1
|
Lutsyk V, Wolski P, Plazinski W. The Conformation of Glycosidic Linkages According to Various Force Fields: Monte Carlo Modeling of Polysaccharides Based on Extrapolation of Short-Chain Properties. J Chem Theory Comput 2024; 20:6350-6368. [PMID: 38985993 PMCID: PMC11270825 DOI: 10.1021/acs.jctc.4c00543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024]
Abstract
The conformational features of the glycosidic linkage are the most important variable to consider when studying di-, oligo-, and polysaccharide molecules using molecular dynamics (MD) simulations. The accuracy of the theoretical model describing this degree of freedom influences the quality of the results obtained from MD calculations based on this model. This article focuses on the following two issues related to the conformation of the glycosidic linkage. First, we describe the results of a comparative analysis of the predictions of three carbohydrate-dedicated classical force fields for MD simulations, namely, CHARMM, GLYCAM, and GROMOS, in the context of different parameters of structural and energetic nature related to the conformation of selected types of glycosidic linkages, α(1 → 4), β(1 → 3), and β(1 → 4), connecting glucopyranose units. This analysis revealed several differences, mainly concerning the energy levels of the secondary and tertiary conformers and the linkage flexibility within the dominant exo-syn conformation for α(1 → 4) and β(1 → 3) linkages. Some aspects of the comparative analysis also included the newly developed, carbohydrate-dedicated Martini 3 coarse-grained force field. Second, to overcome the time-scale problem associated with sampling slow degrees of freedom in polysaccharide chains during MD simulations, we developed a coarse-grained (CG) model based on the data from MD simulations and designed for Monte Carlo modeling. This model (CG MC) is based on information from simulations of short saccharide chains, effectively sampled in atomistic MD simulations, and is capable of extrapolating local conformational properties to the case of polysaccharides of arbitrary length. The CG MC model has the potential to estimate the conformations of very long polysaccharide chains, taking into account the influence of secondary and tertiary conformations of glycosidic linkages. With respect to the comparative analysis of force fields, the application of CG MC modeling showed that relatively small differences in the predictions of individual force fields with respect to a single glycosidic linkage accumulate when considering their effect on the structure of longer chains, leading to drastically different predictions with respect to parameters describing the polymer conformation, such as the persistence length.
Collapse
Affiliation(s)
- Valery Lutsyk
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Pawel Wolski
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Wojciech Plazinski
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
- Department
of Biopharmacy, Medical University of Lublin, Chodzki 4a, 20-093 Lublin, Poland
| |
Collapse
|
2
|
DeLuca M, Sensale S, Lin PA, Arya G. Prediction and Control in DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2024; 7:626-645. [PMID: 36880799 DOI: 10.1021/acsabm.2c01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeling techniques. In this Review, we present various aspects of prediction and control in DNA nanotechnology, including the various scales of molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. We also address the current uses of artificial intelligence and machine learning in DNA nanotechnology. We discuss how experiments and modeling are synergistically combined to provide control over device behavior, allowing scientists to design molecular structures and dynamic devices with confidence that they will function as intended. Finally, we identify processes and scenarios where DNA nanotechnology lacks sufficient prediction ability and suggest possible solutions to these weak areas.
Collapse
Affiliation(s)
- Marcello DeLuca
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Sebastian Sensale
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Po-An Lin
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| |
Collapse
|
3
|
Cui X, Zhang XF, Jagota A. Penetration of Cell Surface Glycocalyx by Enveloped Viruses Is Aided by Weak Multivalent Adhesive Interaction. J Phys Chem B 2023; 127:486-494. [PMID: 36598427 DOI: 10.1021/acs.jpcb.2c06662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Viral infection usually begins with adhesion between the viral particle and viral receptors displayed on the cell membrane. The exterior surface of the cell membrane is typically coated with a brush-like layer of molecules, the glycocalyx, that the viruses need to penetrate. Although there is extensive literature on the biomechanics of virus-cell adhesion, much of it is based on continuum-level models that do not address the question of how virus/cell-membrane adhesion occurs through the glycocalyx. In this work, we present a simulation study of the penetration mechanism. Using a coarse-grained molecular model, we study the force-driven and diffusive penetration of a brush-like glycocalyx by viral particles. For force-driven penetration, we find that viral particles smaller than the spacing of molecules in the brush reach the membrane surface readily. For a given maximum force, viral particles larger than the minimum spacing of brush molecules arrest at some distance from the membrane, governed by the balance of elastic and applied forces. For the diffusive case, we find that weak but multivalent attraction between the glycocalyx molecules and the virus effectively leads to its engulfment by the glycocalyx. Our finding provides potential guidance for developing glycocalyx-targeting drugs and therapies by understanding how virus-cell adhesion works.
Collapse
Affiliation(s)
- Xinyu Cui
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - X Frank Zhang
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Anand Jagota
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States.,Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| |
Collapse
|
4
|
Single-molecule investigations of single-chain cellulose biosynthesis. Proc Natl Acad Sci U S A 2022; 119:e2122770119. [PMID: 36161928 PMCID: PMC9546554 DOI: 10.1073/pnas.2122770119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cellulose biosynthesis in sessile bacterial colonies originates in the membrane-integrated bacterial cellulose synthase (Bcs) AB complex. We utilize optical tweezers to measure single-strand cellulose biosynthesis by BcsAB from Rhodobacter sphaeroides. Synthesis depends on uridine diphosphate glucose, Mg2+, and cyclic diguanosine monophosphate, with the last displaying a retention time of ∼80 min. Below a stall force of 12.7 pN, biosynthesis is relatively insensitive to force and proceeds at a rate of one glucose addition every 2.5 s at room temperature, increasing to two additions per second at 37°. At low forces, conformational hopping is observed. Single-strand cellulose stretching unveiled a persistence length of 6.2 nm, an axial stiffness of 40.7 pN, and an ability for complexes to maintain a tight grip, with forces nearing 100 pN. Stretching experiments exhibited hysteresis, suggesting that cellulose microstructure underpinning robust biofilms begins to form during synthesis. Cellohexaose spontaneously binds to nascent single cellulose strands, impacting polymer mechanical properties and increasing BcsAB activity.
Collapse
|
5
|
Interactions between infernan and calcium: From the molecular level to the mechanical properties of microgels. Carbohydr Polym 2022; 292:119629. [DOI: 10.1016/j.carbpol.2022.119629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/05/2022] [Accepted: 05/14/2022] [Indexed: 11/20/2022]
|
6
|
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: 7] [Impact Index Per Article: 3.5] [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.
Collapse
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.
| |
Collapse
|
7
|
Jiang XZ, Yang L, Ventikos Y, Luo KH. Sodium ion transport across the endothelial glycocalyx layer under electric field conditions: A molecular dynamics study. J Chem Phys 2020; 153:105102. [PMID: 32933268 DOI: 10.1063/5.0014177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In the present research, the sodium ion transport across the endothelial glycocalyx layer (EGL) under an imposed electric field is investigated, for the first time, using a series of molecular dynamics simulations. The electric field is perpendicularly imposed on the EGL with varying strengths. The sodium ion molarity difference between the inner and outer layers of EGL, Δc, is used to quantify the sodium transport in the presence of the negatively charged glycocalyx sugar chains. Results suggest that a weak electric field increases Δc, regardless of whether the electric field is imposed perpendicularly inward or outward. By contrast, a strong electric field drives sodium ions to travel in the same orientation as the electric field. Scrutiny of the charge distribution of the glycocalyx sugar chains suggests that the electric field modifies the spatial layouts of glycocalyx atoms as it drives the transport of sodium ions. The modification in glycocalyx layouts further changes the inter-molecular interactions between glycocalyx sugar chains and sodium ions, thereby limiting the electric field control of ion transport. The sodium ions, in turn, alter the apparent bending stiffness of glycocalyx. Moreover, the negative charges of the glycocalyx sugar chains play an important role in maintaining structural stability of endothelial glycocalyx. Based on the findings, a hypothesis is proposed regarding the existence of a strength threshold of the electric field in controlling charged particles in the endothelium, which offers an alternative explanation for contrasting results in previous experimental observations.
Collapse
Affiliation(s)
- Xi Zhuo Jiang
- Department of Mechanical Engineering, University College London, Torrington Place, London WC1E 7JE, United Kingdom
| | - Lumeng Yang
- Department of Neurology, Huashan Hospital, Fudan University, No. 12 Wulumuqi Zhong Road, Shanghai 200040, People's Republic of China
| | - Yiannis Ventikos
- Department of Mechanical Engineering, University College London, Torrington Place, London WC1E 7JE, United Kingdom
| | - Kai H Luo
- Department of Mechanical Engineering, University College London, Torrington Place, London WC1E 7JE, United Kingdom
| |
Collapse
|
8
|
Wu Z, Beltran-Villegas DJ, Jayaraman A. Development of a New Coarse-Grained Model to Simulate Assembly of Cellulose Chains Due to Hydrogen Bonding. J Chem Theory Comput 2020; 16:4599-4614. [DOI: 10.1021/acs.jctc.0c00225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Zijie Wu
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
| | - Daniel J. Beltran-Villegas
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
| |
Collapse
|
9
|
Li H, Wu H, Li B, Gao Y, Zhao X, Zhang L. Molecular dynamics simulation of fracture mechanism in the double interpenetrated cross-linked polymer. POLYMER 2020. [DOI: 10.1016/j.polymer.2020.122571] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
10
|
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
| |
Collapse
|
11
|
Martin-Bertelsen B, Andersson E, Köhnke T, Hedlund A, Stigsson L, Olsson U. Revisiting the Dissolution of Cellulose in NaOH as "Seen" by X-rays. Polymers (Basel) 2020; 12:E342. [PMID: 32033419 PMCID: PMC7077394 DOI: 10.3390/polym12020342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/16/2020] [Accepted: 01/19/2020] [Indexed: 11/16/2022] Open
Abstract
Cotton production is reaching a global limit, leading to a growing demand for bio-based textile fibers produced by other means. Textile fibers based on regenerated cellulose from wood holds great potential, but in order to produce fibers, the components need to be dissolved in suitable solvents. Furthermore, the dissolution process of cellulose is not yet fully understood. In this study, we investigated the dissolution state of microcrystalline cellulose in aqueous NaOH by using primarily scattering methods. Contrary to previous findings, this study indicated that cellulose concentrations of up to 2 wt % are completely molecularly dissolved in 8 wt % NaOH. Scattering data furthermore revealed the presence of semi-flexible cylinders with stiff segments. In order to improve the dissolution capability of NaOH, the effects of different additives have been of interest. In this study, scattering data indicated that the addition of ZnO decreased the formation of aggregates, while the addition of PEG did not improve the dissolution properties significantly, although preliminary NMR data did suggest a weak attraction between PEG and cellulose. Overall, this study sheds further light on the dissolution of cellulose in NaOH and highlights the use of scattering methods to assess solvent quality.
Collapse
Affiliation(s)
| | - Erika Andersson
- Division of Physical Chemistry, Lund University, 221 00 Lund, Sweden
| | - Tobias Köhnke
- Division Materials and Production, RISE Research Institutes of Sweden, 431 53 Mölndal, Sweden
| | - Artur Hedlund
- Division Materials and Production, RISE Research Institutes of Sweden, 431 53 Mölndal, Sweden
| | - Lars Stigsson
- KIRAM AB, Norra Villavägen 17, 237 34 Bjärred, Sweden
| | - Ulf Olsson
- Division of Physical Chemistry, Lund University, 221 00 Lund, Sweden
| |
Collapse
|
12
|
Mintis DG, Dompé M, Kamperman M, Mavrantzas VG. Effect of Polymer Concentration on the Structure and Dynamics of Short Poly(N,N-dimethylaminoethyl methacrylate) in Aqueous Solution: A Combined Experimental and Molecular Dynamics Study. J Phys Chem B 2019; 124:240-252. [DOI: 10.1021/acs.jpcb.9b08966] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dimitris G. Mintis
- Department of Chemical Engineering, University of Patras & FORTH-ICE/HT, GR 26504 Patras, Greece
| | - Marco Dompé
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Marleen Kamperman
- Polymer Science, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Vlasis G. Mavrantzas
- Department of Chemical Engineering, University of Patras & FORTH-ICE/HT, GR 26504 Patras, Greece
- Particle Technology Laboratory, Department of Mechanical and Process Engineering, ETH Zürich, CH-8092 Zürich, Switzerland
| |
Collapse
|
13
|
Charvet A, Vergelati C, Sotta P, Long DR. Damage Mechanisms of Plasticized Cellulose Acetate under Tensile Deformation Studied by Ultrasmall-Angle X-ray Scattering. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00858] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Agathe Charvet
- Laboratoire des polymères et Matériaux Avancés, UMR 5268 Solvay/CNRS, Solvay in Axel’One, 87 avenue des Frères Perret, 69192 Saint-Fons, France
| | - Caroll Vergelati
- Laboratoire des polymères et Matériaux Avancés, UMR 5268 Solvay/CNRS, Solvay in Axel’One, 87 avenue des Frères Perret, 69192 Saint-Fons, France
| | - Paul Sotta
- Laboratoire des polymères et Matériaux Avancés, UMR 5268 Solvay/CNRS, Solvay in Axel’One, 87 avenue des Frères Perret, 69192 Saint-Fons, France
| | - Didier R. Long
- Laboratoire des polymères et Matériaux Avancés, UMR 5268 Solvay/CNRS, Solvay in Axel’One, 87 avenue des Frères Perret, 69192 Saint-Fons, France
| |
Collapse
|
14
|
Zeman CJ, Schanze KS. Elucidating the Effects of Solvating Side Chains on the Rigidity and Aggregation Tendencies of Conjugated Polymers with Molecular Dynamics Simulations Using DFT Tight Binding. J Phys Chem A 2019; 123:3293-3299. [DOI: 10.1021/acs.jpca.8b12169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Charles J. Zeman
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Kirk S. Schanze
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
| |
Collapse
|
15
|
|
16
|
Jacinto-Méndez D, Villada-Balbuena M, Cruz y Cruz SG, Carbajal-Tinoco MD. Static structure of sodium polystyrene sulfonate solutions obtained through a coarse-grained model. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1471225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Damián Jacinto-Méndez
- Instituto Politécnico Nacional, UPIITA, Cd. de México, Mexico
- Departamento de Física, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Cd. de México, Mexico
| | - Mario Villada-Balbuena
- Departamento de Física, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Cd. de México, Mexico
| | | | - Mauricio D. Carbajal-Tinoco
- Departamento de Física, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Cd. de México, Mexico
| |
Collapse
|
17
|
Weishaupt R, Heuberger L, Siqueira G, Gutt B, Zimmermann T, Maniura-Weber K, Salentinig S, Faccio G. Enhanced Antimicrobial Activity and Structural Transitions of a Nanofibrillated Cellulose-Nisin Biocomposite Suspension. ACS APPLIED MATERIALS & INTERFACES 2018; 10:20170-20181. [PMID: 29767501 DOI: 10.1021/acsami.8b04470] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Resistance to antibiotics has posed a high demand for novel strategies to fight bacterial infections. Antimicrobial peptides (AMPs) are a promising alternative to conventional antibiotics. However, their poor solubility in water and sensitivity to degradation has limited their application. Here, we report the design of a smart, pH-responsive antimicrobial nanobiocomposite material based on the AMP nisin and 2,2,6,6-tetramethyl-1-piperidinyloxyl-oxidized nanofibrillated cellulose (TONFC). Morphological transformations of the nanoscale structure of nisin functionalized-TONFC fibrils were discovered at pH values between 5.8 and 8.0 using small-angle X-ray scattering. Complementary ζ potential measurements indicate that electrostatic attractions between the negatively charged TONFC surface and the positively charged nisin molecules are responsible for the integration of nisin. Modification of the pH level or increasing the ionic strength reduces the nisin binding capacity of TONFC. Biological evaluation studies using a bioluminescence-based reporter strain of Bacillus subtilis and a clinically relevant strain of Staphylococcus aureus indicated a significantly higher antimicrobial activity of the TONFC-nisin biocomposite compared to the pure nisin against both strains under physiological pH and ionic strength conditions. The in-depth characterization of this new class of antimicrobial biocomposite material based on nanocellulose and nisin may guide the rational design of sustainable antimicrobial materials.
Collapse
Affiliation(s)
- Ramon Weishaupt
- Laboratory for Biointerfaces , Empa, Swiss Federal Laboratories for Materials Science and Technology , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
| | - Lukas Heuberger
- Laboratory for Biointerfaces , Empa, Swiss Federal Laboratories for Materials Science and Technology , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
| | - Gilberto Siqueira
- Laboratory for Applied Wood Materials , Empa, Swiss Federal Laboratories for Materials Science and Technology , Überlandstrasse 129 , CH-8600 Dübendorf , Switzerland
| | - Beatrice Gutt
- Laboratory for Biointerfaces , Empa, Swiss Federal Laboratories for Materials Science and Technology , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
| | - Tanja Zimmermann
- Laboratory for Applied Wood Materials , Empa, Swiss Federal Laboratories for Materials Science and Technology , Überlandstrasse 129 , CH-8600 Dübendorf , Switzerland
| | - Katharina Maniura-Weber
- Laboratory for Biointerfaces , Empa, Swiss Federal Laboratories for Materials Science and Technology , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
| | - Stefan Salentinig
- Laboratory for Biointerfaces , Empa, Swiss Federal Laboratories for Materials Science and Technology , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
| | - Greta Faccio
- Laboratory for Biointerfaces , Empa, Swiss Federal Laboratories for Materials Science and Technology , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
| |
Collapse
|
18
|
de Oliveira TE, Marques CM, Netz PA. Molecular dynamics study of the LCST transition in aqueous poly(N-n-propylacrylamide). Phys Chem Chem Phys 2018; 20:10100-10107. [PMID: 29589029 DOI: 10.1039/c8cp00481a] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The breadth of technological applications of smart polymers relies on the possibility of tuning their molecular structure to respond to external stimuli. In this context, N-substituted acrylamide-based polymers are widely studied thermoresponsive polymers. Poly(N-n-propylacrylamide) (PNnPAm), which is a structural isomer of the poly(N-isopropylacrylamide) (PNIPAm) exhibits however, a lower phase transition in aqueous solution. In this work, we use all-atom molecular dynamics simulations of PNnPAm in aqueous solutions to study, from a microscopic point-of-view, the influence of chain size and concentration on the LCST of PNnPAm. Our analysis shows that the collapse of a single oligomer of PNnPAm upon heating is dependent on the chain length and corresponds to a complex interplay between hydration and intermolecular interactions. Analysis of systems with multiple chains shows an aggregation of PNnPAm chains above the LCST.
Collapse
Affiliation(s)
- Tiago E de Oliveira
- Institut Charles Sadron, Université de Strasbourg, CNRS, Strasbourg, France.
| | | | | |
Collapse
|
19
|
Mredha MTI, Guo YZ, Nonoyama T, Nakajima T, Kurokawa T, Gong JP. A Facile Method to Fabricate Anisotropic Hydrogels with Perfectly Aligned Hierarchical Fibrous Structures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30. [PMID: 29341264 DOI: 10.1002/adma.201704937] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/19/2017] [Indexed: 05/11/2023]
Abstract
Natural structural materials (such as tendons and ligaments) are comprised of multiscale hierarchical architectures, with dimensions ranging from nano- to macroscale, which are difficult to mimic synthetically. Here a bioinspired, facile method to fabricate anisotropic hydrogels with perfectly aligned multiscale hierarchical fibrous structures similar to those of tendons and ligaments is reported. The method includes drying a diluted physical hydrogel in air by confining its length direction. During this process, sufficiently high tensile stress is built along the length direction to align the polymer chains and multiscale fibrous structures (from nano- to submicro- to microscale) are spontaneously formed in the bulk material, which are well-retained in the reswollen gel. The method is useful for relatively rigid polymers (such as alginate and cellulose), which are susceptible to mechanical signal. By controlling the drying with or without prestretching, the degree of alignment, size of superstructures, and the strength of supramolecular interactions can be tuned, which sensitively influence the strength and toughness of the hydrogels. The mechanical properties are comparable with those of natural ligaments. This study provides a general strategy for designing hydrogels with highly ordered hierarchical structures, which opens routes for the development of many functional biomimetic materials for biomedical applications.
Collapse
Affiliation(s)
| | - Yun Zhou Guo
- Graduate School of Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Takayuki Nonoyama
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
- Global Station for Soft Matter, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, 001-0021, Japan
| | - Tasuku Nakajima
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
- Global Station for Soft Matter, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, 001-0021, Japan
| | - Takayuki Kurokawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
- Global Station for Soft Matter, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, 001-0021, Japan
| | - Jian Ping Gong
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
- Global Station for Soft Matter, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, 001-0021, Japan
| |
Collapse
|
20
|
Zhang J, Wu P. Grafting Polymers from Poly(2,6-dimethyl-1,4-phenylene oxide) as New Thermoplastics. MACROMOL CHEM PHYS 2017. [DOI: 10.1002/macp.201700023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jiuyang Zhang
- School of Chemistry and Chemical Engineering; Southeast University; Nanjing 211189 China
| | - Peng Wu
- Department of Pathology; Jiangsu Jiankang Vocational College; Nanjing 210029 China
| |
Collapse
|
21
|
Nakano T. Modeling of the morphological change of cellulose microfibrils caused with aqueous NaOH solution: the longitudinal contraction and laterally swelling during decrystallization. J Mol Model 2017; 23:129. [PMID: 28332081 DOI: 10.1007/s00894-017-3307-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 03/06/2017] [Indexed: 11/28/2022]
Abstract
The conformation of cellulose microfibrils treated with aqueous NaOH was modeled as partially decrystallized cellulose chains before completing conversion to cellulose II, in order to elucidate the change in morphology of ramie fiber caused by NaOH treatment. Equations for the relative length and width of the microfibrils were derived on the basis of partially decrystallized microfibrils modeling. Each equation contains four parameters, n, β, w c , and c r , which correspond to the number of glucose residues between periodic defects along the untreated ramie cellulose microfibrils, the extension ratio of amorphous cellulose chain along length, the cross-section crystallinity, and the correction term of crystallinity, respectively. The validity of the derived equations was confirmed by two types of simulations. One is performed using experimental data L/L 0 and W/W 0 as a function of crystallinity, while the other is done using the relationship between the relative length and width obtained from the experimental data, which is independent of crystallinity, was performed. The best-fit simulation was obtained under n = 277, β = 2.813, and c r w c = 0.671 for the former and under n = 301 and β = 2.792 for the latter. These values of n and β correspond closely to the values reported in references for ramie microfibrils. Both simulation results show that macroscopic changes in the morphology of ramie fibers is attributable to the changes in cellulose chain conformation in the decrystallized regions created along the microfibrils upon NaOH treatment.
Collapse
|
22
|
Zhang J, Schneiderman DK, Li T, Hillmyer MA, Bates FS. Design of Graft Block Polymer Thermoplastics. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b02033] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jiuyang Zhang
- School
of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | | | | | | | | |
Collapse
|
23
|
Ricarte RG, Lodge TP, Hillmyer MA. Nanoscale Concentration Quantification of Pharmaceutical Actives in Amorphous Polymer Matrices by Electron Energy-Loss Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:7411-9. [PMID: 27419264 DOI: 10.1021/acs.langmuir.6b01745] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We demonstrated the use of electron energy-loss spectroscopy (EELS) to evaluate the composition of phenytoin:hydroxypropyl methylcellulose acetate succinate (HPMCAS) spin-coated solid dispersions (SDs). To overcome the inability of bright-field and high-angle annular dark-field TEM imaging to distinguish between glassy drug and polymer, we used the π-π* transition peak in the EELS spectrum to detect phenytoin within the HPMCAS matrix of the SD. The concentration of phenytoin within SDs of 10, 25, and 50 wt % drug loading was quantified by a multiple least-squares analysis. Evaluating the concentration of 50 different regions in each SD, we determined that phenytoin and HPMCAS are intimately mixed at a length scale of 200 nm, even for drug loadings up to 50 wt %. At length scales below 100 nm, the variance of the measured phenytoin concentration increases; we speculate that this increase is due to statistical fluctuations in local concentration and chemical changes induced by electron irradiation. We also performed EELS analysis of an annealed 25 wt % phenytoin SD and showed that the technique can resolve concentration differences between regions that are less than 50 nm apart. Our findings indicate that EELS is a useful tool for quantifying, with high accuracy and sub-100 nm spatial resolution, the composition of many pharmaceutical and soft matter systems.
Collapse
Affiliation(s)
- Ralm G Ricarte
- Department of Chemical Engineering and Materials Science and ‡Department of Chemistry, University of Minnesota , Minneapolis, Minnesota 55455-0431, United States
| | - Timothy P Lodge
- Department of Chemical Engineering and Materials Science and ‡Department of Chemistry, University of Minnesota , Minneapolis, Minnesota 55455-0431, United States
| | - Marc A Hillmyer
- Department of Chemical Engineering and Materials Science and ‡Department of Chemistry, University of Minnesota , Minneapolis, Minnesota 55455-0431, United States
| |
Collapse
|
24
|
Zhang T, Luo T. Role of Chain Morphology and Stiffness in Thermal Conductivity of Amorphous Polymers. J Phys Chem B 2016; 120:803-12. [DOI: 10.1021/acs.jpcb.5b09955] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Teng Zhang
- Aerospace and Mechanical Engineering and ‡Center for Sustainable
Energy at
Notre Dame, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Tengfei Luo
- Aerospace and Mechanical Engineering and ‡Center for Sustainable
Energy at
Notre Dame, University of Notre Dame, Notre Dame, Indiana 46556, United States
| |
Collapse
|
25
|
Understanding nanocellulose chirality and structure-properties relationship at the single fibril level. Nat Commun 2015; 6:7564. [PMID: 26108282 PMCID: PMC4491835 DOI: 10.1038/ncomms8564] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 05/19/2015] [Indexed: 12/12/2022] Open
Abstract
Nanocellulose fibrils are ubiquitous in nature and nanotechnologies but their mesoscopic structural assembly is not yet fully understood. Here we study the structural features of rod-like cellulose nanoparticles on a single particle level, by applying statistical polymer physics concepts on electron and atomic force microscopy images, and we assess their physical properties via quantitative nanomechanical mapping. We show evidence of right-handed chirality, observed on both bundles and on single fibrils. Statistical analysis of contours from microscopy images shows a non-Gaussian kink angle distribution. This is inconsistent with a structure consisting of alternating amorphous and crystalline domains along the contour and supports process-induced kink formation. The intrinsic mechanical properties of nanocellulose are extracted from nanoindentation and persistence length method for transversal and longitudinal directions, respectively. The structural analysis is pushed to the level of single cellulose polymer chains, and their smallest associated unit with a proposed 2 × 2 chain-packing arrangement. Cellulose is a material found in many different biological systems, but the fine structure at the single-molecule level is still being assessed. Here, the authors present high-resolution imaging of cellulose structures at the single particle level, finding evidence of chirality in bundles and fibrils.
Collapse
|
26
|
Frank M. Conformational analysis of oligosaccharides and polysaccharides using molecular dynamics simulations. Methods Mol Biol 2015; 1273:359-77. [PMID: 25753720 DOI: 10.1007/978-1-4939-2343-4_22] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).
Collapse
Affiliation(s)
- Martin Frank
- Biognos AB, Generatorsgatan 1, 41705, Göteborg, Sweden,
| |
Collapse
|
27
|
Mostofian B, Cheng X, Smith JC. Replica-exchange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride. J Phys Chem B 2014; 118:11037-49. [PMID: 25180945 DOI: 10.1021/jp502889c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Ionic liquids have become a popular solvent for cellulose pretreatment in biorefineries due to their efficiency in dissolution and their reusability. Understanding the interactions between cations, anions, and cellulose is key to the development of better solvents and the improvement of pretreatment conditions. While previous studies described the interactions between ionic liquids and cellulose fibers, shedding light on the initial stages of the cellulose dissolution process, we study the end state of that process by exploring the structure and dynamics of a single cellulose decamer solvated in 1-butyl-3-methyl-imidazolium chloride (BmimCl) and in water using replica-exchange molecular dynamics. In both solvents, global structural features of the cellulose chain are similar. However, analyses of local structural properties show that cellulose explores greater conformational variability in the ionic liquid than in water. For instance, in BmimCl the cellulose intramolecular hydrogen bond O3H'···O5 is disrupted more often resulting in greater flexibility of the solute. Our results indicate that the cellulose chain is more dynamic in BmimCl than in water, which may play a role in the favorable dissolution of cellulose in the ionic liquid. Calculation of the configurational entropy of the cellulose decamer confirms its higher conformational flexibility in BmimCl than in water at elevated temperatures.
Collapse
Affiliation(s)
- Barmak Mostofian
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | | | | |
Collapse
|
28
|
Cruz-Chu ER, Malafeev A, Pajarskas T, Pivkin IV, Koumoutsakos P. Structure and response to flow of the glycocalyx layer. Biophys J 2014; 106:232-43. [PMID: 24411255 DOI: 10.1016/j.bpj.2013.09.060] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 09/03/2013] [Accepted: 09/30/2013] [Indexed: 12/31/2022] Open
Abstract
The glycocalyx is a sugar-rich layer located at the luminal part of the endothelial cells. It is involved in key metabolic processes and its malfunction is related to several diseases. To understand the function of the glycocalyx, a molecular level characterization is necessary. In this article, we present large-scale molecular-dynamics simulations that provide a comprehensive description of the structure and dynamics of the glycocalyx. We introduce the most detailed, to-date, all-atom glycocalyx model, composed of lipid bilayer, proteoglycan dimers, and heparan sulfate chains with realistic sequences. Our results reveal the folding of proteoglycan ectodomain and the extended conformation of heparan sulfate chains. Furthermore, we study the glycocalyx response under shear flow and its role as a flypaper for binding fibroblast growth factors (FGFs), which are involved in diverse functions related to cellular differentiation, including angiogenesis, morphogenesis, and wound healing. The simulations show that the glycocalyx increases the effective concentration of FGFs, leading to FGF oligomerization, and acts as a lever to transfer mechanical stimulus into the cytoplasmic side of endothelial cells.
Collapse
Affiliation(s)
- Eduardo R Cruz-Chu
- Computational Science and Engineering Laboratory, ETH, Zurich, Switzerland
| | - Alexander Malafeev
- Scientific Computing Group, Institute of Computational Science, University of Lugano, Lugano, Switzerland
| | | | - Igor V Pivkin
- Scientific Computing Group, Institute of Computational Science, University of Lugano, Lugano, Switzerland
| | - Petros Koumoutsakos
- Computational Science and Engineering Laboratory, ETH, Zurich, Switzerland; Scientific Computing Group, Institute of Computational Science, University of Lugano, Lugano, Switzerland.
| |
Collapse
|
29
|
Gumbart JC, Beeby M, Jensen GJ, Roux B. Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations. PLoS Comput Biol 2014; 10:e1003475. [PMID: 24586129 PMCID: PMC3930494 DOI: 10.1371/journal.pcbi.1003475] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 01/05/2014] [Indexed: 12/24/2022] Open
Abstract
Bacteria face the challenging requirement to maintain their shape and avoid rupture due to the high internal turgor pressure, but simultaneously permit the import and export of nutrients, chemical signals, and virulence factors. The bacterial cell wall, a mesh-like structure composed of cross-linked strands of peptidoglycan, fulfills both needs by being semi-rigid, yet sufficiently porous to allow diffusion through it. How the mechanical properties of the cell wall are determined by the molecular features and the spatial arrangement of the relatively thin strands in the larger cellular-scale structure is not known. To examine this issue, we have developed and simulated atomic-scale models of Escherichia coli cell walls in a disordered circumferential arrangement. The cell-wall models are found to possess an anisotropic elasticity, as known experimentally, arising from the orthogonal orientation of the glycan strands and of the peptide cross-links. Other features such as thickness, pore size, and disorder are also found to generally agree with experiments, further supporting the disordered circumferential model of peptidoglycan. The validated constructs illustrate how mesoscopic structure and behavior emerge naturally from the underlying atomic-scale properties and, furthermore, demonstrate the ability of all-atom simulations to reproduce a range of macroscopic observables for extended polymer meshes. The structure of the bacterial cell wall has been a point of controversy and contention since it was first discovered. Although the basic chemical composition of peptidoglycan, the key constituent of the cell wall, is now well established, its long-range organization is not. This dearth of information at the mesoscopic scale is a result of the inability of experimental imaging techniques to simultaneously visualize both the atomic-level detail of the peptidoglycan network and its macroscopic arrangement around the bacterium. Now, using molecular dynamics (MD) simulations, we have carefully constructed and validated models of sections of the Escherichia coli cell wall in full atomic detail. By comparing various properties of these models, including elasticity, pore size, and thickness with experiments, we can discriminate between them, resolving which best represents the native wall structure. In doing so, our study provides approaches for connecting measurements made in atomic-scale MD simulations with large-scale and even macroscopic properties.
Collapse
Affiliation(s)
- James C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail: (JCG); (BR)
| | - Morgan Beeby
- Imperial College London, South Kensington Campus, London, United Kingdom
| | - Grant J. Jensen
- California Institute of Technology and Howard Hughes Medical Institute, Pasadena, California, United States of America
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology and Gordon Center for Integrative Science, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (JCG); (BR)
| |
Collapse
|
30
|
Glass DC, Moritsugu K, Cheng X, Smith JC. REACH Coarse-Grained Simulation of a Cellulose Fiber. Biomacromolecules 2012; 13:2634-44. [DOI: 10.1021/bm300460f] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dennis C. Glass
- UT/ORNL
Center for
Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008 Oak Ridge, Tennessee 37831-6309,
United States
- Graduate School
of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Kei Moritsugu
- Research Program for
Computational Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Xiaolin Cheng
- UT/ORNL
Center for
Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008 Oak Ridge, Tennessee 37831-6309,
United States
- Department of Biochemistry
and Molecular and Cellular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland
Avenue, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- UT/ORNL
Center for
Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008 Oak Ridge, Tennessee 37831-6309,
United States
- Department of Biochemistry
and Molecular and Cellular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland
Avenue, Knoxville, Tennessee 37996, United States
| |
Collapse
|
31
|
Wessig P, Möllnitz K. Building Blocks for Oligospiroketal (OSK) Rods and Evaluation of Their Influence on Rod Rigidity. J Org Chem 2012; 77:3907-20. [DOI: 10.1021/jo300266b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pablo Wessig
- Universität Potsdam, Institut für Chemie, Karl-Liebknecht-Str. 24-25, D-14476
Potsdam, Germany
| | - Kristian Möllnitz
- Universität Potsdam, Institut für Chemie, Karl-Liebknecht-Str. 24-25, D-14476
Potsdam, Germany
| |
Collapse
|
32
|
Borgogna M, Bellich B, Cesàro A. Marine polysaccharides in microencapsulation and application to aquaculture: "from sea to sea". Mar Drugs 2011; 9:2572-2604. [PMID: 22363241 PMCID: PMC3280570 DOI: 10.3390/md9122572] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 11/18/2011] [Accepted: 11/22/2011] [Indexed: 12/15/2022] Open
Abstract
This review's main objective is to discuss some physico-chemical features of polysaccharides as intrinsic determinants for the supramolecular structures that can efficiently provide encapsulation of drugs and other biological entities. Thus, the general characteristics of some basic polysaccharides are outlined in terms of their conformational, dynamic and thermodynamic properties. The analysis of some polysaccharide gelling properties is also provided, including the peculiarity of the charged polysaccharides. Then, the way the basic physical chemistry of polymer self-assembly is made in practice through the laboratory methods is highlighted. A description of the several literature procedures used to influence molecular interactions into the macroscopic goal of the encapsulation is given with an attempt at classification. Finally, a practical case study of specific interest, the use of marine polysaccharide matrices for encapsulation of vaccines in aquaculture, is reported.
Collapse
Affiliation(s)
| | | | - Attilio Cesàro
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 1-I-34127 Trieste, Italy; (M.B.); (B.B.)
| |
Collapse
|
33
|
Muller F, Manet S, Jean B, Chambat G, Boué F, Heux L, Cousin F. SANS Measurements of Semiflexible Xyloglucan Polysaccharide Chains in Water Reveal Their Self-Avoiding Statistics. Biomacromolecules 2011; 12:3330-6. [DOI: 10.1021/bm200881x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- François Muller
- Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif sur Yvette Cedex, France
| | - Sabine Manet
- CERMAV, CNRS UPR 5301, BP 53 38041 Grenoble Cedex, France
| | - Bruno Jean
- CERMAV, CNRS UPR 5301, BP 53 38041 Grenoble Cedex, France
| | - Gérard Chambat
- CERMAV, CNRS UPR 5301, BP 53 38041 Grenoble Cedex, France
| | - François Boué
- Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif sur Yvette Cedex, France
| | - Laurent Heux
- CERMAV, CNRS UPR 5301, BP 53 38041 Grenoble Cedex, France
| | - Fabrice Cousin
- Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif sur Yvette Cedex, France
| |
Collapse
|
34
|
Moon RJ, Martini A, Nairn J, Simonsen J, Youngblood J. Cellulose nanomaterials review: structure, properties and nanocomposites. Chem Soc Rev 2011; 40:3941-94. [PMID: 21566801 DOI: 10.1039/c0cs00108b] [Citation(s) in RCA: 2542] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them. It summarizes cellulose nanoparticles in terms of particle morphology, crystal structure, and properties. Also described are the self-assembly and rheological properties of cellulose nanoparticle suspensions. The methodology of composite processing and resulting properties are fully covered, with an emphasis on neat and high fraction cellulose composites. Additionally, advances in predictive modeling from molecular dynamic simulations of crystalline cellulose to the continuum modeling of composites made with such particles are reviewed (392 references).
Collapse
Affiliation(s)
- Robert J Moon
- The Forest Products Laboratory, US Forest Service, Madison, WI, USA.
| | | | | | | | | |
Collapse
|
35
|
Modeling Textural Processes during Self-Assembly of Plant-Based Chiral-Nematic Liquid Crystals. Polymers (Basel) 2010. [DOI: 10.3390/polym2040766] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
36
|
Hansen HS, Hünenberger PH. A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers. J Comput Chem 2010; 32:998-1032. [PMID: 21387332 DOI: 10.1002/jcc.21675] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 08/12/2010] [Accepted: 08/17/2010] [Indexed: 11/07/2022]
Abstract
This article presents a reoptimization of the GROMOS 53A6 force field for hexopyranose-based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate systems) into a new version 56A(CARBO) (nearly equivalent to 53A6 for non-carbohydrate systems). This reoptimization was found necessary to repair a number of shortcomings of the 53A6 (45A4) parameter set and to extend the scope of the force field to properties that had not been included previously into the parameterization procedure. The new 56A(CARBO) force field is characterized by: (i) the formulation of systematic build-up rules for the automatic generation of force-field topologies over a large class of compounds including (but not restricted to) unfunctionalized polyhexopyranoses with arbritrary connectivities; (ii) the systematic use of enhanced sampling methods for inclusion of experimental thermodynamic data concerning slow or unphysical processes into the parameterization procedure; and (iii) an extensive validation against available experimental data in solution and, to a limited extent, theoretical (quantum-mechanical) data in the gas phase. At present, the 56A(CARBO) force field is restricted to compounds of the elements C, O, and H presenting single bonds only, no oxygen functions other than alcohol, ether, hemiacetal, or acetal, and no cyclic segments other than six-membered rings (separated by at least one intermediate atom). After calibration, this force field is shown to reproduce well the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers. As a result, the 56A(CARBO) force field should be suitable for: (i) the characterization of the dynamics of pyranose ring conformational transitions (in simulations on the microsecond timescale); (ii) the investigation of systems where alternative ring conformations become significantly populated; (iii) the investigation of anomerization or epimerization in terms of free-energy differences; and (iv) the design of simulation approaches accelerating the anomerization process along an unphysical pathway.
Collapse
Affiliation(s)
- Halvor S Hansen
- Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
| | | |
Collapse
|
37
|
Autieri E, Sega M, Pederiva F, Guella G. Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation. J Chem Phys 2010; 133:095104. [DOI: 10.1063/1.3476466] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
38
|
Zakharov VS, Brodskaya EN. Computer simulation of cellulose solvation in polar solvents. POLYMER SCIENCE SERIES A 2009. [DOI: 10.1134/s0965545x09100058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
39
|
Xia J, Margulis CJ. Computational Study of the Conformational Structures of Saccharides in Solution Based on J Couplings and the “Fast Sugar Structure Prediction Software”. Biomacromolecules 2009; 10:3081-8. [DOI: 10.1021/bm900756q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Junchao Xia
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242
| | | |
Collapse
|
40
|
Marsano E, Corsini P, Canetti M, Freddi G. Regenerated cellulose-silk fibroin blends fibers. Int J Biol Macromol 2008; 43:106-14. [DOI: 10.1016/j.ijbiomac.2008.03.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 03/28/2008] [Accepted: 03/31/2008] [Indexed: 10/22/2022]
|
41
|
Kuik JAV, Vincent SJF, Leeflang BR, Kroon-Batenburg LMJ, Kamerling JP. Conformational analysis in aqueous solution and estimation of the persistence length of exopolysaccharides produced by Lactobacillus helveticus Lh59 and Streptococcus macedonicus Sc136. CAN J CHEM 2006. [DOI: 10.1139/v06-055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The conformations of two exopolysaccharides, one produced by Lactobacillus helveticus Lh59 and one by Streptococcus macedonicus Sc136, were investigated by molecular modelling to get insight into their physical properties. In particular, the influence of side chains and glycosidic linkage types on the overall shapes and persistence lengths of the polysaccharides were studied. It appeared that the side chains had only minor effects on the persistence lengths of the polysaccharides, with the exception of the monosaccharide residue directly attached to the backbone. The extensiveness of the backbone is enhanced by β-D-Hexp-(1→4) structural elements, whereas α-D-Hexp-(1→3) and α-D-Hexp-(1→4) elements create structural variability by introducing bends. The occurrence of either (1→5)- or (1→6)-linked monosaccharides, resulting in one extra bond between monosaccharide units, causes the overall flexibility of the polysaccharide chain to be enhanced and extensiveness to be reduced. The presence of such flexible linkages in the backbone leads to a shorter persistence length than when present in the side chain: a value of only 4.5 nm was found for the L. helveticus Lh59 EPS with a (1→5) linkage in the backbone, and a value of 8.5 nm for the S. macedonicus Sc136 EPS with two (1→6) linkages in the side chain.Key words: conformational analysis, exopolysaccharide, Lactobacillus helveticus, molecular modelling, persistence length, Streptococcus macedonicus.
Collapse
|
42
|
Aeberhardt K, Laumer JYDS, Bouquerand PE, Normand V. Ultrasonic wave spectroscopy study of sugar oligomers and polysaccharides in aqueous solutions: The hydration length concept. Int J Biol Macromol 2005; 36:275-82. [PMID: 16095681 DOI: 10.1016/j.ijbiomac.2005.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Accepted: 04/06/2005] [Indexed: 10/25/2022]
Abstract
The determination of apparent persistence length and radius of gyration of maltodextrins in water is achievable through high-resolution ultrasonic spectroscopy measurements. Classical hydration number for those carbohydrates is characteristic of an apparent persistence degree of polymerisation of the polymer. A force-field based molecular modeling of a 10DP malto-oligomer allows measurement of the corresponding length for the lowest energetic conformation in solution. A good agreement between the apparent radii of gyration determined by this technique and the freely rotating polymer chain model is found with radii of gyration calculated from the intrinsic viscosity.
Collapse
Affiliation(s)
- Kasia Aeberhardt
- Firmenich S.A., 7 Rue de la Bergère, 1217 Meyrin 2, Geneva, Switzerland
| | | | | | | |
Collapse
|
43
|
Abstract
A new parameter set (referred to as 45A4) is developed for the explicit-solvent simulation of hexopyranose-based carbohydrates. This set is compatible with the most recent version of the GROMOS force field for proteins, nucleic acids, and lipids, and the SPC water model. The parametrization procedure relies on: (1) reassigning the atomic partial charges based on a fit to the quantum-mechanical electrostatic potential around a trisaccharide; (2) refining the torsional potential parameters associated with the rotations of the hydroxymethyl, hydroxyl, and anomeric alkoxy groups by fitting to corresponding quantum-mechanical profiles for hexopyranosides; (3) adapting the torsional potential parameters determining the ring conformation so as to stabilize the (experimentally predominant) (4)C(1) chair conformation. The other (van der Waals and nontorsional covalent) parameters and the rules for third and excluded neighbors are taken directly from the most recent version of the GROMOS force field (except for one additional exclusion). The new set is general enough to define parameters for any (unbranched) hexopyranose-based mono-, di-, oligo- or polysaccharide. In the present article, this force field is validated for a limited set of monosaccharides (alpha- and beta-D-glucose, alpha- and beta-D-galactose) and disaccharides (trehalose, maltose, and cellobiose) in solution, by comparing the results of simulations to available experimental data. More extensive validation will be the scope of a forthcoming article. (c) 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1400-1412, 2005.
Collapse
Affiliation(s)
- Roberto D Lins
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, CH-1015 Lausanne, Switzerland
| | | |
Collapse
|
44
|
Zhou S, Xu C, Wang J, Golas P, Batteas J, Kreeger L. Phase behavior of cationic hydroxyethyl cellulose-sodium dodecyl sulfate mixtures: effects of molecular weight and ethylene oxide side chain length of polymers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2004; 20:8482-8489. [PMID: 15379464 DOI: 10.1021/la049142n] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Novel cationic hydroxyethyl cellulose (HEC) polymers with different molecular weights (1.1 x 10(5) to 1.7 x 10(6) g/mol) and ethylene oxide (EO) side chain lengths (1.5-2.9 EO units) were mixed with sodium dodecyl sulfate (SDS) in aqueous solutions. The phase diagrams of cationic HEC-SDS complexes were determined in the dilute polymer concentration regime (< 0.5 wt %) with gradual addition of SDS molecules. The viscosity and structures of the complexes during the phase evolution were studied using rheometry and dynamic light scattering. The gradual addition of SDS first induced interchain associations with the bound SDS aggregates serving as cross-linkers to form an open network structure, producing a very broad size distribution and high viscosities of the complex solutions, and then condensed the network and induced a structure reorganization, resulting in globular aggregates with narrow size distributions. The growth of these globular aggregates in size eventually led to macroscopic sedimentation near charge neutralization. Further addition of SDS randomly broke the sedimentary aggregates into small particles and SDS micelles with low solution viscosities. The effects of molecular weight and EO side chain length of polymers on the phase boundary, viscosity, and structure of cationic HEC-SDS complexes were discussed.
Collapse
Affiliation(s)
- Shuiqin Zhou
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, 10314, USA.
| | | | | | | | | | | |
Collapse
|
45
|
Queyroy S, Müller-Plathe F, Brown D. Molecular Dynamics Simulations of Cellulose Oligomers: Conformational Analysis. MACROMOL THEOR SIMUL 2004. [DOI: 10.1002/mats.200300054] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
46
|
Mazeau K, Heux L. Molecular Dynamics Simulations of Bulk Native Crystalline and Amorphous Structures of Cellulose. J Phys Chem B 2003. [DOI: 10.1021/jp0219395] [Citation(s) in RCA: 253] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- K. Mazeau
- CERMAV-CNRS, Université J. Fourier, BP 53, 30841 Grenoble Cedex 9, France
| | - L. Heux
- CERMAV-CNRS, Université J. Fourier, BP 53, 30841 Grenoble Cedex 9, France
| |
Collapse
|
47
|
Comparative analysis of ganglioside conformations by MD simulations: implications for specific recognition by proteins. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0166-1280(01)00813-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
48
|
Vasudevan SV, Balaji PV. Molecular dynamics simulations of alpha2 --> 8-linked disialoside: conformational analysis and implications for binding to proteins. Biopolymers 2002; 63:168-80. [PMID: 11787005 DOI: 10.1002/bip.10019] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Computational methods have played a key role in elucidating the various three-dimensional structures of oligosaccharides. Such structural information, together with other experimental data, leads to a better understanding of the role of oligosaccharide in various biological processes. The disialoside Neu5Ac-alpha2-->8-Neu5Ac appears as the terminal glycan in glycoproteins and glycolipids, and is known to play an important role in various events of cellular communication. Neurotoxins such as botulinum and tetanus require Neu5Ac-alpha2 --> 8-Neu5Ac for infecting the host. Glycoconjugates containing this disialoside and the enzymes catalyzing their biosynthesis are also regulated during cell growth, development, and differentiation. Unlike other biologically relevant disaccharides that have only two linkage bonds, the alpha2-->8-linked disialoside has four: C2-O, O-C8', C8'-C7', and C7'-C6'. The present report describes the results from nine 1 ns MD simulations of alpha2-->8-linked disialoside (Neu5Ac-alpha2-->8-Neu5Ac); simulations were run using GROMOS96 by explicitly considering the solvent molecules. Conformations around the O-C8' bond are restricted to the +sc/+ap regions due to stereochemical reasons. In contrast, conformations around the C2-O and C8'-C7' bonds were found to be largely unrestricted and all the three staggered regions are accessible. The conformations around the C7'-C6' bond were found to be in either the -sc or the anti region. These results are in excellent agreement with the available NMR and potential energy calculation studies. Overall, the disaccharide is flexible and adopts mainly two ensembles of conformations differing in the conformation around the C7'-C6' bond. The flexibility associated with this disaccharide allows for better optimization of intermolecular contacts while binding to proteins and this may partially compensate for the loss of conformational entropy that may be incurred due to disaccharide's flexibility.
Collapse
Affiliation(s)
- Sheeja V Vasudevan
- Biotechnology Center, Indian Institute of Technology, Bombay, Powai, Mumbai 400 076, India
| | | |
Collapse
|
49
|
Boerstoel H, Maatman H, Picken S, Remmers R, Westerink J. Liquid crystalline solutions of cellulose acetate in phosphoric acid. POLYMER 2001. [DOI: 10.1016/s0032-3861(01)00209-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
50
|
Kawanishi H, Tsunashima Y, Horii F. Dynamic Light Scattering Study of Structural Changes of Cellulose Diacetate in Solution under Couette Flow. Macromolecules 2000. [DOI: 10.1021/ma9913055] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroyuki Kawanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | | | - Fumitaka Horii
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| |
Collapse
|