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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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Cortes-Medina M, Bushman AR, Beshay PE, Adorno JJ, Menyhert MM, Hildebrand RM, Agarwal SS, Avendano A, Friedman AK, Song JW. Chondroitin sulfate, dermatan sulfate, and hyaluronic acid differentially modify the biophysical properties of collagen-based hydrogels. Acta Biomater 2024; 174:116-126. [PMID: 38101556 PMCID: PMC10842894 DOI: 10.1016/j.actbio.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 11/30/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Fibrillar collagens and glycosaminoglycans (GAGs) are structural biomolecules that are natively abundant to the extracellular matrix (ECM). Prior studies have quantified the effects of GAGs on the bulk mechanical properties of the ECM. However, there remains a lack of experimental studies on how GAGs alter other biophysical properties of the ECM, including ones that operate at the length scales of individual cells such as mass transport efficiency and matrix microstructure. This study focuses on the GAG molecules chondroitin sulfate (CS), dermatan sulfate (DS), and hyaluronic acid (HA). CS and DS are stereoisomers while HA is the only non-sulfated GAG. We characterized and decoupled the effects of these GAG molecules on the stiffness, transport, and matrix microarchitecture properties of type I collagen hydrogels using mechanical indentation testing, microfluidics, and confocal reflectance imaging, respectively. We complement these biophysical measurements with turbidity assays to profile collagen aggregate formation. Surprisingly, only HA enhanced the ECM indentation modulus, while all three GAGs had no effect on hydraulic permeability. Strikingly, we show that CS, DS, and HA differentially regulate the matrix microarchitecture of hydrogels due to their alterations to the kinetics of collagen self-assembly. In addition to providing information on how GAGs define key physical properties of the ECM, this work shows new ways in which stiffness measurements, microfluidics, microscopy, and turbidity kinetics can be used complementarily to reveal details of collagen self-assembly and structure. STATEMENT OF SIGNIFICANCE: Collagen and glycosaminoglycans (GAGs) are integral to the structure, function, and bioactivity of the extracellular matrix (ECM). Despite widespread interest in collagen-GAG composite hydrogels, there is a lack of quantitative understanding of how different GAGs alter the biophysical properties of the ECM across tissue, cellular, and subcellular length scales. Here we show using mechanical, microfluidic, microscopy, and analytical methods and measurements that the GAG molecules chondroitin sulfate, dermatan sulfate, and hyaluronic acid differentially regulate the mechanical, transport, and microstructural properties of hydrogels due to their alterations to the kinetics of collagen self-assembly. As such, these results will inform improved design and utilization of collagen-based scaffolds of tailored composition, mechanical properties, molecular availability due to mass transport, and microarchitecture.
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Affiliation(s)
- Marcos Cortes-Medina
- Department of Biomedical Engineering, The Ohio State University, Columbus OH 43210, USA
| | - Andrew R Bushman
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus OH 43210, USA
| | - Peter E Beshay
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus OH 43210, USA
| | - Jonathan J Adorno
- Department of Biomedical Engineering, The Ohio State University, Columbus OH 43210, USA
| | - Miles M Menyhert
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus OH 43210, USA
| | - Riley M Hildebrand
- Department of Biomedical Engineering, The Ohio State University, Columbus OH 43210, USA
| | - Shashwat S Agarwal
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus OH 43210, USA
| | - Alex Avendano
- Department of Biomedical Engineering, The Ohio State University, Columbus OH 43210, USA
| | - Alicia K Friedman
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus OH 43210, USA
| | - Jonathan W Song
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus OH 43210, USA; The Comprehensive Cancer Center, The Ohio State University, Columbus OH 43210, USA.
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3
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Torres JE, Meng F, Bhattacharya S, Buno KP, Ahmadzadegan A, Madduri S, Babiak PM, Vlachos PP, Solorio L, Yeo Y, Liu JC. Interpenetrating Networks of Collagen and Hyaluronic Acid That Serve as In Vitro Tissue Models for Assessing Macromolecular Transport. Biomacromolecules 2023; 24:4718-4730. [PMID: 37651737 DOI: 10.1021/acs.biomac.3c00448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
High-fidelity preclinical in vitro tissue models can reduce the failure rate of drugs entering clinical trials. Collagen and hyaluronic acid (HA) are major components of the extracellular matrix of many native tissues and affect therapeutic macromolecule diffusion and recovery through tissues. Although collagen and HA are commonly used in tissue engineering, the physical and mechanical properties of these materials are variable and depend highly on processing conditions. In this study, HA was chemically modified and crosslinked via hydrazone bonds to form interpenetrating networks of crosslinked HA (HAX) with collagen (Col). These networks enabled a wide range of mechanical properties, including stiffness and swellability, and microstructures, such as pore morphology and size, that can better recapitulate diverse tissues. We utilized these interpenetrating ColHAX hydrogels as in vitro tissue models to examine macromolecular transport and recovery for early-stage drug screening. Hydrogel formulations with varying collagen and HAX concentrations imparted different gel properties based on the ratio of collagen to HAX. These gels were stable and swelled up to 170% of their original mass, and the storage moduli of the ColHAX gels increased over an order of magnitude by increasing collagen and HA concentration. Interestingly, when HAX concentration was constant and collagen concentration increased, both the pore size and spatial colocalization of collagen and HA increased. HA in the system dominated the ζ-potentials of the gels. The hydrogel and macromolecule properties impacted the mass transport and recovery of lysozyme, β-lactoglobulin, and bovine serum albumin (BSA) from the ColHAX gels─large molecules were largely impacted by mesh size, whereas small molecules were influenced primarily by electrostatic forces. Overall, the tunable properties demonstrated by the ColHAX hydrogels can be used to mimic different tissues for early-stage assays to understand drug transport and its relationship to matrix properties.
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Affiliation(s)
- Jessica E Torres
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Fanfei Meng
- Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sayantan Bhattacharya
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Kevin P Buno
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Adib Ahmadzadegan
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sathvik Madduri
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Paulina M Babiak
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Pavlos P Vlachos
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Luis Solorio
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yoon Yeo
- Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Julie C Liu
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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4
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Danielsson A, Samsonov SA, Liwo A, Sieradzan AK. Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin. J Chem Theory Comput 2023; 19:6023-6036. [PMID: 37587433 PMCID: PMC10500997 DOI: 10.1021/acs.jctc.3c00511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Indexed: 08/18/2023]
Abstract
Heparin is an unbranched periodic polysaccharide composed of negatively charged monomers and involved in key biological processes, including anticoagulation, angiogenesis, and inflammation. Its structure and dynamics have been studied extensively using experimental as well as theoretical approaches. The conventional approach of computational chemistry applied to the analysis of biomolecules is all-atom molecular dynamics, which captures the interactions of individual atoms by solving Newton's equation of motion. An alternative is molecular dynamics simulations using coarse-grained models of biomacromolecules, which offer a reduction of the representation and consequently enable us to extend the time and size scale of simulations by orders of magnitude. In this work, we extend the UNIfied COarse-gRaiNed (UNICORN) model of biological macromolecules developed in our laboratory to heparin. We carried out extensive tests to estimate the optimal weights of energy terms of the effective energy function as well as the optimal Debye-Hückel screening factor for electrostatic interactions. We applied the model to study unbound heparin molecules of polymerization degree ranging from 6 to 68 residues. We compare the obtained coarse-grained heparin conformations with models obtained from X-ray diffraction studies of heparin. The SUGRES-1P force field was able to accurately predict the general shape and global characteristics of heparin molecules.
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Affiliation(s)
- Annemarie Danielsson
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Sergey A. Samsonov
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam Liwo
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam K. Sieradzan
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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5
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Shakibi S, Onck PR, Van der Giessen E. A One-Bead-Per-Saccharide (1BPS) Model for Glycosaminoglycans. J Chem Theory Comput 2023; 19:5491-5502. [PMID: 37459601 PMCID: PMC10448712 DOI: 10.1021/acs.jctc.3c00238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Indexed: 08/23/2023]
Abstract
Glycosaminoglycans (GAGs) are polysaccharide compounds that play key roles in various biological processes. GAGs are important structural components of cartilage and the extracellular matrix of the brain. Due to the large size of these polysaccharides, coarse-grained approaches are indispensable for modeling these biopolymers. We develop a one-bead-per-saccharide model of chondroitin sulfates and hyaluronic acid based on an existing three-bead-per-saccharide coarse-grained model. Our coarse graining is carried out by using iterative Boltzmann inversion (IBI), including an additional coupling potential to incorporate the correlation between dihedral angles. The predictions of the model are verified against those of the existing three-bead-per-saccharin model and the experimental radius of gyration for hyaluronic acid.
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Affiliation(s)
- Saber Shakibi
- Micromechanics of Materials, Zernike
Institute for Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
| | - Patrick R. Onck
- Micromechanics of Materials, Zernike
Institute for Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
| | - Erik Van der Giessen
- Micromechanics of Materials, Zernike
Institute for Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
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6
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Cortes-Medina M, Bushman AR, Beshay PE, Adorno JJ, Menyhert MM, Hildebrand RM, Agarwal SS, Avendano A, Song JW. Chondroitin sulfate, dermatan sulfate, and hyaluronic acid differentially modify the biophysical properties of collagen-based hydrogels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541626. [PMID: 37293049 PMCID: PMC10245839 DOI: 10.1101/2023.05.22.541626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fibrillar collagens and glycosaminoglycans (GAGs) are structural biomolecules that are natively abundant to the extracellular matrix (ECM). Prior studies have quantified the effects of GAGs on the bulk mechanical properties of the ECM. However, there remains a lack of experimental studies on how GAGs alter other biophysical properties of the ECM, including ones that operate at the length scales of individual cells such as mass transport efficiency and matrix microstructure. Here we characterized and decoupled the effects of the GAG molecules chondroitin sulfate (CS) dermatan sulfate (DS) and hyaluronic acid (HA) on the stiffness (indentation modulus), transport (hydraulic permeability), and matrix microarchitecture (pore size and fiber radius) properties of collagen-based hydrogels. We complement these biophysical measurements of collagen hydrogels with turbidity assays to profile collagen aggregate formation. Here we show that CS, DS, and HA differentially regulate the biophysical properties of hydrogels due to their alterations to the kinetics of collagen self-assembly. In addition to providing information on how GAGs play significant roles in defining key physical properties of the ECM, this work shows new ways in which stiffness measurements, microscopy, microfluidics, and turbidity kinetics can be used complementary to reveal details of collagen self-assembly and structure.
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Affiliation(s)
- Marcos Cortes-Medina
- Department of Biomedical Engineering, The Ohio State University, Columbus OH 43210
| | - Andrew R Bushman
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus OH 43210
| | - Peter E Beshay
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus OH 43210
| | - Jonathan J Adorno
- Department of Biomedical Engineering, The Ohio State University, Columbus OH 43210
| | - Miles M Menyhert
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus OH 43210
| | - Riley M Hildebrand
- Department of Biomedical Engineering, The Ohio State University, Columbus OH 43210
| | - Shashwat S Agarwal
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus OH 43210
| | - Alex Avendano
- Department of Biomedical Engineering, The Ohio State University, Columbus OH 43210
| | - Jonathan W Song
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus OH 43210
- The Comprehensive Cancer Center, The Ohio State University, Columbus OH 43210
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7
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Dubrovin EV, Barinov NA, Ivanov DA, Klinov DV. Single-molecule AFM study of hyaluronic acid softening in electrolyte solutions. Carbohydr Polym 2023; 303:120472. [PMID: 36657830 DOI: 10.1016/j.carbpol.2022.120472] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/30/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Investigation of hyaluronic acid (HA) morphology and mechanical properties at a single-molecule level is important for the development of HA based biomaterials. We have developed the atomic force microscopy (AFM) based approach for quantitative characterization of conformation of HA molecules. HA molecules adsorbed on a modified graphitic surface form oriented linear segments. Conformation of HA molecules can be considered as two-dimensional quasi-projection of a three-dimensional conformation locally straightened by a substrate. The persistence length and Young's modulus of biomolecules estimated using wormlike chain model decrease from 15.7 to 9.9 nm, and from ∼21 to ∼13 GPa, respectively, when KCl concentration increases from 0 to 100 mM. The dependence of the persistence length on ionic strength supports the Odijk-Skolnick-Fixman model of polyelectrolyte stiffening in electrolyte solution. The obtained results represent a new insight into the conformation and mechanical characteristics of HA molecules and complement the characterization of this biopolymer by bulk methods.
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Affiliation(s)
- Evgeniy V Dubrovin
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation; Lomonosov Moscow State University, Leninskie Gory 1 bld. 2, 119991 Moscow, Russian Federation.
| | - Nikolay A Barinov
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation.
| | - Dmitry A Ivanov
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Institut de Sciences des Matériaux de Mulhouse - IS2M, CNRS UMR7361, 15 Jean Starcky, Mulhouse 68057, France.
| | - Dmitry V Klinov
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation.
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8
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Hanssen KØ, Malthe-Sørenssen A. Perineuronal nets restrict transport near the neuron surface: A coarse-grained molecular dynamics study. Front Comput Neurosci 2022; 16:967735. [DOI: 10.3389/fncom.2022.967735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022] Open
Abstract
Perineuronal nets (PNNs) are mesh-like extracellular matrix structures that wrap around certain neurons in the central nervous system. They are hypothesized to stabilize memories in the brain and act as a barrier between cell and extracellular space. As a means to study the impact of PNNs on diffusion, the nets were approximated by negatively charged polymer brushes and simulated by coarse-grained molecular dynamics. Diffusion constants of single neutral and single charged particles were obtained in directions parallel and perpendicular to the brush substrate. The results for the neutral particle were compared to different theories of diffusion in a heuristic manner. Diffusion was found to be considerably reduced for brush spacings smaller than 10 nm, with a pronounced anisotropy for dense brushes. The exact dynamics of the chains was found to have a negligible impact on particle diffusion. The resistance of the brush proved small compared to typical values of the membrane resistance of a neuron, indicating that PNNs likely contribute little to the total resistance of an enwrapped neuron.
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9
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Guvench O. Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes. Molecules 2022; 27:7276. [PMID: 36364098 PMCID: PMC9658939 DOI: 10.3390/molecules27217276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/28/2023] Open
Abstract
This review summarizes the atomic-resolution structural biology of hyaluronan and its complexes available in the Protein Data Bank, as well as published studies of atomic-resolution explicit-solvent molecular dynamics simulations on these and other hyaluronan and hyaluronan-containing systems. Advances in accurate molecular mechanics force fields, simulation methods and software, and computer hardware have supported a recent flourish in such simulations, such that the simulation publications now outnumber the structural biology publications by an order of magnitude. In addition to supplementing the experimental structural biology with computed dynamic and thermodynamic information, the molecular dynamics studies provide a wealth of atomic-resolution information on hyaluronan-containing systems for which there is no atomic-resolution structural biology either available or possible. Examples of these summarized in this review include hyaluronan pairing with other hyaluronan molecules and glycosaminoglycans, with ions, with proteins and peptides, with lipids, and with drugs and drug-like molecules. Despite limitations imposed by present-day computing resources on system size and simulation timescale, atomic-resolution explicit-solvent molecular dynamics simulations have been able to contribute significant insight into hyaluronan's flexibility and capacity for intra- and intermolecular non-covalent interactions.
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Affiliation(s)
- Olgun Guvench
- Department of Pharmaceutical Sciences and Administration, School of Pharmacy, Westbrook College of Health Professions, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA
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10
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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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11
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Hanson P, Arkill KP, Merry CL, Hussain MS, Meersmann T, Randeva HS, Pavlovskaya GE, O'Hare P, Barber TM. Novel perspectives of sodium handling in type 2 diabetes mellitus. Expert Rev Endocrinol Metab 2022; 17:333-341. [PMID: 35729865 DOI: 10.1080/17446651.2022.2092094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/16/2022] [Indexed: 12/07/2022]
Abstract
INTRODUCTION As a key regulator of body water, sodium homeostasis forms an essential component of human physiology. Type 2 Diabetes Mellitus (T2D)-associated sodium overload stems from chronic renal retention of sodium, contributing toward the development of adverse cardiovascular sequelae. AREAS COVERED Our traditional model of sodium regulation invokes two compartments: extracellular fluid (ECF [plasma and interstitial fluid]) and intracellular fluid (ICF). Data from the Mars program reveal inconsistencies with this two-space model, including mismatches between net body sodium and water. Recent data utilizing 23Na magnetic resonance imaging (MRI) show a preponderance of bound sodium within human dermis, consistent with a third space repository and providing compelling evidence to support a three-space model in which dermal sodium binding facilitates sodium homeostasis within the ECF and ICF. This buffer is impaired in T2D, with diminishment of dermal bound sodium that may promote deleterious sequelae of sodium overload within the ECF and ICF. EXPERT OPINION Future studies should focus on novel therapeutic opportunities for sodium regulation in T2D and other conditions of sodium dysregulation. The ratio of free:bound dermal sodium (reflecting sodium storage capacity) could be utilized as a clinical biomarker for salt and water balance, to improve diagnostic accuracy and facilitate clinical decision-making.
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Affiliation(s)
- Petra Hanson
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism, University Hospitals Coventry and Warwickshire, Coventry, UK
| | - Kenton P Arkill
- Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | | | - Mohammed S Hussain
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism, University Hospitals Coventry and Warwickshire, Coventry, UK
| | - Thomas Meersmann
- Sir Peter Mansfield Imaging Centre, University of Nottingham, Nottingham, UK
- Nottingham NIHR Biomedical Research Centre, Nottingham, UK
| | - Harpal S Randeva
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism, University Hospitals Coventry and Warwickshire, Coventry, UK
| | - Galina E Pavlovskaya
- Sir Peter Mansfield Imaging Centre, University of Nottingham, Nottingham, UK
- Nottingham NIHR Biomedical Research Centre, Nottingham, UK
| | - Paul O'Hare
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism, University Hospitals Coventry and Warwickshire, Coventry, UK
| | - Thomas M Barber
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism, University Hospitals Coventry and Warwickshire, Coventry, UK
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12
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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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13
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Rivas F, DeAngelis PL, Rahbar E, Hall AR. Optimizing the sensitivity and resolution of hyaluronan analysis with solid-state nanopores. Sci Rep 2022; 12:4469. [PMID: 35296752 PMCID: PMC8927330 DOI: 10.1038/s41598-022-08533-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
Hyaluronan (HA) is an essential carbohydrate in vertebrates that is a potentially robust bioindicator due to its critical roles in diverse physiological functions in health and disease. The intricate size-dependent function that exists for HA and its low abundance in most biological fluids have highlighted the need for sensitive technologies to provide accurate and quantitative assessments of polysaccharide molecular weight and concentration. We have demonstrated that solid state (SS-) nanopore technology can be exploited for this purpose, given its molecular sensitivity and analytical capacity, but there remains a need to further understand the impacts of experimental variables on the SS-nanopore signal for optimal interpretation of results. Here, we use model quasi-monodisperse HA polymers to determine the dependence of HA signal characteristics on a range of SS-nanopore measurement conditions, including applied voltage, pore diameter, and ionic buffer asymmetry. Our results identify important factors for improving the signal-to-noise ratio, resolution, and sensitivity of HA analysis with SS-nanopores.
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Affiliation(s)
- Felipe Rivas
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA
| | - Paul L DeAngelis
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma, OK, 73104, USA
| | - Elaheh Rahbar
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA
| | - Adam R Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA. .,Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
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14
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Banerjee A, De R, Das B. Hydrodynamic and conformational characterization of aqueous sodium alginate solutions with varying salinity. Carbohydr Polym 2022; 277:118855. [PMID: 34893264 DOI: 10.1016/j.carbpol.2021.118855] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/18/2022]
Abstract
Insight into the role of electrostatic interactions on the hydrodynamics and conformation of aqueous sodium alginate was gained through viscometry. Alginate chains are found to shrink in salt-free solutions more rapidly with increasing polymer concentration compared to salt-solutions. For salt-free solutions, a reduced polymer concentration of less than 1 suffices to make the alginate coil volume half of that at infinite dilution which becomes invariant when the reduced concentration exceeds 8. In saline media having salt concentration greater than 0.1 mol·L-1, the chains become more flexible, caused by the shielding of intra-chain repulsions. The chains effectively reached unperturbed state when the added salt concentration becomes ≥0.5 mol·L-1. Alginate chains are shown to remain stiff up to about 8-10 monomers within the investigated temperature range. This study explores the possible modification of the individual chain behavior induced by the neighboring chains or by the variation of temperature.
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Affiliation(s)
- Arnab Banerjee
- Department of Chemistry, Presidency University, Kolkata 700 073, India
| | - Ranjit De
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Bijan Das
- Department of Chemistry, Presidency University, Kolkata 700 073, India.
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15
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Lin W, Goldberg R, Klein J. Poly-phosphocholination of liposomes leads to highly-extended retention time in mice joints. J Mater Chem B 2022; 10:2820-2827. [PMID: 35099493 PMCID: PMC9007059 DOI: 10.1039/d1tb02346b] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Surface-attached layers of phosphatidylcholine (PC) lipid vesicles (liposomes) may reduce the friction coefficient μ (= force-to-slide/load) between the sliding surfaces down to μ ≈ 10−3–10−4 up to tens of atm contact pressures, as high as those in the major joints (hips or knees). Such friction reduction is attributed to hydration lubrication by the highly-hydrated phosphocholine head-groups exposed at the outer vesicle surfaces. It has been suggested therefore that intra-articular (IA) administration of liposomes as potential boundary lubricants may alleviate degenerative, friction-associated joint conditions such as osteoarthritis (OA), which is associated with insufficient lubrication at the articular cartilage surface. To overcome the problem, common to all nanoparticles, of rapid removal by the mononuclear phagocyte system, as well as to ensure long-term colloidal stability during storage, functionalizing liposomes with poly(ethylene glycol) moieties, PEGylation, is often used. Here we describe a different liposome functionalization approach, using poly(2-methacryloyloxyethyl phosphorylcholine), PMPC, moieties (strictly, lipid–PMPC conjugates), and compare the retention time in mice joints of such PMPCylated liposomes with otherwise-identical but PEGylated vesicles following IA administration. We find, using fluorescence labeling and in vivo optical imaging, that when PMPC-stabilized liposomes are injected into mice knee joints, there is a massive increase of the vesicles’ retention half-life in the joints of about (4–5)-fold (ca. 300–400% increase in retention time) compared with the PEGylated liposomes (and some 100-fold longer than the retention time of intra-articularly injected hyaluronan or HA). Such PMPCylated liposomes are therefore promising candidates as potential long-lived boundary lubricants at the articular cartilage surface, with implication for friction-associated pathologies. Moreover, as lipid vesicles are well known to be efficient drug carriers, such long retention in the joints may enable analgesic or anti-inflammatory agents for joint pathologies to be more efficiently delivered via IA administration using PMPCylated liposomal vehicles relative to PEGylated ones. PMPCylated liposomes injected into mice joints show a massive increase in retention half-life compared with PEGylated liposomes (or hyaluronan, HA), making them promising candidates as boundary lubricants at articular cartilage, or as drug carriers.![]()
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Affiliation(s)
- Weifeng Lin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Ronit Goldberg
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Jacob Klein
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel.
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16
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Dhamankar S, Webb MA. Chemically specific coarse‐graining of polymers: Methods and prospects. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210555] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Satyen Dhamankar
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
| | - Michael A. Webb
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
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17
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Liwo A, Czaplewski C, Sieradzan AK, Lipska AG, Samsonov SA, Murarka RK. Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems. Biomolecules 2021; 11:1347. [PMID: 34572559 PMCID: PMC8465211 DOI: 10.3390/biom11091347] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022] Open
Abstract
Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and the potential of mean force is the physical basis of the coarse-grained force fields. Moreover, the choice of coarse-grained variables and the fact that coarse-grained sites often do not have spherical symmetry implies a non-diagonal inertia tensor. We describe selected coarse-grained models used in molecular dynamics simulations, including the most popular MARTINI model developed by Marrink's group and the UNICORN model of biological macromolecules developed in our laboratory. We conclude by discussing examples of the application of coarse-grained molecular dynamics to study biologically important processes.
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Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Agnieszka G. Lipska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Sergey A. Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Rajesh K. Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, MP, India;
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18
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Guvench O, Whitmore EK. Sulfation and Calcium Favor Compact Conformations of Chondroitin in Aqueous Solutions. ACS OMEGA 2021; 6:13204-13217. [PMID: 34056470 PMCID: PMC8158799 DOI: 10.1021/acsomega.1c01071] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/28/2021] [Indexed: 06/01/2023]
Abstract
The effects of sulfation and calcium cations (Ca2+) on the atomic-resolution conformational properties of chondroitin carbohydrate polymers in aqueous solutions are not well studied owing to experimental challenges. Here, we compare all-atom explicit-solvent molecular dynamics simulations results for pairs of O-type (nonsulfated) and A-type (GlcNAc 4-O-sulfated) chondroitin 20-mers in 140 mM NaCl with and without Ca2+ and find that both sulfation and Ca2+ favor more compact polymer conformations. We also show that subtle differences in force-field parametrization can have dramatic effects on Ca2+ binding to chondroitin carboxylate and sulfate functional groups and thereby determine Ca2+-mediated intra- and interstrand association. In addition to providing an atomic-resolution picture of the interaction of Ca2+ with sulfated and nonsulfated chondroitin polymers, the molecular dynamics data emphasize the importance of careful force-field parametrization to balance ion-water and ion-chondroitin interactions and suggest additional parametrization efforts to tune interactions involving sulfate.
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Affiliation(s)
- Olgun Guvench
- Department
of Pharmaceutical Sciences and Administration, School of Pharmacy, Westbrook College of Health Professions, University
of New England, 716 Stevens
Avenue, Portland, Maine 04103, United States
- Graduate
School of Biomedical Science and Engineering, University of Maine, 5775 Stodder Hall, Orono, Maine 04469, United
States
| | - Elizabeth K. Whitmore
- Department
of Pharmaceutical Sciences and Administration, School of Pharmacy, Westbrook College of Health Professions, University
of New England, 716 Stevens
Avenue, Portland, Maine 04103, United States
- Graduate
School of Biomedical Science and Engineering, University of Maine, 5775 Stodder Hall, Orono, Maine 04469, United
States
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19
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Künze G, Huster D, Samsonov SA. Investigation of the structure of regulatory proteins interacting with glycosaminoglycans by combining NMR spectroscopy and molecular modeling - the beginning of a wonderful friendship. Biol Chem 2021; 402:1337-1355. [PMID: 33882203 DOI: 10.1515/hsz-2021-0119] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/09/2021] [Indexed: 11/15/2022]
Abstract
The interaction of regulatory proteins with extracellular matrix or cell surface-anchored glycosaminoglycans (GAGs) plays important roles in molecular recognition, wound healing, growth, inflammation and many other processes. In spite of their high biological relevance, protein-GAG complexes are significantly underrepresented in structural databases because standard tools for structure determination experience difficulties in studying these complexes. Co-crystallization with subsequent X-ray analysis is hampered by the high flexibility of GAGs. NMR spectroscopy experiences difficulties related to the periodic nature of the GAGs and the sparse proton network between protein and GAG with distances that typically exceed the detection limit of nuclear Overhauser enhancement spectroscopy. In contrast, computer modeling tools have advanced over the last years delivering specific protein-GAG docking approaches successfully complemented with molecular dynamics (MD)-based analysis. Especially the combination of NMR spectroscopy in solution providing sparse structural constraints with molecular docking and MD simulations represents a useful synergy of forces to describe the structure of protein-GAG complexes. Here we review recent methodological progress in this field and bring up examples where the combination of new NMR methods along with cutting-edge modeling has yielded detailed structural information on complexes of highly relevant cytokines with GAGs.
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Affiliation(s)
- Georg Künze
- Center for Structural Biology, Vanderbilt University, 465 21st Ave S, 5140 MRB3, Nashville, TN37240, USA.,Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN37235, USA.,Institute for Drug Discovery, University of Leipzig, Brüderstr. 34, D-04103Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107Leipzig, Germany
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Ul. Wita Stwosza 63, 80-308Gdańsk, Poland
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20
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Bewley MC, Gautam L, Jagadeeshaprasad MG, Gowda DC, Flanagan JM. Molecular architecture and domain arrangement of the placental malaria protein VAR2CSA suggests a model for carbohydrate binding. J Biol Chem 2020; 295:18589-18603. [PMID: 33122198 PMCID: PMC7939466 DOI: 10.1074/jbc.ra120.014676] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/13/2020] [Indexed: 11/29/2022] Open
Abstract
VAR2CSA is the placental-malaria-specific member of the antigenically variant Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family. It is expressed on the surface of Plasmodium falciparum-infected host red blood cells and binds to specific chondroitin-4-sulfate chains of the placental proteoglycan receptor. The functional ∼310 kDa ectodomain of VAR2CSA is a multidomain protein that requires a minimum 12-mer chondroitin-4-sulfate molecule for specific, high affinity receptor binding. However, it is not known how the individual domains are organized and interact to create the receptor-binding surface, limiting efforts to exploit its potential as an effective vaccine or drug target. Using small angle X-ray scattering and single particle reconstruction from negative-stained electron micrographs of the ectodomain and multidomain constructs, we have determined the structural architecture of VAR2CSA. The relative locations of the domains creates two distinct pores that can each accommodate the 12-mer of chondroitin-4-sulfate, suggesting a model for receptor binding. This model has important implications for understanding cytoadherence of infected red blood cells and potentially provides a starting point for developing novel strategies to prevent and/or treat placental malaria.
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Affiliation(s)
- Maria C Bewley
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Lovely Gautam
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Mashanipalya G Jagadeeshaprasad
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - D Channe Gowda
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA.
| | - John M Flanagan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA.
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21
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Singhal A, Schneible JD, Lilova RL, Hall CK, Menegatti S, Grafmüller A. A multiscale coarse-grained model to predict the molecular architecture and drug transport properties of modified chitosan hydrogels. SOFT MATTER 2020; 16:10591-10610. [PMID: 33156313 DOI: 10.1039/d0sm01243b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hydrogels constructed with functionalized polysaccharides are of interest in a multitude of applications, chiefly the design of therapeutic and regenerative formulations. Tailoring the chemical modification of polysaccharide-based hydrogels to achieve specific drug release properties involves the optimization of many tunable parameters, including (i) the type, degree (χ), and pattern of the functional groups, (ii) the water-polymer ratio, and (iii) the drug payload. To guide the design of modified polysaccharide hydrogels for drug release, we have developed a computational toolbox that predicts the structure and physicochemical properties of acylated chitosan chains, and their impact on the transport of drug molecules. Herein, we present a multiscale coarse-grained model to investigate the structure of networks of chitosan chains modified with acetyl, butanoyl, or heptanoyl moieties, as well as the diffusion of drugs doxorubicin (Dox) and gemcitabine (Gem) through the resulting networks. The model predicts the formation of different network structures, in particular the hydrophobically-driven transition from a uniform to a cluster/channel morphology and the formation of fibers of chitin chains. The model also describes the impact of structural and physicochemical properties on drug transport, which was confirmed experimentally by measuring Dox and Gem diffusion through an ensemble of modified chitosan hydrogels.
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Affiliation(s)
- Ankush Singhal
- Department of Theory and Biosystems, Max Planck Institute for Colloids and Interfaces, Potsdam 14476, Germany.
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22
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Hempel C, Kapishnikov S, Perez-Berna AJ, Werner S, Guttmann P, Pereiro E, Qvortrup K, Andresen TL. The need to freeze-Dehydration during specimen preparation for electron microscopy collapses the endothelial glycocalyx regardless of fixation method. Microcirculation 2020; 27:e12643. [PMID: 32542908 DOI: 10.1111/micc.12643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/25/2020] [Accepted: 06/06/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVE The endothelial glycocalyx covers the luminal surface of the endothelium and plays key roles in vascular function. Despite its biological importance, ideal visualization techniques are lacking. The current study aimed to improve the preservation and subsequent imaging quality of the endothelial glycocalyx. METHODS In mice, the endothelial glycocalyx was contrasted with a mixture of lanthanum and dysprosium (LaDy). Standard chemical fixation was compared with high-pressure frozen specimens processed with freeze substitution. Also, isolated brain microvessels and cultured endothelial cells were high-pressure frozen and by transmission soft x-rays, imaged under cryogenic conditions. RESULTS The endothelial glycocalyx was in some tissues significantly more voluminous from chemically fixed specimens compared with high-pressure frozen specimens. LaDy labeling introduced excessive absorption contrast, which impeded glycocalyx measurements in isolated brain microvessels when using transmission soft x-rays. In non-contrasted vessels, the glycocalyx was not resolved. LaDy-contrasted, cultured brain endothelial cells allowed to assess glycocalyx volume in vitro. CONCLUSIONS Both chemical and cryogenic fixation followed by dehydration lead to substantial collapse of the glycocalyx. Cryogenic fixation without freeze substitution could be a way forward although transmission soft x-ray tomography based solely on amplitude contrast seems unsuitable.
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Affiliation(s)
- Casper Hempel
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.,Centre for Medical Parasitology, Department for Clinical Microbiology, Copenhagen University Hospital, Copenhagen, Denmark.,Department for Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Kapishnikov
- Department X-Ray microscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany.,Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Stephan Werner
- Department X-Ray microscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
| | - Peter Guttmann
- Department X-Ray microscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
| | - Eva Pereiro
- MISTRAL Beamline-Experiments Division, ALBA Synchrotron Light Source, Barcelona, Spain
| | - Klaus Qvortrup
- Core Facility for Integrated Microscopy (CFIM), University of Copenhagen, Copenhagen, Denmark
| | - Thomas Lars Andresen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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23
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Graham AJ, Dundas CM, Hillsley A, Kasprak DS, Rosales AM, Keitz BK. Genetic Control of Radical Cross-linking in a Semisynthetic Hydrogel. ACS Biomater Sci Eng 2020; 6:1375-1386. [PMID: 33313392 DOI: 10.1021/acsbiomaterials.9b01773] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Enhancing materials with the qualities of living systems, including sensing, computation, and adaptation, is an important challenge in designing next-generation technologies. Living materials address this challenge by incorporating live cells as actuating components that control material function. For abiotic materials, this requires new methods that couple genetic and metabolic processes to material properties. Toward this goal, we demonstrate that extracellular electron transfer (EET) from Shewanella oneidensis can be leveraged to control radical cross-linking of a methacrylate-functionalized hyaluronic acid hydrogel. Cross-linking rates and hydrogel mechanics, specifically storage modulus, were dependent on various chemical and biological factors, including S. oneidensis genotype. Bacteria remained viable and metabolically active in the networks for a least 1 week, while cell tracking revealed that EET genes also encode control over hydrogel microstructure. Moreover, construction of an inducible gene circuit allowed transcriptional control of storage modulus and cross-linking rate via the tailored expression of a key electron transfer protein, MtrC. Finally, we quantitatively modeled hydrogel stiffness as a function of steady-state mtrC expression and generalized this result by demonstrating the strong relationship between relative gene expression and material properties. This general mechanism for radical cross-linking provides a foundation for programming the form and function of synthetic materials through genetic control over extracellular electron transfer.
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Affiliation(s)
- Austin J Graham
- McKetta Department of Chemical Engineering and Center for Dynamics and Control of Materials, University of Texas at Austin, Austin, Texas 78712, United States
| | - Christopher M Dundas
- McKetta Department of Chemical Engineering and Center for Dynamics and Control of Materials, University of Texas at Austin, Austin, Texas 78712, United States
| | - Alexander Hillsley
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Dain S Kasprak
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Adrianne M Rosales
- McKetta Department of Chemical Engineering and Center for Dynamics and Control of Materials, University of Texas at Austin, Austin, Texas 78712, United States
| | - Benjamin K Keitz
- McKetta Department of Chemical Engineering and Center for Dynamics and Control of Materials, University of Texas at Austin, Austin, Texas 78712, United States
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24
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Santos FM, Barbosa PC, Pereira RF, Silva MM, Gonçalves HM, Nunes SC, Figueiredo FL, Valente AJ, de Zea Bermudez V. Proton conducting electrolytes composed of chondroitin sulfate polysaccharide and citric acid. Eur Polym J 2020. [DOI: 10.1016/j.eurpolymj.2019.109453] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Chondroitin-Sulfate-A-Coated Magnetite Nanoparticles: Synthesis, Characterization and Testing to Predict Their Colloidal Behavior in Biological Milieu. Int J Mol Sci 2019; 20:ijms20174096. [PMID: 31443385 PMCID: PMC6747333 DOI: 10.3390/ijms20174096] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 12/23/2022] Open
Abstract
Biopolymer coated magnetite nanoparticles (MNPs) are suitable to fabricate biocompatible magnetic fluid (MF). Their comprehensive characterization, however, is a necessary step to assess whether bioapplications are feasible before expensive in vitro and in vivo tests. The MNPs were prepared by co-precipitation, and after careful purification, they were coated by chondroitin-sulfate-A (CSA). CSA exhibits high affinity adsorption to MNPs (H-type isotherm). We could only make stable MF of CSA coated MNPs (CSA@MNPs) under accurate conditions. The CSA@MNP was characterized by TEM (size ~10 nm) and VSM (saturation magnetization ~57 emu/g). Inner-sphere metal–carboxylate complex formation between CSA and MNP was proved by FTIR-ATR and XPS. Electrophoresis and DLS measurements show that the CSA@MNPs at CSA-loading > 0.2 mmol/g were stable at pH > 4. The salt tolerance of the product improved up to ~0.5 M NaCl at pH~6.3. Under favorable redox conditions, no iron leaching from the magnetic core was detected by ICP measurements. Thus, the characterization predicts both chemical and colloidal stability of CSA@MNPs in biological milieu regarding its pH and salt concentration. MTT assays showed no significant impact of CSA@MNP on the proliferation of A431 cells. According to these facts, the CSA@MNPs have a great potential in biocompatible MF preparation for medical applications.
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26
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Samsonov SA, Lubecka EA, Bojarski KK, Ganzynkowicz R, Liwo A. Local and long range potentials for heparin‐protein systems for coarse‐grained simulations. Biopolymers 2019; 110:e23269. [DOI: 10.1002/bip.23269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 12/31/2022]
Affiliation(s)
| | - Emilia A. Lubecka
- Faculty of ChemistryUniversity of Gdańsk Gdańsk Poland
- Faculty of Mathematics, Physics and Informatics, Institute of InformaticsUniversity of Gdańsk Gdańsk Poland
| | | | | | - Adam Liwo
- Faculty of ChemistryUniversity of Gdańsk Gdańsk Poland
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27
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Nagarajan B, Sankaranarayanan NV, Desai UR. Perspective on computational simulations of glycosaminoglycans. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2019; 9:e1388. [PMID: 31080520 PMCID: PMC6504973 DOI: 10.1002/wcms.1388] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/07/2018] [Indexed: 01/06/2023]
Abstract
Glycosaminoglycans (GAGs) represent a formidable frontier for chemists, biochemists, biologists, medicinal chemists and drug delivery specialists because of massive structural complexity. GAGs are arguably the most complex, natural linear biopolymers with theoretical diversity orders of magnitude higher than proteins and nucleic acids. Yet, this diversity remains generally untapped. Computational approaches offer major routes to understand GAG structure and dynamics so as to enable novel applications of these biopolymers. In fact, computational algorithms, softwares, online tools and techniques have reached a level of sophistication that help understand atomistic details of conformational variation and protein recognition of individual GAG sequences. This review describes current approaches and challenges in computational study of GAGs. It presents a history of major findings since the earliest mention of GAGs (the 1960s), the development of parameters and force fields specific for GAGs, and the application of these tools in understanding GAG structure-function relationship. This review also presents a section on how to perform simulation of GAGs, which is directed toward researchers interested in entering this promising field with potential to impact therapy.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- 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 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
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Sparks HD, Anjum F, Vallmajo-Martin Q, Ehrbar M, Abbasi S, Kallos MS, Biernaskie J. Flowable Polyethylene Glycol Hydrogels Support the in Vitro Survival and Proliferation of Dermal Progenitor Cells in a Mechanically Dependent Manner. ACS Biomater Sci Eng 2019; 5:950-958. [PMID: 33405787 DOI: 10.1021/acsbiomaterials.8b01294] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cell-based therapies have garnered considerable interest largely because of their potential utility for tissue regeneration in a variety of organs, including skin. Designing vehicles that enable optimal delivery and purposeful integration of donor cells within tissues will be critical for their success. Here, we investigate the utility of an injectable, self-polymerizing, fully synthetic hydrogel in supporting the survival, proliferation, and function of cultured adult dermal progenitor cells (DPCs) which may serve as a source of renewable cells to repair severe skin injuries or restore hair growth. We show that modifying the stiffness of these transglutaminase cross-linked poly(ethylene glycol) (TG-PEG) hydrogels significantly alters DPC behavior and phenotype; increasing stiffness promotes their differentiation and migration whereas softer gels maintained them in a proliferative state. We found that 2-3% TG-PEG was optimal to promote cell expansion and survival. Unexpectedly, DPCs grown in all conditions maintained their inductive function and thus generated de novo hair follicles. Our data suggests that TG-PEG hydrogels may be a versatile platform for stem and progenitor cell transplantation and fate specification while maintaining functional competence.
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Affiliation(s)
| | | | - Queralt Vallmajo-Martin
- Department of Obstetrics, University Hospital Zurich, University of Zurich, Schmelzbergstrasse 12, Zurich 8091, Switzerland
| | - Martin Ehrbar
- Department of Obstetrics, University Hospital Zurich, University of Zurich, Schmelzbergstrasse 12, Zurich 8091, Switzerland
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Karamanos NK, Piperigkou Z, Theocharis AD, Watanabe H, Franchi M, Baud S, Brézillon S, Götte M, Passi A, Vigetti D, Ricard-Blum S, Sanderson RD, Neill T, Iozzo RV. Proteoglycan Chemical Diversity Drives Multifunctional Cell Regulation and Therapeutics. Chem Rev 2018; 118:9152-9232. [DOI: 10.1021/acs.chemrev.8b00354] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Nikos K. Karamanos
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras 26110, Greece
- Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), Patras 26110, Greece
| | - Zoi Piperigkou
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras 26110, Greece
- Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), Patras 26110, Greece
| | - Achilleas D. Theocharis
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras 26110, Greece
| | - Hideto Watanabe
- Institute for Molecular Science of Medicine, Aichi Medical University, Aichi 480-1195, Japan
| | - Marco Franchi
- Department for Life Quality Studies, University of Bologna, Rimini 47100, Italy
| | - Stéphanie Baud
- Université de Reims Champagne-Ardenne, Laboratoire SiRMa, CNRS UMR MEDyC 7369, Faculté de Médecine, 51 rue Cognacq Jay, Reims 51100, France
| | - Stéphane Brézillon
- Université de Reims Champagne-Ardenne, Laboratoire de Biochimie Médicale et Biologie Moléculaire, CNRS UMR MEDyC 7369, Faculté de Médecine, 51 rue Cognacq Jay, Reims 51100, France
| | - Martin Götte
- Department of Gynecology and Obstetrics, Münster University Hospital, Münster 48149, Germany
| | - Alberto Passi
- Department of Medicine and Surgery, University of Insubria, Varese 21100, Italy
| | - Davide Vigetti
- Department of Medicine and Surgery, University of Insubria, Varese 21100, Italy
| | - Sylvie Ricard-Blum
- University Claude Bernard Lyon 1, CNRS, UMR 5246, Institute of Molecular and Supramolecular Chemistry and Biochemistry, Villeurbanne 69622, France
| | - Ralph D. Sanderson
- Department of Pathology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Thomas Neill
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 10107, United States
| | - Renato V. Iozzo
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 10107, United States
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Jiang L, Liu G, Liu H, Han J, Liu Z, Ma H. Molecular weight impact on the mechanical forces between hyaluronan and its receptor. Carbohydr Polym 2018; 197:326-336. [PMID: 30007620 DOI: 10.1016/j.carbpol.2018.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 10/14/2022]
Abstract
Hyaluronan (HA) possesses manifold mechanical and signaling properties in the body. Most of these activities are largely regulated by its molecular weight, which often triggers opposing functions. However the molecular basis for such function distinction between HA size categories remains unclear. Using a combination of biophysical techniques, we measured the physical forces between HA ligand and its specific receptor CD44 in both normal and lateral directions, at different HA molecular weights and bound states. It was found that the impact of HA multivalency is more than just the sum of separate monovalent bindings. The HA-CD44 specific interaction enhances with HA molecular weight and the maximum binding occurs at ∼1000 kD, possibly due to the balance between multivalent HA zipping effect and conformational entropy. High friction patches, probably from CD44 protein clustering, was observed in friction force microscopy (FFM) upon HA shearing, which is also dependent on HA molecular weight. These results could help to understand the biophysical mechanism of HA in regulating CD44-induced physiological activities and thus facilitate the new design of HA-based material in fine tuning the receptor responses.
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Affiliation(s)
- Lei Jiang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, Shandong 266580, PR China.
| | - Guihua Liu
- Department of Common Courses, Weifang Medical University, Weifang, Shandong 261042, PR China.
| | - Hanyun Liu
- Department of Infectious Diseases, the Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003,PR China
| | - Juan Han
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, Shandong 266580, PR China
| | - Zhibin Liu
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, Shandong 266580, PR China
| | - Hongchao Ma
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, Shandong 266580, PR China
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Lane RS, Haller FM, Chavaroche AAE, Almond A, DeAngelis PL. Heparosan-coated liposomes for drug delivery. Glycobiology 2018; 27:1062-1074. [PMID: 29044377 DOI: 10.1093/glycob/cwx070] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 08/03/2017] [Indexed: 11/13/2022] Open
Abstract
Liposomal encapsulation is a useful drug delivery strategy for small molecules, especially chemotherapeutic agents such as doxorubicin. Doxil® is a doxorubicin-containing liposome ("dox-liposome") that passively targets drug to tumors while reducing side effects caused by free drug permeating and poisoning healthy tissues. Polyethylene glycol (PEG) is the hydrophilic coating of Doxil® that protects the formulation from triggering the mononuclear phagocyte system (MPS). Evading the MPS prolongs dox-liposome circulation time thus increasing drug deposition at the tumor site. However, multiple doses of Doxil® sometimes activate an anti-PEG immune response that enhances liposome clearance from circulation and causes hypersensitivity, further limiting its effectiveness against disease. These side effects constrain the utility of PEG-coated liposomes in certain populations, justifying the need for investigation into alternative coatings that could improve drug delivery for better patient quality of life and outcome. We hypothesized that heparosan (HEP; [-4-GlcA-β1-4-GlcNAc-α1-]n) may serve as a PEG alternative for coating liposomes. HEP is a natural precursor to heparin biosynthesis in mammals. Also, bacteria expressing an HEP extracellular capsule during infection escape detection and are recognized as "self," not a foreign threat. By analogy, coating drug-carrying liposomes with HEP should camouflage the delivery vehicle from the MPS, extending circulation time and potentially avoiding immune-mediated clearance. In this study, we characterize the postmodification insertion of HEP-lipids into liposomes by dynamic light scattering and coarse-grain computer modeling, test HEP-lipid immunogenicity in rats, and compare the efficacy of drug delivered by HEP-coated liposomes to PEG-coated liposomes in a human breast cancer xenograft mouse model.
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Affiliation(s)
- Rachel S Lane
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73126, USA
| | - F Michael Haller
- Caisson Biotech, LLC, 655 Research Park, Oklahoma City, OK 73104, USA
| | | | - Andrew Almond
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Paul L DeAngelis
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73126, USA.,Caisson Biotech, LLC, 655 Research Park, Oklahoma City, OK 73104, USA
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Mohtashamian S, Boddohi S, Hosseinkhani S. Preparation and optimization of self-assembled chondroitin sulfate-nisin nanogel based on quality by design concept. Int J Biol Macromol 2018; 107:2730-2739. [DOI: 10.1016/j.ijbiomac.2017.10.156] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 09/26/2017] [Accepted: 10/25/2017] [Indexed: 12/18/2022]
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Richter RP, Baranova NS, Day AJ, Kwok JC. Glycosaminoglycans in extracellular matrix organisation: are concepts from soft matter physics key to understanding the formation of perineuronal nets? Curr Opin Struct Biol 2017; 50:65-74. [PMID: 29275227 DOI: 10.1016/j.sbi.2017.12.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 01/19/2023]
Abstract
Conventional wisdom has it that proteins fold and assemble into definite structures, and that this defines their function. Glycosaminoglycans (GAGs) are different. In most cases the structures they form have a low degree of order, even when interacting with proteins. Here, we discuss how physical features common to all GAGs-hydrophilicity, charge, linearity and semi-flexibility-underpin the overall properties of GAG-rich matrices. By integrating soft matter physics concepts (e.g. polymer brushes and phase separation) with our molecular understanding of GAG-protein interactions, we can better comprehend how GAG-rich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs)-a GAG-rich matrix enveloping neurons-as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions.
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Affiliation(s)
- Ralf P Richter
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Physics and Astronomy, Faculty of Mathematics and Physical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom; Astbury Centre for Strucural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; Biosurfaces Lab, CIC biomaGUNE, Paseo Miramon 182, 20014 San Sebastian, Spain.
| | - Natalia S Baranova
- Biosurfaces Lab, CIC biomaGUNE, Paseo Miramon 182, 20014 San Sebastian, Spain
| | - Anthony J Day
- Wellcome Trust Centre for Cell-Matrix Research, Division of Cell-Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, United Kingdom
| | - Jessica Cf Kwok
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom; Centre for Reconstructive Neuroscience, Institute of Experimental Medicine, Videnska 1083, 14220 Prague 4, Czech Republic.
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Almond A. Multiscale modeling of glycosaminoglycan structure and dynamics: current methods and challenges. Curr Opin Struct Biol 2017; 50:58-64. [PMID: 29253714 DOI: 10.1016/j.sbi.2017.11.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/24/2017] [Accepted: 11/26/2017] [Indexed: 01/24/2023]
Abstract
Glycosaminoglycans are long unbranched and complex polysaccharides that are an essential component of mammalian extracellular matrices. Characterization of their molecular structure, dynamics and interactions are essential to understand important biological phenomena in health and disease, and will lead to novel therapeutics and medical devices. However, this has proven to be a challenge experimentally and theoretical techniques are needed to develop new hypotheses, and interpret experiments. This review aims to examine the current theoretical (rather than experimental) methods used by researchers to investigate glycosaminoglycan structure, dynamics and interactions, from the monosaccharide to the macromolecular scale. It will consider techniques such as quantum mechanics, molecular mechanics, molecular dynamics, coarse graining and docking.
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Affiliation(s)
- Andrew Almond
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK.
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35
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Ma PL, Lavertu M, Winnik FM, Buschmann MD. Stability and binding affinity of DNA/chitosan complexes by polyanion competition. Carbohydr Polym 2017; 176:167-176. [DOI: 10.1016/j.carbpol.2017.08.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 05/24/2017] [Accepted: 08/01/2017] [Indexed: 12/20/2022]
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36
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An accurate coarse-grained model for chitosan polysaccharides in aqueous solution. PLoS One 2017; 12:e0180938. [PMID: 28732036 PMCID: PMC5521771 DOI: 10.1371/journal.pone.0180938] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/24/2017] [Indexed: 01/25/2023] Open
Abstract
Computational models can provide detailed information about molecular conformations and interactions in solution, which is currently inaccessible by other means in many cases. Here we describe an efficient and precise coarse-grained model for long polysaccharides in aqueous solution at different physico-chemical conditions such as pH and ionic strength. The Model is carefully constructed based on all-atom simulations of small saccharides and metadynamics sampling of the dihedral angles in the glycosidic links, which represent the most flexible degrees of freedom of the polysaccharides. The model is validated against experimental data for Chitosan molecules in solution with various degree of deacetylation, and is shown to closely reproduce the available experimental data. For long polymers, subtle differences of the free energy maps of the glycosidic links are found to significantly affect the measurable polymer properties. Therefore, for titratable monomers the free energy maps of the corresponding links are updated according to the current charge of the monomers. We then characterize the microscopic and mesoscopic structural properties of large chitosan polysaccharides in solution for a wide range of solvent pH and ionic strength, and investigate the effect of polymer length and degree and pattern of deacetylation on the polymer properties.
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37
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Anjum F, Carroll A, Young SA, Flynn LE, Amsden BG. Tough, Semisynthetic Hydrogels for Adipose Derived Stem Cell Delivery for Chondral Defect Repair. Macromol Biosci 2017; 17. [DOI: 10.1002/mabi.201600373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/05/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Fraz Anjum
- Department of Chemical Engineering; Queen's University Kingston; ON K7L3N6 Canada
- Human Mobility Research Centre; Queen's University Kingston; ON K7L3N6 Canada
| | - Andrew Carroll
- Department of Chemical Engineering; Queen's University Kingston; ON K7L3N6 Canada
- Human Mobility Research Centre; Queen's University Kingston; ON K7L3N6 Canada
| | - Stuart A. Young
- Department of Chemical Engineering; Queen's University Kingston; ON K7L3N6 Canada
- Human Mobility Research Centre; Queen's University Kingston; ON K7L3N6 Canada
| | - Lauren E. Flynn
- Department of Chemical and Biochemical Engineering; The University of Western Ontario; London ON N6A 3K7 Canada
- Department of Anatomy and Cell Biology; The University of Western Ontario; London ON N6A 3K7 Canada
| | - Brian G. Amsden
- Department of Chemical Engineering; Queen's University Kingston; ON K7L3N6 Canada
- Human Mobility Research Centre; Queen's University Kingston; ON K7L3N6 Canada
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Holtzmann K, Gautier HOB, Christ AF, Guck J, Káradóttir RT, Franze K. Brain tissue stiffness is a sensitive marker for acidosis. J Neurosci Methods 2016; 271:50-4. [PMID: 27378027 PMCID: PMC5012886 DOI: 10.1016/j.jneumeth.2016.07.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/30/2016] [Accepted: 07/01/2016] [Indexed: 12/21/2022]
Abstract
We introduce tissue stiffness as a sensitive indicator for pathophysiological changes to CNS tissue. We applied atomic force microscopy to investigate tissue stiffness. We found that CO2 overexposure-induced acidosis changes brain properties.
Background Carbon dioxide overdose is frequently used to cull rodents for tissue harvesting. However, this treatment may lead to respiratory acidosis, which potentially could change the properties of the investigated tissue. New method Mechanical tissue properties often change in pathological conditions and may thus offer a sensitive generic readout for changes in biological tissues with clinical relevance. In this study, we performed force-indentation measurements with an atomic force microscope on acute cerebellar slices from adult rats to test if brain tissue undergoes changes following overexposure to CO2 compared to other methods of euthanasia. Results The pH significantly decreased in brain tissue of animals exposed to CO2. Concomitant with the drop in pH, cerebellar grey matter significantly stiffened. Tissue stiffening was reproduced by incubation of acute cerebellar slices in acidic medium. Comparison with existing methods Tissue stiffness provides an early, generic indicator for pathophysiological changes in the CNS. Atomic force microscopy offers unprecedented high spatial resolution to detect such changes. Conclusions Our results indicate that the stiffness particularly of grey matter strongly correlates with changes of the pH in the cerebellum. Furthermore, the method of tissue harvesting and preparation may not only change tissue stiffness but very likely also other physiologically relevant parameters, highlighting the importance of appropriate sample preparation.
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Affiliation(s)
- Kathrin Holtzmann
- Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Hélène O B Gautier
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, United Kingdom; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Andreas F Christ
- Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Jochen Guck
- Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom; Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Ragnhildur Thóra Káradóttir
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Kristian Franze
- Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, United Kingdom.
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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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Nazempour A, Van Wie BJ. Chondrocytes, Mesenchymal Stem Cells, and Their Combination in Articular Cartilage Regenerative Medicine. Ann Biomed Eng 2016; 44:1325-54. [PMID: 26987846 DOI: 10.1007/s10439-016-1575-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/17/2016] [Indexed: 01/05/2023]
Abstract
Articular cartilage (AC) is a highly organized connective tissue lining, covering the ends of bones within articulating joints. Its highly ordered structure is essential for stable motion and provides a frictionless surface easing load transfer. AC is vulnerable to lesions and, because it is aneural and avascular, it has limited self-repair potential which often leads to osteoarthritis. To date, no fully successful treatment for osteoarthritis has been reported. Thus, the development of innovative therapeutic approaches is desperately needed. Autologous chondrocyte implantation, the only cell-based surgical intervention approved in the United States for treating cartilage defects, has limitations because of de-differentiation of articular chondrocytes (AChs) upon in vitro expansion. De-differentiation can be abated if initial populations of AChs are co-cultured with mesenchymal stem cells (MSCs), which not only undergo chondrogenesis themselves but also support chondrocyte vitality. In this review we summarize studies utilizing AChs, non-AChs, and MSCs and compare associated outcomes. Moreover, a comprehensive set of recent human studies using chondrocytes to direct MSC differentiation, MSCs to support chondrocyte re-differentiation and proliferation in co-culture environments, and exploratory animal intra- and inter-species studies are systematically reviewed and discussed in an innovative manner allowing side-by-side comparisons of protocols and outcomes. Finally, a comprehensive set of recommendations are made for future studies.
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Affiliation(s)
- A Nazempour
- Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, 99164-6515, USA
| | - B J Van Wie
- Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, 99164-6515, USA.
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41
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Leuty GM, Tsige M, Grest GS, Rubinstein M. Tension Amplification in Tethered Layers of Bottle-Brush Polymers. Macromolecules 2016; 49:1950-1960. [PMID: 27695137 PMCID: PMC5040463 DOI: 10.1021/acs.macromol.5b02305] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Molecular dynamics simulations of a coarse-grained bead-spring model have been used to study the effects of molecular crowding on the accumulation of tension in the backbone of bottle-brush polymers tethered to a flat substrate. The number of bottle-brushes per unit surface area, Σ, as well as the lengths of the bottle-brush backbones Nbb (50 ≤ Nbb ≤ 200) and side chains Nsc (50 ≤ Nsc ≤ 200) were varied to determine how the dimensions and degree of crowding of bottle-brushes give rise to bond tension amplification along the backbone, especially near the substrate. From these simulations, we have identified three separate regimes of tension. For low Σ, the tension is due solely to intramolecular interactions and is dominated by the side chain repulsion that governs the lateral brush dimensions. With increasing Σ, the interactions between bottle-brush polymers induce compression of the side chains, transmitting increasing tension to the backbone. For large Σ, intermolecular side chain repulsion increases, forcing side chain extension and reorientation in the direction normal to the surface and transmitting considerable tension to the backbone.
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Affiliation(s)
- Gary M. Leuty
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Mesfin Tsige
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Gary S. Grest
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Michael Rubinstein
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Anjum F, Lienemann PS, Metzger S, Biernaskie J, Kallos MS, Ehrbar M. Enzyme responsive GAG-based natural-synthetic hybrid hydrogel for tunable growth factor delivery and stem cell differentiation. Biomaterials 2016; 87:104-117. [PMID: 26914701 DOI: 10.1016/j.biomaterials.2016.01.050] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/10/2015] [Accepted: 01/22/2016] [Indexed: 01/22/2023]
Abstract
We describe an enzymatically formed chondroitin sulfate (CS) and poly(ethylene glycol) (PEG) based hybrid hydrogel system, which by tuning the architecture and composition of modular building blocks, allows the application-specific tailoring of growth factor delivery and cellular responses. CS, a negatively charged sulfate-rich glycosaminoglycan of the extracellular matrix (ECM), known for its growth factor binding and stem cell regulatory functions, is used as a starting material for the engineering of this biomimetic materials platform. The functionalization of CS with transglutaminase factor XIII specific substrate sequences is utilized to allow cross-linking of CS with previously described fibrin-mimetic TG-PEG hydrogel precursors. We show that the hydrogel network properties can be tuned by varying the degree of functionalization of CS as well as the ratio and concentrations of PEG and CS precursors. Taking advantage of TG-PEG hydrogel, compatible tagged bio-functional building blocks, including RGD peptides or matrix metalloproteinase sensitive domains, can be incorporated on demand allowing the three-dimensional culture and expansion of human bone marrow mesenchymal stem cells (BM-MSCs). The binding of bone morphogenetic protein-2 (BMP-2) in a CS concentration dependent manner and the BMP-2 release mediated osteogenic differentiation of BM-MSCs indicate the potential of CS-PEG hybrid hydrogels to promote regeneration of bone tissue. Their modular design allows facile incorporation of additional signaling elements, rendering CS-PEG hydrogels a highly flexible platform with potential for multiple biomedical applications.
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Affiliation(s)
- Fraz Anjum
- Pharmaceutical Production Research Facility, University of Calgary, 2500 University Dr., Calgary, AB, T2N 1N4, Canada; Department of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, 2500 University Dr. NW., Calgary, AB, T2N 1N4, Canada.
| | - Philipp S Lienemann
- Department of Obstetrics, University Hospital Zurich, University of Zurich, Schmelzbergstr. 12, 8091, Zurich, Switzerland
| | - Stéphanie Metzger
- Department of Obstetrics, University Hospital Zurich, University of Zurich, Schmelzbergstr. 12, 8091, Zurich, Switzerland
| | - Jeff Biernaskie
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Dr., Calgary, AB, T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Dr., Calgary, AB, T2N 4N1, Canada; Department of Surgery, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr., Calgary, AB, T2N 4N1, Canada
| | - Michael S Kallos
- Pharmaceutical Production Research Facility, University of Calgary, 2500 University Dr., Calgary, AB, T2N 1N4, Canada; Department of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, 2500 University Dr. NW., Calgary, AB, T2N 1N4, Canada
| | - Martin Ehrbar
- Department of Obstetrics, University Hospital Zurich, University of Zurich, Schmelzbergstr. 12, 8091, Zurich, Switzerland.
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43
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Park Y, Jowitt TA, Day AJ, Prestegard JH. Nuclear Magnetic Resonance Insight into the Multiple Glycosaminoglycan Binding Modes of the Link Module from Human TSG-6. Biochemistry 2016; 55:262-76. [PMID: 26685054 PMCID: PMC5073374 DOI: 10.1021/acs.biochem.5b01148] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tumor necrosis factor-stimulated gene-6 (TSG-6) is a hyaluronan (HA)-binding protein that is essential for stabilizing and remodeling the extracellular matrix (ECM) during ovulation and inflammatory disease processes such as arthritis. The Link module, one of the domains of TSG-6, is responsible for binding hyaluronan and other glycosaminoglycans found in the ECM. In this study, we used a well-defined chondroitin sulfate (CS) hexasaccharide (ΔC444S) to determine the structure of the Link module, in solution, in its chondroitin sulfate-bound state. A variety of nuclear magnetic resonance techniques were employed, including chemical shift perturbation, residual dipolar couplings (RDCs), nuclear Overhauser effects, spin relaxation measurements, and paramagnetic relaxation enhancements from a spin-labeled analogue of ΔC444S. The binding site for ΔC444S on the Link module overlapped with that of HA. Surprisingly, ΔC444S binding induced dimerization of the Link module (as confirmed by analytical ultracentrifugation), and a second weak binding site that partially overlapped with a previously identified heparin site was detected. A dimer model was generated using chemical shift perturbations and RDCs as restraints in the docking program HADDOCK. We postulate that the molecular cross-linking enhanced by the multiple binding modes of the Link module might be critical for remodeling the ECM during inflammation/ovulation and might contribute to other functions of TSG-6.
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Affiliation(s)
- Younghee Park
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, USA
| | - Thomas A. Jowitt
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Anthony J. Day
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - James H. Prestegard
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, USA
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44
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Osawa S, Osada K, Hiki S, Dirisala A, Ishii T, Kataoka K. Polyplex Micelles with Double-Protective Compartments of Hydrophilic Shell and Thermoswitchable Palisade of Poly(oxazoline)-Based Block Copolymers for Promoted Gene Transfection. Biomacromolecules 2015; 17:354-61. [PMID: 26682466 DOI: 10.1021/acs.biomac.5b01456] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Improving the stability of polyplex micelles under physiological conditions is a critical issue for promoting gene transfection efficiencies. To this end, hydrophobic palisade was installed between the inner core of packaged plasmid DNA (pDNA) and the hydrophilic shell of polyplex micelles using a triblock copolymer consisting of hydrophilic poly(2-ethyl-2-oxazoline), thermoswitchable amphiphilic poly(2-n-propyl-2-oxazoline) (PnPrOx) and cationic poly(L-lysine). The two-step preparation procedure, mixing the triblock copolymer with pDNA below the lower critical solution temperature (LCST) of PnPrOx, followed by incubation above the LCST to form a hydrophobic palisade of the collapsed PnPrOx segment, induced the formation of spatially aligned hydrophilic-hydrophobic double-protected polyplex micelles. The prepared polyplex micelles exhibited significant tolerance against attacks from nuclease and polyanions compared to those without hydrophobic palisades, thereby promoting gene transfection. These results corroborated the utility of amphiphilic poly(oxazoline) as a molecular thermal switch to improve the stability of polyplex gene carriers relevant for physiological applications.
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Affiliation(s)
| | - Kensuke Osada
- Japan Science and Technology Agency, PRESTO, Tokyo, Japan
| | | | | | | | - Kazunori Kataoka
- Division of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo , 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan.,Innovation Center of NanoMedicine (iCONM), 3-25-14, Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
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Khanlari A, Suekama TC, Detamore MS, Gehrke SH. Structurally diverse and readily tunable photocrosslinked chondroitin sulfate based copolymers. ACTA ACUST UNITED AC 2015. [DOI: 10.1002/polb.23751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Anahita Khanlari
- Department of Chemical and Petroleum Engineering; University of Kansas; Learned Hall, Room 4163 Lawrence Kansas 66045
| | - Tiffany C. Suekama
- Department of Chemical and Petroleum Engineering; University of Kansas; Learned Hall, Room 4163 Lawrence Kansas 66045
| | - Michael S. Detamore
- Department of Chemical and Petroleum Engineering; University of Kansas; Learned Hall, Room 4163 Lawrence Kansas 66045
- Bioengineering Program; University of Kansas; Lawrence Kansas 66045
| | - Stevin H. Gehrke
- Department of Chemical and Petroleum Engineering; University of Kansas; Learned Hall, Room 4163 Lawrence Kansas 66045
- Bioengineering Program; University of Kansas; Lawrence Kansas 66045
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46
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Nia HT, Han L, Bozchalooi IS, Roughley P, Youcef-Toumi K, Grodzinsky AJ, Ortiz C. Aggrecan nanoscale solid-fluid interactions are a primary determinant of cartilage dynamic mechanical properties. ACS NANO 2015; 9:2614-25. [PMID: 25758717 PMCID: PMC6713486 DOI: 10.1021/nn5062707] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Poroelastic interactions between interstitial fluid and the extracellular matrix of connective tissues are critical to biological and pathophysiological functions involving solute transport, energy dissipation, self-stiffening and lubrication. However, the molecular origins of poroelasticity at the nanoscale are largely unknown. Here, the broad-spectrum dynamic nanomechanical behavior of cartilage aggrecan monolayer is revealed for the first time, including the equilibrium and instantaneous moduli and the peak in the phase angle of the complex modulus. By performing a length scale study and comparing the experimental results to theoretical predictions, we confirm that the mechanism underlying the observed dynamic nanomechanics is due to solid-fluid interactions (poroelasticity) at the molecular scale. Utilizing finite element modeling, the molecular-scale hydraulic permeability of the aggrecan assembly was quantified (kaggrecan = (4.8 ± 2.8) × 10(-15) m(4)/N·s) and found to be similar to the nanoscale hydraulic permeability of intact normal cartilage tissue but much lower than that of early diseased tissue. The mechanisms underlying aggrecan poroelasticity were further investigated by altering electrostatic interactions between the molecule's constituent glycosaminoglycan chains: electrostatic interactions dominated steric interactions in governing molecular behavior. While the hydraulic permeability of aggrecan layers does not change across species and age, aggrecan from adult human cartilage is stiffer than the aggrecan from newborn human tissue.
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Affiliation(s)
- Hadi Tavakoli Nia
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Lin Han
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Iman Soltani Bozchalooi
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Peter Roughley
- Shriners Hospital for Children, Montreal, Quebec H3G 1A6, Canada
| | - Kamal Youcef-Toumi
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alan J. Grodzinsky
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Address correspondence to: ,
| | - Christine Ortiz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Address correspondence to: ,
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47
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Khanlari A, Schulteis JE, Suekama TC, Detamore MS, Gehrke SH. Designing crosslinked hyaluronic acid hydrogels with tunable mechanical properties for biomedical applications. J Appl Polym Sci 2015. [DOI: 10.1002/app.42009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Anahita Khanlari
- Department of Chemical and Petroleum Engineering; University of Kansas; Lawrence Kansas 66045
| | - Jason E. Schulteis
- Department of Chemical and Petroleum Engineering; University of Kansas; Lawrence Kansas 66045
| | - Tiffany C. Suekama
- Department of Chemical and Petroleum Engineering; University of Kansas; Lawrence Kansas 66045
| | - Michael S. Detamore
- Department of Chemical and Petroleum Engineering; University of Kansas; Lawrence Kansas 66045
- Bioengineering Graduate Program; University of Kansas; Lawrence Kansas 66045
| | - Stevin H. Gehrke
- Department of Chemical and Petroleum Engineering; University of Kansas; Lawrence Kansas 66045
- Bioengineering Graduate Program; University of Kansas; Lawrence Kansas 66045
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48
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Abstract
Recent findings in several organ systems show that cytoneme-mediated signaling transports signaling proteins along cellular extensions and targets cell-to-cell exchanges to synaptic contacts. This mechanism of paracrine signaling may be a general one that is used by many (or all) cell types in many (or all) organs. We briefly review these findings in this perspective. We also describe the properties of several signaling systems that have previously been interpreted to support a passive diffusion mechanism of signaling protein dispersion, but can now be understood in the context of the cytoneme mechanism. Also watch the Video Abstract.
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Affiliation(s)
- Sougata Roy
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Thomas B. Kornberg
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
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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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50
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Yu Y, Chau Y. Formulation of in situ chemically cross-linked hydrogel depots for protein release: from the blob model perspective. Biomacromolecules 2014; 16:56-65. [PMID: 25314589 DOI: 10.1021/bm501063n] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The fast release rate and the undesirable covalent binding are two major problems often encountered in formulating in situ chemically cross-linked hydrogel as protein release depot, particularly when prolonged release over months is desirable. In this study, we applied the De Gennes' blob theory to analyze and tackle these two problems using a vinylsulfone-thiol (VS-SH) reaction based in situ hydrogel system. We showed that the simple scaling relation ξb ≈ Rg(c/c*)(-v/(3v-1)) is applicable to the in situ hydrogel and the mesh size estimated from the precursor polymer parameters is a reasonable match to experimental results. On the other hand, as predicted by the theory and confirmed by experiments, the drug diffusion within hydrogel depends mainly on polymer concentration but not the degree of modification (DM). The covalent binding was found to be caused by the mismatch of location between the reactive groups and the entanglement points. The mismatch and, thus, the protein binding were minimized by increasing the DM and concentration of the SH polymer relative to the VS polymer, as predicted by theory. Using these principles, an in situ hydrogel system for the controlled release of an antiangiogenic antibody therapeutics bevacizumab for 3 months was developed.
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Affiliation(s)
- Yu Yu
- Division of Biomedical Engineering and ‡Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong, China
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