1
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Bakó I, Pusztai L, Pothoczki S. Outstanding Properties of the Hydration Shell around β-d-Glucose: A Computational Study. ACS OMEGA 2024; 9:20331-20337. [PMID: 38737074 PMCID: PMC11080014 DOI: 10.1021/acsomega.4c00798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/14/2024]
Abstract
Ab initio molecular dynamics (AIMD) simulations have been performed on aqueous solutions of four simple sugars, α-d-glucose, β-d-glucose, α-d-mannose, and α-d-galactose. Hydrogen-bonding (HB) properties, such as the number of donor- and acceptor-type HB-s, and the lengths and strengths of hydrogen bonds between sugar and water molecules, have been determined. Related electronic properties, such as the dipole moments of water molecules and partial charges of the sugar O atoms, have also been calculated. The hydrophilic and hydrophobic shells were characterized by means of spatial distribution functions. β-d-Glucose was found to form the highest number of hydrophilic and the smallest number of hydrophobic connections to neighboring water molecules. The average sugar-water H-bond length was the shortest for β-d-glucose, which suggests that these are the strongest such H-bonds. Furthermore, β-d-glucose appears to stand out in terms of the symmetry properties of both its hydrophilic and hydrophobic hydration shells. In summary, in all aspects considered here, there seems to be a correlation between the distinct characteristics of β-d-glucose reported here and its outstanding solubility in water. Admittedly, our findings represent only some of the important factors that influence the solubility.
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Affiliation(s)
- Imre Bakó
- HUN-REN
Research Centre for Natural Sciences, Magyar tudósok körútja 2., H-1117 Budapest, Hungary
| | - László Pusztai
- HUN-REN
Wigner Research Centre for Physics, Konkoly-Thege M. út 29-33., H-1121 Budapest, Hungary
- International
Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Szilvia Pothoczki
- HUN-REN
Wigner Research Centre for Physics, Konkoly-Thege M. út 29-33., H-1121 Budapest, Hungary
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2
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Deng JL, Tang MJ, Su XX, Ye YT, Wei JY, Chen ZX, Qin YM. Rapid Kinetic Interactions of Sugar and Sugar Alcohol with Sweet Taste Receptors on Live Cells Using Stopped-Flow Spectroscopy. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14731-14741. [PMID: 37773006 DOI: 10.1021/acs.jafc.3c05144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
The subjective measurement of the dynamic perception of sweetness is a problem in food science. Herein, the rapid interactions of sugars and sugar alcohols with sweet taste receptors on living cells on a millisecond timescale were studied via stopped-flow fluorescence spectroscopy. According to the rapid-kinetic parameters, sweeteners were divided into two groups. Sweeteners in group I disrupted the hydrogen bond network structure of water, and the apparent rate constant (kobs) was in the range of 0.45-0.6 s-1. Sweeteners in group II promoted the hydrogen bond formation of water, and the kobs was mostly in the range of 0.6-0.75 s-1. For most sweeteners, the kobs of cell responses was negatively correlated with the apparent specific volume of sweeteners. The differences in the cellular responses may be attributed to the disturbance in the water structure. Experimental results showed that the kinetic parameters of sweet cell responses reflected the dynamic perception of sweetness. Rapid kinetics, solution thermodynamic analysis, and water structure analysis enriched the physicochemical study of the sweetness mechanism and can be used to objectively evaluate the dynamic perception of sweetness.
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Affiliation(s)
- Jun-Ling Deng
- Molecular Food Science Laboratory, College of Food & Biology Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Meng-Jie Tang
- Molecular Food Science Laboratory, College of Food & Biology Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Xiao-Xia Su
- Molecular Food Science Laboratory, College of Food & Biology Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
- COFCO Nutrition and Health Research Institute Co., Ltd., Beijing 102209, China
| | - Yu-Tong Ye
- Molecular Food Science Laboratory, College of Food & Biology Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Jie-Ying Wei
- Molecular Food Science Laboratory, College of Food & Biology Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Zhong-Xiu Chen
- Molecular Food Science Laboratory, College of Food & Biology Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Yu-Mei Qin
- Molecular Food Science Laboratory, College of Food & Biology Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
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3
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Wang X, Yang X, Hu Y, Guo S, Lu J. Bionic Assembly of Layered Double Hydroxides Nanosheets and Positively Charged Micelles by Counterions Balance and Their Selective Detection of Mannose. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:14686-14694. [PMID: 36437733 DOI: 10.1021/acs.langmuir.2c02225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The selective detection of mannose is significant for tumor early diagnosis. However, current methods for detecting mannose are expensive and time-consuming, limiting their application. In this paper, we have obtained a 25-layer positively charged micellar/LDHs nanocomposite film system by electrostatic layer-by-layer assembly with reference to the unique properties of homogeneous charge ion attraction and charge overcompensation in biomolecules: hexadecyl trimethylammonium bromide (CTAB) was used to coat neutral molecules of fluorescein (FLU) to form (FLU@CTAB) cationic micelles, which were electrostatically assembled with laminate positively charged layered double hydroxides (LDHs) nanosheets to form (FLU@CTAB/LDHs)n ultrathin films (UTFs) by the layer-by-layer electrostatic assembly, where the mediating role of the Br- counteranion had a profound effect on the success of the assembly. Moreover, compared to pure FLU solution, the fluorescence intensity and the lifetime of (FLU@CTAB/LDHs)20 UTFs were enhanced by 1.6 and 2 times, respectively. (FLU@CTAB/LDHs)20 UTFs exhibited selective detection for d-mannose with a detection limit of 0.05 mg·mL-1. Therefore, the (FLU@CTAB/LDHs)n UTFs can be a novel biosensor. Compared to conventional powder sensors, (FLU@CTAB/LDHs)n thin-film fluorescent sensors are more promising for device implementation. Moreover, the design strategy of positively charged micellar/LDHs nanocomposite systems breaks the current limitation that LDHs can only be assembled with anions or neutral molecules and extends the scope of counterion-mediated host-guest to the nanosheet-micellar system.
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Affiliation(s)
- Xiaoyan Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, P.O. Box 98, Beisanhuan East Road 15, Beijing, 100029, China
| | - Xueting Yang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, P.O. Box 98, Beisanhuan East Road 15, Beijing, 100029, China
| | - Yuehua Hu
- Shanghai Research Institute Sinopec Lubricant, 455 Gaoyang Road, Shanghai, 200080, China
| | - Shuaitian Guo
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, P.O. Box 98, Beisanhuan East Road 15, Beijing, 100029, China
| | - Jun Lu
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, P.O. Box 98, Beisanhuan East Road 15, Beijing, 100029, China
- Beijing Advanced Innovation Center for Soft Mater Science and Engineering, P.O. Box 98, Beisanhuan East Road 15, Beijing, 100029, China
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4
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Food sustainability trends - How to value the açaí production chain for the development of food inputs from its main bioactive ingredients? Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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5
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Terban MW, Billinge SJL. Structural Analysis of Molecular Materials Using the Pair Distribution Function. Chem Rev 2022; 122:1208-1272. [PMID: 34788012 PMCID: PMC8759070 DOI: 10.1021/acs.chemrev.1c00237] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Indexed: 12/16/2022]
Abstract
This is a review of atomic pair distribution function (PDF) analysis as applied to the study of molecular materials. The PDF method is a powerful approach to study short- and intermediate-range order in materials on the nanoscale. It may be obtained from total scattering measurements using X-rays, neutrons, or electrons, and it provides structural details when defects, disorder, or structural ambiguities obscure their elucidation directly in reciprocal space. While its uses in the study of inorganic crystals, glasses, and nanomaterials have been recently highlighted, significant progress has also been made in its application to molecular materials such as carbons, pharmaceuticals, polymers, liquids, coordination compounds, composites, and more. Here, an overview of applications toward a wide variety of molecular compounds (organic and inorganic) and systems with molecular components is presented. We then present pedagogical descriptions and tips for further implementation. Successful utilization of the method requires an interdisciplinary consolidation of material preparation, high quality scattering experimentation, data processing, model formulation, and attentive scrutiny of the results. It is hoped that this article will provide a useful reference to practitioners for PDF applications in a wide realm of molecular sciences, and help new practitioners to get started with this technique.
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Affiliation(s)
- Maxwell W. Terban
- Max
Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Simon J. L. Billinge
- Department
of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Condensed
Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, New York 11973, United States
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6
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Lima-Oliveira G, Brennan-Bourdon LM, Varela B, Arredondo ME, Aranda E, Flores S, Ochoa P. Clot activators and anticoagulant additives for blood collection. A critical review on behalf of COLABIOCLI WG-PRE-LATAM. Crit Rev Clin Lab Sci 2020; 58:207-224. [PMID: 33929278 DOI: 10.1080/10408363.2020.1849008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In the clinical laboratory, knowledge of and the correct use of clot activators and anticoagulant additives are critical to preserve and maintain samples in optimal conditions prior to analysis. In 2017, the Latin America Confederation of Clinical Biochemistry (COLABIOCLI) commissioned the Latin American Working Group for Preanalytical Phase (WG-PRE-LATAM) to study preanalytical variability and establish guidelines for preanalytical procedures to be applied by clinical laboratories and health care professionals. The aim of this critical review, on behalf of COLABIOCLI WG-PRE-LATAM, is to provide information to understand the mechanisms of the interactions and reactions that occur between blood and clot activators and anticoagulant additives inside evacuated tubes used for laboratory testing. Clot activators - glass, silica, kaolin, bentonite, and diatomaceous earth - work by surface dependent mechanism whereas extrinsic biomolecules - thrombin, snake venoms, ellagic acid, and thromboplastin - start in vitro coagulation when added to blood. Few manufacturers of evacuated tubes state the type and concentration of clot activators used in their products. With respect to anticoagulant additives, sodium citrate and oxalate complex free calcium and ethylenediaminetetraacetic acid chelates calcium. Heparin potentiates antithrombin and hirudin binds to active thrombin, inactivating the thrombin irreversibly. Blood collection tubes have improved continually over the years, from the glass tubes containing clot activators or anticoagulant additives that were prepared by laboratory personnel to the current standardized evacuated systems that permit more precise blood/additive ratios. Each clot activator and anticoagulant additive demonstrates specific functionality, and both manufacturers of tubes and laboratory professional strive to provide suitable interference-free sample matrices for laboratory testing. Both manufacturers of in vitro diagnostic devices and laboratory professionals need to understand all aspects of venous blood sampling so that they do not underestimate the impact of tube additives on laboratory testing.
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Affiliation(s)
- G Lima-Oliveira
- Latin American Working Group for Preanalytical Phase (WG-PRE-LATAM), Latin America Confederation of Clinical Biochemistry (COLABIOCLI), Montevideo, Uruguay.,Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - L M Brennan-Bourdon
- Latin American Working Group for Preanalytical Phase (WG-PRE-LATAM), Latin America Confederation of Clinical Biochemistry (COLABIOCLI), Montevideo, Uruguay.,Comisión Para la Protección Contra Riesgos Sanitarios del Estado de Jalisco (COPRISJAL), Secretaria de Salud, Guadalajara, México
| | - B Varela
- Latin American Working Group for Preanalytical Phase (WG-PRE-LATAM), Latin America Confederation of Clinical Biochemistry (COLABIOCLI), Montevideo, Uruguay.,Quality Assurance, LAC, Montevideo, Uruguay
| | - M E Arredondo
- Latin American Working Group for Preanalytical Phase (WG-PRE-LATAM), Latin America Confederation of Clinical Biochemistry (COLABIOCLI), Montevideo, Uruguay.,Management Area, Clinical Laboratory, BIONET S.A, Santiago, Chile
| | - E Aranda
- Latin American Working Group for Preanalytical Phase (WG-PRE-LATAM), Latin America Confederation of Clinical Biochemistry (COLABIOCLI), Montevideo, Uruguay.,Laboratory of Thrombosis and Hemostasis, Department of Hematology-Oncology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - S Flores
- Latin American Working Group for Preanalytical Phase (WG-PRE-LATAM), Latin America Confederation of Clinical Biochemistry (COLABIOCLI), Montevideo, Uruguay.,Clinical Laboratory, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - P Ochoa
- Latin American Working Group for Preanalytical Phase (WG-PRE-LATAM), Latin America Confederation of Clinical Biochemistry (COLABIOCLI), Montevideo, Uruguay.,Facultad de Medicina, Universidad Católica de Cuenca, Cuenca, Ecuador
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7
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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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8
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Pullicin AJ, Penner MH, Lim J. The Sweet Taste of Acarbose and Maltotriose: Relative Detection and Underlying Mechanism. Chem Senses 2020; 44:123-128. [PMID: 30590468 DOI: 10.1093/chemse/bjy081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Although sweet-tasting saccharides possess similar molecular structures, their relative sweetness often varies to a considerable degree. Current understanding of saccharide structure/sweetness interrelationships is limited. Understanding how certain structural features of saccharides and/or saccharide analogs correlate to their relative sweetness can provide insight on the mechanisms underlying sweetness potency. Maltotriose is a short-chain glucose-based oligosaccharide, which we recently reported to elicit sweet taste. Acarbose, an α-glucosidase inhibitor, is a pseudo-saccharide that has an overall resemblance to a glucose-based oligosaccharide and thus may be viewed as a structural analog. During other studies, we recognized that acarbose can also elicit sweet taste. Here, we formally investigated the underlying taste detection mechanism of acarbose, while confirming our previous findings for maltotriose. We found that subjects could detect the sweet taste of acarbose and maltotriose in aqueous solutions but were not able to detect them in the presence of a sweet taste inhibitor lactisole. These findings support that both are ligands of the human sweet taste receptor, hT1R2/hT1R3. In a separate experiment, we measured the relative sweetness detection of acarbose, maltotriose, and other sweet-tasting mono- and disaccharides (glucose, fructose, maltose, and sucrose). Whereas maltotriose was found to have a similar discriminability profile to glucose and maltose, the discriminability of acarbose matched that of fructose at the concentrations tested (18, 32, and 56 mM). These findings are discussed in terms of how specific molecular features (e.g., degree of polymerization and monomer composition) may contribute to the relative sweetness of saccharides.
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Affiliation(s)
- Alexa J Pullicin
- Department of Food Science and Technology, Oregon State University, Corvallis, OR, USA
| | - Michael H Penner
- Department of Food Science and Technology, Oregon State University, Corvallis, OR, USA
| | - Juyun Lim
- Department of Food Science and Technology, Oregon State University, Corvallis, OR, USA
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9
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Imberti S, McLain SE, Rhys NH, Bruni F, Ricci MA. Role of Water in Sucrose, Lactose, and Sucralose Taste: The Sweeter, The Wetter? ACS OMEGA 2019; 4:22392-22398. [PMID: 31909321 PMCID: PMC6941182 DOI: 10.1021/acsomega.9b02794] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/15/2019] [Indexed: 05/16/2023]
Abstract
Natural sugars combine energy supply and, except a few cases, a pleasant taste. On the other hand, exaggerated consumption may impact population health. This has busted the research for the synthesis of increasingly cheaper artificial sweeteners, with low energy content and intense taste. Here, we suggest that studies of the hydration properties of three disaccharides, namely, the natural sucrose and lactose and the artificial sucralose, may explain the difference by orders of magnitude among their sweetness. This is done by analyzing via Monte Carlo simulations the neutron diffraction differential cross sections of aqueous solutions of the three sugars and their isotopes. Our results show that the strength of the sugar-water hydrogen bond interaction is one of the factors influencing sweetness, another being the number of water molecules within the first neighboring shell of the sugar whether bonded or not.
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Affiliation(s)
- Silvia Imberti
- UKRI-STFC,
ISIS Neutron and Muon Source, Rutherford
Appleton Laboratory, Harwell Campus, OX11 0QX Didcot, United Kingdom
- E-mail: ,
| | - Sylvia E. McLain
- Department
of Chemistry, School of Life Sciences, University
of Sussex, Falmer, BN1 9RH Brighton, United Kingdom
| | - Natasha H. Rhys
- Department
of Physics, King’s College London, WC2R 2LS London, United Kingdom
| | - Fabio Bruni
- Dipartimento
di Scienze, Sezione di Nanoscienze, Università
degli Studi “Roma Tre”, Via della Vasca Navale 84, 00146 Roma, Italy
| | - Maria Antonietta Ricci
- Dipartimento
di Scienze, Sezione di Nanoscienze, Università
degli Studi “Roma Tre”, Via della Vasca Navale 84, 00146 Roma, Italy
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10
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Moore JE, McCoy TM, Sokolova AV, de Campo L, Pearson GR, Wilkinson BL, Tabor RF. Worm-like micelles and vesicles formed by alkyl-oligo(ethylene glycol)-glycoside carbohydrate surfactants: The effect of precisely tuned amphiphilicity on aggregate packing. J Colloid Interface Sci 2019; 547:275-290. [DOI: 10.1016/j.jcis.2019.03.068] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 10/27/2022]
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11
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Rhys NH, Duffy IB, Sowden CL, Lorenz CD, McLain SE. On the hydration of DOPE in solution. J Chem Phys 2019; 150:115104. [PMID: 30902020 DOI: 10.1063/1.5085736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The atomic-scale hydration structure around the 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) headgroup in a chloroform/water solution has been investigated using neutron diffraction enhanced by isotopic substitution and NMR, coupled with empirical potential structure refinement and molecular dynamics simulations. The results obtained show the preferential binding sites for water molecules on the DOPE headgroups, with the most predominant interactions being with the ammonium and phosphate groups. Interestingly, the level of hydration, as well as the association of DOPE molecules, varies according to the simulation method used. The results here suggest the presence of a tight water network around these lipid headgroups that could affect the permeability of the membrane for lipid-mediated diffusion.
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Affiliation(s)
- Natasha H Rhys
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Imogen B Duffy
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Christopher L Sowden
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Christian D Lorenz
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Sylvia E McLain
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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12
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Zeng Z, Bernstein ER. Studies of Arabinose- and Mannose-Related Anionic Species and Comparison to Ribose and Fructose. J Phys Chem A 2019; 123:2340-2350. [PMID: 30807168 DOI: 10.1021/acs.jpca.8b11838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gas phase, isolated monosaccharides arabinose- and mannose-related anionic species generated through the matrix-assisted laser desorption ionization (MALDI) method are investigated via negative ion photoelectron spectroscopy (PES) and density functional theory (DFT) calculations. The vertical detachment energies (VDEs) of the observed anionic species are experimentally determined: the corresponding structures are assigned based on good agreement between experimental and theoretical VDEs. Arabinose- parent anion is found to exist as open chain structures in the gas phase, while mannose- parent anionic species are not observed. Both monosaccharides undergo dissociation through loss of H and loss of H2O. (saccharide-H)- anions evidence coexisting positional and conformational isomers. (saccharide-H2O)- species have only two positional isomers, each with conformational differences. The present results for arabinose and mannose are further compared to those previously reported for ribose and fructose. This comparison is based on the anions observed and identified through the same PES/DFT techniques for the four saccharides (arabinose, mannose, ribose, and fructose). The issue of natural selection of ribose as the sugar backbone constituent of RNA is thereby explored from the point of view of anionic electronic structure and stability of the four species. Saccharide phosphates are also discussed in the present work with regard to addressing the unique natural selection of ribose for the backbone support of RNA and DNA.
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Affiliation(s)
- Zhen Zeng
- Department of Chemistry, NSF ERC for Extreme Ultraviolet Science and Technology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Elliot R Bernstein
- Department of Chemistry, NSF ERC for Extreme Ultraviolet Science and Technology , Colorado State University , Fort Collins , Colorado 80523 , United States
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13
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Di Gioacchino M, Bruni F, Ricci MA. N-Methylacetamide Aqueous Solutions: A Neutron Diffraction Study. J Phys Chem B 2019; 123:1808-1814. [PMID: 30739453 DOI: 10.1021/acs.jpcb.9b00246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydration of N-methylacetamide (NMA) in solution has been determined by neutron diffraction with isotopic Hydrogen/Deuterium substitution (NDIS), augmented by Monte Carlo simulation. This study is representative of the hydration of the peptide bonds characteristic of proteins and might shed light on aggregation phenomena in intrinsically disordered proteins. It is found that NMA forms hydrogen bonds with water at both O and H peptide sites, although of different lengths and strengths. The comparison with the case of tripeptide glutathione evidences differences in both hydration and propensity for aggregation.
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Affiliation(s)
- Michael Di Gioacchino
- Dipartimento di Scienze , Universitá degli Studi Roma Tre , via della Vasca Navale 84 , 00146 Roma , Italy
| | - Fabio Bruni
- Dipartimento di Scienze , Universitá degli Studi Roma Tre , via della Vasca Navale 84 , 00146 Roma , Italy
| | - Maria Antonietta Ricci
- Dipartimento di Scienze , Universitá degli Studi Roma Tre , via della Vasca Navale 84 , 00146 Roma , Italy
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14
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Estimating Metabolic Equilibrium Constants: Progress and Future Challenges. Trends Biochem Sci 2018; 43:960-969. [DOI: 10.1016/j.tibs.2018.09.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 01/03/2023]
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15
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Lenton S, Rhys NH, Towey JJ, Soper AK, Dougan L. Temperature-Dependent Segregation in Alcohol-Water Binary Mixtures Is Driven by Water Clustering. J Phys Chem B 2018; 122:7884-7894. [PMID: 30039970 DOI: 10.1021/acs.jpcb.8b03543] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previous neutron scattering work, combined with computer simulated structure analysis, has established that binary mixtures of methanol and water partially segregate into water-rich and alcohol-rich components. It has furthermore been noted that, between methanol mole fractions of 0.27 and 0.54, both components, water and methanol, simultaneously form percolating clusters. This partial segregation is enhanced with decreasing temperature. The mole fraction of 0.27 also corresponds to the point of maximum excess entropy for ethanol-water mixtures. Here, we study the degree of molecular segregation in aqueous ethanol solutions at a mole fraction of 0.27 and compare it with that in methanol-water solutions at the same concentration. Structural information is extracted for these solutions using neutron diffraction coupled with empirical potential structure refinement. We show that ethanol, like methanol, bi-percolates at this concentration and that, in a similar manner to methanol, alcohol segregation, as measured by the proximity of neighboring methyl sidechains, is increased upon cooling the solution. Water clustering is found to be significantly enhanced in both alcohol solutions compared to the water clustering that occurs for random, hard sphere-like, mixing with no hydrogen bonds between molecules. Alcohol clustering via the hydrophobic groups is, on the other hand, only slightly sensitive to the water hydrogen bond network. These results support the idea that it is the water clustering that drives the partial segregation of the two components, and hence the observed excess entropy of mixing.
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Affiliation(s)
- Samuel Lenton
- School of Physics and Astronomy , University of Leeds , Leeds LS2 9JT , U.K
| | - Natasha H Rhys
- School of Physics and Astronomy , University of Leeds , Leeds LS2 9JT , U.K
| | - James J Towey
- School of Physics and Astronomy , University of Leeds , Leeds LS2 9JT , U.K
| | - Alan K Soper
- ISIS Facility , STFC Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , U.K
| | - Lorna Dougan
- School of Physics and Astronomy , University of Leeds , Leeds LS2 9JT , U.K
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16
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Abstract
Trehalose, commonly found in living organisms, is believed to help them survive severe environmental conditions, such as drought or extreme temperatures. With the aim of trying to understand these properties, two recent neutron scattering studies investigate the structure of trehalose water solutions but come to seemingly opposite conclusions. In the first study, which looks at two concentrations of trehalose-water mole ratios of 1:100 and 1:25, the conclusion is that trehalose hydrogen-bonds to water rather weakly and has a relatively minor impact on the structure of water in solution compared to bulk water. On the other hand, for the other, using a mole ratio of 1:38, the conclusion is that the water structure is rather substantially modified by the presence of trehalose and that the hydrogen bonding between water and trehalose hydroxyl groups is significant. In an attempt to try to understand the origin of these divergent views, which arise from similar but independent analyses of different neutron diffraction data, we have performed additional X-ray scattering experiments, which are highly sensitive to water structure, at the same trehalose-water concentrations used in the first study, and combined these with empirical potential structure refinement on the previously collected neutron data. The new analysis unequivocally confirms that trehalose does indeed have only a minor impact on the structure of water, at all three concentrations, and forms relatively weak hydrogen bonds with water. Far from being discrepant with the existing literature, our new analysis of the different datasets suggests a natural explanation for the increased glass-transition temperature of trehalose compared to other sugars and hence its enhanced effectiveness as a protectant against drought stress.
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Affiliation(s)
- Alan K Soper
- ISIS Facility, STFC Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , U.K
| | - Maria Antonietta Ricci
- Dipartimento di Scienze , Università degli Studi "Roma Tre" , via della Vasca Navale 84 , 00146 Roma , Italy
| | - Fabio Bruni
- Dipartimento di Scienze , Università degli Studi "Roma Tre" , via della Vasca Navale 84 , 00146 Roma , Italy
| | - Natasha H Rhys
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Sylvia E McLain
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
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17
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Bruni F, Di Mino C, Imberti S, McLain SE, Rhys NH, Ricci MA. Hydrogen Bond Length as a Key To Understanding Sweetness. J Phys Chem Lett 2018; 9:3667-3672. [PMID: 29920095 DOI: 10.1021/acs.jpclett.8b01280] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Neutron diffraction experiments have been performed to investigate and compare the structure of the hydration shell of three monosaccharides, namely, fructose, glucose, and mannose. It is found that despite their differences with respect to many thermodynamical quantities, bioprotective properties against environmental stresses, and taste, the influence of these monosaccharides on the bulk water solvent structure is virtually identical. Conversely, these sugars interact with the neighboring water molecules by forming H bonds of different length and strength. Interestingly, the sweetness of these monosaccharides, along with that of the disaccharide trehalose, is correlated with the length of these H bonds. This suggests that the small differences in stereochemistry between the different sugars determine a relevant change in polarity, which has a fundamental impact on the behavior of these molecules in vivo.
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Affiliation(s)
- F Bruni
- Dipartimento di Scienze, Sezione di Nanoscienze , Università degli Studi "Roma Tre" , Via della Vasca Navale 84 , 00146 Roma , Italy
| | - C Di Mino
- Dipartimento di Scienze, Sezione di Nanoscienze , Università degli Studi "Roma Tre" , Via della Vasca Navale 84 , 00146 Roma , Italy
| | - S Imberti
- ISIS Neutron and Muon Source, STFC, Rutherford Appleton Laboratory , Harwell Campus , Didcot , Oxfordshire OX11 0QX , United Kingdom
| | - S E McLain
- Department of Biochemistry , University of Oxford , South Park Road , Oxford , Oxfordshire OX1 3QU , United Kingdom
| | - N H Rhys
- Department of Biochemistry , University of Oxford , South Park Road , Oxford , Oxfordshire OX1 3QU , United Kingdom
| | - M A Ricci
- Dipartimento di Scienze, Sezione di Nanoscienze , Università degli Studi "Roma Tre" , Via della Vasca Navale 84 , 00146 Roma , Italy
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18
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Rhys NH, Al-Badri MA, Ziolek RM, Gillams RJ, Collins LE, Lawrence MJ, Lorenz CD, McLain SE. On the solvation of the phosphocholine headgroup in an aqueous propylene glycol solution. J Chem Phys 2018; 148:135102. [DOI: 10.1063/1.5024850] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Natasha H. Rhys
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | | | - Robert M. Ziolek
- Department of Physics, King’s College London, London WC2R 2LS, United Kingdom
| | - Richard J. Gillams
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
- Earth-Life Sciences Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Louise E. Collins
- Department of Pharmaceutical Sciences, King’s College London, London SE1 9NH, United Kingdom
| | - M. Jayne Lawrence
- Division of Pharmacy and Optometry, University of Manchester, Manchester ML13 9PL, United Kingdom
| | - Christian D. Lorenz
- Department of Physics, King’s College London, London WC2R 2LS, United Kingdom
| | - Sylvia E. McLain
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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19
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Zeng Z, Bernstein ER. Photoelectron spectroscopy and density functional theory studies of (fructose + (H 2O) n) − ( n = 1–5) anionic clusters. Phys Chem Chem Phys 2017; 19:31121-31137. [DOI: 10.1039/c7cp06625b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
(Fructose + (H2O)n)− (n = 1–5) cluster anions mainly exist as open chain structures. Some cyclic structures of (fructose + (H2O)n)− (n = 3, 4) are present too.
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Affiliation(s)
- Zhen Zeng
- Department of Chemistry
- NSF ERC for Extreme Ultraviolet Science and Technology
- Colorado State University
- Fort Collins
- USA
| | - Elliot R. Bernstein
- Department of Chemistry
- NSF ERC for Extreme Ultraviolet Science and Technology
- Colorado State University
- Fort Collins
- USA
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