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Hu K, Shirakashi R. Molecular dynamics study of water rotational relaxation in saccharide solution for the development of bioprotective agent. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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2
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Masaya TW, Goulay F. A Molecular Dynamic Study of the Effects of Surface Partitioning on the OH Radical Interactions with Solutes in Multicomponent Aqueous Aerosols. J Phys Chem A 2023; 127:751-764. [PMID: 36639126 DOI: 10.1021/acs.jpca.2c07419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The surface-bulk partitioning of small saccharide and amide molecules in aqueous droplets was investigated using molecular dynamics. The air-particle interface was modeled using a 80 Å cubic water box containing a series of organic molecules and surrounded by gaseous OH radicals. The properties of the organic solutes within the interface and the water bulk were examined at a molecular level using density profiles and radial pair distribution functions. Molecules containing only polar functional groups such as urea and glucose are found predominantly in the water bulk, forming an exclusion layer near the water surface. Substitution of a single polar group by an alkyl group in sugars and amides leads to the migration of the molecule toward the interface. Within the first 2 nm from the water surface, surface-active solutes lose their rotational freedom and adopt a preferred orientation with the alkyl group pointing toward the surface. The different packing within the interface leads to different solvation shell structures and enhanced interaction between the organic molecules and absorbed OH radicals. The simulations provide quantitative information about the dimension, composition, and organization of the air-water interface as well as about the nonreactive interaction of the OH radicals with the organic solutes. It suggests that increased concentrations, preferred orientations, and decreased solvation near the air-water surface may lead to differences in reactivities between surface-active and surface-inactive molecules. The results are important to explain how heterogeneous oxidation mechanisms and kinetics within interfaces may differ from those of the bulk.
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Affiliation(s)
- Tadini Wenyika Masaya
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia26506, United States
| | - Fabien Goulay
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia26506, United States
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3
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Ćorković I, Rajchl A, Škorpilová T, Pichler A, Šimunović J, Kopjar M. Evaluation of Chokeberry/Carboxymethylcellulose Hydrogels with the Addition of Disaccharides: DART-TOF/MS and HPLC-DAD Analysis. Int J Mol Sci 2022; 24:ijms24010448. [PMID: 36613889 PMCID: PMC9820810 DOI: 10.3390/ijms24010448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022] Open
Abstract
With the growing awareness of the importance of a healthy diet, the need for the development of novel formulations is also on the rise. Chokeberry products are popular among consumers since they are a rich source of polyphenols that are responsible for antioxidant activity and other positive effects on human health. However, other natural food ingredients, such as disaccharides, can affect their stability. The aim of this study was to investigate the influence of disaccharides addition on the polyphenol composition of chokeberry hydrogels. Hydrogels were prepared from chokeberry juice and 2% of carboxymethylcellulose (CMC) with the addition of 30%, 40%, or 50% of disaccharides (sucrose or trehalose). Samples were analyzed using DART-TOF/MS. The method was optimized, and the fingerprints of the mass spectra have been statistically processed using PCA analysis. Prepared samples were evaluated for total polyphenols, monomeric anthocyanins, and antioxidant activity (FRAP, CUPRAC, DPPH, ABTS assays) using spectrophotometric methods. Individual polyphenols were evaluated using HPLC-DAD analysis. Results showed the addition of disaccharides to 2% CMC hydrogels caused a decrease of total polyphenols. These findings confirm proper formulation is important to achieve appropriate retention of polyphenols.
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Affiliation(s)
- Ina Ćorković
- Faculty of Food Technology, Josip Juraj Strossmayer University, F. Kuhača 18, 31000 Osijek, Croatia
| | - Aleš Rajchl
- Department of Food Preservation, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 3, Dejvice, 166 28 Prague, Czech Republic
| | - Tereza Škorpilová
- Department of Food Preservation, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 3, Dejvice, 166 28 Prague, Czech Republic
| | - Anita Pichler
- Faculty of Food Technology, Josip Juraj Strossmayer University, F. Kuhača 18, 31000 Osijek, Croatia
| | - Josip Šimunović
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695-7624, USA
| | - Mirela Kopjar
- Faculty of Food Technology, Josip Juraj Strossmayer University, F. Kuhača 18, 31000 Osijek, Croatia
- Correspondence: ; Tel.: +385-3122-4309
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4
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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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Encapsulation of Blackberry Phenolics and Volatiles Using Apple Fibers and Disaccharides. Polymers (Basel) 2022; 14:polym14112179. [PMID: 35683852 PMCID: PMC9182803 DOI: 10.3390/polym14112179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
The objective of this study was to determine the effect of disaccharides on the encapsulation of the phenolics and volatiles of blackberry juice with the use of apple fiber. For this purpose, apple fiber/blackberry microparticles were prepared as the control, as well as microparticles additionally containing disaccharides, i.e., sucrose or trehalose. Fiber:disaccharide ratios were 1:0.5, 1:1, and 1:2. Formulated microparticles were characterized for total phenolics, proanthocyanidins, individual phenolics, antioxidant activity, flavor profiles, and color parameters. Both applied disaccharides affected the encapsulation of phenolics and volatiles by the apple fibers. Control microparticles had a higher content of phenolics than microparticles with disaccharides. Comparing disaccharides, the microparticles with trehalose had a higher content of phenolics than the ones containing sucrose. The amount of proanthocyanidins in the control microparticles was 47.81 mg PB2/100 g; in trehalose, the microparticles ranged from 39.88 to 42.99 mg PB2/100 g, and in sucrose, the microparticles ranged from 12.98 to 26.42 mg PB2/100 g, depending on the fiber:disaccharide ratio. Cyanidin-3-glucoside was the dominant anthocyanin. Its amount in the control microparticles was 151.97 mg/100 g, while in the trehalose microparticles, this ranged from 111.97 to 142.56 mg /100 g and in sucrose microparticles, from 100.28 to 138.74 mg /100 g. On the other hand, microparticles with disaccharides had a higher content of volatiles than the control microparticles. Trehalose microparticles had a higher content of volatiles than sucrose ones. These results show that the formulation of microparticles, i.e., the selection of carriers, had an important role in the final quality of the encapsulates.
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Kubbutat P, Leitão L, Kulozik U. Stability of Foams in Vacuum Drying Processes. Effects of Interactions between Sugars, Proteins, and Surfactants on Foam Stability and Dried Foam Properties. Foods 2021; 10:foods10081876. [PMID: 34441652 PMCID: PMC8392398 DOI: 10.3390/foods10081876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 01/16/2023] Open
Abstract
The hypothesis was that saccharides mediate interactions between surface-active components and that this will have an impact on foam decay during the drying process. Static light scattering was performed to determine changes in interactions between the foam stabilizer on a molecular level. Furthermore, pendant drop and oscillating drop measurements were performed to examine the surface tension and surface rheology. Foams were dried in conventional dryers as well as microwave-supported vacuum dryers. Final foam properties were determined. It was shown that the addition of sugars, often added as protective substances for sensitive organic molecules, resulted in lower repulsion between different types of surface-active components, namely polysorbate 80 and β-lactoglobulin (β-lg). Differences in impact of the types of sugars and between different types of surfactant, protein, and small molecules were observed influencing the foam decay behavior. The interfacial properties of polysorbate 80 and β-lg were influenced by the type of the used sugars. The surface elasticity of protein stabilized surfaces was higher compared to that of polysorbate stabilized systems. Protein stabilized systems remained more stable compared to polysorbate systems, which was also affected by the used saccharide. Overall, a correlation between molecular interactions and foam decay behavior was found.
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Vukoja J, Buljeta I, Ivić I, Šimunović J, Pichler A, Kopjar M. Disaccharide Type Affected Phenolic and Volatile Compounds of Citrus Fiber-Blackberry Cream Fillings. Foods 2021; 10:foods10020243. [PMID: 33530336 PMCID: PMC7912440 DOI: 10.3390/foods10020243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 11/16/2022] Open
Abstract
The food industry is continuously developing ingredients, processing methods and packaging materials to improve the quality of fruit products. The aim of this work was to study the possibility of using citrus fiber in the preparation of blackberry cream fillings in combination with disaccharides (sucrose, maltose and trehalose). Evaluations of the phenolics, proanthocyanidins, antioxidant activity, color and volatiles of blackberry cream fillings were conducted after preparation and after three months of storage. Blackberry cream fillings were prepared from citrus fiber (5%), blackberry juice and disaccharides (50%). Disaccharide type had an effect on all investigated parameters. The highest phenol content was in fillings with trehalose (4.977 g/100 g) and the lowest was in fillings prepared with sucrose (4.249 g/100 g). The same tendency was observed after storage. Fillings with maltose had the highest proanthocyanidins content (473.05 mg/100 g) while fillings with sucrose had the lowest amount (299.03 mg/100 g) of these compounds. Regarding volatile compounds, terpenes and aldehydes and ketones were evaluated in the highest concentration. Terpenes were determined in the highest concentration in fillings with trehalose (358.05 µg/kg), while aldehydes and ketones were highest in fillings with sucrose (250.87 µg/kg). After storage, concentration of volatiles decreased. These results indicate that the selection of adequate disaccharides is very important since it can influence the final quality of the product.
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Affiliation(s)
- Josipa Vukoja
- Faculty of Food Technology Osijek, F. Kuhača 18, Josip Juraj Strossmayer University in Osijek, 31000 Osijek, Croatia; (J.V.); (I.B.); (I.I.); (A.P.)
| | - Ivana Buljeta
- Faculty of Food Technology Osijek, F. Kuhača 18, Josip Juraj Strossmayer University in Osijek, 31000 Osijek, Croatia; (J.V.); (I.B.); (I.I.); (A.P.)
| | - Ivana Ivić
- Faculty of Food Technology Osijek, F. Kuhača 18, Josip Juraj Strossmayer University in Osijek, 31000 Osijek, Croatia; (J.V.); (I.B.); (I.I.); (A.P.)
| | - Josip Šimunović
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA;
| | - Anita Pichler
- Faculty of Food Technology Osijek, F. Kuhača 18, Josip Juraj Strossmayer University in Osijek, 31000 Osijek, Croatia; (J.V.); (I.B.); (I.I.); (A.P.)
| | - Mirela Kopjar
- Faculty of Food Technology Osijek, F. Kuhača 18, Josip Juraj Strossmayer University in Osijek, 31000 Osijek, Croatia; (J.V.); (I.B.); (I.I.); (A.P.)
- Correspondence:
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8
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Anumalla B, Prabhu NP. Surface hydration and preferential interaction directs the charged amino acids-induced changes in protein stability. J Mol Graph Model 2020; 98:107602. [PMID: 32251994 DOI: 10.1016/j.jmgm.2020.107602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 01/23/2023]
Abstract
In the present study, we investigate the interaction of amino acid osmolytes, Arg, Lys, Asp and Glu, and a denaturant, guanidinium chloride (Gdm) with proteins. To achieve this, molecular dynamics (MD) simulation of RNase A and α-lactalbumin was performed in the presence of three charged amino acids Arg, Lys, and Asp and the molecular mechanism of amino acid-induced (de)stabilization of the proteins was examined by combining with our earlier report on Glu. As Arg has the side chain similar to that of Gdm and destabilizes the proteins, MD simulation was carried out in the presence of Gdm as well. Radial distribution function and hydration fraction around the protein surface reveals that preferential hydration increases upon the addition of any of the cosolvent; however, the extent of increase is more in the presence of stabilizing cosolvents (stAAs: Lys, Asp and Glu) compared to destabilizing cosolvents (Arg and Gdm). Moreover, the preferential interaction of Arg and Gdm with the proteins is higher than that of stAAs. Residue-level interaction analysis suggests that stAAs preferably interacts with charged amino acids of the proteins whereas Arg and Gdm interactions could be found on almost all the surface exposed residues which might provide higher preferential interaction for these residues. From the results, we propose that the net outcome of preferential hydration versus preferential interaction of the amino acids might determine their effect on the stability of proteins.
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Affiliation(s)
- Bramhini Anumalla
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500 046, India
| | - N Prakash Prabhu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500 046, India.
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Abstract
![]()
The
two sugar molecules sucrose and trehalose are both considered
as stabilizing molecules for the purpose of preserving biological
materials during, for example, lyophilization or cryo-preservation.
Although these molecules share a similar molecular structure, there
are several important differences in their properties when they interact
with water, such as differences in solubility, viscosity, and glass
transition temperature. In general, trehalose has been shown to be
more efficient than other sugar molecules in preserving different
biological molecules against stress, and thus by investigating how
these two disaccharides differ in their water interaction, it is possible
to further understand what makes trehalose special in its stabilizing
properties. For this purpose, the structure of aqueous solutions of
these disaccharides was studied by using neutron and X-ray diffraction
in combination with empirical potential structure refinement (EPSR)
modeling. The results show that there are surprisingly few differences
in the overall structure of the solutions, although there are indications
for that trehalose perturbs the water structure slightly more than
sucrose.
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Affiliation(s)
- Christoffer Olsson
- Department of Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Jan Swenson
- Department of Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
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10
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Heid E, Honegger P, Braun D, Szabadi A, Stankovic T, Steinhauser O, Schröder C. Computational spectroscopy of trehalose, sucrose, maltose, and glucose: A comprehensive study of TDSS, NQR, NOE, and DRS. J Chem Phys 2019; 150:175102. [DOI: 10.1063/1.5095058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Esther Heid
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
| | - Philipp Honegger
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
| | - Daniel Braun
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - András Szabadi
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
| | - Toda Stankovic
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
| | - Othmar Steinhauser
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
| | - Christian Schröder
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
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Zlatic E, Pichler A, Vidrih R, Hribar J, Piližota V, Kopjar M. Volatile profile of sour cherry puree as affected by sucrose and trehalose. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2018. [DOI: 10.1080/10942912.2017.1374289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Emil Zlatic
- Biotechnical Faculty, University in Ljubljana, Ljubljana, Slovenia
| | - Anita Pichler
- Faculty of Food Technology, Josip Juraj Strossmayer University in Osijek, Osijek, Croatia
| | - Rajko Vidrih
- Biotechnical Faculty, University in Ljubljana, Ljubljana, Slovenia
| | - Janez Hribar
- Biotechnical Faculty, University in Ljubljana, Ljubljana, Slovenia
| | - Vlasta Piližota
- Faculty of Food Technology, Josip Juraj Strossmayer University in Osijek, Osijek, Croatia
| | - Mirela Kopjar
- Faculty of Food Technology, Josip Juraj Strossmayer University in Osijek, Osijek, Croatia
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Lončarić A, Pablo Lamas J, Guerra E, Kopjar M, Lores M. Thermal stability of catechin and epicatechin upon disaccharides addition. Int J Food Sci Technol 2017. [DOI: 10.1111/ijfs.13696] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ante Lončarić
- Department of Food Technologies; Faculty of Food Technology Osijek; Josip Juraj Strossmayer University of Osijek; Franje Kuhača 20 HR 31000 Osijek Croatia
| | - Juan Pablo Lamas
- Department of Analytical Chemistry, Nutrition and Food Science; Faculty of Chemistry; University of Santiago de Compostela; E-15782 Santiago de Compostela Spain
| | - Eugenia Guerra
- Department of Analytical Chemistry, Nutrition and Food Science; Faculty of Chemistry; University of Santiago de Compostela; E-15782 Santiago de Compostela Spain
| | - Mirela Kopjar
- Department of Food Technologies; Faculty of Food Technology Osijek; Josip Juraj Strossmayer University of Osijek; Franje Kuhača 20 HR 31000 Osijek Croatia
| | - Marta Lores
- Department of Analytical Chemistry, Nutrition and Food Science; Faculty of Chemistry; University of Santiago de Compostela; E-15782 Santiago de Compostela Spain
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Zlatić E, Pichler A, Kopjar M. Disaccharides: Influence on Volatiles and Phenolics of Sour Cherry Juice. Molecules 2017; 22:E1939. [PMID: 29120375 PMCID: PMC6150359 DOI: 10.3390/molecules22111939] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/04/2017] [Accepted: 11/08/2017] [Indexed: 11/16/2022] Open
Abstract
The food industry is continuously developing ingredients, processing methods and packaging materials to improve the quality of fruit products. The aim of this work was to study the effect of sugars, a common ingredient in the food industry, on phenolics and volatiles of sour cherry juice. Sucrose, trehalose and maltose chemical isomers were chosen for this investigation. All sugars influenced the evaluated parameters. Samples with maltose addition had lower, while samples with sucrose and trehalose addition had higher anthocyanin content than the control sample. Generally, trehalose had a higher positive effect on volatiles with the desired flavor note.
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Affiliation(s)
- Emil Zlatić
- Biotechnical Faculty, Jamnikarjeva 101, Ljubljana 1000, Slovenia.
| | - Anita Pichler
- Faculty of Food Technology, Josip Juraj Strossmayer University in Osijek, F. Kuhača 20, Osijek 31000, Croatia.
| | - Mirela Kopjar
- Faculty of Food Technology, Josip Juraj Strossmayer University in Osijek, F. Kuhača 20, Osijek 31000, Croatia.
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Lacetera A, Berbís MÁ, Nurisso A, Jiménez-Barbero J, Martín-Santamaría S. Computational Chemistry Tools in Glycobiology: Modelling of Carbohydrate–Protein Interactions. COMPUTATIONAL TOOLS FOR CHEMICAL BIOLOGY 2017. [DOI: 10.1039/9781788010139-00145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular modelling provides a major impact in the field of glycosciences, helping in the characterisation of the molecular basis of the recognition between lectins from pathogens and human glycoconjugates, and in the design of glycocompounds with anti-infectious properties. The conformational properties of oligosaccharides are complex, and therefore, the simulation of these properties is a challenging task. Indeed, the development of suitable force fields is required for the proper simulation of important problems in glycobiology, such as the interatomic interactions responsible for oligosaccharide and glycoprotein dynamics, including O-linkages in oligo- and polysaccharides, and N- and O-linkages in glycoproteins. The computational description of representative examples is discussed, herein, related to biologically active oligosaccharides and their interaction with lectins and other proteins, and the new routes open for the design of glycocompounds with promising biological activities.
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Affiliation(s)
- Alessandra Lacetera
- Center for Biological Research CIB-CSIC. Ramiro de Maeztu, 9 28040-Madrid Spain
| | - M. Álvaro Berbís
- Center for Biological Research CIB-CSIC. Ramiro de Maeztu, 9 28040-Madrid Spain
| | - Alessandra Nurisso
- School of Pharmaceutical Sciences University of Geneva, University of Lausanne, Rue Michel Servet 1 CH-1211 Geneva 4 Switzerland
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15
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Petelski AN, Pamies SC, Benítez EI, Rovaletti MML, Sosa GL. Molecular Insights into Protein-Polyphenols Aggregation: A Dynamic and Topological Description. ChemistrySelect 2017. [DOI: 10.1002/slct.201700726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- André N. Petelski
- Chemical Engineering Department. Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Facultad Regional Resistencia; Universidad Tecnológica Nacional; French 414 H3500CHJ) Resistencia, Chaco Argentina
- Instituto de Química Básica y Aplicada del Nordeste Argentino (IQUIBA-NEA), UNNE-CONICET.; Avenida Libertad 5460 3400) Corrientes Argentina
| | - Silvana C. Pamies
- Chemical Engineering Department. Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Facultad Regional Resistencia; Universidad Tecnológica Nacional; French 414 H3500CHJ) Resistencia, Chaco Argentina
| | - Elisa I. Benítez
- Chemical Engineering Department. Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Facultad Regional Resistencia; Universidad Tecnológica Nacional; French 414 H3500CHJ) Resistencia, Chaco Argentina
- Instituto de Química Básica y Aplicada del Nordeste Argentino (IQUIBA-NEA), UNNE-CONICET.; Avenida Libertad 5460 3400) Corrientes Argentina
| | - María M. Lataza Rovaletti
- Chemical Engineering Department. Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Facultad Regional Resistencia; Universidad Tecnológica Nacional; French 414 H3500CHJ) Resistencia, Chaco Argentina
| | - Gladis L. Sosa
- Chemical Engineering Department. Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Facultad Regional Resistencia; Universidad Tecnológica Nacional; French 414 H3500CHJ) Resistencia, Chaco Argentina
- Instituto de Química Básica y Aplicada del Nordeste Argentino (IQUIBA-NEA), UNNE-CONICET.; Avenida Libertad 5460 3400) Corrientes Argentina
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16
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Pamies SC, Petelski AN, Castro EA, Sosa GL. Static and Dynamic Study of Disaccharides Trehalose, Maltose and Sucrose. Struct Chem 2016. [DOI: 10.1007/s11224-016-0896-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Pandey P, Mallajosyula SS. Influence of Polarization on Carbohydrate Hydration: A Comparative Study Using Additive and Polarizable Force Fields. J Phys Chem B 2016; 120:6621-33. [PMID: 27266974 DOI: 10.1021/acs.jpcb.6b05546] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Carbohydrates are known to closely modulate their surrounding solvent structures and influence solvation dynamics. Spectroscopic investigations studying far-IR regions (below 1000 cm(-1)) have observed spectral shifts in the libration band (around 600 cm(-1)) of water in the presence of monosaccharides and polysaccharides. In this paper, we use molecular dynamics simulations to gain atomistic insight into carbohydrate-water interactions and to specifically highlight the differences between additive (nonpolarizable) and polarizable simulations. A total of six monosaccharide systems, α and β anomers of glucose, galactose, and mannose, were studied using additive and polarizable Chemistry at HARvard Macromolecular Mechanics (CHARMM) carbohydrate force fields. Solvents were modeled using three additive water models TIP3P, TIP4P, and TIP5P in additive simulations and polarizable water model SWM4 in polarizable simulations. The presence of carbohydrate has a significant effect on the microscopic water structure, with the effects being pronounced for proximal water molecules. Notably, disruption of the tetrahedral arrangement of proximal water molecules was observed due to the formation of strong carbohydrate-water hydrogen bonds in both additive and polarizable simulations. However, the inclusion of polarization resulted in significant water-bridge occupancies, improved ordered water structures (tetrahedral order parameter), and longer carbohydrate-water H-bond correlations as compared to those for additive simulations. Additionally, polarizable simulations also allowed the calculation of power spectra from the dipole-dipole autocorrelation function, which corresponds to the IR spectra. From the power spectra, we could identify spectral signatures differentiating the proximal and bulk water structures, which could not be captured from additive simulations.
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Affiliation(s)
- Poonam Pandey
- Department of Chemistry, Indian Institute of Technology Gandhinagar , Simkheda, Gandhinagar, Gujarat 382355, India
| | - Sairam S Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar , Simkheda, Gandhinagar, Gujarat 382355, India
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Patel DS, Pendrill R, Mallajosyula SS, Widmalm G, MacKerell AD. Conformational properties of α- or β-(1→6)-linked oligosaccharides: Hamiltonian replica exchange MD simulations and NMR experiments. J Phys Chem B 2014; 118:2851-71. [PMID: 24552401 PMCID: PMC3979472 DOI: 10.1021/jp412051v] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Conformational sampling for a set of 10 α- or β-(1→6)-linked oligosaccharides has been studied using explicit solvent Hamiltonian replica exchange (HREX) simulations and NMR spectroscopy techniques. Validation of the force field and simulation methodology is done by comparing calculated transglycosidic J coupling constants and proton-proton distances with the corresponding NMR data. Initial calculations showed poor agreement, for example, with >3 Hz deviation of the calculated (3)J(H5,H6R) values from the experimental data, prompting optimization of the ω torsion angle parameters associated with (1→6)-linkages. The resulting force field is in overall good agreement (i.e., within ∼0.5 Hz deviation) from experimental (3)J(H5,H6R) values, although some small limitations are evident. Detailed hydrogen bonding analysis indicates that most of the compounds lack direct intramolecular H-bonds between the two monosaccharides; however, minor sampling of the O6···HO2' hydrogen bond is present in three compounds. The results verify the role of the gauche effect between O5 and O6 atoms in gluco- and manno-configured pyranosides causing the ω torsion angle to sample an equilibrium between the gt and gg rotamers. Conversely, galacto-configured pyranosides sample a population distribution in equilibrium between gt and tg rotamers, while the gg rotamer populations are minor. Water radial distribution functions suggest decreased accessibility to the O6 atom in the (1→6)-linkage as compared to the O6' atom in the nonreducing sugar. The role of bridging water molecules between two sugar moieties on the distributions of ω torsion angles in oligosaccharides is also explored.
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Affiliation(s)
- Dhilon S Patel
- Department of Pharmaceutical Sciences, University of Maryland , 20 Penn Street HSF II, Baltimore, Maryland 21201, United States
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Vilén EM, Sandström C. NMR study on the interaction of trehalose with lactose and its effect on the hydrogen bond interaction in lactose. Molecules 2013; 18:9735-54. [PMID: 23948714 PMCID: PMC6270309 DOI: 10.3390/molecules18089735] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 07/31/2013] [Accepted: 08/07/2013] [Indexed: 11/16/2022] Open
Abstract
Trehalose, a well-known stress-protector of biomolecules, has been investigated for its effect on the mobility, hydration and hydrogen bond interaction of lactose using diffusion-ordered NMR spectroscopy and NMR of hydroxy protons. In ternary mixtures of trehalose, lactose and water, the two sugars have the same rate of diffusion. The chemical shifts, temperature coefficients, vicinal coupling constants and ROE of the hydroxy protons in trehalose, lactose and sucrose were measured for the disaccharides alone in water/acetone-d6 solutions as well as in mixtures. The data indicated that addition of trehalose did not change significantly the strength of the hydrogen bond interaction between GlcOH3 and GalO5' in lactose. Small upfield shifts were however measured for all hydroxy protons when the sugar concentration was increased. The chemical shift of the GlcOH3 signal in lactose showed less change, attributed to the spatial proximity to GalO5'. Chemical exchange between hydroxy protons of lactose and trehalose was observed in the ROESY NMR spectra. Similar effects were observed with sucrose indicating no specific effect of trehalose at the concentrations investigated (73 to 763 mg/mL) and suggesting that it is the concentration of hydroxy groups more than the type of sugars which is guiding intermolecular interactions.
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Affiliation(s)
- Eric Morssing Vilén
- Department of Chemistry, Swedish University of Agricultural Sciences, Biocenter P.O. Box 7015, Uppsala SE-75007, Sweden.
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20
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Naziga EB, Schweizer F, Wetmore SD. Solvent interactions stabilize the polyproline II conformation of glycosylated oligoprolines. J Phys Chem B 2013; 117:2671-81. [PMID: 23363073 DOI: 10.1021/jp312487v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In nature, proline residues carry several post-translational modifications (PTMs), including 4R hydroxylation and glycosylation. A recent study synthesized contiguously hydroxylated and glycosylated nonaproline peptides and revealed that both PTMs lead to a significant increase in the thermal stability of PPII relative to the unmodified oligoproline. The increased stability of the hydroxylated peptide can be explained by increased stability of the trans isomer due to stereoelectronic effects. However, the effects of glycosylation cannot be completely explained by stereoelectronics since previous experimental results indicate that 4R-glycosylation does not produce observable changes in the trans preference compared to 4R-hydroxylation. We therefore used sophisticated molecular modeling techniques to determine the reason for the further increase in thermal stability upon glycosylation. Free energy estimates obtained from adaptively biased molecular dynamics calculations in implicit (explicit) solvent are -9 kcal mol(-1) (-20 kcal mol(-1)) for the hydroxylated compound and -9 kcal mol(-1) (-46 kcal mol(-1)) for the glycosylated compound, indicating that direct solvent-peptide interactions are vital for explaining the glycosylation effects on PPII stability. Our data reveals for the first time that interactions between the hydroxyl groups in the glycosylated compound and water act in a complementary fashion with stereoelectronic effects to stabilize the PPII conformation in these substituted oligoproline peptides.
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Affiliation(s)
- Emmanuel B Naziga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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Nikolakis V, Mushrif SH, Herbert B, Booksh KS, Vlachos DG. Fructose–Water–Dimethylsulfoxide Interactions by Vibrational Spectroscopy and Molecular Dynamics Simulations. J Phys Chem B 2012; 116:11274-83. [DOI: 10.1021/jp3056703] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimiros Nikolakis
- Department of Chemical and Biomolecular Engineering,
Catalysis Center for Energy Innovation, University of Delaware, 150 Academy Street, Newark,
Delaware 19716, United States
- Department of Chemistry and Biochemistry, University of Delaware, 102 Brown Laboratory,
Newark, Delaware 19716, United States
| | - Samir H. Mushrif
- Department of Chemical and Biomolecular Engineering,
Catalysis Center for Energy Innovation, University of Delaware, 150 Academy Street, Newark,
Delaware 19716, United States
- Department of Chemistry and Biochemistry, University of Delaware, 102 Brown Laboratory,
Newark, Delaware 19716, United States
| | - Bryon Herbert
- Department of Chemical and Biomolecular Engineering,
Catalysis Center for Energy Innovation, University of Delaware, 150 Academy Street, Newark,
Delaware 19716, United States
- Department of Chemistry and Biochemistry, University of Delaware, 102 Brown Laboratory,
Newark, Delaware 19716, United States
| | - Karl S. Booksh
- Department of Chemical and Biomolecular Engineering,
Catalysis Center for Energy Innovation, University of Delaware, 150 Academy Street, Newark,
Delaware 19716, United States
- Department of Chemistry and Biochemistry, University of Delaware, 102 Brown Laboratory,
Newark, Delaware 19716, United States
| | - Dionisios G. Vlachos
- Department of Chemical and Biomolecular Engineering,
Catalysis Center for Energy Innovation, University of Delaware, 150 Academy Street, Newark,
Delaware 19716, United States
- Department of Chemistry and Biochemistry, University of Delaware, 102 Brown Laboratory,
Newark, Delaware 19716, United States
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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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Xia J, Case DA. Sucrose in aqueous solution revisited, Part 1: molecular dynamics simulations and direct and indirect dipolar coupling analysis. Biopolymers 2012; 97:276-88. [PMID: 22189655 PMCID: PMC3290335 DOI: 10.1002/bip.22017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 11/29/2011] [Accepted: 12/01/2011] [Indexed: 11/10/2022]
Abstract
Although the crystal structure of the disaccharide sucrose was solved more than 30 years ago, its conformational distribution in aqueous solution is still a matter of debate. We report here a variety of molecular dynamics simulations (mostly of 100 ns) using the GLYCAM06 force field and various water models, paying particular attention to comparisons to NMR measurements of residual dipolar couplings and electron-mediated spin-spin couplings. We focus on the glycosidic linkage conformation, the puckering phase angle of the fructose ring, and intramolecular hydrogen bonds between the two sugars. Our results show that sucrose is indeed a dynamic molecule, but the crystal conformation is qualitatively the dominant one in dilute solution. A second conformational basin, populated in many force fields, is probably overstabilized in the calculations.
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Affiliation(s)
- Junchao Xia
- Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ 08854, USA
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24
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Patyk E, Skumiel J, Podsiadło M, Katrusiak A. High-Pressure (+)-Sucrose Polymorph. Angew Chem Int Ed Engl 2012; 51:2146-50. [DOI: 10.1002/anie.201107283] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Indexed: 11/10/2022]
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25
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Patyk E, Skumiel J, Podsiadło M, Katrusiak A. High-Pressure (+)-Sucrose Polymorph. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Mushrif SH, Caratzoulas S, Vlachos DG. Understanding solvent effects in the selective conversion of fructose to 5-hydroxymethyl-furfural: a molecular dynamics investigation. Phys Chem Chem Phys 2012; 14:2637-44. [DOI: 10.1039/c2cp22694d] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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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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28
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Xia J, Case DA. Sucrose in aqueous solution revisited, Part 2: adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation. Biopolymers 2011; 97:289-302. [PMID: 22058066 DOI: 10.1002/bip.22004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 10/21/2011] [Accepted: 10/26/2011] [Indexed: 11/07/2022]
Abstract
We report 100 ns molecular dynamics simulations, at various temperatures, of sucrose in water (with concentrations of sucrose ranging from 0.02 to 4M), and in a 7:3 water-DMSO mixture. Convergence of the resulting conformational ensembles was checked using adaptive-biased simulations along the glycosidic Φ and ψ torsion angles. NMR relaxation parameters, including longitudinal (R₁) and transverse (R₂) relaxation rates, nuclear Overhauser enhancements (NOE), and generalized order parameter (S²) were computed from the resulting time-correlation functions. The amplitude and time scales of molecular motions change with temperature and concentration in ways that track closely with experimental results, and are consistent with a model in which sucrose conformational fluctuations are limited (with 80-90% of the conformations having ϕ-ψ values within 20° of an average conformation), but with some important differences in conformation between pure water and DMSO-water mixtures.
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Affiliation(s)
- Junchao Xia
- Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ 08854, USA
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29
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Mallajosyula SS, MacKerell AD. Influence of solvent and intramolecular hydrogen bonding on the conformational properties of o-linked glycopeptides. J Phys Chem B 2011; 115:11215-29. [PMID: 21823626 PMCID: PMC3179525 DOI: 10.1021/jp203695t] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A detailed investigation of the conformational properties of all the biologically relevant O-glycosidic linkages using the Hamiltonian replica exchange (HREX) simulation methodology and the recently developed CHARMM carbohydrate force field parameters is presented. Fourteen biologically relevant O-linkages between the five sugars N-acetylgalactosamine (GalNAc), N-acetylglucosamine (GlcNAc), D-glucose (Glc), D-mannose (Man), and L-fucose (Fuc) and the amino acids serine and threonine were studied. The force field was tested by comparing the simulation results of the model glycopeptides to various NMR (3)J coupling constants, NOE distances, and data from molecular dynamics with time-averaged restraints (tar-MD). The results show the force field to be in overall agreement with experimental and previous tar-MD simulations, although some small limitations are identified. An in-depth hydrogen bond and bridging water analysis revealed an interplay of hydrogen bonding and bridge water interactions influencing the geometry of the underlying peptide backbone, with the O-linkages favoring extended β-sheet and polyproline type II (PPII) conformations over the compact α(R)-helical conformation. The newly developed parameters were also able to identify hydrogen bonding and water mediated interactions between O-linked sugars and proteins. These results indicate that the newly developed parameters in tandem with HREX conformational sampling provide the means to study glycoproteins in the absence of targeted NMR restraint data.
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Affiliation(s)
- Sairam S. Mallajosyula
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
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30
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Vila Verde A, Campen RK. Disaccharide Topology Induces Slowdown in Local Water Dynamics. J Phys Chem B 2011; 115:7069-84. [DOI: 10.1021/jp112178c] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ana Vila Verde
- FOM Institute AMOLF, 104 Science Park, 1098 XG Amsterdam, The Netherlands
- Centro de Física, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - R. Kramer Campen
- FOM Institute AMOLF, 104 Science Park, 1098 XG Amsterdam, The Netherlands
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31
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Zhu L, Cai T, Huang J, Stringfellow TC, Wall M, Yu L. Water Self-Diffusion in Glassy and Liquid Maltose Measured by Raman Microscopy and NMR. J Phys Chem B 2011; 115:5849-55. [DOI: 10.1021/jp202663r] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lei Zhu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53706, United States
| | - Ting Cai
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53706, United States
| | - Jun Huang
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53706, United States
| | - Thomas C. Stringfellow
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53706, United States
| | - Mark Wall
- Thermo Fisher Scientific, 5225 Verona Road, Madison, Wisconsin 53711, United States
| | - Lian Yu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53706, United States
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32
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Boscaino A, Naidoo KJ. The Extent of Conformational Rigidity Determines Hydration in Nonaromatic Hexacyclic Systems. J Phys Chem B 2011; 115:2608-16. [DOI: 10.1021/jp110248j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Annalisa Boscaino
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kevin J. Naidoo
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
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Cheng S, Edwards SA, Jiang Y, Gräter F. Glycosylation enhances peptide hydrophobic collapse by impairing solvation. Chemphyschem 2010; 11:2367-74. [PMID: 20583025 DOI: 10.1002/cphc.201000205] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Post-translational N-glycosylation of proteins is ubiquitous in eukaryotic cells, and has been shown to influence the thermodynamics of protein collapse and folding. However, the mechanism for this influence is not well understood. All-atom molecular dynamics simulations are carried out to study the collapse of a peptide linked to a single N-glycan. The glycan is shown to perturb the local water hydrogen-bonding network, rendering it less able to solvate the peptide and thus enhancing the hydrophobic contribution to the free energy of collapse. The enhancement of the hydrophobic collapse compensates for the weakened entropic coiling due to the bulky glycan chain and leads to a stronger burial of hydrophobic surface, presumably enhancing folding. This conclusion is reinforced by comparison with coarse-grained simulations, which contain no explicit solvent and correspondingly exhibit no significant thermodynamic changes on glycosylation.
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Affiliation(s)
- Shanmei Cheng
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China
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Venable RM, Hatcher E, Guvench O, MacKerell AD, Pastor RW. Comparing simulated and experimental translation and rotation constants: range of validity for viscosity scaling. J Phys Chem B 2010; 114:12501-7. [PMID: 20831149 PMCID: PMC3040444 DOI: 10.1021/jp105549s] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proper simulation of dynamic properties, including molecular diffusion, is an important goal of empirical force fields. However, the widely used TIP3P water model does not reproduce the experimental viscosity of water. Consequently, scaling of simulated diffusion constants of solutes in aqueous solutions is required to effectively compare them with experiment. It is proposed that scaling by the ratio of viscosities of model and real water is appropriate in the regime where the concentration dependence of simulated and experimental solution viscosities is parallel. With this ansatz, viscosity scaling can be carried out for glucose and trehalose up to 20 wt % for simulations carried out with the CHARMM additive carbohydrate force field C35 and TIP3P water; above this value, the concentration dependence of simulated viscosities lags that of experiment, and scaling is not advised. Scaled translational diffusion constants for glucose and the disaccharides trehalose, maltose, and melibiose at low concentration agree nearly quantitatively with experiment, as do NMR (13)C T(1)'s for glucose, trehalose, and maltose; these results support the use of C35 for simulations of sugar transport properties at low concentration. At high concentrations the scaled diffusion constants for glucose and trehalose underestimate and overestimate experiment, respectively. Hydrodynamic bead model calculations indicate a hydration level of approximately 1 water/hydroxyl for glucose. Patterns for the disaccharides are more complicated, though trehalose binds 0.5 to 1 more water than does maltose depending on the analysis.
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Affiliation(s)
- Richard M. Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elizabeth Hatcher
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, MD 21201
| | - Olgun Guvench
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, MD 21201
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, 716 Stevens Ave, Portland, ME 04103
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, MD 21201
| | - Richard W. Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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35
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Perić-Hassler L, Hansen HS, Baron R, Hünenberger PH. Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling. Carbohydr Res 2010; 345:1781-801. [PMID: 20576257 DOI: 10.1016/j.carres.2010.05.026] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 05/20/2010] [Accepted: 05/22/2010] [Indexed: 10/19/2022]
Abstract
Explicit-solvent molecular dynamics (MD) simulations of the 11 glucose-based disaccharides in water at 300K and 1bar are reported. The simulations were carried out with the GROMOS 45A4 force-field and the sampling along the glycosidic dihedral angles phi and psi was artificially enhanced using the local elevation umbrella sampling (LEUS) method. The trajectories are analyzed in terms of free-energy maps, stable and metastable conformational states (relative free energies and estimated transition timescales), intramolecular H-bonds, single molecule configurational entropies, and agreement with experimental data. All disaccharides considered are found to be characterized either by a single stable (overwhelmingly populated) state ((1-->n)-linked disaccharides with n=1, 2, 3, or 4) or by two stable (comparably populated and differing in the third glycosidic dihedral angle omega ; gg or gt) states with a low interconversion barrier ((1-->6)-linked disaccharides). Metastable (anti-phi or anti-psi) states are also identified with relative free energies in the range of 8-22 kJ mol(-1). The 11 compounds can be classified into four families: (i) the alpha(1-->1)alpha-linked disaccharide trehalose (axial-axial linkage) presents no metastable state, the lowest configurational entropy, and no intramolecular H-bonds; (ii) the four alpha(1-->n)-linked disaccharides (n=1, 2, 3, or 4; axial-equatorial linkage) present one metastable (anti-psi) state, an intermediate configurational entropy, and two alternative intramolecular H-bonds; (iii) the four beta(1-->n)-linked disaccharides (n=1, 2, 3, or 4; equatorial-equatorial linkage) present two metastable (anti-phi and anti-psi) states, an intermediate configurational entropy, and one intramolecular H-bond; (iv) the two (1-->6)-linked disaccharides (additional glycosidic dihedral angle) present no (isomaltose) or a pair of (gentiobiose) metastable (anti-phi) states, the highest configurational entropy, and no intramolecular H-bonds. The observed conformational preferences appear to be dictated by four main driving forces (ring conformational preferences, exo-anomeric effect, steric constraints, and possible presence of a third glycosidic dihedral angle), leaving a secondary role to intramolecular H-bonding and specific solvation effects. In spite of the weak conformational driving force attributed to solvent-exposed H-bonds in water (highly polar protic solvent), intramolecular H-bonds may still have a significant influence on the physico-chemical properties of the disaccharide by decreasing its hydrophilicity. Along with previous work, the results also complete the suggestion of a spectrum of approximate transition timescales for carbohydrates up to the disaccharide level, namely: approximately 30 ps (hydroxyl groups), approximately 1 ns (free lactol group, free hydroxymethyl groups, glycosidic dihedral angleomega in (1-->6)-linked disaccharides), approximately 10 ns to 2 micros (ring conformation, glycosidic dihedral angles phi and psi). The calculated average values of the glycosidic torsional angles agree well with the available experimental data, providing validation for the force-field and simulation methodology employed.
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Affiliation(s)
- Lovorka Perić-Hassler
- Laboratory of Physical Chemistry, ETH Zürich, ETH Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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36
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Damager I, Engelsen SB, Blennow A, Lindberg Møller B, Motawia MS. First principles insight into the alpha-glucan structures of starch: their synthesis, conformation, and hydration. Chem Rev 2010; 110:2049-80. [PMID: 20302376 PMCID: PMC2854524 DOI: 10.1021/cr900227t] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Indexed: 12/02/2022]
Affiliation(s)
| | | | | | | | - Mohammed Saddik Motawia
- To whom correspondence should be addressed. E-mail: . Tel: +45 35 33 33 69. Fax: +45 35 33 33 33
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37
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Schnupf U, Willett JL, Momany FA. 27 ps DFT molecular dynamics simulation of α-maltose: A reduced basis set study. J Comput Chem 2010; 31:2087-97. [DOI: 10.1002/jcc.21495] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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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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39
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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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40
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Hansen PI, Spraul M, Dvortsak P, Larsen FH, Blennow A, Motawia MS, Engelsen SB. Starch phosphorylation--maltosidic restrains upon 3'- and 6'-phosphorylation investigated by chemical synthesis, molecular dynamics and NMR spectroscopy. Biopolymers 2009; 91:179-93. [PMID: 18985674 DOI: 10.1002/bip.21111] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Phosphorylation is the only known in vivo substitution of starch, yet no structural evidence has been provided to explain its implications of the amylosidic backbone and its stimulating effects on starch degradation in plants. In this study, we provide evidence for a major influence on the glucosidic bond in starch specifically induced by the 3-O-phosphate. Two phosphorylated maltose model compounds were synthesized and subjected to combined molecular dynamics (MD) studies and 950 MHz NMR studies. The two phosphorylated disaccharides represent the two possible phosphorylation sites observed in natural starches, namely maltose phosphorylated at the 3'- and 6'-position (maltose-3'-O-phosphate and maltose-6'-O-phosphate). When compared with maltose, both of the maltose-phosphates exhibit a restricted conformational space of the alpha(1-->4) glycosidic linkage. When maltose is phosphorylated in the 3'-position, MD and NMR show that the glucosidic space is seriously restricted to one narrow potential energy well which is strongly offset from the global potential energy well of maltose and almost 50 degrees degrees from the Phi angle of the alpha-maltose crystal structure. The driving force is primarily steric, but the configuration of the structural waters is also significantly altered. Both the favored conformation of the maltose-3'-phosphate and the maltose-6'-phosphate align well into the 6-fold double helical structure of amylopectin when the effects on the glucosidic bond are not taken into account. However, the restrained geometry of the glucosidic linkage of maltose-3'-phosphate cannot be accommodated in the helical structure, suggesting a major local disturbing effect, if present in the starch granule semi-crystalline lattice.
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Affiliation(s)
- Peter I Hansen
- Department of Food Science, Quality and Technology, University of Copenhagen, Rolighedsvej 30, DK-1958 Frederiksberg C, Denmark
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41
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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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42
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Abstract
Carbohydrates are crucial for living cells, playing myriads of functional roles that range from being structural or energy-storage devices to molecular labels that, through non-covalent interaction with proteins, impart exquisite selectivity in processes such as molecular trafficking and cellular recognition. The molecular bases that govern the recognition between carbohydrates and proteins have not been fully understood yet. In the present study, we have obtained a surface-area-based model for the formation heat capacity of protein–carbohydrate complexes, which includes separate terms for the contributions of the two molecular types. The carbohydrate model, which was calibrated using carbohydrate dissolution data, indicates that the heat capacity contribution of a given group surface depends on its position in the saccharide molecule, a picture that is consistent with previous experimental and theoretical studies showing that the high abundance of hydroxy groups in carbohydrates yields particular solvation properties. This model was used to estimate the carbohydrate's contribution in the formation of a protein–carbohydrate complex, which in turn was used to obtain the heat capacity change associated with the protein's binding site. The model is able to account for protein–carbohydrate complexes that cannot be explained using a previous model that only considered the overall contribution of polar and apolar groups, while allowing a more detailed dissection of the elementary contributions that give rise to the formation heat capacity effects of these adducts.
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Shpigelman A, Portnaya I, Ramon O, Livney YD. Saccharide-structure effects on polyN-isopropylacrylamide phase transition in aqueous media; Reflections on protein stability. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/polb.21562] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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44
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Hansen PI, Larsen FH, Motawia SM, Blennow A, Spraul M, Dvortsak P, Engelsen SB. Structure and hydration of the amylopectin trisaccharide building blocks-Synthesis, NMR, and molecular dynamics. Biopolymers 2008; 89:1179-93. [DOI: 10.1002/bip.21075] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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Depiction of the forces participating in the 2-O-sulfo-alpha-L-iduronic acid conformational preference in heparin sequences in aqueous solutions. Carbohydr Res 2008; 343:1435-45. [PMID: 18452898 DOI: 10.1016/j.carres.2008.04.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Revised: 04/03/2008] [Accepted: 04/13/2008] [Indexed: 11/22/2022]
Abstract
2-O-Sulfo-alpha-l-iduronic acid (IdoA2S) is one of the main components of heparin, an anticoagulant and antithrombotic polysaccharide able to potentiate the inhibitory effect of antithrombin over plasma serine proteases. This monosaccharide unit adopts an equilibrium between chair (1C4) and skew-boat (2SO) forms as a function of heparin sequence size and composition. Although the prevalence of the 1C4 chair conformation in monosaccharides is understood, the reasons for the increase in 2SO contribution in the whole polysaccharide chain are still uncertain. In this context, 0.2 mus molecular dynamics simulations of IdoA2S-containing oligosaccharides indicated that stabilization due to intramolecular hydrogen bonds around IdoA2S is highly correlated (p0.001) with the expected conformational equilibrium for this residue in solution. This behavior explains the known effect of different heparin compositions, at the monosaccharide level, on IdoA2S conformation in biological solutions.
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46
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Lerbret A, Affouard F, Bordat P, Hédoux A, Guinet Y, Descamps M. Molecular dynamics simulations of lysozyme in water/sugar solutions. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.09.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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47
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Gharsallaoui A, Rogé B, Mathlouthi M. Water–disaccharides interactions in saturated solution and the crystallisation conditions. Food Chem 2008. [DOI: 10.1016/j.foodchem.2006.12.068] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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48
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Kräutler V, Müller M, Hünenberger PH. Conformation, dynamics, solvation and relative stabilities of selected β-hexopyranoses in water: a molecular dynamics study with the gromos 45A4 force field. Carbohydr Res 2007; 342:2097-124. [PMID: 17573054 DOI: 10.1016/j.carres.2007.05.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 04/06/2007] [Accepted: 05/01/2007] [Indexed: 11/23/2022]
Abstract
The present article reports long timescale (200 ns) simulations of four beta-D-hexopyranoses (beta-D-glucose, beta-D-mannose, beta-D-galactose and beta-D-talose) using explicit-solvent (water) molecular dynamics and vacuum stochastic dynamics simulations together with the GROMOS 45A4 force field. Free-energy and solvation free-energy differences between the four compounds are also calculated using thermodynamic integration. Along with previous experimental findings, the present results suggest that the formation of intramolecular hydrogen-bonds in water is an 'opportunistic' consequence of the close proximity of hydrogen-bonding groups, rather than a major conformational driving force promoting this proximity. In particular, the conformational preferences of the hydroxymethyl group in aqueous environment appear to be dominated by 1,3-syn-diaxial repulsion, with gauche and solvation effects being secondary, and intramolecular hydrogen-bonding essentially negligible. The rotational dynamics of the exocyclic hydroxyl groups, which cannot be probed experimentally, is found to be rapid (10-100 ps timescale) and correlated (flip-flop hydrogen-bonds interconverting preferentially through an asynchronous disrotatory pathway). Structured solvent environments are observed between the ring and lactol oxygen atoms, as well as between the 4-OH and hydroxymethyl groups. The calculated stability differences between the four compounds are dominated by intramolecular effects, while the corresponding differences in solvation free energies are small. An inversion of the stereochemistry at either C(2) or C(4) from equatorial to axial is associated with a raise in free energy. Finally, the particularly low hydrophilicity of beta-D-talose appears to be caused by the formation of a high-occurrence hydrogen-bonded bridge between the 1,3-syn-diaxial 2-OH and 4-OH groups. Overall, good agreement is found with available experimental and theoretical data on the structural, dynamical, solvation and energetic properties of these compounds. However, this detailed comparison also reveals some discrepancies, suggesting the need (and providing a solid basis) for further refinement.
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Affiliation(s)
- Vincent Kräutler
- Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
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49
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Pereira CS, Hünenberger PH. Interaction of the sugars trehalose, maltose and glucose with a phospholipid bilayer: a comparative molecular dynamics study. J Phys Chem B 2007; 110:15572-81. [PMID: 16884281 DOI: 10.1021/jp060789l] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics simulations are used to investigate the interaction of the sugars trehalose, maltose, and glucose with a phospholipid bilayer at atomic resolution. Simulations of the bilayer in the absence or in the presence of sugar (2 molal concentration for the disaccharides, 4 molal for the monosaccharide) are carried out at 325 and 475 K. At 325 K, the three sugars are found to interact directly with the lipid headgroups through hydrogen bonds, replacing water at about one-fifth to one-quarter of the hydrogen-bonding sites provided by the membrane. Because of its small size and of the reduced topological constraints imposed on the hydroxyl group locations and orientations, glucose interacts more tightly (at identical effective hydroxyl group concentration) with the lipid headgroups when compared to the disaccharides. At high temperature, the three sugars are able to prevent the thermal disruption of the bilayer. This protective effect is correlated with a significant increase in the number of sugar-headgroups hydrogen bonds. For the disaccharides, this change is predominantly due to an increase in the number of sugar molecules bridging three or more lipid molecules. For glucose, it is primarily due to an increase in the number of sugar molecules bound to one or bridging two lipid molecules.
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Affiliation(s)
- Cristina S Pereira
- Laboratory of Physical Chemistry, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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50
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Lerbret A, Bordat P, Affouard F, Descamps M, Migliardo F. How homogeneous are the trehalose, maltose, and sucrose water solutions? An insight from molecular dynamics simulations. J Phys Chem B 2007; 109:11046-57. [PMID: 16852346 DOI: 10.1021/jp0468657] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural properties resulting from the reciprocal influence between water and three well-known homologous disaccharides, namely, trehalose, maltose, and sucrose, in aqueous solutions have been investigated in the 4-66 wt % concentration range by means of molecular dynamics computer simulations. Hydration numbers clearly show that trehalose binds to a larger number of water molecules than do maltose or sucrose, thus affecting the water structure to a deeper extent. Two-dimensional radial distribution functions of trehalose solutions definitely reveal that water is preferentially localized at the hydration sites found in the trehalose dihydrate crystal, this tendency being enhanced when increasing trehalose concentration. Over a rather wide concentration range (4-49 wt %), the fluctuations of the radius of gyration and of the glycosidic dihedral angles of trehalose indicate a higher flexibility with respect to maltose and sucrose. At sugar concentrations between 33 and 66 wt %, the mean sugar cluster size and the number of sugar-sugar hydrogen bonds formed within sugar clusters reveal that trehalose is able to form larger clusters than sucrose but smaller than maltose. These features suggest that trehalose-water mixtures would be more homogeneous than the two others, thus reducing both desiccation stresses and ice formation.
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Affiliation(s)
- A Lerbret
- Laboratoire de Dynamique et Structure des Matériaux Moléculaires, UMR CNRS 8024, Université Lille I, 59655 Villeneuve d'Ascq Cedex, France.
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