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Masclef JB, Acs EMN, Koehnke J, Prunet J, Schmidt BVKJ. PEGose Block Poly(lactic acid) Nanoparticles for Cargo Delivery. Macromolecules 2024; 57:6013-6023. [PMID: 39005948 PMCID: PMC11238580 DOI: 10.1021/acs.macromol.4c00528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/15/2024] [Accepted: 06/04/2024] [Indexed: 07/16/2024]
Abstract
Hydrophilic polymers have found ubiquitous use in drug delivery and novel polymer materials to advance drug delivery systems are highly sought after. Herein, an amylose mimic (PEGose) was combined with poly(lactic acid) (PLA) in an amphiphilic block copolymer to form PEG-free nanoparticles as an alternative to PEG-based nanomedicines. The block copolymer self-assembled into 150-200 nm particles with a narrow dispersity in aqueous environment. The formed nanoparticles were capable of encapsulation, the sustained release of both hydrophilic and hydrophobic dyes. Moreover, the nanoparticles were found to be remarkably stable and had a very low cytotoxicity and a high propensity to penetrate cells. These results highlight the potential of PEGose-b-PLA to be used in drug delivery with a new hydrophilic building block.
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Affiliation(s)
- Jean-Baptiste Masclef
- School
of Chemistry, University of Glasgow, Joseph Black Building, G12 8QQ Glasgow, U.K.
| | - Emmanuelle M. N. Acs
- School
of Chemistry, University of Glasgow, Joseph Black Building, G12 8QQ Glasgow, U.K.
| | - Jesko Koehnke
- School
of Chemistry, University of Glasgow, Joseph Black Building, G12 8QQ Glasgow, U.K.
- Institute
of Food Chemistry, Leibniz University Hannover, 30167 Hannover, Germany
| | - Joëlle Prunet
- School
of Chemistry, University of Glasgow, Joseph Black Building, G12 8QQ Glasgow, U.K.
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2
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Wang G, Huang X, Wang S, Yang F, Sun S, Yan P, Chen Y, Fang F, Guo J. Effect of food-to-microorganisms ratio on aerobic granular sludge settleability: Microbial community, potential roles and sequential responses of extracellular proteins and polysaccharides. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118814. [PMID: 37591089 DOI: 10.1016/j.jenvman.2023.118814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/18/2023] [Accepted: 08/12/2023] [Indexed: 08/19/2023]
Abstract
The food-to-microorganism ratio (F/M) is an important parameter in wastewater biotreatment that significantly affects the granulation and settleability of aerobic granular sludge (AGS). Hence, understanding the long-term effects and internal mechanisms of F/M on AGS settling performance is essential. This study investigated the relationship between F/M and the sludge volume index (SVI) within a range of 0.23-2.50 kgCOD/(kgMLVSS·d). Thiothrix and Candidatus_Competibacter were identified as two dominant bacterial genera influencing AGS settling performance. With F/M increased from 0.27 kgCOD/(kgMLVSS·d) to 1.53 kgCOD/(kgMLVSS·d), the abundance of Thiothrix significantly increased from 0.20% to 27.02%, and the hydrophobicity of extracellular proteins (PN) decreased, which collectively reduced AGS settling performance. However, under high-F/M conditions, the gel-like polysaccharides (PS) effectively retained the granular biomass by binding to the highly abundant Thiothrix (53.65%). The progressive increment in biomass led to a concomitant reduction in F/M, resulting in the recovery of AGS settleability. In addition, two-dimensional correlation infrared spectroscopy analysis revealed the preferential responses of PN and PS to the increase and decrease of F/M, and the content and characteristics of PN and PS played important roles in granular settling. The study provides insight into the microbial composition and the potential role of extracellular polymer substances in the AGS sedimentation behavior, offering valuable theoretical support for stable AGS operation.
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Affiliation(s)
- Gonglei Wang
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Xiaoxiao Huang
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Shuai Wang
- College of Environment Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Fan Yang
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Shiting Sun
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Peng Yan
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Youpeng Chen
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Fang Fang
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China.
| | - Jinsong Guo
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
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3
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Lalithamaheswari B, Anu Radha C. Structural and binding studies of 2'- and 3-fucosyllactose and its complexes with norovirus capsid protein by molecular dynamics simulations. J Biomol Struct Dyn 2023; 41:10230-10243. [PMID: 36476051 DOI: 10.1080/07391102.2022.2153923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
Human breast milk contains free oligosaccharides (Human Milk Oligosaccharides-HMOs) that help to protect breastfed infants against a variety of infectious diseases and act as decoy receptors. In breast milk, HMOs are the third most abundant compounds after lactose and lipids. Structural and conformational models of HMOs are quite crucial to studying the interaction with proteins and molecular recognition phenomenon. Molecular dynamics simulations for two trisaccharides HMOs (2'-FL and 3-FL) were carried out for 250 ns and the conformational models were subsequently substantiated by three replicate simulations. The conformer models of HMOs 2'-FL and 3-FL were deposited in the 3-Dimensional Structural Database for Sialic acid-containing CARbohydrates (3DSDSCAR) database website (www.3dsdscar.in). HMOs were then docked into the active site of norovirus capsid protein and are simulated for 100 ns duration. Each complex system was stabilized by direct and water-mediated hydrogen bonding interactions. Binding free energy calculations predict two possible binding modes for each complex system. The conformational flexibility and binding stability of the complex systems were calculated. The protein folding/unfolding and compactness seem to be better for the two HMOs. From a general perspective, we found that both 2'-FL and 3-FL exhibited higher binding efficacy towards norovirus capsid protein and according to the structural stability, 3-FL might be used as a preventive inhibitor for norovirus infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- B Lalithamaheswari
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C Anu Radha
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Roy R, Poddar S, Kar P. Comparison of the conformational dynamics of an N-glycan in implicit and explicit solvents. Carbohydr Res 2022; 522:108700. [DOI: 10.1016/j.carres.2022.108700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/28/2022]
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5
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Shebis Y, Vanegas A, Tish N, Fallik E, Rodov V, Poverenov E. Facile method for preparation of oligo-carboxymethyl cellulose and other oligosaccharides: Physicochemical properties and bioactivity. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107530] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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6
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Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations. J Biomol Struct Dyn 2022; 41:3305-3320. [PMID: 35262462 DOI: 10.1080/07391102.2022.2047109] [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] [Indexed: 01/22/2023]
Abstract
In the current study, we have investigated the conformational dynamics of a triantennary (N-glycan1) and tetraantennary (N-glycan2) hybrid N-glycans found on the surface of the HIV glycoprotein using 20 μs long all-atom molecular dynamics (MD) simulations. The main objective of the present study is to elucidate the influence of adding a complex branch on the overall glycan structural dynamics. Our investigation suggests that the average RMSD value increases when a complex branch is added to N-glycan1. However, the RMSD distribution is relatively wider in the case of N-glycan1 compared to N-glycan2, which indicates that multiple complex branches restrict the conformational variability of glycans. A similar observation is obtained from the principal component analysis of both glycans. All the puckering states (4C1 to 1C4) of each monosaccharide except mannose are sampled in our simulations, although the 4C1 chair form is energetically more favorable than 1C4. In N-glycan1, the 1-6 linkage in the mannose branch [Man(9)-α(1-6)-Man(5)] stays in the gauche-gauche cluster, whereas it moves towards trans-gauche in N-glycan2. For both glycans, mannose branches are more flexible than the complex branches, and adding a complex branch does not influence the dynamics of the mannose branches. We have noticed that the end-to-end distance of the complex branch shortens by ∼ 10 Å in the presence of another complex branch. This suggests that in the presence of an additional complex branch, the other complex branch adopts a close folded structure. All these conformational changes involve the selective formation of inter-residue and water-mediated hydrogen-bond networks.
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7
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Huda MM, Saha C, Jahan N, Wilson WN, Rai N. Insights into Sorption and Molecular Transport of Aqueous Glucose into Zeolite Nanopores. J Phys Chem B 2022; 126:1352-1364. [PMID: 35119855 DOI: 10.1021/acs.jpcb.1c10572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Liquid-phase heterogeneous catalysis using zeolites is important for biomass conversion to fuels and chemicals. There is a substantial body of work on gas-phase sorption in zeolites with different topologies; however, studies investigating the diffusion of complex molecules in liquid medium into zeolitic nanopores are scarce. Here, we present a molecular dynamics study to understand the sorption and diffusion of aqueous β-d-glucose into β-zeolite silicate at T = 395 K and P = 1 bar. Through 2-μs-long molecular dynamics trajectories, we reveal the role of the solvent, the kinetics of the pore filling, and the effect of the water model on these properties. We find that the glucose and water loading is a function of the initial glucose concentration. Although the glucose concentration increases monotonically with the initial glucose concentration, the water loading exhibits a nonmonotonic behavior. At the highest initial concentration (∼20 wt %), we find that the equilibrium loading of glucose is approximately five molecules per unit cell and displays a weak dependence on the water model. Glucose molecules follow a single-file diffusion in the nanopores due to confinement. The dynamics of glucose and water molecules slows significantly at the interface. The average residence time for glucose molecules is an order of magnitude larger than that in the bulk solution, while it is about twice as large for the water molecules. Our simulations reveal critical molecular details of the glucose molecule's local environment inside the zeolite pore relevant to catalytic conversion of biomass to valuable chemicals.
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Affiliation(s)
- Md Masrul Huda
- Dave C. Swalm School of Chemical Engineering and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Chinmoy Saha
- Dave C. Swalm School of Chemical Engineering and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Nusrat Jahan
- Dave C. Swalm School of Chemical Engineering and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Woodrow N Wilson
- Dave C. Swalm School of Chemical Engineering and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Neeraj Rai
- Dave C. Swalm School of Chemical Engineering and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, United States
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8
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Identification of the Primary Structure of Selenium-Containing Polysaccharides Selectively Inhibiting T-Cell Proliferation. Molecules 2021; 26:molecules26175404. [PMID: 34500837 PMCID: PMC8434567 DOI: 10.3390/molecules26175404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 11/19/2022] Open
Abstract
We previously described the biosynthesis, isolation, and immunosuppressive activity of the selenium-containing polysaccharide fraction isolated from the mycelial culture of Lentinula edodes. Structural studies have shown that the fraction was a protein-containing mixture of high molar mass polysaccharides α- and β-glucans. However, which of the components of the complex fraction is responsible for the immunosuppressive activity non-typical for polysaccharides of fungal origin has not been explained. In the current study, we defined four-polysaccharide components of the Se-containing polysaccharide fraction determined their primary structure and examined the effect on T- and B-cell proliferation. The isolated Se-polysaccharides, α-1,4-glucan (Mw 2.25 × 106 g/mol), unbranched β-1,6-d-glucan, unbranched β-1,3-d-glucan and β-1,3-branched β-1,6-d-glucan (Mw 1.10 × 105 g/mol), are not typical as components of the cell wall of L. edodes. All are biologically active, but the inhibitory effect of the isolated polysaccharides on lymphocyte proliferation was weaker, though more selective than that of the crude fraction.
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9
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Sastre Toraño J, Aizpurua‐Olaizola O, Wei N, Li T, Unione L, Jiménez‐Osés G, Corzana F, Somovilla VJ, Falcon‐Perez JM, Boons G. Identification of Isomeric N-Glycans by Conformer Distribution Fingerprinting using Ion Mobility Mass Spectrometry. Chemistry 2021; 27:2149-2154. [PMID: 33047840 PMCID: PMC7898647 DOI: 10.1002/chem.202004522] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Indexed: 12/14/2022]
Abstract
Glycans possess unparalleled structural complexity arising from chemically similar monosaccharide building blocks, configurations of anomeric linkages and different branching patterns, potentially giving rise to many isomers. This level of complexity is one of the main reasons that identification of exact glycan structures in biological samples still lags behind that of other biomolecules. Here, we introduce a methodology to identify isomeric N-glycans by determining gas phase conformer distributions (CDs) by measuring arrival time distributions (ATDs) using drift-tube ion mobility spectrometry-mass spectrometry. Key to the approach is the use of a range of well-defined synthetic glycans that made it possible to investigate conformer distributions in the gas phase of isomeric glycans in a systematic manner. In addition, we have computed CD fingerprints by molecular dynamics (MD) simulation, which compared well with experimentally determined CDs. It supports that ATDs resemble conformational populations in the gas phase and offer the prospect that such an approach can contribute to generating a library of CCS distributions (CCSDs) for structure identification.
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Affiliation(s)
- Javier Sastre Toraño
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | - Oier Aizpurua‐Olaizola
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
- Exosomes LabCIC bioGUNE, CIBERehdDerioSpain
| | - Na Wei
- The University of GeorgiaComplex Carbohydrate Research CenterAthensGAUSA
| | - Tiehai Li
- The University of GeorgiaComplex Carbohydrate Research CenterAthensGAUSA
| | - Luca Unione
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | - Gonzalo Jiménez‐Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNEBasque Research and Technology Alliance (BRTA)Bizkaia Technology Park, Building 801A48160DerioSpain
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis QuímicaUniversidad de La Rioja26006LogroñoSpain
| | - Victor J. Somovilla
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | | | - Geert‐Jan Boons
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
- The University of GeorgiaComplex Carbohydrate Research CenterAthensGAUSA
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Abstract
The conformation of a molecule strongly affects its function, as demonstrated for peptides and nucleic acids. This correlation is much less established for carbohydrates, the most abundant organic materials in nature. Recent advances in synthetic and analytical techniques have enabled the study of carbohydrates at the molecular level. Recurrent structural features were identified as responsible for particular biological activities or material properties. In this Minireview, recent achievements in the structural characterization of carbohydrates, enabled by systematic studies of chemically defined oligosaccharides, are discussed. These findings can guide the development of more potent glycomimetics. Synthetic carbohydrate materials by design can be envisioned.
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Affiliation(s)
- Yang Yu
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Martina Delbianco
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
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11
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Nagarajan B, Sankaranarayanan NV, Desai UR. Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools. Glycobiology 2020; 30:516-527. [PMID: 32080710 PMCID: PMC8179626 DOI: 10.1093/glycob/cwaa015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 11/15/2022] Open
Abstract
Heparin/heparan sulfates (H/HS) are ubiquitous biopolymers that interact with many proteins to induce a range of biological functions. Unfortunately, how these biopolymers recognize their preferred protein targets remain poorly understood. It is suggested that computational simulations offer attractive avenues but a number of challenges, e.g., difficulty of selecting a comprehensive force field, few simple tools to interpret data, among others, remain. This work addresses several such challenges so as to help ease the implementation and analysis of computational experiments. First, this work presents a rigorous comparison of two different recent force fields, CHARMM36 and GLYCAM06, for H/HS studies. Second, it introduces two new straightforward parameters, i.e., end-to-end distance and minimum volume enclosing ellipsoid, to understand the myriad conformational forms of oligosaccharides that evolve over time in water. Third, it presents an application to elucidate the number and nature of inter and intramolecular, nondirect bridging water molecules, which help stabilize unique forms of H/HS. The results show that nonspecialists can use either CHARMM36 or GLYCAM06 force fields because both gave comparable results, albeit with small differences. The comparative study shows that the HS hexasaccharide samples a range of conformations with nearly equivalent energies, which could be the reason for its recognition by different proteins. Finally, analysis of the nondirect water bridges across the dynamics trajectory shows their importance in stabilization of certain conformational forms, which may become important for protein recognition. Overall, the work aids nonspecialists employ computational studies for understanding the solution behavior of H/HS.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Umesh R Desai
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
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Fernandes LM, Guimarães JT, Silva R, Rocha RS, Coutinho NM, Balthazar CF, Calvalcanti RN, Piler CW, Pimentel TC, Neto RP, Tavares MIB, Esmerino EA, Freitas MQ, Silva MC, Cruz AG. Whey protein films added with galactooligosaccharide and xylooligosaccharide. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2020.105755] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Variation in Cell Surface Hydrophobicity among Cryptococcus neoformans Strains Influences Interactions with Amoebas. mSphere 2020; 5:5/2/e00310-20. [PMID: 32350094 PMCID: PMC7193044 DOI: 10.1128/msphere.00310-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cryptococcus neoformans and Cryptococcus gattii are pathogenic fungi that cause significant morbidity and mortality. Cell surface hydrophobicity (CSH) is a biophysical parameter that influences the adhesion of fungal cells or spores to biotic and abiotic surfaces. C. neoformans is encased by polysaccharide capsule that is highly hydrophilic and is a critical determinant of virulence. In this study, we report large differences in the CSH of some C. neoformans and C. gattii strains. The capsular polysaccharides of C. neoformans strains differ in repeating motifs and therefore vary in the number of hydroxyl groups, which, along with higher-order structure of the capsule, may contribute to the variation in hydrophobicity that we observed. We found that cell wall composition, in the context of chitin-chitosan content, does not influence CSH. For C. neoformans, CSH correlated with phagocytosis by natural soil predator Acanthamoeba castellanii Furthermore, capsular binding of the protective antibody (18B7), but not the nonprotective antibody (13F1), altered the CSH of C. neoformans strains. Variability in CSH could be an important characteristic in comparing the biological properties of cryptococcal strains.IMPORTANCE The interaction of a microbial cell with its environment is influenced by the biophysical properties of a cell. The affinity of the cell surface for water, defined by the cell surface hydrophobicity (CSH), is a biophysical parameter that varies among different strains of Cryptococcus neoformans The CSH influences the phagocytosis of the yeast by its natural predator in the soil, the amoeba. Studying variation in biophysical properties like CSH gives us insight into the dynamic host-predator interaction and host-pathogen interaction in a damage-response framework.
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Smilek J, Jarábková S, Velcer T, Pekař M. Compositional and Temperature Effects on the Rheological Properties of Polyelectrolyte-Surfactant Hydrogels. Polymers (Basel) 2019; 11:polym11050927. [PMID: 31137862 PMCID: PMC6571672 DOI: 10.3390/polym11050927] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 11/19/2022] Open
Abstract
The rheological properties of hydrogels prepared by physical interactions between oppositely charged polyelectrolyte and surfactant in micellar form were studied. Specifically, hyaluronan was employed as a negatively charged polyelectrolyte and Septonex (carbethopendecinium bromide) as a cationic surfactant. Amino-modified dextran was used as a positively charged polyelectrolyte interacting with sodium dodecylsulphate as an anionic surfactant. The effects of the preparation method, surfactant concentration, ionic strength (the concentration of NaCl background electrolyte), pH (buffers), multivalent cations, and elevated temperature on the properties were investigated. The formation of gels required an optimum ionic strength (set by the NaCl solution), ranging from 0.15–0.3 M regardless of the type of hydrogel system and surfactant concentration. The other compositional effects and the effect of temperature were dependent on the polyelectrolyte type or its molecular weight. General differences between the behaviour of hyaluronan-based and cationized dextran-based materials were attributed to differences in the chain conformations of the two biopolymers and in the accessibility of their charged groups.
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Affiliation(s)
- Jiří Smilek
- Faculty of Chemistry, Brno University of Technology, Purkynova 464/118, 612 00 Brno, Czech Republic.
| | - Sabína Jarábková
- Faculty of Chemistry, Brno University of Technology, Purkynova 464/118, 612 00 Brno, Czech Republic.
| | - Tomáš Velcer
- Faculty of Chemistry, Brno University of Technology, Purkynova 464/118, 612 00 Brno, Czech Republic.
| | - Miloslav Pekař
- Faculty of Chemistry, Brno University of Technology, Purkynova 464/118, 612 00 Brno, Czech Republic.
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15
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ECS Dynamism and Its Influence on Neuronal Excitability and Seizures. Neurochem Res 2019; 44:1020-1036. [DOI: 10.1007/s11064-019-02773-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 02/08/2023]
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16
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Nagarajan B, Sankaranarayanan NV, Desai UR. Perspective on computational simulations of glycosaminoglycans. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2019; 9:e1388. [PMID: 31080520 PMCID: PMC6504973 DOI: 10.1002/wcms.1388] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/07/2018] [Indexed: 01/06/2023]
Abstract
Glycosaminoglycans (GAGs) represent a formidable frontier for chemists, biochemists, biologists, medicinal chemists and drug delivery specialists because of massive structural complexity. GAGs are arguably the most complex, natural linear biopolymers with theoretical diversity orders of magnitude higher than proteins and nucleic acids. Yet, this diversity remains generally untapped. Computational approaches offer major routes to understand GAG structure and dynamics so as to enable novel applications of these biopolymers. In fact, computational algorithms, softwares, online tools and techniques have reached a level of sophistication that help understand atomistic details of conformational variation and protein recognition of individual GAG sequences. This review describes current approaches and challenges in computational study of GAGs. It presents a history of major findings since the earliest mention of GAGs (the 1960s), the development of parameters and force fields specific for GAGs, and the application of these tools in understanding GAG structure-function relationship. This review also presents a section on how to perform simulation of GAGs, which is directed toward researchers interested in entering this promising field with potential to impact therapy.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
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17
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Aguirre Montesdeoca V, Bakker J, Boom R, Janssen AE, Van der Padt A. Ultrafiltration of non-spherical molecules. J Memb Sci 2019. [DOI: 10.1016/j.memsci.2018.10.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Chen G, Huang K, Miao M, Feng B, Campanella OH. Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art. Compr Rev Food Sci Food Saf 2018; 18:243-263. [PMID: 33337012 DOI: 10.1111/1541-4337.12406] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/07/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022]
Abstract
Molecular dynamics (MD) simulation is a useful technique to study the interaction between molecules and how they are affected by various processes and processing conditions. This review summarizes the application of MD simulations in food processing and safety, with an emphasis on the effects that emerging nonthermal technologies (for example, high hydrostatic pressure, pulsed electric field) have on the molecular and structural characteristics of foods and biomaterials. The advances and potential projection of MD simulations in the science and engineering aspects of food materials are discussed and focused on research work conducted to study the effects of emerging technologies on food components. It is expected by showing key case studies that it will stir novel developments as a valuable tool to study the effects of emerging food technologies on biomaterials. This review is useful to food researchers and the food industry, as well as researchers and practitioners working on flavor and nutraceutical encapsulations, dietary carbohydrate product developments, modified starches, protein engineering, and other novel food applications.
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Affiliation(s)
- Gang Chen
- School of Food Science and Technology, Henan Univ. of Technology, 100 Lianhua St., Zhengzhou 450001, Henan, P. R. China.,State Key Laboratory of Food Science and Technology, Jiangnan Univ., 1800 Lihu Ave., Wuxi, 214122, Jiangsu, P. R. China
| | - Kai Huang
- State Key Laboratory of Food Science and Technology, Jiangnan Univ., 1800 Lihu Ave., Wuxi, 214122, Jiangsu, P. R. China
| | - Ming Miao
- State Key Laboratory of Food Science and Technology, Jiangnan Univ., 1800 Lihu Ave., Wuxi, 214122, Jiangsu, P. R. China
| | - Biao Feng
- State Key Laboratory of Food Science and Technology, Jiangnan Univ., 1800 Lihu Ave., Wuxi, 214122, Jiangsu, P. R. China
| | - Osvaldo H Campanella
- State Key Laboratory of Food Science and Technology, Jiangnan Univ., 1800 Lihu Ave., Wuxi, 214122, Jiangsu, P. R. China.,Agricultural and Biological Engineering, and Dept. of Food Science, Whistler Center for Carbohydrate Research, Purdue Univ., 745 Agriculture Mall Dr., West Lafayette, IN, 47906, U.S.A
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19
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Almond A. Multiscale modeling of glycosaminoglycan structure and dynamics: current methods and challenges. Curr Opin Struct Biol 2017; 50:58-64. [PMID: 29253714 DOI: 10.1016/j.sbi.2017.11.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/24/2017] [Accepted: 11/26/2017] [Indexed: 01/24/2023]
Abstract
Glycosaminoglycans are long unbranched and complex polysaccharides that are an essential component of mammalian extracellular matrices. Characterization of their molecular structure, dynamics and interactions are essential to understand important biological phenomena in health and disease, and will lead to novel therapeutics and medical devices. However, this has proven to be a challenge experimentally and theoretical techniques are needed to develop new hypotheses, and interpret experiments. This review aims to examine the current theoretical (rather than experimental) methods used by researchers to investigate glycosaminoglycan structure, dynamics and interactions, from the monosaccharide to the macromolecular scale. It will consider techniques such as quantum mechanics, molecular mechanics, molecular dynamics, coarse graining and docking.
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Affiliation(s)
- Andrew Almond
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK.
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20
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Perkins KL, Arranz AM, Yamaguchi Y, Hrabetova S. Brain extracellular space, hyaluronan, and the prevention of epileptic seizures. Rev Neurosci 2017; 28:869-892. [PMID: 28779572 PMCID: PMC5705429 DOI: 10.1515/revneuro-2017-0017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/03/2017] [Indexed: 01/08/2023]
Abstract
Mutant mice deficient in hyaluronan (HA) have an epileptic phenotype. HA is one of the major constituents of the brain extracellular matrix. HA has a remarkable hydration capacity, and a lack of HA causes reduced extracellular space (ECS) volume in the brain. Reducing ECS volume can initiate or exacerbate epileptiform activity in many in vitro models of epilepsy. There is both in vitro and in vivo evidence of a positive feedback loop between reduced ECS volume and synchronous neuronal activity. Reduced ECS volume promotes epileptiform activity primarily via enhanced ephaptic interactions and increased extracellular potassium concentration; however, the epileptiform activity in many models, including the brain slices from HA synthase-3 knockout mice, may still require glutamate-mediated synaptic activity. In brain slice epilepsy models, hyperosmotic solution can effectively shrink cells and thus increase ECS volume and block epileptiform activity. However, in vivo, the intravenous administration of hyperosmotic solution shrinks both brain cells and brain ECS volume. Instead, manipulations that increase the synthesis of high-molecular-weight HA or decrease its breakdown may be used in the future to increase brain ECS volume and prevent seizures in patients with epilepsy. The prevention of epileptogenesis is also a future target of HA manipulation. Head trauma, ischemic stroke, and other brain insults that initiate epileptogenesis are known to be associated with an early decrease in high-molecular-weight HA, and preventing that decrease in HA may prevent the epileptogenesis.
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Affiliation(s)
- Katherine L. Perkins
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Amaia M. Arranz
- VIB Center for Brain and Disease Research, 3000 Leuven, Belgium; and KU Leuven Department for Neurosciences, Leuven Institute for Neurodegenerative Disorders (LIND) and Universitaire Ziekenhuizen Leuven, University of Leuven, 3000 Leuven, Belgium
| | - Yu Yamaguchi
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
| | - Sabina Hrabetova
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
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21
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Restrepo-Espinosa DC, Román Y, Colorado-Ríos J, de Santana-Filho AP, Sassaki GL, Cipriani TR, Martínez A, Iacomini M, Pavão MSG. Structural analysis of a sulfated galactan from the tunic of the ascidian Microcosmus exasperatus and its inhibitory effect of the intrinsic coagulation pathway. Int J Biol Macromol 2017; 105:1391-1400. [PMID: 28867226 DOI: 10.1016/j.ijbiomac.2017.08.166] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/24/2017] [Accepted: 08/30/2017] [Indexed: 01/22/2023]
Abstract
Several bioactive sulfated galactans have been isolated from the tunic of different species of ascidians. The biological activity of this kind of polysaccharides has been related with the presence and position of sulfate groups, and by the chemical composition of this kind of polysaccharides. A sulfated galactan (1000RS) was isolated from the tunic of the Brazilian ascidia Microcosmus exasperatus through proteolytic digestion, ethanol precipitation, dialysis and freeze-thaw cycles. Homogeneity and molecular weight were estimated by using size exclusion chromatography. Monosaccharide composition and type of linkage were assessed by Gas chromatography coupled to mass spectrometry and the sulfate content was quantified through gelatin/BaCl2 method. These experiments along with NMR and FTIR analysis allowed to claim that the galactan backbone is mainly composed of 4-linked α-l-Galp units. In addition, they permitted to establish that some of the galactose residues are sulfated at the 3-position. This sulfated polysaccharide, which has an average molecular mass of 439.5kDa, presents anticoagulant effect in a dose-dependent manner through the inhibition of the intrinsic coagulation pathway.
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Affiliation(s)
- Diana C Restrepo-Espinosa
- Productos Naturales Marinos, Departamento de Farmacia, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Calle 70 N° 52-21, CP 050010234, Medellín, Colombia.
| | - Yony Román
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Paraná, CEP 81531-980, CP 19046, Curitiba, Paraná, Brazil.
| | - Jhonny Colorado-Ríos
- Productos Naturales Marinos, Departamento de Farmacia, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Calle 70 N° 52-21, CP 050010234, Medellín, Colombia.
| | | | - Guilherme Lanzi Sassaki
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Paraná, CEP 81531-980, CP 19046, Curitiba, Paraná, Brazil.
| | - Thales R Cipriani
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Paraná, CEP 81531-980, CP 19046, Curitiba, Paraná, Brazil.
| | - Alejandro Martínez
- Productos Naturales Marinos, Departamento de Farmacia, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Calle 70 N° 52-21, CP 050010234, Medellín, Colombia.
| | - Marcello Iacomini
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Paraná, CEP 81531-980, CP 19046, Curitiba, Paraná, Brazil.
| | - Mauro S G Pavão
- Laboratório de Bioquímica e Biologia Celular de Glicoconjugados, Instituto de Bioquímica Médica Leopoldo de Méis-Universidade Federal do Rio de Janeiro, CEP 21941-913, Rio de Janeiro, Brazil.
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22
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Cao F, Bourven I, van Hullebusch ED, Pechaud Y, Lens PN, Guibaud G. Hydrophobic molecular features of EPS extracted from anaerobic granular sludge treating wastewater from a paper recycling plant. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.04.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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23
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Nestor G, Sandström C. NMR study of hydroxy and amide protons in hyaluronan polymers. Carbohydr Polym 2017; 157:920-928. [DOI: 10.1016/j.carbpol.2016.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/03/2016] [Accepted: 10/04/2016] [Indexed: 11/26/2022]
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24
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Wendling RJ, Christensen AM, Quast AD, Atzet SK, Mann BK. Effect of Carboxymethylation on the Rheological Properties of Hyaluronan. PLoS One 2016; 11:e0162849. [PMID: 27611817 PMCID: PMC5017724 DOI: 10.1371/journal.pone.0162849] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/28/2016] [Indexed: 11/18/2022] Open
Abstract
Chemical modifications made to hyaluronan to enable covalent crosslinking to form a hydrogel or to attach other molecules may alter the physical properties as well, which have physiological importance. Here we created carboxymethyl hyaluronan (CMHA) with varied degree of modification and investigated the effect on the viscosity of CMHA solutions. Viscosity decreased initially as modification increased, with a minimum viscosity for about 30-40% modification. This was followed by an increase in viscosity around 45-50% modification. The pH of the solution had a variable effect on viscosity, depending on the degree of carboxymethyl modification and buffer. The presence of phosphates in the buffer led to decreased viscosity. We also compared large-scale production lots of CMHA to lab-scale and found that large-scale required extended reaction times to achieve the same degree of modification. Finally, thiolated CMHA was disulfide crosslinked to create hydrogels with increased viscosity and shear-thinning aspects compared to CMHA solutions.
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Affiliation(s)
- Rian J. Wendling
- Department of Bioengineering, University of Utah, Salt Lake City, Utah, United States of America
| | | | - Arthur D. Quast
- Department of Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Sarah K. Atzet
- SentrX Animal Care, Inc., Salt Lake City, Utah, United States of America
| | - Brenda K. Mann
- Department of Bioengineering, University of Utah, Salt Lake City, Utah, United States of America
- SentrX Animal Care, Inc., Salt Lake City, Utah, United States of America
- * E-mail:
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25
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Jo S, Qi Y, Im W. Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins. Glycobiology 2015; 26:19-29. [PMID: 26405106 DOI: 10.1093/glycob/cwv083] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/14/2015] [Indexed: 11/13/2022] Open
Abstract
N-linked glycans are on protein surfaces and have direct and water/ion-mediated interactions with surrounding amino acids. Such contacts could restrict their conformational freedom compared to the same glycans free in solution. In this work, we have examined the conformational freedom of the N-glycan core pentasaccharide moiety in solution using standard molecular dynamics (MD) simulations as well as temperature replica-exchange MD simulations. Both simulations yield the comparable conformational variability of the pentasaccharide in solution, indicating the convergence of both simulations. The glycoprotein crystal structures are analyzed to compare the conformational freedom of the N-glycan on the protein surface with the simulation result. Surprisingly, the pentasaccharide free in solution shows more restricted conformational variability than the N-glycan on the protein surface. The interactions between the carbohydrate and the protein side chain appear to be responsible for the increased conformational diversity of the N-glycan on the protein surface. Finally, the transfer entropy analysis of the simulation trajectory also reveals an unexpected causality relationship between intramolecular hydrogen bonds and the conformational states in that the hydrogen bonds play a role in maintaining the conformational states rather than driving the change in glycosidic torsional states.
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Affiliation(s)
- Sunhwan Jo
- Leadership Computing Center, Argonne National Laboratory, 9700 Cass Ave Bldg. 240, Argonne, IL 60439, USA
| | - Yifei Qi
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA
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26
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Debranching of soluble wheat arabinoxylan dramatically enhances recalcitrant binding to cellulose. Biotechnol Lett 2014; 37:633-41. [DOI: 10.1007/s10529-014-1705-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
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27
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Selig MJ, Thygesen LG, Felby C. Correlating the ability of lignocellulosic polymers to constrain water with the potential to inhibit cellulose saccharification. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:159. [PMID: 25426165 PMCID: PMC4243321 DOI: 10.1186/s13068-014-0159-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/08/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Studies in bioconversions have continuously sought the development of processing strategies to overcome the "close physical association" between plant cell wall polymers thought to significantly contribute to biomass recalcitrance [Adv Space Res 18:251-265, 1996],[ Science 315:804-807, 2007]. To a lesser extent, studies have sought to understand biophysical factors responsible for the resistance of lignocelluloses to enzymatic degradation. Provided here are data supporting our hypothesis that the inhibitory potential of different cell wall polymers towards enzymatic cellulose hydrolysis is related to how much these polymers constrain the water surrounding them. We believe the entropy-reducing constraint imparted to polymer associated water plays a negative role by increasing the probability of detrimental interactions such as junction zone formation and the non-productive binding of enzymes. RESULTS Selected commercial lignocellulose-derived polymers, including hemicelluloses, pectins, and lignin, showed varied potential to inhibit 24-h cellulose conversion by a mix of purified cellobiohydrolase I and β-glucosidase. At low dry matter loadings (0.5% w/w), insoluble hemicelluloses were most inhibitory (reducing conversion relative to cellulose-only controls by about 80%) followed by soluble xyloglucan and wheat arabinoxylan (reductions of about 70% and 55%, respectively), while the lignin and pectins tested were the least inhibitory (approximately 20% reduction). Low field nuclear magnetic resonance (LF-NMR) relaxometry used to observe water-related proton relaxation in saturated polymer suspensions (10% dry solids, w/w) showed spin-spin, T2, relaxation time curves generally approached zero faster for the most inhibitory polymer preparations. The manner of this decline varied between polymers, indicating different biophysical aspects may differentially contribute to overall water constraint in each case. To better compare the LF-NMR data to inhibitory potential, T2 values from monocomponent exponential fits of relaxation curves were used as a measure of overall water constraint. These values generally correlated faster relaxation times (greater water constraint) with greater inhibition of the model cellulase system by the polymers. CONCLUSIONS The presented correlation of cellulase inhibition and proton relaxation data provides support for our water constraint-biomass recalcitrance hypothesis. Deeper investigation into polymer-cellulose-cellulase interactions should help elucidate the types of interactions that may be propagating this correlation. If these observations can be verified to be more than correlative, the hypothesis and data presented suggest that a focus on water-polymer interactions and ways to alter them may help resolve key biological lignocellulose processing bottlenecks.
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Affiliation(s)
- Michael J Selig
- IGN, Faculty of Science, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg, Denmark
| | - Lisbeth G Thygesen
- IGN, Faculty of Science, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg, Denmark
| | - Claus Felby
- IGN, Faculty of Science, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg, Denmark
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28
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Rahkila J, Ekholm FS, Panchadhayee R, Ardá A, Cañada FJ, Jiménez-Barbero J, Leino R. Synthesis and conformational analysis of phosphorylated β-(1→2) linked mannosides. Carbohydr Res 2014; 383:58-68. [DOI: 10.1016/j.carres.2013.10.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 11/28/2022]
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29
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Barry C, Cocinero EJ, Çarçabal P, Gamblin D, Stanca-Kaposta EC, Remmert SM, Fernández-Alonso MC, Rudić S, Simons JP, Davis BG. 'Naked' and hydrated conformers of the conserved core pentasaccharide of N-linked glycoproteins and its building blocks. J Am Chem Soc 2013; 135:16895-903. [PMID: 24127839 PMCID: PMC3901393 DOI: 10.1021/ja4056678] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Indexed: 12/11/2022]
Abstract
N-glycosylation of eukaryotic proteins is widespread and vital to survival. The pentasaccharide unit -Man3GlcNAc2- lies at the protein-junction core of all oligosaccharides attached to asparagine side chains during this process. Although its absolute conservation implies an indispensable role, associated perhaps with its structure, its unbiased conformation and the potential modulating role of solvation are unknown; both have now been explored through a combination of synthesis, laser spectroscopy, and computation. The proximal -GlcNAc-GlcNAc- unit acts as a rigid rod, while the central, and unusual, -Man-β-1,4-GlcNAc- linkage is more flexible and is modulated by the distal Man-α-1,3- and Man-α-1,6- branching units. Solvation stiffens the 'rod' but leaves the distal residues flexible, through a β-Man pivot, ensuring anchored projection from the protein shell while allowing flexible interaction of the distal portion of N-glycosylation with bulk water and biomolecular assemblies.
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Affiliation(s)
- Conor
S. Barry
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Emilio J. Cocinero
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ United Kingdom
| | - Pierre Çarçabal
- Institut
des Sciences Moléculaire d’Orsay-CNRS, Université Paris Sud, Bâtiment 210, 91405 Orsay Cedex, France
| | - David
P. Gamblin
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - E. Cristina Stanca-Kaposta
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ United Kingdom
| | - Sarah M. Remmert
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ United Kingdom
| | | | - Svemir Rudić
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ United Kingdom
| | - John P. Simons
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ United Kingdom
| | - Benjamin G. Davis
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
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30
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Çarçabal P, Cocinero EJ, Simons JP. Binding energies of micro-hydrated carbohydrates: measurements and interpretation. Chem Sci 2013. [DOI: 10.1039/c3sc50135c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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31
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Seviour T, Yuan Z, van Loosdrecht MCM, Lin Y. Aerobic sludge granulation: a tale of two polysaccharides? WATER RESEARCH 2012; 46:4803-4813. [PMID: 22776210 DOI: 10.1016/j.watres.2012.06.018] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/28/2012] [Accepted: 06/09/2012] [Indexed: 06/01/2023]
Abstract
Aerobic sludge granules are suspended biofilms with the potential to reduce the cost and footprint of secondary wastewater treatment. Attempts to answer how and why they form leads to a consideration of the role of their extracellular polymeric substances (EPS) in determining their physical and microbiological properties. The exopolysaccharide components of this matrix, in particular, have received attention as putative structural, gel-forming agents. Two quite different exopolysaccharides have been proposed as the gel-forming constituents, with their gel properties clearly different from those of activated sludge EPS. This review aims to address the question of whether more than one gel-forming exopolysaccharide exist in granules. Based on the available structural data, it seems likely that they are different gel-forming polymers and their differences are not artifacts of the analytical methods used. Nonetheless, both proposed structural gel polymers are extracted and purified based on procedures selecting for anionic polar polysaccharides soluble at high pH, and both contain hexuronic acids. Granulation does not result from EPS synthesis by any single microbial population, nor from production of a single exopolysaccharide. Future studies using solvents suitable for recalcitrant polysaccharides are likely to reveal important structural roles for other polysaccharides. It is hoped that this article will serve as a guide for subsequent studies into understanding the roles of exopolysaccharides in aerobic granular sludge.
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Affiliation(s)
- Thomas Seviour
- Singapore Centre on Environmental Life Sciences Engineering-SCELSE, Nanyang Technological University, SBS-B2n-27, 60 Nanyang Drive, Singapore 637551, Singapore.
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32
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Re S, Nishima W, Miyashita N, Sugita Y. Conformational flexibility of N-glycans in solution studied by REMD simulations. Biophys Rev 2012; 4:179-187. [PMID: 28510079 DOI: 10.1007/s12551-012-0090-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 06/21/2012] [Indexed: 01/09/2023] Open
Abstract
Protein-glycan recognition regulates a wide range of biological and pathogenic processes. Conformational diversity of glycans in solution is apparently incompatible with specific binding to their receptor proteins. One possibility is that among the different conformational states of a glycan, only one conformer is utilized for specific binding to a protein. However, the labile nature of glycans makes characterizing their conformational states a challenging issue. All-atom molecular dynamics (MD) simulations provide the atomic details of glycan structures in solution, but fairly extensive sampling is required for simulating the transitions between rotameric states. This difficulty limits application of conventional MD simulations to small fragments like di- and tri-saccharides. Replica-exchange molecular dynamics (REMD) simulation, with extensive sampling of structures in solution, provides a valuable way to identify a family of glycan conformers. This article reviews recent REMD simulations of glycans carried out by us or other research groups and provides new insights into the conformational equilibria of N-glycans and their alteration by chemical modification. We also emphasize the importance of statistical averaging over the multiple conformers of glycans for comparing simulation results with experimental observables. The results support the concept of "conformer selection" in protein-glycan recognition.
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Affiliation(s)
- Suyong Re
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Wataru Nishima
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Naoyuki Miyashita
- RIKEN Quantitative Biology Center, IMDA 6F, 1-6-5 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Yuji Sugita
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,RIKEN Quantitative Biology Center, IMDA 6F, 1-6-5 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan. .,RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
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33
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Nishima W, Miyashita N, Yamaguchi Y, Sugita Y, Re S. Effect of bisecting GlcNAc and core fucosylation on conformational properties of biantennary complex-type N-glycans in solution. J Phys Chem B 2012; 116:8504-12. [PMID: 22530754 DOI: 10.1021/jp212550z] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The introduction of bisecting GlcNAc and core fucosylation in N-glycans is essential for fine functional regulation of glycoproteins. In this paper, the effect of these modifications on the conformational properties of N-glycans is examined at the atomic level by performing replica-exchange molecular dynamics (REMD) simulations. We simulate four biantennary complex-type N-glycans, namely, unmodified, two single-substituted with either bisecting GlcNAc or core fucose, and disubstituted forms. By using REMD as an enhanced sampling technique, five distinct conformers in solution, each of which is characterized by its local orientation of the Manα1-6Man glycosidic linkage, are observed for all four N-glycans. The chemical modifications significantly change their conformational equilibria. The number of major conformers is reduced from five to two and from five to four upon the introduction of bisecting GlcNAc and core fucosylation, respectively. The population change is attributed to specific inter-residue hydrogen bonds, including water-mediated ones. The experimental NMR data, including nuclear Overhauser enhancement and scalar J-coupling constants, are well reproduced taking the multiple conformers into account. Our structural model supports the concept of "conformer selection", which emphasizes the conformational flexibility of N-glycans in protein-glycan interactions.
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Affiliation(s)
- Wataru Nishima
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Bauer BA, Patel S. Recent applications and developments of charge equilibration force fields for modeling dynamical charges in classical molecular dynamics simulations. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1153-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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35
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Zhong Y, Bauer BA, Patel S. Solvation properties of N-acetyl-β-glucosamine: molecular dynamics study incorporating electrostatic polarization. J Comput Chem 2011; 32:3339-53. [PMID: 21898464 PMCID: PMC3193586 DOI: 10.1002/jcc.21873] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 04/25/2011] [Accepted: 05/28/2011] [Indexed: 12/13/2022]
Abstract
N-Acetyl-β-glucosamine (NAG) is an important moiety of glycoproteins and is involved in many biological functions. However, conformational and dynamical properties of NAG molecules in aqueous solution, the most common biological environment, remain ambiguous due to limitations of experimental methods. Increasing efforts are made to probe structural properties of NAG and NAG-containing macromolecules, like peptidoglycans and polymeric chitin, at the atomic level using molecular dynamics simulations. In this work, we develop a polarizable carbohydrate force field for NAG and contrast simulation results of various properties using this novel force field and an analogous nonpolarizable (fixed charge) model. Aqueous solutions of NAG and its oligomers are investigated; we explore conformational properties (rotatable bond geometry), electrostatic properties (dipole moment distribution), dynamical properties (self-diffusion coefficient), hydrogen bonding (water bridge structure and dynamics), and free energy of hydration. The fixed-charge carbohydrate force field exhibits deviations from the gas phase relative rotation energy of exocyclic hydroxymethyl side chain and of chair/boat ring distortion. The polarizable force field predicts conformational properties in agreement with corresponding first-principles results. NAG-water hydrogen bonding pattern is studied through radial distribution functions (RDFs) and correlation functions. Intermolecular hydrogen bonding between solute and solvent is found to stabilize NAG solution structures while intramolecular hydrogen bonds define glycosidic linkage geometry of NAG oligomers. The electrostatic component of hydration free energy is highly dependent on force field atomic partial charges, influencing a more favorable free energy of hydration in the fixed-charge model compared to the polarizable model.
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Affiliation(s)
- Yang Zhong
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Brad A. Bauer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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36
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Hyaluronan-surfactant interactions in physiological solution studied by tensiometry and fluorescence probe techniques. Colloids Surf A Physicochem Eng Asp 2011. [DOI: 10.1016/j.colsurfa.2011.05.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Parthasarathi R, Tian J, Redondo A, Gnanakaran S. Quantum Chemical Study of Carbohydrate–Phospholipid Interactions. J Phys Chem A 2011; 115:12826-40. [DOI: 10.1021/jp204015j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- R. Parthasarathi
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Jianhui Tian
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Antonio Redondo
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - S. Gnanakaran
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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38
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Guzzi C, Angulo J, Doro F, Reina JJ, Thépaut M, Fieschi F, Bernardi A, Rojo J, Nieto PM. Insights into molecular recognition of LewisX mimics by DC-SIGN using NMR and molecular modelling. Org Biomol Chem 2011; 9:7705-12. [DOI: 10.1039/c1ob05938f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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39
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Less is more when simulating unsulfated glycosaminoglycan 3D-structure: Comparison of GLYCAM06/TIP3P, PM3-CARB1/TIP3P, and SCC-DFTB-D/TIP3P predictions with experiment. J Comput Chem 2010; 31:2932-47. [DOI: 10.1002/jcc.21589] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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40
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Nestor G, Kenne L, Sandström C. Experimental evidence of chemical exchange over the β(1→3) glycosidic linkage and hydrogen bonding involving hydroxy protons in hyaluronan oligosaccharides by NMR spectroscopy. Org Biomol Chem 2010; 8:2795-802. [DOI: 10.1039/b927159g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Conformational Analysis of Trimannoside and Bisected Trimannoside Using Aqueous Molecular Dynamics Simulations. B KOREAN CHEM SOC 2009. [DOI: 10.5012/bkcs.2009.30.11.2723] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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42
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Ramadugu SK, Chung YH, Xia J, Margulis CJ. When sugars get wet. A comprehensive study of the behavior of water on the surface of oligosaccharides. J Phys Chem B 2009; 113:11003-15. [PMID: 19588947 DOI: 10.1021/jp904981v] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this article, we characterize the behavior of water on the surface of a diverse group of carbohydrates and attempt to determine the role of saccharide size, linkage, and branching as well as secondary structure on the dynamics and structure of water at the surface. In order to better understand the similarities and differences in the behavior of the solvent on the carbohydrate surface, we explore residence times, rotational correlation functions, local solvent occupancy numbers, and diffusivities. We find that due to the differences in secondary structure water residence times are longer and translational and rotational dynamics are retarded when in contact with wide helices and branched sugars. In the case of extended helices and smaller oligosaccharides, water dynamics is faster and less hindered. This indicates that branching, the type of linkage between monomers, and the anomeric configuration all play a major role in determining the structure and dynamics of water on the surface of carbohydrates.
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43
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Membrane technology for purification of enzymatically produced oligosaccharides: Molecular and operational features affecting performance. Sep Purif Technol 2009. [DOI: 10.1016/j.seppur.2009.08.010] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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44
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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
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45
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Su Z, Wagner B, Cocinero EJ, Ernst B, Simons JP. The intrinsic conformation of a Lewis antigen: The Lewis×trisaccharide. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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46
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Zhang W, Zhao H, Carmichael I, Serianni AS. An NMR investigation of putative interresidue H-bonding in methyl alpha-cellobioside in solution. Carbohydr Res 2009; 344:1582-7. [PMID: 19632671 DOI: 10.1016/j.carres.2009.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 06/02/2009] [Accepted: 06/03/2009] [Indexed: 11/28/2022]
Abstract
Methyl alpha-cellobioside (methyl beta-D-glucopyranosyl-(1-->4)-alpha-D-glucopyranoside) was labeled with (13)C at C4' for use in NMR studies in DMSO-d(6) solvent to attempt the detection of a trans-H-bond J-coupling ((3h)J(CCOH)) between C4' and OH3. Analysis of the OH3 signal at 600 MHz revealed only the presence of two homonuclear J-couplings: (3)J(H3,OH3) and a smaller, longer range J(HH). No evidence for (3h)J(C4',OH3) was found. The longer range J(HH) was traced to (4)J(H4,OH3) based on 2D (1)H-(1)H COSY data and inspection of the H2 and H4 signal lineshapes. A limited set of DFT calculations was performed on a methyl cellobioside mimic to evaluate the structural dependencies of (4)J(H2,O3H) and (4)J(H4,O3H) on the H3-C3-O3-H torsion angle. Computed couplings range from about -0.7 to about +1.1 Hz, with maximal values observed when the C-H and O-H bonds are roughly diaxial.
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Affiliation(s)
- Wenhui Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
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47
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48
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Salisburg AM, Deline AL, Lexa KW, Shields GC, Kirschner KN. Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field. J Comput Chem 2009; 30:910-21. [DOI: 10.1002/jcc.21099] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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49
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Mackeen MM, Almond A, Deschamps M, Cumpstey I, Fairbanks AJ, Tsang C, Rudd PM, Butters TD, Dwek RA, Wormald MR. The conformational properties of the Glc3Man unit suggest conformational biasing within the chaperone-assisted glycoprotein folding pathway. J Mol Biol 2009; 387:335-47. [PMID: 19356590 DOI: 10.1016/j.jmb.2009.01.043] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Revised: 01/19/2009] [Accepted: 01/23/2009] [Indexed: 11/16/2022]
Abstract
A major puzzle is: are all glycoproteins routed through the ER calnexin pathway irrespective of whether this is required for their correct folding? Calnexin recognizes the terminal Glcalpha1-3Manalpha linkage, formed by trimming of the Glcalpha1-2Glcalpha1-3Glcalpha1-3Manalpha (Glc3Man) unit in Glc3Man9GlcNAc2. Different conformations of this unit have been reported. We have addressed this problem by studying the conformation of a series of N-glycans; i.e. Glc3ManOMe, Glc3Man(4,5,7)GlcNAc2 and Glc1Man9GlcNAc2 using 2D NMR NOESY, ROESY, T-ROESY and residual dipolar coupling experiments in a range of solvents, along with solution molecular dynamics simulations of Glc3ManOMe. Our results show a single conformation for the Glcalpha1-2Glcalpha and Glcalpha1-3Glcalpha linkages, and a major (65%) and a minor (30%) conformer for the Glcalpha1-3Manalpha linkage. Modeling of the binding of Glc1Man9GlcNAc2 to calnexin suggests that it is the minor conformer that is recognized by calnexin. This may be one of the mechanisms for controlling the rate of recruitment of proteins into the calnexin/calreticulin chaperone system and enabling proteins that do not require such assistance for folding to bypass the system. This is the first time evidence has been presented on glycoprotein folding that suggests the process may be optimized to balance the chaperone-assisted and chaperone-independent pathways.
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Affiliation(s)
- Mukram M Mackeen
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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50
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Slynko V, Schubert M, Numao S, Kowarik M, Aebi M, Allain FHT. NMR Structure Determination of a Segmentally Labeled Glycoprotein Using in Vitro Glycosylation. J Am Chem Soc 2009; 131:1274-81. [DOI: 10.1021/ja808682v] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vadim Slynko
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Mario Schubert
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Shin Numao
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Michael Kowarik
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Markus Aebi
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Frédéric H.-T. Allain
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
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