface modified polymer films. ACS APPLIED MATERIALS & INTERFACES 2014; 6:5891-5899. [PMID: 24646074 DOI: 10.1021/am500794q] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Preparation of smart materials by coatings of established surfaces with biomolecules will lead to the next generation of functionalized biomaterials. Rejection of implants is still a major problem in medical applications but masking the implant material with protein coatings is a promising approach. These layers not only disguise the material but also equip it with a certain biological function. The anti-inflammatory chemokine stromal cell-derived factor 1α (SDF-1α) is well suited to take over this function, because it efficiently attracts stem cells and promotes their differentiation and proliferation. At least the initial stem cell homing requires the formation of a concentration gradient. Thus, a reliable and robust release mechanism of SDF-1α from the material is essential. Several proteases, most notably matrix metalloproteinases, are upregulated during inflammation, which, in principle, can be exploited for a tightly controlled release of SDF-1α. Herein, we present the covalent immobilization of M-[S4V]-SDF-1α on novel biodegradable polymer films, which consist of heterobifunctional poly(ethylene glycol) and oligolactide-based functionalized macromers. A peptidic linker with a trimeric matrix metalloproteinase 9 (MMP-9) cleavage site (MCS) was used as connection and the linkage between the three components was achieved by combination of expressed protein ligation and Cu(I) catalyzed azide/alkyne cycloaddition. The MCS was used for MMP-9 mediated release of M-[S4V]-SDF-1α from the biomaterial and the released SDF-1α derivative was biologically active and induced strong cell migration, which demonstrates the great potential of this system.
Collapse
Affiliation(s)
- Max Steinhagen
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig , Brüderstraße 34, 04103 Leipzig, Germany
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Mobius K, Nordsieck K, Pichert A, Samsonov SA, Thomas L, Schiller J, Kalkhof S, Teresa Pisabarro M, Beck-Sickinger AG, Huster D. Investigation of lysine side chain interactions of interleukin-8 with heparin and other glycosaminoglycans studied by a methylation-NMR approach. Glycobiology 2013; 23:1260-9. [DOI: 10.1093/glycob/cwt062] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
|
20
|
Nieto L, Canales Á, Fernández IS, Santillana E, González-Corrochano R, Redondo-Horcajo M, Cañada FJ, Nieto P, Martín-Lomas M, Giménez-Gallego G, Jiménez-Barbero J. Heparin Modulates the Mitogenic Activity of Fibroblast Growth Factor by Inducing Dimerization of its Receptor. A 3D View by Using NMR. Chembiochem 2013; 14:1732-44. [DOI: 10.1002/cbic.201300313] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Indexed: 11/08/2022]
|
21
|
Steinhagen M, Zunker K, Nordsieck K, Beck-Sickinger AG. Large scale modification of biomolecules using immobilized sortase A from Staphylococcus aureus. Bioorg Med Chem 2013; 21:3504-10. [PMID: 23598248 DOI: 10.1016/j.bmc.2013.03.039] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 03/02/2013] [Accepted: 03/11/2013] [Indexed: 01/24/2023]
Abstract
Recently, sortase A (SrtA) from Staphyloccus aureus moved into the focus of bioscience because of its ability to incorporate site specific modifications into proteins. The enzyme was mostly used to modify target proteins in an analytical scale, to study biomolecules in their cellular context. In this study, we show the applicability of SrtA mediated ligation for site specific modification of proteins in a large scale. Therefore, the reaction was first optimized using peptides and subsequently new reaction conditions were applied for the large scale biotinylation of interleukin-8. Furthermore, we established C-terminal immobilization of the SrtA on a PEG based resin and could demonstrate maintaining enzymatic activity. Immobilized SrtA significantly facilitates previous ligation protocols as the enzyme can be easily recycled. Also, the removal of excess reaction solution and the whole washing process is significantly accelerated, as centrifugation or filtration techniques can be applied instead of time-consuming chromatography steps.
Collapse
Affiliation(s)
- Max Steinhagen
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig, Brüderstr. 34, 04103 Leipzig, Germany.
| | | | | | | |
Collapse
|
22
|
Académie des Sciences Prizes / New Members of the Deutsche Akademie der Naturforscher Leopoldina. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/anie.201209796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
23
|
Preise der französischen Akademie der Wissenschaften / Neue Mitglieder der Deutschen Akademie der Naturforscher Leopoldina. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
24
|
Berger C, Berndt S, Pichert A, Theisgen S, Huster D. Efficient isotopic tryptophan labeling of membrane proteins by an indole controlled process conduct. Biotechnol Bioeng 2013; 110:1681-90. [DOI: 10.1002/bit.24830] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/11/2012] [Accepted: 12/17/2012] [Indexed: 12/18/2022]
|