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Shivgan AT, Marzinek JK, Krah A, Matsudaira P, Verma CS, Bond PJ. Coarse-Grained Model of Glycosaminoglycans for Biomolecular Simulations. J Chem Theory Comput 2024; 20:3308-3321. [PMID: 38358378 DOI: 10.1021/acs.jctc.3c01088] [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: 02/16/2024]
Abstract
Proteoglycans contain glycosaminoglycans (GAGs) which are negatively charged linear polymers made of repeating disaccharide units of uronic acid and hexosamine units. They play vital roles in numerous physiological and pathological processes, particularly in governing cellular communication and attachment. Depending on their sulfonation state, acetylation, and glycosidic linkages, GAGs belong to different families. The high molecular weight, heterogeneity, and flexibility of GAGs hamper their characterization at atomic resolution, but this may be circumvented via coarse-grained (CG) approaches. In this work, we report a CG model for a library of common GAG types in their isolated or proteoglycan-linked states compatible with version 2.2 (v2.2) of the widely popular CG Martini force field. The model reproduces conformational and thermodynamic properties for a wide variety of GAGs, as well as matching structural and binding data for selected proteoglycan test systems. The parameters developed here may thus be employed to study a range of GAG-containing biomolecular systems, thereby benefiting from the efficiency and broad applicability of the Martini framework.
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Affiliation(s)
- Aishwary T Shivgan
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Jan K Marzinek
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Alexander Krah
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Paul Matsudaira
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
| | - Chandra S Verma
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
- School of Biological sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551, Singapore
| | - Peter J Bond
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
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2
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Kogut MM, Danielsson A, Ricard-Blum S, Samsonov SA. Impact of calcium ions on the structural and dynamic properties of heparin oligosaccharides by computational analysis. Comput Biol Chem 2022; 99:107727. [PMID: 35841830 DOI: 10.1016/j.compbiolchem.2022.107727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/24/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022]
Abstract
Heparin (HP) belongs to glycosaminoglycans (GAGs), anionic linear polysaccharides composed of repetitive disaccharide units. They are key players in many biological processes occurring in the extracellular matrix and at the cell surface. GAGs are challenging molecules for computational research due to their high chemical heterogeneity, flexibility, periodicity, pseudosymmetry, predominantly electrostatics-driven nature of interactions with their protein partners and potential multipose binding. The molecular mechanisms underlying GAG interactions mediated by divalent ions, which are important for GAG binding to several proteins, are not well understood. The goal of this study was to characterize the binding of Ca2+ to two HP oligosaccharides of different lengths (dp10 and dp18, dp: degree of polymerization) and their impact on HP conformational space and their dynamic behavior with the use of molecular dynamics (MD)-based approaches with two Ca2+ parameter sets. MD data suggested that the flexibility of the monosaccharides, the glycosidic linkages and ring puckering were not affected by the presence of Ca2+, in contrast to H-bond propensities and the calculated Rg for a fraction of the oligosaccharide populations in both dp10 and dp18. Moreover, the essential differences in the data obtained by using two Ca2+ parameter sets were reported.
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Affiliation(s)
- Małgorzata M Kogut
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Annemarie Danielsson
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Sylvie Ricard-Blum
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, Institute of Molecular and Supramolecular Chemistry and Biochemistry, UMR 5246, Villeurbanne CEDEX F-69622, France
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, Gdańsk 80-308, Poland.
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3
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Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states. Curr Opin Struct Biol 2022; 74:102356. [DOI: 10.1016/j.sbi.2022.102356] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/08/2022] [Accepted: 02/13/2022] [Indexed: 11/18/2022]
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4
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Modeling glycosaminoglycan–protein complexes. Curr Opin Struct Biol 2022; 73:102332. [DOI: 10.1016/j.sbi.2022.102332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/20/2021] [Accepted: 01/06/2022] [Indexed: 12/23/2022]
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5
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Janke JJ, Yu Y, Pomin VH, Zhao J, Wang C, Linhardt RJ, García AE. Characterization of Heparin's Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy. J Chem Theory Comput 2022; 18:1894-1904. [PMID: 35108013 PMCID: PMC9027489 DOI: 10.1021/acs.jctc.1c00760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Heparin is a highly charged, polysulfated polysaccharide and serves as an anticoagulant. Heparin binds to multiple proteins throughout the body, suggesting a large range of potential therapeutic applications. Although its function has been characterized in multiple physiological contexts, heparin's solution conformational dynamics and structure-function relationships are not fully understood. Molecular dynamics (MD) simulations facilitate the analysis of a molecule's underlying conformational ensemble, which then provides important information necessary for understanding structure-function relationships. However, for MD simulations to afford meaningful results, they must both provide adequate sampling and accurately represent the energy properties of a molecule. The aim of this study is to compare heparin's conformational ensemble using two well-developed force fields for carbohydrates, known as GLYCAM06 and CHARMM36, using replica exchange molecular dynamics (REMD) simulations, and to validate these results with NMR experiments. The anticoagulant sequence, an ultra-low-molecular-weight heparin, known as Arixtra (fondaparinux, sodium), was simulated with both parameter sets. The results suggest that GLYCAM06 matches experimental nuclear magnetic resonance three-bond J-coupling values measured for Arixtra better than CHARMM36. In addition, NOESY and ROESY experiments suggest that Arixtra is very flexible in the sub-millisecond time scale and does not adopt a unique structure at 25 C. Moreover, GLYCAM06 affords a much more dynamic conformational ensemble for Arixtra than CHARMM36.
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Affiliation(s)
- J Joel Janke
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Yanlei Yu
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Vitor H Pomin
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Jing Zhao
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Angel E García
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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6
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Kim SH, Kearns FL, Rosenfeld MA, Casalino L, Papanikolas MJ, Simmerling C, Amaro RE, Freeman R. GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses. ACS CENTRAL SCIENCE 2022; 8:22-42. [PMID: 35106370 PMCID: PMC8796303 DOI: 10.1021/acscentsci.1c01080] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Indexed: 05/02/2023]
Abstract
Inspired by the role of cell-surface glycoproteins as coreceptors for pathogens, we report the development of GlycoGrip: a glycopolymer-based lateral flow assay for detecting SARS-CoV-2 and its variants. GlycoGrip utilizes glycopolymers for primary capture and antispike antibodies labeled with gold nanoparticles for signal-generating detection. A lock-step integration between experiment and computation has enabled efficient optimization of GlycoGrip test strips which can selectively, sensitively, and rapidly detect SARS-CoV-2 and its variants in biofluids. Employing the power of the glycocalyx in a diagnostic assay has distinct advantages over conventional immunoassays as glycopolymers can bind to antigens in a multivalent capacity and are highly adaptable for mutated strains. As new variants of SARS-CoV-2 are identified, GlycoGrip will serve as a highly reconfigurable biosensor for their detection. Additionally, via extensive ensemble-based docking simulations which incorporate protein and glycan motion, we have elucidated important clues as to how heparan sulfate and other glycocalyx components may bind the spike glycoprotein during SARS-CoV-2 host-cell infection. GlycoGrip is a promising and generalizable alternative to costly, labor-intensive RT-PCR, and we envision it will be broadly useful, including for rural or low-income populations that are historically undertested and under-reported in infection statistics.
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Affiliation(s)
- Sang Hoon Kim
- University
of North Carolina−Chapel Hill, Department of Applied Physical Sciences, 1112 Murray Hall, CB#3050, Chapel Hill, North Carolina 27599-2100, United States
| | - Fiona L. Kearns
- University
of California−San Diego, Department of Chemistry and Biochemistry, 3234 Urey Hall, MC-0340, La Jolla, California 92093-0340, United States
| | - Mia A. Rosenfeld
- University
of California−San Diego, Department of Chemistry and Biochemistry, 3234 Urey Hall, MC-0340, La Jolla, California 92093-0340, United States
| | - Lorenzo Casalino
- University
of California−San Diego, Department of Chemistry and Biochemistry, 3234 Urey Hall, MC-0340, La Jolla, California 92093-0340, United States
| | - Micah J. Papanikolas
- University
of North Carolina−Chapel Hill, Department of Applied Physical Sciences, 1112 Murray Hall, CB#3050, Chapel Hill, North Carolina 27599-2100, United States
| | - Carlos Simmerling
- SUNY
Stony Brook, Department of Chemistry, 537 Chemistry/119 Laufer Center,
100 Nicolls Road, 104 Chemistry, Stony Brook, New York 11790-3400, United States
| | - Rommie E. Amaro
- University
of California−San Diego, Department of Chemistry and Biochemistry, 3234 Urey Hall, MC-0340, La Jolla, California 92093-0340, United States
| | - Ronit Freeman
- University
of North Carolina−Chapel Hill, Department of Applied Physical Sciences, 1112 Murray Hall, CB#3050, Chapel Hill, North Carolina 27599-2100, United States
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7
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Nagarajan B, Desai U. Aqueous Molecular Dynamics for Understanding Glycosaminoglycan Recognition by Proteins. Methods Mol Biol 2022; 2303:49-62. [PMID: 34626369 DOI: 10.1007/978-1-0716-1398-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Glycosaminoglycans (GAGs) are biopolymers that exist in most organisms. GAGs are known to bind to hundreds of proteins and partake in multiple biological processes such as growth, morphogenesis, inflammation, infection, and others. Their intrinsic structural heterogeneity and conformational variability introduce major challenges in experimental studies. On the other hand, recent advances in force field development and computational technology have yielded phenomenal opportunity to study thousands of GAG sequences simultaneously to understand recognition of target protein(s). Here, we describe experimental setup for conventional molecular dynamics simulations of GAGs to position an experimental biologist favorably in performance, analysis and interpretation of stability, specificity, and conformational properties of GAGs, while also elucidating their interactions with amino acid residues of a protein at an atomistic level in presence of water.
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Affiliation(s)
- Balaji Nagarajan
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA.
| | - Umesh Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
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8
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Marcisz M, Maszota-Zieleniak M, Huard B, Samsonov SA. Advanced Molecular Dynamics Approaches to Model a Tertiary Complex APRIL/TACI with Long Glycosaminoglycans. Biomolecules 2021; 11:biom11091349. [PMID: 34572563 PMCID: PMC8465899 DOI: 10.3390/biom11091349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 02/05/2023] Open
Abstract
Glycosaminoglycans (GAGs) are linear anionic periodic polysaccharides participating in a number of biologically relevant processes in the extracellular matrix via interactions with their protein targets. Due to their periodicity, conformational flexibility, pseudo-symmetry of the sulfation pattern, and the key role of electrostatics, these molecules are challenging for both experimental and theoretical approaches. In particular, conventional molecular docking applied for GAGs longer than 10-mer experiences severe difficulties. In this work, for the first time, 24- and 48-meric GAGs were docked using all-atomic repulsive-scaling Hamiltonian replica exchange molecular dynamics (RS-REMD), a novel methodology based on replicas with van der Waals radii of interacting molecules being scaled. This approach performed well for proteins complexed with oligomeric GAGs and is independent of their length, which distinguishes it from other molecular docking approaches. We built a model of long GAGs in complex with a proliferation-inducing ligand (APRIL) prebound to its receptors, the B cell maturation antigen and the transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI). Furthermore, the prediction power of the RS-REMD for this tertiary complex was evaluated. We conclude that the TACI–GAG interaction could be potentially amplified by TACI’s binding to APRIL. RS-REMD outperformed Autodock3, the docking program previously proven the best for short GAGs.
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Affiliation(s)
- Mateusz Marcisz
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland; (M.M.); (M.M.-Z.)
- Intercollegiate Faculty of Biotechnology of UG and MUG, ul. Abrahama 58, 80-307 Gdańsk, Poland
| | - Martyna Maszota-Zieleniak
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland; (M.M.); (M.M.-Z.)
| | - Bertrand Huard
- Laboratory TIMC-IMAG, University Grenoble-Alpes, CNRS UMR 5525, 38700 La Tronche, France;
| | - Sergey A. Samsonov
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland; (M.M.); (M.M.-Z.)
- Correspondence: ; Tel.: +48-58-523-51-66
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9
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Sankaranarayanan NV, Nagarajan B, Desai UR. Combinatorial Virtual Library Screening Study of Transforming Growth Factor-β2-Chondroitin Sulfate System. Int J Mol Sci 2021; 22:7542. [PMID: 34299163 PMCID: PMC8305211 DOI: 10.3390/ijms22147542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022] Open
Abstract
Transforming growth factor-beta (TGF-β), a member of the TGF-β cytokine superfamily, is known to bind to sulfated glycosaminoglycans (GAGs), but the nature of this interaction remains unclear. In a recent study, we found that preterm human milk TGF-β2 is sequestered by chondroitin sulfate (CS) in its proteoglycan form. To understand the molecular basis of the TGF-β2-CS interaction, we utilized the computational combinatorial virtual library screening (CVLS) approach in tandem with molecular dynamics (MD) simulations. All possible CS oligosaccharides were generated in a combinatorial manner to give 24 di- (CS02), 192 tetra- (CS04), and 1536 hexa- (CS06) saccharides. This library of 1752 CS oligosaccharides was first screened against TGF-β2 using the dual filter CVLS algorithm in which the GOLDScore and root-mean-square-difference (RMSD) between the best bound poses were used as surrogate markers for in silico affinity and in silico specificity. CVLS predicted that both the chain length and level of sulfation are critical for the high affinity and high specificity recognition of TGF-β2. Interestingly, CVLS led to identification of two distinct sites of GAG binding on TGF-β2. CVLS also deduced the preferred composition of the high specificity hexasaccharides, which were further assessed in all-atom explicit solvent MD simulations. The MD results confirmed that both sites of binding form stable GAG-protein complexes. More specifically, the highly selective CS chains were found to engage the TGF-β2 monomer with high affinity. Overall, this work present key principles of recognition with regard to the TGF-β2-CS system. In the process, it led to the generation of the in silico library of all possible CS oligosaccharides, which can be used for advanced studies on other protein-CS systems. Finally, the study led to the identification of unique CS sequences that are predicted to selectively recognize TGF-β2 and may out-compete common natural CS biopolymers.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; (N.V.S.); (B.N.)
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; (N.V.S.); (B.N.)
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; (N.V.S.); (B.N.)
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
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10
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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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11
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Solid state structure of sodium β-1-thiophenyl glucuronate identifies 5-coordinate sodium with three independent glucoronates. Carbohydr Res 2021; 502:108281. [PMID: 33770633 DOI: 10.1016/j.carres.2021.108281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/21/2022]
Abstract
Glucuronic acid is a key component of the glycosaminoglycans (GAGs) Chrondroitin Sulfate (CS), Heparin/Heparan sulfate (HS) and Hyaluronic Acid (HA), as well an important metabolite derivative. In biological systems the carboxylate of uronic acids in GAGs is involved in important H-binding interactions, and the role of metal coordination, such as sodiated systems, has indications associated with a number of biological effects, and physiological GAG-related processes. In synthetic approaches to GAG fragments, thioglycoside intermediates, or derivatives from these, are commonly employed. Of the reported examples of sodium coordination in carbohydrates, 6-coordinate systems are usually observed often with water ligands involved, Herein we report an unexpected 5-coordinate sodiated GlcA crystal structure of the parent GlcA, but as a thioglycoside derivative, whose crystal coordination differs from previous examples, with no involvement of water as a ligand and containing a distorted trigonal bypramidal sodium with each GlcA having five of 6 oxygens sodium-coordinated.
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12
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Gómez Toledo A, Sorrentino JT, Sandoval DR, Malmström J, Lewis NE, Esko JD. A Systems View of the Heparan Sulfate Interactome. J Histochem Cytochem 2021; 69:105-119. [PMID: 33494649 PMCID: PMC7841697 DOI: 10.1369/0022155420988661] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 12/28/2022] Open
Abstract
Heparan sulfate proteoglycans consist of a small family of proteins decorated with one or more covalently attached heparan sulfate glycosaminoglycan chains. These chains have intricate structural patterns based on the position of sulfate groups and uronic acid epimers, which dictate their ability to engage a large repertoire of heparan sulfate-binding proteins, including extracellular matrix proteins, growth factors and morphogens, cytokines and chemokines, apolipoproteins and lipases, adhesion and growth factor receptors, and components of the complement and coagulation system. This review highlights recent progress in the characterization of the so-called "heparan sulfate interactome," with a major focus on systems-wide strategies as a tool for discovery and characterization of this subproteome. In addition, we compiled all heparan sulfate-binding proteins reported in the literature to date and grouped them into a few major functional classes by applying a networking approach.
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Affiliation(s)
- Alejandro Gómez Toledo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
- Department of Clinical Sciences, Lund, Division of Infection Medicine, Lund University, Lund, Sweden
| | - James T Sorrentino
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California
- Department of Bioengineering, University of California, San Diego, La Jolla, California
| | - Daniel R Sandoval
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
| | - Johan Malmström
- Department of Clinical Sciences, Lund, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego, La Jolla, California
- Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
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13
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Nagarajan B, Sankaranarayanan NV, Desai UR. Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools. Glycobiology 2020; 30:516-527. [PMID: 32080710 PMCID: PMC8179626 DOI: 10.1093/glycob/cwaa015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 11/15/2022] Open
Abstract
Heparin/heparan sulfates (H/HS) are ubiquitous biopolymers that interact with many proteins to induce a range of biological functions. Unfortunately, how these biopolymers recognize their preferred protein targets remain poorly understood. It is suggested that computational simulations offer attractive avenues but a number of challenges, e.g., difficulty of selecting a comprehensive force field, few simple tools to interpret data, among others, remain. This work addresses several such challenges so as to help ease the implementation and analysis of computational experiments. First, this work presents a rigorous comparison of two different recent force fields, CHARMM36 and GLYCAM06, for H/HS studies. Second, it introduces two new straightforward parameters, i.e., end-to-end distance and minimum volume enclosing ellipsoid, to understand the myriad conformational forms of oligosaccharides that evolve over time in water. Third, it presents an application to elucidate the number and nature of inter and intramolecular, nondirect bridging water molecules, which help stabilize unique forms of H/HS. The results show that nonspecialists can use either CHARMM36 or GLYCAM06 force fields because both gave comparable results, albeit with small differences. The comparative study shows that the HS hexasaccharide samples a range of conformations with nearly equivalent energies, which could be the reason for its recognition by different proteins. Finally, analysis of the nondirect water bridges across the dynamics trajectory shows their importance in stabilization of certain conformational forms, which may become important for protein recognition. Overall, the work aids nonspecialists employ computational studies for understanding the solution behavior of H/HS.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Umesh R Desai
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
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14
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Rajarathnam K, Desai UR. Structural Insights Into How Proteoglycans Determine Chemokine-CXCR1/CXCR2 Interactions: Progress and Challenges. Front Immunol 2020; 11:660. [PMID: 32391006 PMCID: PMC7193095 DOI: 10.3389/fimmu.2020.00660] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/23/2020] [Indexed: 01/01/2023] Open
Abstract
Proteoglycans (PGs), present in diverse environments, such as the cell membrane surface, extracellular milieu, and intracellular granules, are fundamental to life. Sulfated glycosaminoglycans (GAGs) are covalently attached to the core protein of proteoglycans. PGs are complex structures, and are diverse in terms of amino acid sequence, size, shape, and in the nature and number of attached GAG chains, and this diversity is further compounded by the phenomenal diversity in GAG structures. Chemokines play vital roles in human pathophysiology, from combating infection and cancer to leukocyte trafficking, immune surveillance, and neurobiology. Chemokines mediate their function by activating receptors that belong to the GPCR class, and receptor interactions are regulated by how, when, and where chemokines bind GAGs. GAGs fine-tune chemokine function by regulating monomer/dimer levels and chemotactic/haptotactic gradients, which are also coupled to how they are presented to their receptors. Despite their small size and similar structures, chemokines show a range of GAG-binding geometries, affinities, and specificities, indicating that chemokines have evolved to exploit the repertoire of chemical and structural features of GAGs. In this review, we summarize the current status of research on how GAG interactions regulate ELR-chemokine activation of CXCR1 and CXCR2 receptors, and discuss knowledge gaps that must be overcome to establish causal relationships governing the impact of GAG interactions on chemokine function in human health and disease.
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Affiliation(s)
- Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States.,Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch at Galveston, Galveston, TX, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Umesh R Desai
- Department of Medicinal Chemistry, Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
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15
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Analysis of Procollagen C-Proteinase Enhancer-1/Glycosaminoglycan Binding Sites and of the Potential Role of Calcium Ions in the Interaction. Int J Mol Sci 2019; 20:ijms20205021. [PMID: 31658765 PMCID: PMC6829435 DOI: 10.3390/ijms20205021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 12/15/2022] Open
Abstract
In this study, we characterize the interactions between the extracellular matrix protein, procollagen C-proteinase enhancer-1 (PCPE-1), and glycosaminoglycans (GAGs), which are linear anionic periodic polysaccharides. We applied molecular modeling approaches to build a structural model of full-length PCPE-1, which is not experimentally available, to predict GAG binding poses for various GAG lengths, types and sulfation patterns, and to determine the effect of calcium ions on the binding. The computational data are analyzed and discussed in the context of the experimental results previously obtained using surface plasmon resonance binding assays. We also provide experimental data on PCPE-1/GAG interactions obtained using inhibition assays with GAG oligosaccharides ranging from disaccharides to octadecasaccharides. Our results predict the localization of GAG-binding sites at the amino acid residue level onto PCPE-1 and is the first attempt to describe the effects of ions on protein-GAG binding using modeling approaches. In addition, this study allows us to get deeper insights into the in silico methodology challenges and limitations when applied to GAG-protein interactions.
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16
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Samsonov SA, Freza S, Zsila F. In silico analysis of heparin and chondroitin sulfate binding mechanisms of the antiprotozoal drug berenil and pentamidine. Carbohydr Res 2019; 482:107742. [DOI: 10.1016/j.carres.2019.107742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/18/2022]
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17
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Penk A, Baumann L, Huster D, Samsonov SA. NMR and molecular modeling reveal specificity of the interactions between CXCL14 and glycosaminoglycans. Glycobiology 2019; 29:715-725. [DOI: 10.1093/glycob/cwz047] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/25/2019] [Accepted: 06/25/2019] [Indexed: 12/13/2022] Open
Abstract
Abstract
CXCL14, chemokine (C-X-C motif) ligand 14, is a novel highly conserved chemokine with unique features. Despite exhibiting the typical chemokine fold, it has a very short N-terminus of just two amino acid residues responsible for chemokine receptor activation. CXCL14 actively participates in homeostatic immune surveillance of skin and mucosae, is linked to metabolic disorders and fibrotic lung diseases and possesses strong anti-angiogenic properties in early tumor development. In this work, we investigated the interaction of CXCL14 with various glycosaminoglycans (GAGs) by nuclear magnetic resonance spectroscopy, microscale thermophoresis, analytical heparin (HE) affinity chromatography and in silico approaches to understand the molecular basis of GAG-binding. We observed different GAG-binding modes specific for the GAG type used in the study. In particular, the CXCL14 epitope for HE suggests a binding pose distinguishable from the ones of the other GAGs investigated (hyaluronic acid, chondroitin sulfate-A/C, −D, dermatan sulfate). This observation is also supported by computational methods that included molecular docking, molecular dynamics and free energy calculations. Based on our results, we suggest that distinct GAG sulfation patterns confer specificity beyond simple electrostatic interactions usually considered to represent the driving forces in protein–GAG interactions. The CXCL14–GAG system represents a promising approach to investigate the specificity of GAG–protein interactions, which represents an important topic for developing the rational approaches to novel strategies in regenerative medicine.
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Affiliation(s)
- Anja Penk
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. Leipzig, Germany
| | - Lars Baumann
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. Leipzig, Germany
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, Poland
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18
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Bojarski KK, Sieradzan AK, Samsonov SA. Molecular dynamics insights into protein‐glycosaminoglycan systems from microsecond‐scale simulations. Biopolymers 2019; 110:e23252. [DOI: 10.1002/bip.23252] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/26/2018] [Accepted: 12/21/2018] [Indexed: 12/30/2022]
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19
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Caputo HE, Straub JE, Grinstaff MW. Design, synthesis, and biomedical applications of synthetic sulphated polysaccharides. Chem Soc Rev 2019; 48:2338-2365. [DOI: 10.1039/c7cs00593h] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review summarizes the synthetic methods to sulphated polysaccharides, describes their compositional and structural diversity in regards to activity, and showcases their biomedical applications.
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Affiliation(s)
| | | | - Mark W. Grinstaff
- Department of Chemistry
- Boston University
- Boston
- USA
- Department of Biomedical Engineering
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20
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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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21
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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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22
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Vallet SD, Miele AE, Uciechowska-Kaczmarzyk U, Liwo A, Duclos B, Samsonov SA, Ricard-Blum S. Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners. Sci Rep 2018; 8:11768. [PMID: 30082873 PMCID: PMC6078952 DOI: 10.1038/s41598-018-30190-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 07/20/2018] [Indexed: 01/29/2023] Open
Abstract
Lysyl oxidase (LOX) catalyzes the oxidative deamination of lysine and hydroxylysine residues in collagens and elastin, which is the first step of the cross-linking of these extracellular matrix proteins. It is secreted as a proenzyme activated by bone morphogenetic protein-1, which releases the LOX catalytic domain and its bioactive N-terminal propeptide. We characterized the recombinant human propeptide by circular dichroism, dynamic light scattering, and small-angle X-ray scattering (SAXS), and showed that it is elongated, monomeric, disordered and flexible (Dmax: 11.7 nm, Rg: 3.7 nm). We generated 3D models of the propeptide by coarse-grained molecular dynamics simulations restrained by SAXS data, which were used for docking experiments. Furthermore, we have identified 17 new binding partners of the propeptide by label-free assays. They include four glycosaminoglycans (hyaluronan, chondroitin, dermatan and heparan sulfate), collagen I, cross-linking and proteolytic enzymes (lysyl oxidase-like 2, transglutaminase-2, matrix metalloproteinase-2), a proteoglycan (fibromodulin), one growth factor (Epidermal Growth Factor, EGF), and one membrane protein (tumor endothelial marker-8). This suggests new roles for the propeptide in EGF signaling pathway.
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Affiliation(s)
- Sylvain D Vallet
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry, UMR 5246, F-69622, Villeurbanne cedex, France
| | - Adriana E Miele
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry, UMR 5246, F-69622, Villeurbanne cedex, France
| | - Urszula Uciechowska-Kaczmarzyk
- Laboratory of Molecular Modeling, Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Adam Liwo
- Laboratory of Molecular Modeling, Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Bertrand Duclos
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry, UMR 5246, F-69622, Villeurbanne cedex, France
| | - Sergey A Samsonov
- Laboratory of Molecular Modeling, Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Sylvie Ricard-Blum
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry, UMR 5246, F-69622, Villeurbanne cedex, France.
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23
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Molecular interactions of the anticancer agent ellipticine with glycosaminoglycans by in silico analysis. Carbohydr Res 2018; 462:28-33. [DOI: 10.1016/j.carres.2018.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 12/18/2022]
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24
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Sankaranarayanan NV, Nagarajan B, Desai UR. So you think computational approaches to understanding glycosaminoglycan-protein interactions are too dry and too rigid? Think again! Curr Opin Struct Biol 2018; 50:91-100. [PMID: 29328962 PMCID: PMC6037615 DOI: 10.1016/j.sbi.2017.12.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/17/2017] [Accepted: 12/15/2017] [Indexed: 12/20/2022]
Abstract
Glycosaminoglycans (GAGs) play key roles in virtually all biologic responses through their interaction with proteins. A major challenge in understanding these roles is their massive structural complexity. Computational approaches are extremely useful in navigating this bottleneck and, in some cases, the only avenue to gain comprehensive insight. We discuss the state-of-the-art on computational approaches and present a flowchart to help answer most basic, and some advanced, questions on GAG-protein interactions. For example, firstly, does my protein bind to GAGs?; secondly, where does the GAG bind?; thirdly, does my protein preferentially recognize a particular GAG type?; fourthly, what is the most optimal GAG chain length?; fifthly, what is the structure of the most favored GAG sequence?; and finally, is my GAG-protein system 'specific', 'non-specific', or a combination of both? Recent advances show the field is now poised to enable a non-computational researcher perform advanced experiments through the availability of various tools and online servers.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Balaji Nagarajan
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA.
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25
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Uciechowska-Kaczmarzyk U, Babik S, Zsila F, Bojarski KK, Beke-Somfai T, Samsonov SA. Molecular dynamics-based model of VEGF-A and its heparin interactions. J Mol Graph Model 2018; 82:157-166. [DOI: 10.1016/j.jmgm.2018.04.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 11/28/2022]
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26
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David G, Turin-Moleavin I, Ursu LE, Peptanariu D, Ailincai D. Multilayer biopolymer/poly(ε-caprolactone)/polycation nanoparticles. IRANIAN POLYMER JOURNAL 2018. [DOI: 10.1007/s13726-018-0629-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Peng Y, Tellier LE, Temenoff JS. Heparin-based hydrogels with tunable sulfation & degradation for anti-inflammatory small molecule delivery. Biomater Sci 2018; 4:1371-80. [PMID: 27447003 DOI: 10.1039/c6bm00455e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Sustained release of anti-inflammatory agents remains challenging for small molecule drugs due to their low molecular weight and hydrophobicity. Therefore, the goal of this study was to control the release of a small molecule anti-inflammatory agent, crystal violet (CV), from hydrogels fabricated with heparin, a highly sulfated glycosaminoglycan capable of binding positively-charged molecules such as CV. In this system, both electrostatic interactions between heparin and CV and hydrogel degradation were tuned simultaneously by varying the level of heparin sulfation and varying the amount of dithiothreitol within hydrogels, respectively. It was found that heparin sulfation significantly affected CV release, whereby more sulfated heparin hydrogels (Hep and Hep(-N)) released CV with near zero-order release kinetics (R-squared values between 0.96-0.99). Furthermore, CV was released more quickly from fast-degrading hydrogels than slow-degrading hydrogels, providing a method to tune total CV release between 5-15 days while maintaining linear release kinetics. In particular, N-desulfated heparin hydrogels exhibited efficient CV loading (∼90% of originally included CV), near zero-order CV release kinetics, and maintenance of CV bioactivity after release, making this hydrogel formulation a promising CV delivery vehicle for a wide range of inflammatory diseases.
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Affiliation(s)
- Yifeng Peng
- W.H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA.
| | - Liane E Tellier
- W.H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA.
| | - Johnna S Temenoff
- W.H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA. and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA
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28
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Nordsieck K, Baumann L, Hintze V, Pisabarro MT, Schnabelrauch M, Beck-Sickinger AG, Samsonov SA. The effect of interleukin-8 truncations on its interactions with glycosaminoglycans. Biopolymers 2018; 109:e23103. [DOI: 10.1002/bip.23103] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/23/2017] [Accepted: 01/08/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Karoline Nordsieck
- Institute of Biochemistry, Universität Leipzig, Brüderstr. 34; Leipzig 04103 Germany
| | - Lars Baumann
- Institute of Biochemistry, Universität Leipzig, Brüderstr. 34; Leipzig 04103 Germany
- Institute for Medical Physics and Biophysics, Universität Leipzig, Härtelstr. 16-18; Leipzig 04107 Germany
| | - Vera Hintze
- Institute of Materials Science, Max Bergmann Center of Biomaterials, TU Dresden, Budapester Strasse 27; Dresden 01069 Germany
| | - M. Teresa Pisabarro
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg 47-49; Dresden 01307 Germany
| | | | | | - Sergey A. Samsonov
- Faculty of Chemistry; University of Gdańsk, ul. Wita Stwosza 63; Gdańsk 80-308 Poland
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29
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Babik S, Samsonov SA, Pisabarro MT. Computational drill down on FGF1-heparin interactions through methodological evaluation. Glycoconj J 2017; 34:427-440. [PMID: 27858202 PMCID: PMC5487771 DOI: 10.1007/s10719-016-9745-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 01/22/2023]
Abstract
Glycosaminoglycans (GAGs) exhibit a key role in cellular communication processes through interactions with target proteins of the extracellular matrix (ECM). The sandwich-like interaction established between Fibroblast growth factor (FGF) and heparin (HE) represents quite a peculiar protein-GAG-protein system, which has been both structurally and functionally intensively studied. The molecular recognition characteristics of this system have been exploited in various computational studies in order to deepen understanding of GAG-protein interactions. Here, we drill down on the interactions established in this peculiar macromolecular complex by analyzing the applicability of docking techniques and molecular dynamics (MD)-based approaches, and we dissect the molecular recognition properties exhibited by FGF towards a series of HE derivatives. We examine the sensitivity of MM-GBSA free energy calculations in terms of receptor conformational space sampling and changes in the ligand structures. Furthermore, we investigate its predictive power in combination with other computational methods, namely the well-established Autodock3 (AD3) and dynamic molecular docking (DMD), a targeted MD-based docking method specifically developed to account for flexibility and solvent in computer simulations of protein-GAG systems. Our results show that a site-mapping approach can be effectively combined with AD3 and DMD calculations to accurately reproduce available experimental data and, furthermore, to determine specific GAG recognition patterns. This study deepens our understanding of the applicability of available theoretical approaches to the investigation of molecular recognition in protein-GAG systems.
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Affiliation(s)
- Sándor Babik
- Structural Bioinformatics, BIOTEC TU Dresden, Dresden, 01307, Germany
| | - Sergey A Samsonov
- Structural Bioinformatics, BIOTEC TU Dresden, Dresden, 01307, Germany
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30
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Gao Q, Chen CY, Zong C, Wang S, Ramiah A, Prabhakar P, Morris LC, Boons GJ, Moremen KW, Prestegard JH. Structural Aspects of Heparan Sulfate Binding to Robo1-Ig1-2. ACS Chem Biol 2016; 11:3106-3113. [PMID: 27653286 PMCID: PMC5148660 DOI: 10.1021/acschembio.6b00692] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Roundabout 1, or Robo1, is a cell surface signaling molecule important in axon guidance. Its interaction with heparan sulfate (HS) and members of the Slit protein family is essential to its activity, making characterization of these interactions by structural methods, such as NMR, highly desirable. However, the fact that Robo1 is a glycosylated protein prevents employment of commonly used bacterial hosts for expression of properly glycosylated forms with the uniform 15N, 13C, and 2H labeling needed for NMR studies. Here, we apply an alternative methodology, based on labeling with a single amino acid type and high structural content NMR data, to characterize a two-domain construct of glycosylated Robo1 (Robo1-Ig1-2) interacting with a synthetic HS tetramer (IdoA-GlcNS6S-IdoA2S-GlcNS6S-(CH2)5NH2). Significant chemical shift perturbations of the crosspeak from K81 on titration with the tetramer provide initial evidence for the location of a binding site and allow determination of a 255 μM disassociation constant. The binding epitopes, bound conformation, and binding site placement of the HS tetramer have been further characterized by saturation transfer difference (STD), transferred nuclear Overhauser effect (trNOE), and paramagnetic perturbation experiments. A model of the complex has been generated using constraints derived from the various NMR experiments. Postprocessing energetic analysis of this model provides a rationale for the role each glycan residue plays in the binding event, and examination of the binding site in the context of a previous Robo-Slit structure provides a rationale for modulation of Robo-Slit interactions by HS.
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Affiliation(s)
- Qi Gao
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Cheng-Yu Chen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Chengli Zong
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Shuo Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Annapoorani Ramiah
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Pradeep Prabhakar
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Laura C. Morris
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Kelley W. Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
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31
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Sarkar A, Yu W, Desai UR, MacKerell AD, Mosier PD. Estimating glycosaminoglycan-protein interaction affinity: water dominates the specific antithrombin-heparin interaction. Glycobiology 2016; 26:1041-1047. [PMID: 27496757 DOI: 10.1093/glycob/cww073] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/01/2016] [Accepted: 07/12/2016] [Indexed: 11/13/2022] Open
Abstract
Glycosaminoglycan (GAG)-protein interactions modulate many important biological processes. Structure-function studies on GAGs may reveal probes and drugs, but their structural complexity and highly acidic nature confound such work. Productivity will increase if we are able to identify tight-binding oligosaccharides in silico. An extension of the CHARMM force field is presented to enable modeling of polysaccharides containing sulfamate functionality, and is used to develop a reliable alchemical free-energy perturbation protocol that estimates changes in affinity for the prototypical heparin-antithrombin system to within 2.3 kcal/mol using modest simulation times. Inclusion of water is crucial during simulation as solvation energy was equal in magnitude to the sum of all other thermodynamic factors. In summary, we have identified and optimized a reliable method for estimation of GAG-protein binding affinity, and shown that solvation is a crucial component in GAG-protein interactions.
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Affiliation(s)
- Aurijit Sarkar
- Department of Basic Pharmaceutical Sciences, Fred Wilson School of Pharmacy, High Point University, One University Parkway, High Point, NC 27268, USA .,Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, PO Box 980133, Richmond, VA 23298, USA
| | - Wenbo Yu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, PO Box 980133, Richmond, VA 23298, USA
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Philip D Mosier
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, PO Box 980133, Richmond, VA 23298, USA
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32
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Samsonov SA, Pisabarro MT. Computational analysis of interactions in structurally available protein-glycosaminoglycan complexes. Glycobiology 2016; 26:850-861. [PMID: 27496767 DOI: 10.1093/glycob/cww055] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 04/26/2016] [Indexed: 01/01/2023] Open
Abstract
Glycosaminoglycans represent a class of linear anionic periodic polysaccharides, which play a key role in a variety of biological processes in the extracellular matrix via interactions with their protein targets. Computationally, glycosaminoglycans are very challenging due to their high flexibility, periodicity and electrostatics-driven nature of the interactions with their protein counterparts. In this work, we carry out a detailed computational characterization of the interactions in protein-glycosaminoglycan complexes from the Protein Data Bank (PDB), which are split into two subsets accounting for their intrinsic nature: non-enzymatic-protein-glycosaminoglycan and enzyme-glycosaminoglycan complexes. We apply molecular dynamics to analyze the differences in these two subsets in terms of flexibility, retainment of the native interactions in the simulations, free energy components of binding and contributions of protein residue types to glycosaminoglycan binding. Furthermore, we systematically demonstrate that protein electrostatic potential calculations, previously found to be successful for glycosaminoglycan binding sites prediction for individual systems, are in general very useful for proposing protein surface regions as putative glycosaminoglycan binding sites, which can be further used for local docking calculations with these particular polysaccharides. Finally, the performance of six different docking programs (Autodock 3, Autodock Vina, MOE, eHiTS, FlexX and Glide), some of which proved to perform well for particular protein-glycosaminoglycan complexes in previous work, is evaluated on the complete protein-glycosaminoglycan data set from the PDB. This work contributes to widen our knowledge of protein-glycosaminoglycan molecular recognition and could be useful to steer a choice of the strategies to be applied in theoretical studies of these systems.
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Affiliation(s)
- Sergey A Samsonov
- Structural Bioinformatics, BIOTEC TU Dresden, Dresden 01307, Germany
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33
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Sarkar A, Desai UR. A Simple Method for Discovering Druggable, Specific Glycosaminoglycan-Protein Systems. Elucidation of Key Principles from Heparin/Heparan Sulfate-Binding Proteins. PLoS One 2015; 10:e0141127. [PMID: 26488293 PMCID: PMC4619353 DOI: 10.1371/journal.pone.0141127] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/05/2015] [Indexed: 01/25/2023] Open
Abstract
Glycosaminoglycans (GAGs) affect human physiology and pathology by modulating more than 500 proteins. GAG-protein interactions are generally assumed to be ionic and nonspecific, but specific interactions do exist. Here, we present a simple method to identify the GAG-binding site (GBS) on proteins that in turn helps predict high specific GAG-protein systems. Contrary to contemporary thinking, we found that the electrostatic potential at basic arginine and lysine residues neither identifies the GBS consistently, nor its specificity. GBSs are better identified by considering the potential at neutral hydrogen bond donors such as asparagine or glutamine sidechains. Our studies also reveal that an unusual constellation of ionic and non-ionic residues in the binding site leads to specificity. Nature engineers the local environment of Asn45 of antithrombin, Gln255 of 3-O-sulfotransferase 3, Gln163 and Asn167 of 3-O-sulfotransferase 1 and Asn27 of basic fibroblast growth factor in the respective GBSs to induce specificity. Such residues are distinct from other uncharged residues on the same protein structure in possessing a significantly higher electrostatic potential, resultant from the local topology. In contrast, uncharged residues on nonspecific GBSs such as thrombin and serum albumin possess a diffuse spread of electrostatic potential. Our findings also contradict the paradigm that GAG-binding sites are simply a collection of contiguous Arg/Lys residues. Our work demonstrates the basis for discovering specifically interacting and druggable GAG-protein systems based on the structure of protein alone, without requiring access to any structure-function relationship data.
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Affiliation(s)
- Aurijit Sarkar
- Institute for Structural Biology, Drug Discovery & Development and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery & Development and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
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34
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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35
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Singh A, Kett WC, Severin IC, Agyekum I, Duan J, Amster IJ, Proudfoot AEI, Coombe DR, Woods RJ. The Interaction of Heparin Tetrasaccharides with Chemokine CCL5 Is Modulated by Sulfation Pattern and pH. J Biol Chem 2015; 290:15421-15436. [PMID: 25907556 DOI: 10.1074/jbc.m115.655845] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Indexed: 12/28/2022] Open
Abstract
Interactions between chemokines such as CCL5 and glycosaminoglycans (GAGs) are essential for creating haptotactic gradients to guide the migration of leukocytes into inflammatory sites, and the GAGs that interact with CCL5 with the highest affinity are heparan sulfates/heparin. The interaction between CCL5 and its receptor on monocytes, CCR1, is mediated through residues Arg-17 and -47 in CCL5, which overlap with the GAG-binding (44)RKNR(47) "BBXB" motifs. Here we report that heparin and tetrasaccharide fragments of heparin are able to inhibit CCL5-CCR1 binding, with IC50 values showing strong dependence on the pattern and extent of sulfation. Modeling of the CCL5-tetrasaccharide complexes suggested that interactions between specific sulfate and carboxylate groups of heparin and residues Arg-17 and -47 of the protein are essential for strong inhibition; tetrasaccharides lacking the specific sulfation pattern were found to preferentially bind CCL5 in positions less favorable for inhibition of the interaction with CCR1. Simulations of a 12-mer heparin fragment bound to CCL5 indicated that the oligosaccharide preferred to interact simultaneously with both (44)RKNR(47) motifs in the CCL5 homodimer and engaged residues Arg-47 and -17 from both chains. Direct engagement of these residues by the longer heparin oligosaccharide provides a rationalization for its effectiveness as an inhibitor of CCL5-CCR1 interaction. In this mode, histidine (His-23) may contribute to CCL5-GAG interactions when the pH drops just below neutral, as occurs during inflammation. Additionally, an examination of the contribution of pH to modulating CCL5-heparin interactions suggested a need for careful interpretation of experimental results when experiments are performed under non-physiological conditions.
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Affiliation(s)
- Arunima Singh
- Complex Carbohydrate Research Center and, University of Georgia, Athens, Georgia 30602
| | - Warren C Kett
- Molecular Immunology, School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, Perth 6102, Australia
| | - India C Severin
- Merck Serono Geneva Research Centre, 9 chemin des Mines, 1202 Geneva, Switzerland
| | - Isaac Agyekum
- Department of Chemistry, University of Georgia, Athens, Georgia 30602
| | - Jiana Duan
- Department of Chemistry, University of Georgia, Athens, Georgia 30602
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, Georgia 30602
| | - Amanda E I Proudfoot
- Merck Serono Geneva Research Centre, 9 chemin des Mines, 1202 Geneva, Switzerland
| | - Deirdre R Coombe
- Molecular Immunology, School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, Perth 6102, Australia.
| | - Robert J Woods
- Complex Carbohydrate Research Center and, University of Georgia, Athens, Georgia 30602.
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36
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Sankaranarayanan NV, Sarkar A, Desai UR, Mosier PD. Designing "high-affinity, high-specificity" glycosaminoglycan sequences through computerized modeling. Methods Mol Biol 2015; 1229:289-314. [PMID: 25325961 DOI: 10.1007/978-1-4939-1714-3_24] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The prediction of high-affinity and/or high-specificity protein-glycosaminoglycan (GAG) interactions is an inherently difficult task, due to several factors including the shallow nature of the typical GAG-binding site and the inherent size, flexibility, diversity, and polydisperse nature of the GAG molecules. Here, we present a generally applicable methodology termed Combinatorial Library Virtual Screening (CVLS) that can identify potential high-affinity, high-specificity protein-GAG interactions from very large GAG combinatorial libraries and a suitable GAG-binding protein. We describe the CVLS approach along with the rationale behind it and provide validation for the method using the well-known antithrombin-thrombin-heparin system.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, 800 E. Leigh Street, Suite 212, Richmond, VA, 23298, USA
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37
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Samsonov SA, Bichmann L, Pisabarro MT. Coarse-Grained Model of Glycosaminoglycans. J Chem Inf Model 2014; 55:114-24. [DOI: 10.1021/ci500669w] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sergey A. Samsonov
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg
47-51, D-01307 Dresden, Germany
| | - Leon Bichmann
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg
47-51, D-01307 Dresden, Germany
| | - M. Teresa Pisabarro
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg
47-51, D-01307 Dresden, Germany
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38
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Yang J, Furuta T, Sakurai M, Tsutsumi H, Mihara H. A Computational Study of the Interaction of Amphiphilic α-Helical Cell-Penetrating Peptides with Heparan Sulfate. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20140136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ji Yang
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology
| | - Hiroshi Tsutsumi
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Hisakazu Mihara
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
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39
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Agostino M, Gandhi NS, Mancera RL. Development and application of site mapping methods for the design of glycosaminoglycans. Glycobiology 2014; 24:840-51. [DOI: 10.1093/glycob/cwu045] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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40
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Samsonov SA, Gehrcke JP, Pisabarro MT. Flexibility and Explicit Solvent in Molecular-Dynamics-Based Docking of Protein–Glycosaminoglycan Systems. J Chem Inf Model 2014; 54:582-92. [DOI: 10.1021/ci4006047] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sergey A. Samsonov
- Structural Bioinformatics,
BIOTEC, TU Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Jan-Philip Gehrcke
- Structural Bioinformatics,
BIOTEC, TU Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - M. Teresa Pisabarro
- Structural Bioinformatics,
BIOTEC, TU Dresden, Tatzberg 47-51, 01307 Dresden, Germany
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41
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Mishra SK, Kara M, Zacharias M, Koca J. Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation. Glycobiology 2013; 24:70-84. [PMID: 24134878 DOI: 10.1093/glycob/cwt093] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost.
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Affiliation(s)
- Sushil Kumar Mishra
- Central European Institute of Technology, Masaryk University, Kamenice 5, 61137 Brno, Czech Republic
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42
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Zhu T, Lee H, Lei H, Jones C, Patel K, Johnson ME, Hevener KE. Fragment-based drug discovery using a multidomain, parallel MD-MM/PBSA screening protocol. J Chem Inf Model 2013; 53:560-72. [PMID: 23432621 PMCID: PMC3752004 DOI: 10.1021/ci300502h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have developed a rigorous computational screening protocol to identify novel fragment-like inhibitors of N(5)-CAIR mutase (PurE), a key enzyme involved in de novo purine synthesis that represents a novel target for the design of antibacterial agents. This computational screening protocol utilizes molecular docking, graphics processing unit (GPU)-accelerated molecular dynamics, and Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) free energy estimations to investigate the binding modes and energies of fragments in the active sites of PurE. PurE is a functional octamer comprised of identical subunits. The octameric structure, with its eight active sites, provided a distinct advantage in these studies because, for a given simulation length, we were able to place eight separate fragment compounds in the active sites to increase the throughput of the MM/PBSA analysis. To validate this protocol, we have screened an in-house fragment library consisting of 352 compounds. The theoretical results were then compared with the results of two experimental fragment screens, Nuclear Magnetic Resonance (NMR) and Surface Plasmon Resonance (SPR) binding analyses. In these validation studies, the protocol was able to effectively identify the competitive binders that had been independently identified by experimental testing, suggesting the potential utility of this method for the identification of novel fragments for future development as PurE inhibitors.
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Affiliation(s)
- Tian Zhu
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Ave., Suite 3100, Chicago, IL 60607-7173 (USA)
| | - Hyun Lee
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Ave., Suite 3100, Chicago, IL 60607-7173 (USA)
| | - Hao Lei
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Ave., Suite 3100, Chicago, IL 60607-7173 (USA)
| | - Christopher Jones
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Ave., Suite 3100, Chicago, IL 60607-7173 (USA)
| | - Kavankumar Patel
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Ave., Suite 3100, Chicago, IL 60607-7173 (USA)
| | - Michael E. Johnson
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Ave., Suite 3100, Chicago, IL 60607-7173 (USA)
| | - Kirk E. Hevener
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Ave., Suite 3100, Chicago, IL 60607-7173 (USA)
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43
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Jana M, Bandyopadhyay S. Restricted dynamics of water around a protein-carbohydrate complex: computer simulation studies. J Chem Phys 2012; 137:055102. [PMID: 22894384 DOI: 10.1063/1.4739421] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Water-mediated protein-carbohydrate interaction is a complex phenomenon responsible for different biological processes in cellular environment. One of the unexplored but important issues in this area is the role played by water during the recognition process and also in controlling the microscopic properties of the complex. In this study, we have carried out atomistic molecular dynamics simulations of a protein-carbohydrate complex formed between the hyaluronan binding domain of the murine Cd44 protein and the octasaccharide hyaluronan in explicit water. Efforts have been made to explore the heterogeneous influence of the complex on the dynamic properties of water present in different regions around it. It is revealed from our analyses that the heterogeneous dynamics of water around the complex are coupled with differential time scales of formation and breaking of hydrogen bonds at the interface. Presence of a highly rigid thin layer of motionally restricted water molecules bridging the protein and the carbohydrate in the common region of the complex has been identified. Such water molecules are expected to play a crucial role in controlling properties of the complex. Importantly, it is demonstrated that the formation of the protein-carbohydrate complex affects the transverse and longitudinal degrees of freedom of the interfacial water molecules in a heterogeneous manner.
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Affiliation(s)
- Madhurima Jana
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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44
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Vorup-Jensen T. On the roles of polyvalent binding in immune recognition: perspectives in the nanoscience of immunology and the immune response to nanomedicines. Adv Drug Deliv Rev 2012; 64:1759-81. [PMID: 22705545 DOI: 10.1016/j.addr.2012.06.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Revised: 06/06/2012] [Accepted: 06/08/2012] [Indexed: 12/31/2022]
Abstract
Immunology often conveys the image of large molecules, either in the soluble state or in the membrane of leukocytes, forming multiple contacts with a target for actions of the immune system. Avidity names the ability of a polyvalent molecule to form multiple connections of the same kind with ligands tethered to the same surface. Polyvalent interactions are vastly stronger than their monovalent equivalent. In the present review, the functional consequences of polyvalent interactions are explored in a perspective of recent theoretical advances in understanding the thermodynamics of such binding. From insights on the structural biology of soluble pattern recognition molecules as well as adhesion molecules in the cell membranes or in their proteolytically shed form, this review documents the prominent role of polyvalent interactions in making the immune system a formidable barrier to microbial infection as well as constituting a significant challenge to the application of nanomedicines.
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45
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Biomimetic hydrogels for controlled biomolecule delivery to augment bone regeneration. Adv Drug Deliv Rev 2012; 64:1078-89. [PMID: 22465487 DOI: 10.1016/j.addr.2012.03.010] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2011] [Revised: 02/12/2012] [Accepted: 03/05/2012] [Indexed: 11/21/2022]
Abstract
The regeneration of large bone defects caused by trauma or disease remains a significant clinical problem. Although osteoinductive growth factors such as bone morphogenetic proteins have entered clinics, transplantation of autologous bone remains the gold standard to treat bone defects. The effective treatment of bone defects by protein therapeutics in humans requires quantities that exceed the physiological doses by several orders of magnitude. This not only results in very high treatment costs but also bears considerable risks for adverse side effects. These issues have motivated the development of biomaterials technologies allowing to better control biomolecule delivery from the solid phase. Here we review recent approaches to immobilize biomolecules by affinity binding or by covalent grafting to biomaterial matrices. We focus on biomaterials concepts that are inspired by extracellular matrix (ECM) biology and in particular the dynamic interaction of growth factors with the ECM. We highlight the value of synthetic, ECM-mimicking matrices for future technologies to study bone biology and develop the next generation of 'smart' implants.
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46
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Da Pozzo E, Barsotti MC, Bendinelli S, Martelli A, Calderone V, Balbarini A, Martini C, Di Stefano R. Differential effects of fondaparinux and bemiparin on angiogenic and vasculogenesis-like processes. Thromb Res 2012; 130:e113-22. [PMID: 22497885 DOI: 10.1016/j.thromres.2012.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 02/14/2012] [Accepted: 03/13/2012] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Conventional therapy for venous thromboembolism or acute coronary syndrome involves the administration of glycoanticoagulants (heparins) or oligosaccharides (fondaparinux). We evaluated the effects of such drugs on angiogenesis and vasculogenesis-like models. MATERIALS AND METHODS Human umbilical vein endothelial cells or human endothelial progenitor cells were treated with bemiparin, fondaparinux or unfractionated heparin, at concentrations reflecting the doses used in clinical practice. After 24h, cell viability, proliferation, tubule formation and angiogenic molecular mechanisms, such as activation of the serine/threonine kinase AKT, were assessed. In vivo angiogenesis was studied using a Matrigel sponge assay in mice. RESULTS Bemiparin gave a significant decrease of in vitro angiogenesis as shown by the reduction of endothelial cell tubule network, while both fondaparinux and unfractionated heparin did not show any significant effect. In assays of Matrigel sponge invasion in mice, unfractionated heparin was able to stimulate angiogenesis and, conversely, bemiparin inhibited angiogenesis. Furthermore, both bemiparin and fondaparinux caused a significant reduction in an in vitro vasculogenesis-like model, as demonstrated by the decrease of tubule network after co-seeding of endothelial progenitor cells and human umbilical vein endothelial cells. In addition, unfractionated heparin but not bemiparin was able to increase AKT phosphorylation. CONCLUSIONS In in vitro experiments, bemiparin was the only drug to show an anti-angiogenic and vasculogenic-like effect, unfractionated heparin showed only a trend to increase in angiogenesis assay and fondaparinux affected only the vasculogenesis-like model. Notably, the in vivo experiments corroborated these data. Such results are important for the choice of a patient-tailored therapy.
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Affiliation(s)
- Eleonora Da Pozzo
- Department of Psychiatry, Neurobiology, Pharmacology and Biotechnology, University of Pisa, Pisa, Italy.
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Kaushik S, Mohanty D, Surolia A. Molecular Dynamics Simulations onPars Intercerebralis MajorPeptide-C (PMP-C) Reveal the Role of Glycosylation and Disulfide Bonds in its Enhanced Structural Stability and Function. J Biomol Struct Dyn 2012; 29:905-20. [DOI: 10.1080/073911012010525026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Jana M, Bandyopadhyay S. Conformational flexibility of a protein-carbohydrate complex and the structure and ordering of surrounding water. Phys Chem Chem Phys 2012; 14:6628-38. [PMID: 22460826 DOI: 10.1039/c2cp24104h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein-carbohydrate non-covalent interactions are important to understand various biological processes in living organisms. One of the important issues in protein-carbohydrate binding is how the protein identifies the target carbohydrate and recognizes its conformational features. Surrounding water molecules are expected to play a critical role not only in mediating the recognition process but also in maintaining the structure of the complex. We carried out atomistic molecular dynamics (MD) simulations of an aqueous solution of the protein-carbohydrate complex formed between the hyaluronan binding domain (HABD) of the murine Cd44 protein and the octasaccharide hyaluronan (HA(8)). The conformational flexibilities of the protein and the carbohydrate, and the microscopic structure and ordering of water molecules around them in the complexed form have been explored. It is revealed that the formation of the complex is associated with significant immobilization of the monosaccharide units of the carbohydrate moiety that are involved in binding. Further, reduction in water densities around the binding residues of the two molecules in the complex with respect to their free forms clearly demonstrated that the recognition between the protein and the carbohydrate is facilitated by removal of a fraction of water molecules from regions around the binding domains.
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Affiliation(s)
- Madhurima Jana
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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Tian F, Lv Y, Yang L. Structure-based prediction of protein–protein binding affinity with consideration of allosteric effect. Amino Acids 2011; 43:531-43. [DOI: 10.1007/s00726-011-1101-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 09/21/2011] [Indexed: 11/28/2022]
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Gandhi NS, Freeman C, Parish CR, Mancera RL. Computational analyses of the catalytic and heparin-binding sites and their interactions with glycosaminoglycans in glycoside hydrolase family 79 endo-β-d-glucuronidase (heparanase). Glycobiology 2011; 22:35-55. [DOI: 10.1093/glycob/cwr095] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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