1
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Tomezsko PJ, Ford CT, Meyer AE, Michaleas AM, Jaimes R. Human cytokine and coronavirus nucleocapsid protein interactivity using large-scale virtual screens. FRONTIERS IN BIOINFORMATICS 2024; 4:1397968. [PMID: 38855143 PMCID: PMC11157076 DOI: 10.3389/fbinf.2024.1397968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/26/2024] [Indexed: 06/11/2024] Open
Abstract
Understanding the interactions between SARS-CoV-2 and the human immune system is paramount to the characterization of novel variants as the virus co-evolves with the human host. In this study, we employed state-of-the-art molecular docking tools to conduct large-scale virtual screens, predicting the binding affinities between 64 human cytokines against 17 nucleocapsid proteins from six betacoronaviruses. Our comprehensive in silico analyses reveal specific changes in cytokine-nucleocapsid protein interactions, shedding light on potential modulators of the host immune response during infection. These findings offer valuable insights into the molecular mechanisms underlying viral pathogenesis and may guide the future development of targeted interventions. This manuscript serves as insight into the comparison of deep learning based AlphaFold2-Multimer and the semi-physicochemical based HADDOCK for protein-protein docking. We show the two methods are complementary in their predictive capabilities. We also introduce a novel algorithm for rapidly assessing the binding interface of protein-protein docks using graph edit distance: graph-based interface residue assessment function (GIRAF). The high-performance computational framework presented here will not only aid in accelerating the discovery of effective interventions against emerging viral threats, but extend to other applications of high throughput protein-protein screens.
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Affiliation(s)
| | - Colby T. Ford
- Tuple LLC, Charlotte, NC, United States
- University of North Carolina at Charlotte, Department of Bioinformatics and Genomics, Charlotte, NC, United States
- University of North Carolina at Charlotte, Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Charlotte, NC, United States
| | | | | | - Rafael Jaimes
- MIT Lincoln Laboratory, Lexington, MA, United States
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2
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Dhurua S, Jana M. Sulfation Effects of Chondroitin Sulfate to Bind a Chemokine in Aqueous Medium: Conformational Heterogeneity and Dynamics from Molecular Simulation. J Chem Inf Model 2023; 63:5660-5675. [PMID: 37611186 DOI: 10.1021/acs.jcim.3c00668] [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: 08/25/2023]
Abstract
The sulfation patterns and degree of sulfation of chondroitin sulfate (CS), an important class of glycosaminoglycans (GAG), and their interactions with chemokines are accountable for various diseases. To realize the underlying mechanism of such complex biological phenomena at a molecular level and their application in rational drug design, a study on conformations and dynamics of CSs is necessary. To explore this, in this study, we performed a series of atomistic molecular dynamics (MD) simulations with different sulfated variants of octadecasaccharide CS, like CS-C, CS-E, and CS-T, in their free forms and when bound to the protein chemokine CXCL8 dimer in an aqueous medium. The calculated binding free energy of CSs with the CXCL8 dimer is favorable, and the degree of sulfation favors the complexation process further with prominent hydrophobic and hydrogen-bonded interactions. We find that the recognition is associated with the configurational entropy loss of the CS molecules as calculated from the Gaussian mixture approach, which supports that the degree of sulfation regulates the process. Cluster analysis through the k-means algorithm and end-to-end distance measurement revealed that although the free CS molecules adopted linear conformations, the nonlinear conformations during binding with protein were noted. Adaptation of nonlinear forms in the bound forms is noteworthy for the less-sulfated CS-C and CS-E. Apart from favorable 4C1 conformations, the occasional appearance of skew-boat forms from the free-energy map of ring pucker for the GlcUA unit was observed, which remains unaffected by the sulfation. We find that during recognition, the average relaxation time of intra-CS and inter-CS-CXCL8 hydrogen bonds (HBs) is about a magnitude lesser than that of CS-water HBs, most prominent on the involvement of higher sulfated CS-T analogues. The translational motion of surrounded water molecules in CSs exhibited sublinear diffusion, and the degree of sublinearity increases around the heavily sulfated molecules due to the hindrance created by them as well as the presence of the chemokine and exhibited markedly slow heterogeneous diffusion.
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Affiliation(s)
- Shakuntala Dhurua
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
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3
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Hogwood J, Mulloy B, Lever R, Gray E, Page CP. Pharmacology of Heparin and Related Drugs: An Update. Pharmacol Rev 2023; 75:328-379. [PMID: 36792365 DOI: 10.1124/pharmrev.122.000684] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 02/17/2023] Open
Abstract
Heparin has been used extensively as an antithrombotic and anticoagulant for close to 100 years. This anticoagulant activity is attributed mainly to the pentasaccharide sequence, which potentiates the inhibitory action of antithrombin, a major inhibitor of the coagulation cascade. More recently it has been elucidated that heparin exhibits anti-inflammatory effect via interference of the formation of neutrophil extracellular traps and this may also contribute to heparin's antithrombotic activity. This illustrates that heparin interacts with a broad range of biomolecules, exerting both anticoagulant and nonanticoagulant actions. Since our previous review, there has been an increased interest in these nonanticoagulant effects of heparin, with the beneficial role in patients infected with SARS2-coronavirus a highly topical example. This article provides an update on our previous review with more recent developments and observations made for these novel uses of heparin and an overview of the development status of heparin-based drugs. SIGNIFICANCE STATEMENT: This state-of-the-art review covers recent developments in the use of heparin and heparin-like materials as anticoagulant, now including immunothrombosis observations, and as nonanticoagulant including a role in the treatment of SARS-coronavirus and inflammatory conditions.
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Affiliation(s)
- John Hogwood
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Barbara Mulloy
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Rebeca Lever
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, 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., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, 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., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
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4
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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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5
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Spiller S, Wippold T, Bellmann-Sickert K, Franz S, Saalbach A, Anderegg U, Beck-Sickinger AG. Protease-Triggered Release of Stabilized CXCL12 from Coated Scaffolds in an Ex Vivo Wound Model. Pharmaceutics 2021; 13:pharmaceutics13101597. [PMID: 34683890 PMCID: PMC8539926 DOI: 10.3390/pharmaceutics13101597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022] Open
Abstract
Biomaterials are designed to improve impaired healing of injured tissue. To accomplish better cell integration, we suggest to coat biomaterial surfaces with bio-functional proteins. Here, a mussel-derived surface-binding peptide is used and coupled to CXCL12 (stromal cell-derived factor 1α), a chemokine that activates CXCR4 and consequently recruits tissue-specific stem and progenitor cells. CXCL12 variants with either non-releasable or protease-mediated-release properties were designed and compared. Whereas CXCL12 was stabilized at the N-terminus for protease resistance, a C-terminal linker was designed that allowed for specific cleavage-mediated release by matrix metalloproteinase 9 and 2, since both enzymes are frequently found in wound fluid. These surface adhesive CXCL12 derivatives were produced by expressed protein ligation. Functionality of the modified chemokines was assessed by inositol phosphate accumulation and cell migration assays. Increased migration of keratinocytes and primary mesenchymal stem cells was demonstrated. Immobilization and release were studied for bioresorbable PCL-co-LC scaffolds, and accelerated wound closure was demonstrated in an ex vivo wound healing assay on porcine skin grafts. After 24 h, a significantly improved CXCL12-specific growth stimulation of the epithelial tips was already observed. The presented data display a successful application of protein-coated biomaterials for skin regeneration.
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Affiliation(s)
- Sabrina Spiller
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany; (S.S.); (K.B.-S.)
| | - Tom Wippold
- Department of Dermatology, Venerology and Allergology, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany; (T.W.); (S.F.); (A.S.)
| | - Kathrin Bellmann-Sickert
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany; (S.S.); (K.B.-S.)
| | - Sandra Franz
- Department of Dermatology, Venerology and Allergology, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany; (T.W.); (S.F.); (A.S.)
| | - Anja Saalbach
- Department of Dermatology, Venerology and Allergology, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany; (T.W.); (S.F.); (A.S.)
| | - Ulf Anderegg
- Department of Dermatology, Venerology and Allergology, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany; (T.W.); (S.F.); (A.S.)
- Correspondence: (U.A.); (A.G.B.-S.); Tel.: +49-341-972-5881 (U.A.); +49-341-973-6900 (A.G.B.-S.); Fax: +49-341-972-5878 (U.A.); +49-341-973-6909 (A.G.B.-S.)
| | - Annette G. Beck-Sickinger
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany; (S.S.); (K.B.-S.)
- Correspondence: (U.A.); (A.G.B.-S.); Tel.: +49-341-972-5881 (U.A.); +49-341-973-6900 (A.G.B.-S.); Fax: +49-341-972-5878 (U.A.); +49-341-973-6909 (A.G.B.-S.)
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6
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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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7
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Spiller S, Clauder F, Bellmann-Sickert K, Beck-Sickinger AG. Improvement of wound healing by the development of ECM-inspired biomaterial coatings and controlled protein release. Biol Chem 2021; 402:1271-1288. [PMID: 34392636 DOI: 10.1515/hsz-2021-0144] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/19/2021] [Indexed: 12/22/2022]
Abstract
Implant design has evolved from biochemically inert substrates, minimizing cell and protein interaction, towards sophisticated bioactive substrates, modulating the host response and supporting the regeneration of the injured tissue. Important aspects to consider are the control of cell adhesion, the discrimination of bacteria and non-local cells from the desired tissue cell type, and the stimulation of implant integration and wound healing. Here, the extracellular matrix acts as a role model providing us with inspiration for sophisticated designs. Within this scope, small bioactive peptides have proven to be miscellaneously deployable for the mediation of surface, cell and matrix interactions. Combinations of adhesion ligands, proteoglycans, and modulatory proteins should guide multiple aspects of the regeneration process and cooperativity between the different extracellular matrix components, which bears the chance to maximize the therapeutic efficiency and simultaneously lower the doses. Hence, efforts to include multiple of these factors in biomaterial design are well worth. In the following, multifunctional implant coatings based on bioactive peptides are reviewed and concepts to implement strong surface anchoring for stable cell adhesion and a dynamic delivery of modulator proteins are discussed.
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Affiliation(s)
- Sabrina Spiller
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, D-04103Leipzig, Germany
| | - Franziska Clauder
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, D-04103Leipzig, Germany
| | - Kathrin Bellmann-Sickert
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, D-04103Leipzig, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, D-04103Leipzig, Germany
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8
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Salbach-Hirsch J, Rauner M, Hofbauer C, Hofbauer LC. New insights into the role of glycosaminoglycans in the endosteal bone microenvironment. Biol Chem 2021; 402:1415-1425. [PMID: 34323057 DOI: 10.1515/hsz-2021-0174] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 07/14/2021] [Indexed: 12/19/2022]
Abstract
The bone microenvironment is a complex tissue in which heterogeneous cell populations of hematopoietic and mesenchymal origin interact with environmental cues to maintain tissue integrity. Both cellular and matrix components are subject to physiologic challenges and can dynamically respond by modifying cell/matrix interactions. When either component is impaired, the physiologic balance is lost. Here, we review the current state of knowledge of how glycosaminoglycans - organic components of the bone extracellular matrix - influence the bone micromilieu. We point out how they interact with mediators of distinct signaling pathways such as the RANKL/OPG axis, BMP and WNT signaling, and affect the activity of bone remodeling cells within the endosteal niche summarizing their potential for therapeutic intervention.
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Affiliation(s)
- Juliane Salbach-Hirsch
- Division of Endocrinology, Diabetes, and Metabolic Bone Diseases, Department of Medicine III, Medical Center, Technische Universität Dresden, D-01307 Dresden, Germany
- Center for Healthy Aging, Medical Center, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Martina Rauner
- Division of Endocrinology, Diabetes, and Metabolic Bone Diseases, Department of Medicine III, Medical Center, Technische Universität Dresden, D-01307 Dresden, Germany
- Center for Healthy Aging, Medical Center, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Christine Hofbauer
- NCT Dresden and University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Lorenz C Hofbauer
- Division of Endocrinology, Diabetes, and Metabolic Bone Diseases, Department of Medicine III, Medical Center, Technische Universität Dresden, D-01307 Dresden, Germany
- Center for Healthy Aging, Medical Center, Technische Universität Dresden, D-01307 Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), D-01307 Dresden, Germany
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9
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Schiller J, Lemmnitzer K, Dürig JN, Rademann J. Insights into structure, affinity, specificity, and function of GAG-protein interactions through the chemoenzymatic preparation of defined sulfated oligohyaluronans. Biol Chem 2021; 402:1375-1384. [PMID: 34291624 DOI: 10.1515/hsz-2021-0165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/04/2021] [Indexed: 11/15/2022]
Abstract
High amounts of glycosaminoglycans (GAG) such as hyaluronan (HA) occur in connective tissues. There is nowadays increasing evidence that a "sulfation code" exists which mediates numerous GAG functions. High molecular weight and inhomogeneity of GAG, however, aggravated detailed studies. Thus, synthetic oligosaccharides were urgently required. We will review here chemoenzymatic and analytic strategies to provide defined sulfated and anomerically modified GAG oligosaccharides of the HA type. Representative studies of protein/GAG interactions by (bio)chemical and biophysical methods are reported yielding novel insights into GAG-protein binding. Finally, the biological conclusions and in vivo applications of defined sulfated GAG oligosaccharides will be discussed.
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Affiliation(s)
- Jürgen Schiller
- Faculty of Medicine, Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstraße 16-18, 04107Leipzig, Germany
| | - Katharina Lemmnitzer
- Faculty of Medicine, Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstraße 16-18, 04107Leipzig, Germany
| | - Jan-Niklas Dürig
- Department of Biology, Chemistry, and Pharmacy, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195Berlin, Germany
| | - Jörg Rademann
- Department of Biology, Chemistry, and Pharmacy, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195Berlin, Germany
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10
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Kühn S, Freyse J, Atallah P, Rademann J, Freudenberg U, Werner C. Tuning the network charge of biohybrid hydrogel matrices to modulate the release of SDF-1. Biol Chem 2021; 402:1453-1464. [PMID: 34218538 DOI: 10.1515/hsz-2021-0175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/10/2021] [Indexed: 11/15/2022]
Abstract
The delivery of chemotactic signaling molecules via customized biomaterials can effectively guide the migration of cells to improve the regeneration of damaged or diseased tissues. Here, we present a novel biohybrid hydrogel system containing two different sulfated glycosaminoglycans (sGAG)/sGAG derivatives, namely either a mixture of short heparin polymers (Hep-Mal) or structurally defined nona-sulfated tetrahyaluronans (9s-HA4-SH), to precisely control the release of charged signaling molecules. The polymer networks are described in terms of their negative charge, i.e. the anionic sulfate groups on the saccharides, using two parameters, the integral density of negative charge and the local charge distribution (clustering) within the network. The modulation of both parameters was shown to govern the release characteristics of the chemotactic signaling molecule SDF-1 and allows for seamless transitions between burst and sustained release conditions as well as the precise control over the total amount of delivered protein. The obtained hydrogels with well-adjusted release profiles effectively promote MSC migration in vitro and emerge as promising candidates for new treatment modalities in the context of bone repair and wound healing.
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Affiliation(s)
- Sebastian Kühn
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Str. 6, D-01069Dresden, Germany
| | - Joanna Freyse
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, D-14195Berlin, Germany
| | - Passant Atallah
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Str. 6, D-01069Dresden, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, D-14195Berlin, Germany
| | - Uwe Freudenberg
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Str. 6, D-01069Dresden, Germany
| | - Carsten Werner
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Str. 6, D-01069Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Fetscherstraße 105, D-01307Dresden, Germany
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11
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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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12
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Gaardløs M, Samsonov SA, Sletmoen M, Hjørnevik M, Sætrom GI, Tøndervik A, Aachmann FL. Insights into the roles of charged residues in substrate binding and mode of action of mannuronan C-5 epimerase AlgE4. Glycobiology 2021; 31:1616-1635. [PMID: 33822050 DOI: 10.1093/glycob/cwab025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/10/2021] [Indexed: 01/18/2023] Open
Abstract
Mannuronan C-5 epimerases catalyse the epimerization of monomer residues in the polysaccharide alginate, changing the physical properties of the biopolymer. The enzymes are utilized to tailor alginate to numerous biological functions by alginate-producing organisms. The underlying molecular mechanisms that control the processive movement of the epimerase along the substrate chain is still elusive. To study this, we have used an interdisciplinary approach combining molecular dynamics simulations with experimental methods from mutant studies of AlgE4, where initial epimerase activity and product formation were addressed with NMR spectroscopy, and characteristics of enzyme-substrate interactions were obtained with isothermal titration calorimetry and optical tweezers. Positive charges lining the substrate-binding groove of AlgE4 appear to control the initial binding of poly-mannuronate, and binding also seems to be mediated by both electrostatic and hydrophobic interactions. After the catalytic reaction, negatively charged enzyme residues might facilitate dissociation of alginate from the positive residues, working like electrostatic switches, allowing the substrate to translocate in the binding groove. Molecular simulations show translocation increments of two monosaccharide units before the next productive binding event resulting in MG-block formation, with the epimerase moving with its N-terminus towards the reducing end of the alginate chain. Our results indicate that the charge pair R343-D345 might be directly involved in conformational changes of a loop that can be important for binding and dissociation. The computational and experimental approaches used in this study complement each other, allowing for a better understanding of individual residues' roles in binding and movement along the alginate chains.
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Affiliation(s)
- Margrethe Gaardløs
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | | | - Marit Sletmoen
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | - Maya Hjørnevik
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | - Gerd Inger Sætrom
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | - Anne Tøndervik
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands veg 3 B, N-7491 Trondheim, Norway
| | - Finn Lillelund Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
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13
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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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14
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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.
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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
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15
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Spiller S, Panitz N, Limasale YDP, Atallah PM, Schirmer L, Bellmann-Sickert K, Blaszkiewicz J, Koehling S, Freudenberg U, Rademann J, Werner C, Beck-Sickinger AG. Modulation of Human CXCL12 Binding Properties to Glycosaminoglycans To Enhance Chemotactic Gradients. ACS Biomater Sci Eng 2019; 5:5128-5138. [DOI: 10.1021/acsbiomaterials.9b01139] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sabrina Spiller
- Universität Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Nydia Panitz
- Universität Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Yanuar Dwi Putra Limasale
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Strasse 6, 01069 Dresden, Germany
| | - Passant Morsi Atallah
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Strasse 6, 01069 Dresden, Germany
| | - Lucas Schirmer
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Strasse 6, 01069 Dresden, Germany
| | - Kathrin Bellmann-Sickert
- Universität Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Joanna Blaszkiewicz
- Freie Universität Berlin, Medicinal Chemistry, Königin-Luise-Strasse 2+4, Berlin 14195, Germany
| | - Sebastian Koehling
- Freie Universität Berlin, Medicinal Chemistry, Königin-Luise-Strasse 2+4, Berlin 14195, Germany
| | - Uwe Freudenberg
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Strasse 6, 01069 Dresden, Germany
| | - Jörg Rademann
- Freie Universität Berlin, Medicinal Chemistry, Königin-Luise-Strasse 2+4, Berlin 14195, Germany
| | - Carsten Werner
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Strasse 6, 01069 Dresden, Germany
| | - Annette G. Beck-Sickinger
- Universität Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstrasse 34, 04103 Leipzig, Germany
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16
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Köhling S, Blaszkiewicz J, Ruiz-Gómez G, Fernández-Bachiller MI, Lemmnitzer K, Panitz N, Beck-Sickinger AG, Schiller J, Pisabarro MT, Rademann J. Syntheses of defined sulfated oligohyaluronans reveal structural effects, diversity and thermodynamics of GAG-protein binding. Chem Sci 2018; 10:866-878. [PMID: 30774881 PMCID: PMC6346292 DOI: 10.1039/c8sc03649g] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/22/2018] [Indexed: 01/14/2023] Open
Abstract
High binding affinities of GAG toward extracellular regulatory proteins are governed by recognition diversity, sulfation pattern, length, and anomeric functionalization.
Binding of sulfated glycosaminoglycans (GAG) to a wide spectrum of extracellular regulatory proteins is crucial for physiological processes such as cell growth, migration, tissue homeostasis and repair. Thus, GAG derivatives exhibit great relevance in the development of innovative biomaterials for tissue regeneration therapies. We present a synthetic strategy for the preparation of libraries of defined sulfated oligohyaluronans as model GAG systematically varied in length, sulfation pattern and anomeric substitution in order to elucidate the effects of these parameters on GAG recognition by regulatory proteins. Through an experimental and computational approach using fluorescence polarization, ITC, docking and molecular dynamics simulations we investigate the binding of these functionalized GAG derivatives to ten representative regulatory proteins including IL-8, IL-10, BMP-2, sclerostin, TIMP-3, CXCL-12, TGF-β, FGF-1, FGF-2, and AT-III, and we establish structure–activity relationships for GAG recognition. Binding is mainly driven by enthalpy with only minor entropic contributions. In several cases binding is determined by GAG length, and in all cases by the position and number of sulfates. Affinities strongly depend on the anomeric modification of the GAG. Highest binding affinities are effected by anomeric functionalization with large fluorophores and by GAG dimerization. Our experimental and theoretical results suggest that the diversity of GAG binding sites and modes is responsible for the observed high affinities and other binding features. The presented new insights into GAG–protein recognition will be of relevance to guide the design of GAG derivatives with customized functions for the engineering of new biomaterials.
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Affiliation(s)
- Sebastian Köhling
- Institute of Pharmacy - Medicinal Chemistry , Freie Universität Berlin , Königin-Luise-Str. 2+4 , 14195 Berlin , Germany .
| | - Joanna Blaszkiewicz
- Institute of Pharmacy - Medicinal Chemistry , Freie Universität Berlin , Königin-Luise-Str. 2+4 , 14195 Berlin , Germany .
| | - Gloria Ruiz-Gómez
- Structural Bioinformatics , BIOTEC TU Dresden , Tatzberg 47-51 , Dresden 01307 , Germany .
| | | | - Katharina Lemmnitzer
- Institute of Medical Physics and Biophysics , University of Leipzig , Härtelstr. 16/18 , 04107 Leipzig , Germany
| | - Nydia Panitz
- Institute of Biochemistry , University of Leipzig , Brüderstr. 34 , 04103 Leipzig , Germany
| | | | - Jürgen Schiller
- Institute of Medical Physics and Biophysics , University of Leipzig , Härtelstr. 16/18 , 04107 Leipzig , Germany
| | - M Teresa Pisabarro
- Structural Bioinformatics , BIOTEC TU Dresden , Tatzberg 47-51 , Dresden 01307 , Germany .
| | - Jörg Rademann
- Institute of Pharmacy - Medicinal Chemistry , Freie Universität Berlin , Königin-Luise-Str. 2+4 , 14195 Berlin , Germany .
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17
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Sepuru KM, Nagarajan B, Desai UR, Rajarathnam K. Structural basis, stoichiometry, and thermodynamics of binding of the chemokines KC and MIP2 to the glycosaminoglycan heparin. J Biol Chem 2018; 293:17817-17828. [PMID: 30257866 DOI: 10.1074/jbc.ra118.004866] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/10/2018] [Indexed: 01/21/2023] Open
Abstract
Keratinocyte-derived chemokine (KC or mCXCL1) and macrophage inflammatory protein 2 (MIP2 or mCXCL2) play nonredundant roles in trafficking blood neutrophils to sites of infection and injury. The functional responses of KC and MIP2 are intimately coupled to their interactions with glycosaminoglycans (GAGs). GAG interactions orchestrate chemokine concentration gradients and modulate receptor activity, which together regulate neutrophil trafficking. Here, using NMR, molecular dynamics (MD) simulations, and isothermal titration calorimetry (ITC), we characterized the molecular basis of KC and MIP2 binding to the GAG heparin. Both chemokines reversibly exist as monomers and dimers, and the NMR analysis indicates that the dimer binds heparin with higher affinity. The ITC experiments indicate a stoichiometry of two GAGs per KC or MIP2 dimer and that the enthalpic and entropic contributions vary significantly between the two chemokine-heparin complexes. NMR-based structural models of heparin-KC and heparin-MIP2 complexes reveal that different combinations of residues from the N-loop, 40s turn, β3-strand, and C-terminal helix form a binding surface within a monomer and that both conserved residues and residues unique to a particular chemokine mediate the binding interactions. MD simulations indicate significant residue-specific differences in their contribution to binding and affinity for a given chemokine and between chemokines. On the basis of our observations that KC and MIP2 bind to GAG via distinct molecular interactions, we propose that the differences in these GAG interactions lead to differences in neutrophil recruitment and play nonoverlapping roles in resolution of inflammation.
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Affiliation(s)
- Krishna Mohan Sepuru
- From the Departments of Biochemistry and Molecular Biology; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555
| | - Balaji Nagarajan
- Department of Medicinal Chemistry and Institute for Structural Biology, and Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Umesh R Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, and Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Krishna Rajarathnam
- From the Departments of Biochemistry and Molecular Biology; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555; Microbiology and Immunology.
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