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The influence of hydrogen bonds on the glass transition in amorphous binary systems. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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2
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Investigation of the Hydration Behavior of Different Sugars by Time Domain-NMR. Foods 2022; 11:foods11081148. [PMID: 35454735 PMCID: PMC9031088 DOI: 10.3390/foods11081148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/19/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
The hydration behavior of sugars varies from each other and examining the underlying mechanism is challenging. In this study, the hydration behavior of glucose, fructose, allulose (aka rare sugar), and sucrose have been explored using different Time Domain Nuclear Magnetic Resonance (TD-NMR) approaches (relaxation times, self-diffusion, and Magic Sandwich Echo (MSE)). For that purpose, the effects of different sugar concentrations (2.5%, 5%, 10%, 15%, 20%, 30%, and 40%) (w/v) and hydration at different times for 1 day were investigated by T2 relaxation times and self-diffusion coefficients. Crystallinity values of the solid and hydrated sugars were also determined with MSE. Change in T2 relaxation times with concentration showed that the fastest binding with water (parallel with the shortest T2 values) was observed for sucrose for all concentrations followed by glucose, fructose, and allulose. Furthermore, dependency of T2 relaxation times with hydration time showed that sucrose was the fastest in binding with water followed by glucose, fructose, and allulose. The study showed that allulose, one of the most famous rare sugars that is known to be a natural low-calorie sugar alternative, had the lowest interaction with water than the other sugars. TD-NMR was suggested as a practical, quick, and accurate technique to determine the hydration behavior of sugars.
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3
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Influence of Extraction Method on the Rheological Properties of Jackfruit (Artocarpus heterophyllus) Seed Starch Dispersions. FOOD BIOPHYS 2018. [DOI: 10.1007/s11483-018-9521-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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4
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Patra S, Erwin N, Winter R. Translational Dynamics of Lipidated Ras Proteins in the Presence of Crowding Agents and Compatible Osmolytes. Chemphyschem 2016; 17:2164-9. [PMID: 27028423 DOI: 10.1002/cphc.201600179] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Indexed: 11/07/2022]
Abstract
Ras proteins are small GTPases and are involved in transmitting signals that control cell growth, differentiation, and proliferation. Since the cell cytoplasm is crowded with different macromolecules, understanding the translational dynamics of Ras proteins in crowded environments is crucial to yielding deeper insight into their reactivity and function. Herein, the translational dynamics of lipidated N-Ras and K-Ras4B is studied in the bulk and in the presence of a macromolecular crowder (Ficoll) and the compatible osmolyte and microcrowder sucrose by fluorescence correlation spectroscopy. The results reveal that N-Ras forms dimers due to the presence of its lipid moiety in the hypervariable region, whereas K-Ras4B remains in its monomeric form in the bulk. Addition of a macromolecular crowding agent gradually favors clustering of the Ras proteins. In 20 wt % Ficoll N-Ras forms trimers and K-Ras4B dimers. Concentrations of sucrose up to 10 wt % foster formation of N-Ras trimers and K-Ras dimers as well. The results can be rationalized in terms of the excluded-volume effect, which enhances the association of the proteins, and, for the higher concentrations, by limited-hydration conditions. The results of this study shed new light on the association state of these proteins in a crowded environment. This is of particular interest for the Ras proteins, because their solution state-monomeric or clustered-influences their membrane-partitioning behavior and their interplay with cytosolic interaction partners.
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Affiliation(s)
- Satyajit Patra
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Nelli Erwin
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany.
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5
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Pendrill R, Säwén E, Widmalm G. Conformation and dynamics at a flexible glycosidic linkage revealed by NMR spectroscopy and molecular dynamics simulations: analysis of β-L-Fucp-(1→6)-α-D-Glcp-OMe in water solution. J Phys Chem B 2013; 117:14709-22. [PMID: 24175957 DOI: 10.1021/jp409985h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The intrinsic flexibility of carbohydrates facilitates different 3D structures in response to altered environments. At glycosidic (1→6)-linkages, three torsion angles are variable, and herein the conformation and dynamics of β-L-Fucp-(1→6)-α-D-Glcp-OMe are investigated using a combination of NMR spectroscopy and molecular dynamics (MD) simulations. The disaccharide shows evidence of conformational averaging for the ψ and ω torsion angles, best explained by a four-state conformational distribution. Notably, there is a significant population of conformations having ψ = 85° (clinal) in addition to those having ψ = 180° (antiperiplanar). Moderate differences in (13)C R1 relaxation rates are found to be best explained by axially symmetric tumbling in combination with minor differences in librational motion for the two residues, whereas the isomerization motions are occurring too slowly to be contributing significantly to the observed relaxation rates. The MD simulation was found to give a reasonably good agreement with experiment, especially with respect to diffusive properties, among which the rotational anisotropy, D∥/D⊥, is found to be 2.35. The force field employed showed too narrow ω torsion angles in the gauche-trans and gauche-gauche states as well as overestimating the population of the gauche-trans conformer. This information can subsequently be used in directing parameter developments and emphasizes the need for refinement of force fields for (1→6)-linked carbohydrates.
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Affiliation(s)
- Robert Pendrill
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
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Chen CS, Yu YP, Hsu CH, Zou W, Fang JM, Wu SH. Evaluation of the regioselective delactonization of tri-sialic acid lactone by in-solution molecular dynamics simulation. Carbohydr Res 2012; 354:87-93. [PMID: 22572126 DOI: 10.1016/j.carres.2012.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 02/18/2012] [Accepted: 02/22/2012] [Indexed: 11/29/2022]
Abstract
An approximate model for the delactonization of tri-sialic acid lactone is presented with two water-layers that led to neutral hydrolysis of δ-lactone. The hydrolytic reactivity was studied with a 10-ns in-solution molecular dynamics simulation. The initial step of this hydrolysis involves a reactant water nucleophile complex via a proton transfer with another water molecule. Therefore, the probability of water molecules localized at the hydrolytic center correlates to the hydrolysis of δ-lactone. The stepwise delactonization of α2,8-(NeuAc)(3) lactone results/resulted from water concentration discrepancy near the carbonyl carbon of lactones in two water oxygen···carbonyl carbon shells, and the distances of OC···O(water) layers were 2.8 Å and 5.1 Å. Based on in-solution molecular dynamics study, the motion of water molecules over the re-face of the carbonyl groups was used for the quantitative description of the residence probability, p, whose value is 0.11 for lactone I and 0.33 for lactone II. The geometric criteria used to determine the residence statistics are (1) the distance of water-oxygen···carbonyl carbon in less than 5.1 Å and (2) the cone angle, θ, of carbonyl OC···O(water) in the range of 85-115°. As expected, a higher residence probability at lactone II led to its faster hydrolysis. Both the radial g(r) and angular p(θ) pair distribution functions of water oxygen and carbonyl groups of lactones ensure a better surrounding hydration encounter for lactone II. In contrast, water molecules around lactone I are deduced due to a steric hindrance by the turn structure of α2,8-(NeuAc)(3) lactone.
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Affiliation(s)
- Chien-Sheng Chen
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
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7
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Burakowski A, Gliński J. Hydration numbers of nonelectrolytes from acoustic methods. Chem Rev 2011; 112:2059-81. [PMID: 22148760 DOI: 10.1021/cr2000948] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrzej Burakowski
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
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8
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Biswas A, Bharara M, Hurst C, Gruessner R, Armstrong D, Rilo H. Use of sugar on the healing of diabetic ulcers: a review. J Diabetes Sci Technol 2010; 4:1139-45. [PMID: 20920433 PMCID: PMC2956799 DOI: 10.1177/193229681000400512] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
With the advent of several innovative wound care management tools, the choice of products and treatment modalities available to clinicians continues to expand. High costs associated with wound care, especially diabetic foot wounds, make it important for clinician scientists to research alternative therapies and optimally incorporate them into wound care protocols appropriately. This article reviews using sugar as a treatment option in diabetic foot care and provides a guide to its appropriate use in healing foot ulcers. In addition to a clinical case study, the physiological significance and advantages of sugar are discussed.
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Affiliation(s)
- Atanu Biswas
- Department of Surgery, Center for Cellular Transplantation, University of Arizona College of MedicineTucson, Arizona
| | - Manish Bharara
- Department of Surgery, Southern Arizona Limb Salvage Alliance, University of Arizona College of MedicineTucson, Arizona
| | - Craig Hurst
- Department of Surgery, Division of Plastic and Reconstructive Surgery, University of Arizona College of MedicineTucson, Arizona
| | - Rainer Gruessner
- Department of Surgery, Center for Cellular Transplantation, University of Arizona College of MedicineTucson, Arizona
- Department of Surgery, Division of Abdominal Transplant Surgery, University of Arizona College of MedicineTucson, Arizona
| | - David Armstrong
- Department of Surgery, Southern Arizona Limb Salvage Alliance, University of Arizona College of MedicineTucson, Arizona
| | - Horacio Rilo
- Department of Surgery, Center for Cellular Transplantation, University of Arizona College of MedicineTucson, Arizona
- Department of Surgery, Southern Arizona Limb Salvage Alliance, University of Arizona College of MedicineTucson, Arizona
- Department of Surgery, Division of Abdominal Transplant Surgery, University of Arizona College of MedicineTucson, Arizona
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9
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Te JA, Tan ML, Ichiye T. Solvation of Glucose, Trehalose, and Sucrose by the Soft Sticky Dipole-Quadrupole-Octupole Water Model. Chem Phys Lett 2010; 491:218-223. [PMID: 21072255 PMCID: PMC2975465 DOI: 10.1016/j.cplett.2010.04.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Water structure around sugars modeled by partial charges is compared for soft-sticky dipole-quadrupole-octupole (SSDQO), a fast single-site multipole model, and commonly used multi-site models in Monte Carlo simulations. Radial distribution functions and coordination numbers of all the models indicate similar hydration by hydrogen-bond donor and acceptor waters. However, the new optimized SSDQO1 parameters as well as TIP4P-Ew and TIP5P predict a "lone-pair" orientation for the water accepting the sugar hydroxyl hydrogen bond that is more consistent with the limited experimental data than the "dipole" orientation in SPC/E, which has important implications for studies of the cryoprotectant properties of sugars.
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Affiliation(s)
- Jerez A. Te
- Department of Chemistry, Georgetown University, Washington, DC, 20057
| | - Ming-Liang Tan
- Department of Chemistry, Georgetown University, Washington, DC, 20057
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC, 20057
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10
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Kaminski K, Kaminska E, Wlodarczyk P, Pawlus S, Kimla D, Kasprzycka A, Paluch M, Ziolo J, Szeja W, Ngai KL. Dielectric Studies on Mobility of the Glycosidic Linkage in Seven Disaccharides. J Phys Chem B 2008; 112:12816-23. [DOI: 10.1021/jp804240a] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. Kaminski
- Institute of Physics, Silesian Univ., ul. Uniwersytecka 4, 40-007 Katowice, Poland, Silesian University of Technology, Department of Chemistry, Division of Organic, Chemistry, Biochemistry and Biotechnology, ul. Krzywoustego 4, 44-100 Gliwice, Poland, and Naval Research Laboratory, Washington, DC 20375-5320
| | - E. Kaminska
- Institute of Physics, Silesian Univ., ul. Uniwersytecka 4, 40-007 Katowice, Poland, Silesian University of Technology, Department of Chemistry, Division of Organic, Chemistry, Biochemistry and Biotechnology, ul. Krzywoustego 4, 44-100 Gliwice, Poland, and Naval Research Laboratory, Washington, DC 20375-5320
| | - P. Wlodarczyk
- Institute of Physics, Silesian Univ., ul. Uniwersytecka 4, 40-007 Katowice, Poland, Silesian University of Technology, Department of Chemistry, Division of Organic, Chemistry, Biochemistry and Biotechnology, ul. Krzywoustego 4, 44-100 Gliwice, Poland, and Naval Research Laboratory, Washington, DC 20375-5320
| | - S. Pawlus
- Institute of Physics, Silesian Univ., ul. Uniwersytecka 4, 40-007 Katowice, Poland, Silesian University of Technology, Department of Chemistry, Division of Organic, Chemistry, Biochemistry and Biotechnology, ul. Krzywoustego 4, 44-100 Gliwice, Poland, and Naval Research Laboratory, Washington, DC 20375-5320
| | - D. Kimla
- Institute of Physics, Silesian Univ., ul. Uniwersytecka 4, 40-007 Katowice, Poland, Silesian University of Technology, Department of Chemistry, Division of Organic, Chemistry, Biochemistry and Biotechnology, ul. Krzywoustego 4, 44-100 Gliwice, Poland, and Naval Research Laboratory, Washington, DC 20375-5320
| | - A. Kasprzycka
- Institute of Physics, Silesian Univ., ul. Uniwersytecka 4, 40-007 Katowice, Poland, Silesian University of Technology, Department of Chemistry, Division of Organic, Chemistry, Biochemistry and Biotechnology, ul. Krzywoustego 4, 44-100 Gliwice, Poland, and Naval Research Laboratory, Washington, DC 20375-5320
| | - M. Paluch
- Institute of Physics, Silesian Univ., ul. Uniwersytecka 4, 40-007 Katowice, Poland, Silesian University of Technology, Department of Chemistry, Division of Organic, Chemistry, Biochemistry and Biotechnology, ul. Krzywoustego 4, 44-100 Gliwice, Poland, and Naval Research Laboratory, Washington, DC 20375-5320
| | - J. Ziolo
- Institute of Physics, Silesian Univ., ul. Uniwersytecka 4, 40-007 Katowice, Poland, Silesian University of Technology, Department of Chemistry, Division of Organic, Chemistry, Biochemistry and Biotechnology, ul. Krzywoustego 4, 44-100 Gliwice, Poland, and Naval Research Laboratory, Washington, DC 20375-5320
| | - W. Szeja
- Institute of Physics, Silesian Univ., ul. Uniwersytecka 4, 40-007 Katowice, Poland, Silesian University of Technology, Department of Chemistry, Division of Organic, Chemistry, Biochemistry and Biotechnology, ul. Krzywoustego 4, 44-100 Gliwice, Poland, and Naval Research Laboratory, Washington, DC 20375-5320
| | - K. L. Ngai
- Institute of Physics, Silesian Univ., ul. Uniwersytecka 4, 40-007 Katowice, Poland, Silesian University of Technology, Department of Chemistry, Division of Organic, Chemistry, Biochemistry and Biotechnology, ul. Krzywoustego 4, 44-100 Gliwice, Poland, and Naval Research Laboratory, Washington, DC 20375-5320
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11
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Kaminski K, Kaminska E, Hensel-Bielowka S, Chelmecka E, Paluch M, Ziolo J, Wlodarczyk P, Ngai KL. Identification of the Molecular Motions Responsible for the Slower Secondary (β) Relaxation in Sucrose. J Phys Chem B 2008; 112:7662-8. [DOI: 10.1021/jp711502a] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. Kaminski
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
| | - E. Kaminska
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
| | - S. Hensel-Bielowka
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
| | - E. Chelmecka
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
| | - M. Paluch
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
| | - J. Ziolo
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
| | - P. Wlodarczyk
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
| | - K. L. Ngai
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
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12
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Affiliation(s)
- Kjeld Rasmussen
- a Department of Chemistry, Building 207 , Technical University of Denmark , DK - 2800 Lyngby, Denmark
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13
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Simperler A, Kornherr A, Chopra R, Jones W, Motherwell WDS, Zifferer G. The glass transition temperatures of amorphous trehalose–water mixtures and the mobility of water: an experimental and in silico study. Carbohydr Res 2007; 342:1470-9. [PMID: 17511976 DOI: 10.1016/j.carres.2007.04.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 04/06/2007] [Accepted: 04/11/2007] [Indexed: 11/24/2022]
Abstract
Isothermal-isobaric molecular dynamics simulations are used to calculate the specific volume of models of trehalose and three amorphous trehalose-water mixtures (2.9%, 4.5% and 5.3% (w/w) water, respectively) as a function of temperature. Plots of specific volume versus temperature exhibit a characteristic change in slope when the amorphous systems change from the glassy to the rubbery state and the intersection of the two regression lines provides an estimate of the glass transition temperature T(g). A comparison of the calculated and experimental T(g) values, as obtained from differential scanning calorimetry, shows that despite the predicted values being systematically higher (about 21-26K), the trend and the incremental differences between the T(g) values have been computed correctly: T(g)(5.3%(w/w))<T(g)(4.5%(w/w))<T(g)(2.9%(w/w))<T(g)(0.0%(w/w)). The mobility of water has been investigated over temperature ranges covering the rubbery and the glassy phases of the trehalose-water mixtures by calculating the diffusion coefficients of water. The temperature dependence of the diffusion coefficient changes in the region of the glass transition and can be used as well to estimate T(g) values. The activation energies for water diffusion were found to be independent of the amount of water in amorphous trehalose.
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Affiliation(s)
- Alexandra Simperler
- The Pfizer Institute for Pharmaceutical Materials Science, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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14
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Chen CS, Yu YP, Hsu CH, Wu YT, Zou W, Fang JM, Wu SH. Conformation of Trisialic Acid Lactone: NMR Spectroscopic Analysis and Molecular Dynamics Simulation. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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15
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Marigheto N, Venturi L, Hibberd D, Wright KM, Ferrante G, Hills BP. Methods for peak assignment in low-resolution multidimensional NMR cross-correlation relaxometry. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 187:327-42. [PMID: 17587616 DOI: 10.1016/j.jmr.2007.04.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 03/29/2007] [Accepted: 04/25/2007] [Indexed: 05/16/2023]
Abstract
Several NMR protocols are presented for assigning peaks in complex T1-T2 spectra, including the effects of varying the spectrometer frequency and the CPMG pulsing rate. Extensions into a third dimension based on chemical-shift; diffusion- and field-cycled weighted T1-T2 cross-correlation methods are also explored as a means of peak assignment. We illustrate the power of these novel techniques with reference to simple aqueous sucrose solutions, but the methodology should be generally applicable.
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Affiliation(s)
- N Marigheto
- Institute of Food Research, Norwich Research Park, Colney, Norwich, UK
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16
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Humeres E, Mascayano C, Riadi G, González-Nilo F. Molecular dynamics simulation of the aqueous solvation shell of cellulose and xanthate ester derivatives. J PHYS ORG CHEM 2007. [DOI: 10.1002/poc.1074] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Fabri D, Williams MAK, Halstead TK. Water T2 relaxation in sugar solutions. Carbohydr Res 2005; 340:889-905. [PMID: 15780255 DOI: 10.1016/j.carres.2005.01.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2004] [Accepted: 01/27/2005] [Indexed: 10/25/2022]
Abstract
1H spin-spin relaxation times of water were measured with the CPMG sequence in dilute aqueous solutions of glucitol, mannitol, glycerol, glycol, the methyl D-pyranosides of alpha-glucose, beta-glucose, alpha-galactose, beta-galactose, alpha-xylose, beta-xylose, beta-arabinose and sucrose, alpha,alpha-trehalose, beta-maltose, maltotriose and maltoheptaose. The relaxation-time dispersion was measured by varying the CPMG pulse spacing, tau. These data were interpreted by means of the Carver-Richards model in which exchange between water protons and labile solute hydroxyl protons provides a significant contribution to the relaxation. From the dependences on temperature and tau, parameters characteristic of the pool of hydroxyls belonging to a given solute were extracted by nonlinear regression, including: the fraction of exchangeable protons, P, the chemical-shift difference between water protons and hydroxyl protons, deltaomega, the intrinsic spin-spin relaxation time, T2, and the chemical exchange rate, k. These solute-specific parameters are related, respectively, to the concentration, identity, mobility and exchange life-time of the hydroxyl site. At 298 K, values of deltaomega, T2 and k were found to be of the order of 1 ppm, 100 ms and 1000 s(-1), respectively. Effects of molecular size, conformation and solute concentration were investigated. The exchange mechanism was characterised by Eyring activation enthalpies and entropies with values in the ranges 50-70 kJ mol(-1) and -10 to 60 J K(-1)mol(-1), respectively.
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Affiliation(s)
- Deborah Fabri
- Department of Chemistry, University of York, Heslington, York YO19 6AL, UK.
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18
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Corzana F, Motawia MS, Du Penhoat CH, Perez S, Tschampel SM, Woods RJ, Engelsen SB. A hydration study of (1-->4) and (1-->6) linked alpha-glucans by comparative 10 ns molecular dynamics simulations and 500-MHz NMR. J Comput Chem 2004; 25:573-86. [PMID: 14735575 PMCID: PMC4201036 DOI: 10.1002/jcc.10405] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The hydration behavior of two model disaccharides, methyl-alpha-D-maltoside (1) and methyl-alpha-D-isomaltoside (2), has been investigated by a comparative 10 ns molecular dynamics study. The detailed hydration of the two disaccharides was described using three force fields especially developed for modeling of carbohydrates in explicit solvent. To validate the theoretical results the two compounds were synthesized and subjected to 500 MHz NMR spectroscopy, including pulsed field gradient diffusion measurements (1: 4.0. 10(-6) cm(2). s(-1); 2: 4.2. 10(-6) cm(2). s(-1)). In short, the older CHARMM-based force field exhibited a more structured carbohydrate-water interaction leading to better agreement with the diffusional properties of the two compounds, whereas especially the alpha-(1-->6) linkage and the primary hydroxyl groups were inaccurately modeled. In contrast, the new generation of the CHARMM-based force field (CSFF) and the most recent version of the AMBER-based force field (GLYCAM-2000a) exhibited less structured carbohydrate-water interactions with the result that the diffusional properties of the two disaccharides were underestimated, whereas the simulations of the alpha-(1-->6) linkage and the primary hydroxyl groups were significantly improved and in excellent agreement with homo- and heteronuclear coupling constants. The difference between the two classes of force field (more structured and less structured carbohydrate-water interaction) was underlined by calculation of the isotropic hydration as calculated by radial pair distributions. At one extreme, the radial O em leader O pair distribution function yielded a peak density of 2.3 times the bulk density in the first hydration shell when using the older CHARMM force field, whereas the maximum density observed in the GLYCAM force field was calculated to be 1.0, at the other extreme.
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Affiliation(s)
- Francisco Corzana
- Food Technology, Department of Dairy and Food Science, The Royal Veterinary and Agricultural University, Rolighedsvej 30, DK-1958 Frederiksberg C, Denmark
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19
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Laederach A, Reilly PJ. Specific empirical free energy function for automated docking of carbohydrates to proteins. J Comput Chem 2003; 24:1748-57. [PMID: 12964193 DOI: 10.1002/jcc.10288] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We present an automated docking protocol specifically optimized to predict the structure and affinity of a protein-carbohydrate complex. A scoring function was developed based on a training set of 30 protein-carbohydrate complexes of known structure and affinity. Combinations of several models for hydrogen bonding, torsional entropy loss, and solvation were tested for their ability to fit the training set data, and the best model was used with AutoDock. The electrostatic empirical coefficient is larger than in a previously obtained model using a training set comprised of various types of protein-ligand complexes, indicating that electrostatic interactions play a more important role in determining the affinity between a carbohydrate and a protein. The differences in the relative weighting of the empirical coefficients in the model yields predicted free energies for the training set with a standard error of 1.403 kcal/mol. The new scoring function was tested on 17 Aspergillus niger glucoamylase inhibitors for which binding energies had been determined experimentally. Free energies of complex formation were predicted with a residual standard error of 1.101 kcal/mol. The new scoring function therefore provides a robust method for predicting free energies of formation and optimal conformations of carbohydrate-protein complexes.
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Affiliation(s)
- Alain Laederach
- Department of Chemical Engineering, Iowa State University, 2114 Sweeney Hall, Ames, IA 50011, USA
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20
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Loris R, Imberty A, Beeckmans S, Van Driessche E, Read JS, Bouckaert J, De Greve H, Buts L, Wyns L. Crystal structure of Pterocarpus angolensis lectin in complex with glucose, sucrose, and turanose. J Biol Chem 2003; 278:16297-303. [PMID: 12595543 DOI: 10.1074/jbc.m211148200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The crystal structure of the Man/Glc-specific seed lectin from Pterocarpus angolensis was determined in complex with methyl-alpha-d-glucose, sucrose, and turanose. The carbohydrate binding site contains a classic Man/Glc type specificity loop. Its metal binding loop on the other hand is of the long type, different from what is observed in other Man/Glc-specific legume lectins. Glucose binding in the primary binding site is reminiscent of the glucose complexes of concanavalin A and lentil lectin. Sucrose is found to be bound in a conformation similar as seen in the binding site of lentil lectin. A direct hydrogen bond between Ser-137(OG) to Fru(O2) in Pterocarpus angolensis lectin replaces a water-mediated interaction in the equivalent complex of lentil lectin. In the turanose complex, the binding site of the first molecule in the asymmetric unit contains the alphaGlc1-3betaFruf form of furanose while the second molecule contains the alphaGlc1-3betaFrup form in its binding site.
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Affiliation(s)
- Remy Loris
- Laboratorium voor Ultrastructuur, Instituut voor Moleculaire Biologie, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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21
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Iannilli E, Tettamanti E, Galantini L, Magazù S. An Integrated Quasi-Elastic Light-Scattering, Pulse-Gradient-Spin−Echo Study on the Transport Properties of α,α-Trehalose, Sucrose, and Maltose Deuterium Oxide Solutions. J Phys Chem B 2001. [DOI: 10.1021/jp011275j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emilia Iannilli
- Istituto Nazionale di Fisica della Materia (INFM), Dipartimento di Fisica, Università di L'Aquila, Via Vetoio, 67010 Coppito, L'Aquila, Italy
| | - Enzo Tettamanti
- Istituto Nazionale di Fisica della Materia (INFM), Dipartimento di Fisica, Università di L'Aquila, Via Vetoio, 67010 Coppito, L'Aquila, Italy
| | - Luciano Galantini
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Salvatore Magazù
- Dipartimento di Fisica and INFM, Università di Messina, P.O. Box 55, Papardo, 98166 S. Agata di Messina, Italy
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22
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Martorana V, La Fata L, Bulone D, San Biagio P. Potential of mean force between two ions in a sucrose rich aqueous solution. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)01028-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Abstract
Sugar in its pure form, or incorporated into a paste containing an adhesive hydropolymer (gum), is a non-toxic treatment for a variety of wounds. Not only does it provide a suitable clean environment for angiogenesis to take place, but it will debride the wound surface and reduce odour. The presence of an adhesive hydropolymer seems to prevent hypergranulation, scarring and contraction.
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24
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Frecer V, Ho B, Ding JL. Molecular dynamics study on lipid A from Escherichia coli: insights into its mechanism of biological action. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1466:87-104. [PMID: 10825434 DOI: 10.1016/s0005-2736(00)00174-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Structural properties of the Escherichia coli lipid A moiety were analysed by means of molecular mechanics and molecular dynamics simulations and compared to synthetic monophospho and dephospho analogues with different biological activities in the Limulus assay. The conformation of glucosamine disaccharide headgroup, order and packing of fatty acid chains, solvation of phosphate groups, coordination by water molecules, sodium counterions and models of cationic amino acid side chains were described in terms of mean values, mean residence times, radial distribution functions, coordination numbers, solvation and interaction energies. Solvation and polar interactions of the phosphate groups were correlated to known biological activities the lipid A variants. The observed relationship between the biological effect and the number and position of the phosphate groups were explained with the help of simple mechanistic models of lipid A action. The possible mechanism of action involving specific binding of lipid A disaccharide headgroup to cationic residues of a receptor model was compared with an alternative mechanism, which assumes a relationship between the ability to adopt non-lamellar supramolecular structures and the biological activity. Conclusions are drawn about the probable mode of lipid A action. Implications for rational drug design of endotoxin-neutralising agents are discussed.
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Affiliation(s)
- V Frecer
- Departmnt of Biological Sciences, Faculty of Science, Naitonal University of Singapore, Singapore
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25
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Andersson C, Engelsen SB. The mean hydration of carbohydrates as studied by normalized two-dimensional radial pair distributions. J Mol Graph Model 1999; 17:101-5, 131-3. [PMID: 10680115 DOI: 10.1016/s1093-3263(99)00022-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The hydration of carbohydrates plays a key role in many biological processes. Molecular dynamics simulations provide an effective tool for investigating the hydration of complex solutes such as carbohydrates. In this article we devise an algorithm for the calculation of two-dimensional radial pair distributions describing the probability of finding a water molecule in a site defined by two reference atoms. The normalized 2D radial pair distribution is proposed as an effective tool for investigating and comparing localized or ordered water sites around flexible molecules such as carbohydrates when analyzing molecular dynamics simulations and the utility of 2D radial pair distributions is demonstrated using sucrose as an example. In this relatively simple structure, 2D radial pair distributions were able to characterize and quantify the importance of two unique interresidue hydration sites in which a water molecule is forming a bridge between the glycopyranosyl and fructofuranosyl residues. The approach is proposed to be a valuable tool for comparing and understanding the hydration of flexible biomolecules such as carbohydrates.
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Affiliation(s)
- C Andersson
- Department of Dairy and Food Science, Royal Veterinary and Agricultural University, Frederiksberg, Denmark
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