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Mohandas N, Edwards PJB, Kent LM, Jameson GB, Williams MAK. Biotinylation of reducing and non-reducing termini to create plug-and-play polysaccharides. Carbohydr Polym 2023; 305:120569. [PMID: 36737207 DOI: 10.1016/j.carbpol.2023.120569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/14/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Single-molecule studies continue to grow in popularity. In cases where biopolymer samples of interest exhibit variations in fine-structure between individual chains such single-molecule studies uniquely offer the promise of revealing deep structure-function relationships. Polysaccharides are typically studied in bulk and, as such, their study could greatly benefit from the application of single-molecule techniques. However, while for example single-molecule optical tweezers (OT) studies have become commonplace for DNA, studies of polysaccharides have lagged behind somewhat, complicated by the difficulty of studying molecules that amongst other things have more complex end-group chemistry. Recently, divalent streptavidin linkers have been shown to be capable of concatenating two pieces of biotin-terminated DNA to produce robust composite strings that run intact through conventional gels, and can be used in single-molecule OT experiments (Mohandas, Kent, Raudsepp, Jameson, & Williams, 2022). By using two such streptavidin linkers, biotin-terminated polymers could be inserted between two sections of DNA in order to facilitate single-molecule experiments on biopolymers that are currently difficult to address by other means. Here, we describe a generic approach for placing the required biotin moieties at both ends of polysaccharide chains, producing plug-and-play polysaccharide inserts that can be incorporated into composite polymer strings using streptavidin linking hubs.
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Affiliation(s)
- Nimisha Mohandas
- School of Natural Sciences, Massey University, Palmerston North, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Patrick J B Edwards
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Lisa M Kent
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Geoffrey B Jameson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
| | - Martin A K Williams
- School of Natural Sciences, Massey University, Palmerston North, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
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2
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Zhang Y, Yu J, Wang X, Durachko DM, Zhang S, Cosgrove DJ. Molecular insights into the complex mechanics of plant epidermal cell walls. Science 2021; 372:706-711. [PMID: 33986175 DOI: 10.1126/science.abf2824] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/29/2021] [Indexed: 12/26/2022]
Abstract
Plants have evolved complex nanofibril-based cell walls to meet diverse biological and physical constraints. How strength and extensibility emerge from the nanoscale-to-mesoscale organization of growing cell walls has long been unresolved. We sought to clarify the mechanical roles of cellulose and matrix polysaccharides by developing a coarse-grained model based on polymer physics that recapitulates aspects of assembly and tensile mechanics of epidermal cell walls. Simple noncovalent binding interactions in the model generate bundled cellulose networks resembling that of primary cell walls and possessing stress-dependent elasticity, stiffening, and plasticity beyond a yield threshold. Plasticity originates from fibril-fibril sliding in aligned cellulose networks. This physical model provides quantitative insight into fundamental questions of plant mechanobiology and reveals design principles of biomaterials that combine stiffness with yielding and extensibility.
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Affiliation(s)
- Yao Zhang
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Jingyi Yu
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Xuan Wang
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Daniel M Durachko
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sulin Zhang
- Department of Engineering Science and Mechanics and Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
| | - Daniel J Cosgrove
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
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3
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Mani S, Cosgrove DJ, Voth GA. Anisotropic Motions of Fibrils Dictated by Their Orientations in the Lamella: A Coarse-Grained Model of a Plant Cell Wall. J Phys Chem B 2020; 124:3527-3539. [DOI: 10.1021/acs.jpcb.0c01697] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sriramvignesh Mani
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Daniel J. Cosgrove
- Department of Biology and Center for Lignocellulose Structure and Formation, Pennsylvania State University, University Park, State College, Pennsylvania 16801, United States
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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4
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John J, Ray D, Aswal VK, Deshpande AP, Varughese S. Dissipation and strain-stiffening behavior of pectin-Ca gels under LAOS. SOFT MATTER 2019; 15:6852-6866. [PMID: 31410439 DOI: 10.1039/c9sm00709a] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Non-linear mechanical responses observed in networks of many biopolymers such as pectin are important for their functioning as biological systems. Additionally, pectins derived from plant sources are also used for several food and biomedical applications. In the present work, the possible contributions of egg-box bundles in the large deformation response of calcium crosslinked gels of low methoxy pectin are explored using large amplitude oscillatory shear (LAOS). The gels exhibit a significant overshoot in the loss modulus (G'') and intra-cycle strain-stiffening, more prominent at greater extents of egg-box bundling. This observation signifies the dissipation characteristics of the egg-box bundles in pectin gels, hitherto not reported. The observed non-linear signatures diminish when the extent of bundling as well as the bundle radius decreases below a critical value. We identify different pectin/Ca concentration regimes based on the semi-flexible/flexible nature of the gel network and the non-linear signatures. Monovalent salt addition prior to crosslinking is shown to modify the extent of bundling, thereby influencing the magnitude of G'' overshoot and strain-stiffening. The intensity of the G'' overshoot and the extent of strain-stiffening are correlated with the radius of the egg-box bundles obtained from small angle neutron scattering (SANS) data. However, analysis using strain-stiffening models indicates the possible contributions from the semi-flexible nature of egg-box bundles and single chains.
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Affiliation(s)
- Jacob John
- Department of Chemical Engineering, Indian Institute of Technology, Madras, India.
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Irani AH, Mercadante D, Williams MAK. On the electrophoretic mobilities of partially charged oligosaccharides as a function of charge patterning and degree of polymerization. Electrophoresis 2018; 39:1497-1503. [PMID: 29603292 DOI: 10.1002/elps.201800050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/03/2018] [Accepted: 03/04/2018] [Indexed: 11/11/2022]
Abstract
Fully or partially charged oligosaccharide molecules play a key role in many areas of biology, where their fine structures are crucial in determining their functionality. However, the separation of specific charged oligosaccharides from similar moieties that typically coexist in extracted samples, even for those that are unbranched, and in cases where each saccharide moiety can only carry a single charge or not, is far from trivial. Typically such molecules are characterized by a degree of polymerization n and a number m (and distribution) of charged residues, and must be separated from a plethora of similar species possessing different combinations of n and m. Furthermore, the separation of the possible n!/m!(n-m)! isomers of each species of fixed n and m is a formidable challenge to analytical chemists. Herein, we report the results of molecular dynamics simulations that have been performed in order to calculate the free solution electrophoretic mobilities of galacturonides and charged oligosaccharides derived from digests of the important plant cell-wall polysaccharide pectin. The simulations are compared with an experiment and are found to correctly predict the loss of resolution of fully charged species above a critical degree of polymerization n and the ionic strength dependence of the electrophoretic mobilities of different partially charged oligosaccharides. It is expected that having a predictive tool for the calculation of the electrophoretic mobilities of differently charged oligosaccharide species in hand will allow experimental conditions that optimize the resolution of particular species to be ascertained and understood.
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Affiliation(s)
- Amir H Irani
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - Martin A K Williams
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,The MacDiarmid Institute of Advanced Materials and Nanotechnology, Wellington, New Zealand
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Irani AH, Owen JL, Mercadante D, Williams MAK. Molecular Dynamics Simulations Illuminate the Role of Counterion Condensation in the Electrophoretic Transport of Homogalacturonans. Biomacromolecules 2017; 18:505-516. [DOI: 10.1021/acs.biomac.6b01599] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Amir H. Irani
- Institute
of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Jessie L. Owen
- Institute
of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - Martin A. K. Williams
- Institute
of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The MacDiarmid Institute
of Advanced Materials and Nanotechnology, Wellington, New Zealand
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Influence of Pectin as a green polymer electrolyte on the transport properties of Chitosan-Pectin membranes. Carbohydr Polym 2016; 157:1759-1768. [PMID: 27987892 DOI: 10.1016/j.carbpol.2016.11.061] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/17/2016] [Accepted: 11/20/2016] [Indexed: 12/11/2022]
Abstract
Novel blend membranes have been prepared from Chitosan (CH), Pectin (PEC) and their mixtures. The obtained samples were cross-linked and sulfonated before characterization. The results show that CH/PEC membranes display structural changes on the chemical and physical properties as a function of composition. DSC analysis reveals an endothermic peak due to the scission of the ionic pairs between carboxylic groups and ammonium groups, which produces a strong change on physical properties such as methanol permeability and proton conductivity. The methanol permeability decreases with the amount of Pectin from (4.24±0.04)×10-6cm2/s for pure Chitosan membrane to (1.51±0.03)×10-6cm2/s for blend CH/PEC membranes when the amount of Pectin is 50% (v/v). The proton conductivities of the blend membranes follow a similar behavior. For a pure CH membrane the conductivity is 2.44×10-3S/cm, decreasing with pectin content until the composition 50/50 (v/v), in which the conductivity drops almost one order of magnitude.
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Cybulska J, Brzyska A, Zdunek A, Woliński K. Simulation of force spectroscopy experiments on galacturonic acid oligomers. PLoS One 2014; 9:e107896. [PMID: 25229407 PMCID: PMC4168238 DOI: 10.1371/journal.pone.0107896] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 08/23/2014] [Indexed: 11/19/2022] Open
Abstract
Pectins, forming a matrix for cellulose and hemicellulose, determine the mechanics of plant cell walls. They undergo salient structural changes during their development. In the presence of divalent cations, usually calcium, pectins can form gel-like structures. Because of their importance they have been the subject of many force spectroscopy experiments, which have examined the conformational changes and molecular tensions due to external forces. The most abundant unit present in the pectin backbone is polygalacturonic acid. Unfortunately, experimental force spectroscopy on polygalacturonic acid molecules is still not a trivial task. The mechanism of the single-molecule response to external forces can be inferred by theoretical methods. Therefore, in this work we simulated such force spectroscopy experiments using the Enforced Geometry Optimization (EGO) method. We examined the oligomeric (up to hexamer) structures of α-D-galacturonic acid exposed to external stretching forces. The EGO simulation of the force spectroscopy appropriately reproduced the experimental course of the enforced conformational transition: chair →inverted chair via the twisted boat conformation(s) in the pyranose ring of α-D-galacturonic acid. Additionally, our theoretical approach also allowed to determine the minimum oligomer size adequate for the description of nano-mechanical properties of (poly)-α-D-galacturonic acid.
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Affiliation(s)
- Justyna Cybulska
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
- * E-mail:
| | - Agnieszka Brzyska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Poland
| | - Artur Zdunek
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Krzysztof Woliński
- Department of Chemistry, Maria Curie-Skłodowska University, Lublin, Poland
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Schuster E, Lundin L, Williams MAK. Investigating the Relationship between Network Mechanics and Single-Chain Extension Using Biomimetic Polysaccharide Gels. Macromolecules 2012. [DOI: 10.1021/ma300724n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Erich Schuster
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Leif Lundin
- Food Future Flagship and Division
of Food and Nutritional Sciences, CSIRO, Werribee, Australia
| | - Martin A. K. Williams
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Food Future Flagship and Division
of Food and Nutritional Sciences, CSIRO, Werribee, Australia
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington,
New Zealand
- The Riddet Institute, Palmerston North, New Zealand
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Facilitating high-force single-polysaccharide stretching using covalent attachment of one end of the chain. Carbohydr Polym 2012; 87:806-815. [PMID: 34663040 DOI: 10.1016/j.carbpol.2011.08.073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 08/23/2011] [Indexed: 11/24/2022]
Abstract
Single polysaccharide force spectroscopy has yielded particularly interesting data, the interpretation of which requires the marriage of statistical-mechanical theories of polymer physics to the complexities afforded by possible force-induced conformational transitions of the constituent sugar rings. However, the difficulty of designing handles for the specific attachment of the different ends of polysaccharide chains to substrates, such as piezoelectric scanners, cantilevers or microbeads has meant that the majority of studies to date have been carried out with the polymer physisorbed to the substrates between which it is stretched, or at best chemically attached via bonds formed at uncontrolled locations along the length of the molecule. This means that the lengths of obtained polysaccharide stretches, as well as the forces that can be placed on the molecule without generating detachment, are generally smaller than those obtainable for polymers that offer the ability to be covalently attached to substrates specifically at their ends. As a consequence it is troublesome and tedious to record a statistically significant number of force curves that extend chains to high enough forces to investigate certain conformational transitions, such as the boat-to-inverted chair, exhibited by polysaccharides such as pectin. Herein, single molecule force-extension curves have been measured for the several pectin samples using AFM. The results are compared when either (1) the polymers have been physisorbed between the cantilever and the surface of the piezo-electric scanner, under several different solvent conditions of pH and ionic strength, or (2) the polymer molecule has been chemically attached at one end to the piezo surface using a recently reported coupling procedure. In fact, using such a chemical attachment to tether the end of the polysaccharide, reduced the frequency of successful stretching events obtained in a particular location, confirming the role of surface diffusion in the physisorbed experiments. Nevertheless, when polymer stretches were successfully recorded, the force that could be applied before detachment was significantly increased, indicating that this methodology has great potential for improving the acquisition of data reporting on force-induced conformational transitions of the sugar ring that require the application of significant stresses.
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Fellah A, Anjukandi P, Hemar Y, Otter D, Williams MA. Towards polysaccharide handles for single molecule experiments: Spectroscopic evidence for the selective covalent coupling of terminal sugar residues to desired substrates. Carbohydr Polym 2011. [DOI: 10.1016/j.carbpol.2011.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Schuster E, Lundin L, Williams MAK. Insights into the potential functionality of single-chain force-induced conformational transitions in polymer networks: implications for polysaccharide signaling in the plant cell wall. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:051927. [PMID: 21230520 DOI: 10.1103/physreve.82.051927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 09/08/2010] [Indexed: 05/30/2023]
Abstract
The behavior of biopolymer networks comprised of clickable polysaccharide chains that can undergo force-induced conformational transitions was investigated during straining using a simulation technique. The simulation was carried out both using an affine deformation field and alternatively using Lees-Edwards boundary conditions as an example of a nonaffine case. In the affine situation the simulated stress-strain curves were found to be consistent with results obtained by evaluating the molecular force-extension curve at a single average extension and calculating the bulk modulus as an average over all possible orientations with respect to the deformation. While in all cases examined the macroscopic mechanical responses of networks of randomly oriented chains, consisting either of simple extensible wormlike chains or their clickable analogs, were found to be indistinguishable, the simulation additionally allowed the number of chains containing sugar rings in different conformational states to be monitored, and this was found to change significantly during straining. This supports the hypothesis that in networks of randomly oriented clickable polysaccharide chains, such conformational transitions could have biological significance as stress switches in signaling processes but that they are unlikely to affect the bulk rheological properties of tissue.
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Affiliation(s)
- E Schuster
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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Fellah A, Anjukandi P, Waterland MR, Williams MA. Determining the degree of methylesterification of pectin by ATR/FT-IR: Methodology optimisation and comparison with theoretical calculations. Carbohydr Polym 2009. [DOI: 10.1016/j.carbpol.2009.07.003] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Conformational free energy maps for globobiose (α-d-Galp-(1→4)-β-d-Galp) in implicit and explict aqueous solution. Carbohydr Res 2008; 343:1091-8. [DOI: 10.1016/j.carres.2008.01.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 12/20/2007] [Accepted: 01/07/2008] [Indexed: 11/21/2022]
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Haverkamp RG, Marshall AT, Williams MAK. Entropic and Enthalpic Contributions to the Chair−Boat Conformational Transformation in Dextran under Single Molecule Stretching. J Phys Chem B 2007; 111:13653-7. [DOI: 10.1021/jp076052t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Richard G. Haverkamp
- Institute of Technology and Engineering, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Aaron T. Marshall
- Institute of Technology and Engineering, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Martin A. K. Williams
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
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