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Lupi L, Gallo P. Mode coupling behavior and fragile to strong transition of trehalose in a binary mixture with water upon supercooling. J Chem Phys 2024; 160:244501. [PMID: 38912627 DOI: 10.1063/5.0218369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024] Open
Abstract
We perform molecular dynamics simulations of a binary mixture of water and trehalose with the TIP4P/Ice water model. We analyze the slow dynamics of trehalose molecules in the mildly supercooled region for concentrations of 3.66 and 18.57 wt. %. We previously studied the dynamics of water in the same mixtures. Supercooled TIP4P/Ice water solvating trehalose molecules was found to follow the Mode Coupling Theory (MCT) and to undergo a transition from a fragile to a strong behavior for both concentrations. Here, we show that also the dynamics of trehalose molecules follows the MCT and displays a fragile to strong crossover (FSC). The results show that trehalose in binary mixtures with water shares with it the dynamical behavior typical of glass forming liquids. Moreover, the FSC for trehalose structural relaxation times is found to occur at temperatures close to those previously obtained for water in the same solutions, showing that the dynamics of the solute is strongly coupled to that of the solvent. We also perform a MCT test showing that the trehalose dynamics obeys the MCT time-temperature superposition principle and that the exponents derived from the theory and the ones obtained from fitting procedure of the relaxation times are comparable, confirming that trehalose molecules in supercooled water solutions follow the MCT of glassy dynamics. Moreover, as predicted by the theory, trehalose particles have MCT parameters comparable to those of water in the same mixtures. This is an important result, given that MCT was originally formulated for monoatomic particles.
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Affiliation(s)
- Laura Lupi
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - Paola Gallo
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
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2
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Lupi L, Gallo P. Glassy dynamics of water in TIP4P/Ice aqueous solutions of trehalose in comparison with the bulk phase. J Chem Phys 2023; 159:154504. [PMID: 37850697 DOI: 10.1063/5.0168933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
We perform molecular dynamics simulations of TIP4P/Ice water in solution with trehalose for 3.65 and 18.57 wt. % concentrations and of bulk TIP4P/Ice water at ambient pressure, to characterize the structure and dynamics of water in a sugar aqueous solution in the supercooled region. We find here that TIP4P/Ice water in solution with trehalose molecules follows the Mode Coupling Theory and undergoes a fragile to strong transition up to the highest concentration investigated, similar to the bulk. Moreover, we perform a Mode Coupling Theory test, showing that the Time Temperature Superposition principle holds for both bulk TIP4P/Ice water and for TIP4P/Ice water in the solutions and we calculate the exponents of the theory. The direct comparison of the dynamical results for bulk water and water in the solutions shows upon cooling along the isobar a fastening of water dynamics for lower temperatures, T < 240 K. We found that the counter-intuitive behavior for the low temperature solutions can be explained with the diffusion anomaly of water leading us to the conclusion that the fastening observed below T = 240 K in water dynamics is only fictitious, due to the fact that the density of water molecules in the solutions is higher than the density of the bulk at the same temperature and pressure. This result should be taken into account in experimental investigations which are often carried out at constant pressure.
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Affiliation(s)
- Laura Lupi
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - Paola Gallo
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
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3
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Vinod SM, Murugan Sreedevi S, Krishnan A, Perumal T, Chinnadurai R, Rajendran K. Interaction of an Aldose Sugar with Photoinduced Electron Transfer (PET) and Non-PET Based Acridinedione Dyes in Water: Hydrogen-bonding Evidences from Fluorescence Spectral Techniques Assisted by Molecular Docking Approach. J Fluoresc 2023; 33:471-486. [PMID: 36445509 DOI: 10.1007/s10895-022-03062-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022]
Abstract
Fluorescence spectral techniques aided by molecular docking (Mol.Doc) approach were employed in probing the molecular interactions existing between D-glucose and resorcinol based acridinedione (ADR) dyes. ADR dyes has been classified into PET and non-PET dyes based on the substitution in the 9th position of acridinedione ring structure. Addition of glucose to PET dye (ADR1) resulted in a decrease in the absorbance whereas to that of ADR2 dye (non-PET character in aqueous medium) resulted in a significant increase in the absorbance. The formation of an isosbestic point reveals the existence of a ground state interaction existing between the dye and sugar molecule. Addition of glucose to PET dye resulted in a drastic increase in the fluorescent enhancement (FE) and subsequent addition resulted in a marked decrease in the fluorescent intensity with no apparent shift of emission maximum. Interestingly, neither characteristic shift nor variation in emission intensity was observed in the case of ADR2 dye. Fluorescence lifetime studies of ADR1 dye in the presence of glucose illustrate the existence of multiple distinguishable micro environments of dye. Mol.Doc studies authenticate the co-existence of hydrogen bonding (HB) and hydrophobic interaction wherein the dye and sugar molecule acts as HB donor and acceptor resulting in a stable conformer. These conformers are governed predominantly by HB interactions. The nature of interaction of a simple sugar with ADR dyes are explored in depth by fluorescent techniques in coordination with docking studies is imparted in the present study.
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Affiliation(s)
- Seba Merin Vinod
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous)(University of Madras)Tamil Nadu, Gokul Bagh, E.V.R.Periyar Road, 833, Arumbakkam, Chennai, India
| | - Sangeetha Murugan Sreedevi
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous)(University of Madras)Tamil Nadu, Gokul Bagh, E.V.R.Periyar Road, 833, Arumbakkam, Chennai, India
| | - Anju Krishnan
- Department of Chemistry, Sathyabama Institute of Science and Technology, Tamil Nadu, Kamaraj Nagar, Semmancheri, Chennai, 600119, India
| | - Tamizhdurai Perumal
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous)(University of Madras)Tamil Nadu, Gokul Bagh, E.V.R.Periyar Road, 833, Arumbakkam, Chennai, India
| | - Raghupathi Chinnadurai
- Department of Chemistry, Sriram College of Arts and Science, Tamil Nadu, Perumalpattu, Tiruvallur, 602024, India
| | - Kumaran Rajendran
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous)(University of Madras)Tamil Nadu, Gokul Bagh, E.V.R.Periyar Road, 833, Arumbakkam, Chennai, India.
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Morita M, Matsumura F, Shikata T, Ogawa Y, Kondo N, Shiraga K. Hydrogen-Bond Configurations of Hydration Water around Glycerol Investigated by HOH Bending and OH Stretching Analysis. J Phys Chem B 2022; 126:9871-9880. [PMID: 36350734 DOI: 10.1021/acs.jpcb.2c05445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Toward a comprehensive understanding of the mechanism of glycerol as a moisturizer, studies on the hydrogen-bond (HB) structure of hydration water, which is known to be disordered by glycerol, are insufficient. To this aim, we evaluated the HB configurations based on the HOH bending and OH stretching spectra of the hydration water from those of glycerol/water mixtures by subtracting the contributions of bulk water and glycerol using dielectric relaxation spectroscopy. Analysis of the HOH bending band showed that hydration water-donating HBs lose the intermolecular bending coupling with increasing glycerol by replacing the water-water HBs with water-glycerol HBs. The OH stretching band provided more detailed insight into the HB configuration, indicating that the double-donor double-acceptor and double-donor single-acceptor configurations in bulk water change to a predominantly double-donor single-acceptor configuration in hydration water around glycerol. The formation of more donor HBs than acceptor HBs may be due to the steric constrains by glycerol and/or differences in the partial charge on the oxygen atom between water and glycerol.
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Affiliation(s)
- Miho Morita
- Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Fumiki Matsumura
- Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Toshiyuki Shikata
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo183-8509, Japan
| | - Yuichi Ogawa
- Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Naoshi Kondo
- Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Keiichiro Shiraga
- Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi332-0012, Japan
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5
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Yeole SD. Quantum chemical study of molecular hydration of phenylxylopyranose sugar. J CHEM SCI 2022. [DOI: 10.1007/s12039-022-02100-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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6
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Han Z, Wang P, Lu Y, Jia Z, Qu S, Yang W. A versatile hydrogel network-repairing strategy achieved by the covalent-like hydrogen bond interaction. SCIENCE ADVANCES 2022; 8:eabl5066. [PMID: 35196089 PMCID: PMC8865770 DOI: 10.1126/sciadv.abl5066] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Hydrogen bond engineering is widely exploited to impart stretchability, toughness, and self-healing capability to hydrogels. However, the enhancement effect of conventional hydrogen bonds is severely limited by their weak interaction strength. In nature, some organisms tolerate extreme conditions due to the strong hydrogen bond interactions induced by trehalose. Here, we report a trehalose network-repairing strategy achieved by the covalent-like hydrogen bonding interactions to improve the hydrogels' mechanical properties while simultaneously enabling them to tolerate extreme environmental conditions and retain synthetic simplicity, which proves to be useful for various kinds of hydrogels. The mechanical properties of trehalose-modified hydrogels including strength, stretchability, and fracture toughness are substantially enhanced under a wide range of temperatures. After dehydration, the modified hydrogels maintain their hyperelasticity and functions, while the unmodified hydrogels collapse. This strategy provides a versatile methodology for synthesizing extremotolerant, highly stretchable, and tough hydrogels, which expand their potential applications to various conditions.
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Affiliation(s)
| | - Peng Wang
- Corresponding author. (P.W.); (S.Q.)
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7
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Hu J, Liao Z, Yano Y, Yamahara H, Tabata H. Broadband Dielectric Spectroscopic Analysis toward Characterization of the Hydration State and Bioprotective Superiority of Trehalose. J Phys Chem B 2022; 126:708-715. [PMID: 35040322 DOI: 10.1021/acs.jpcb.1c09941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alteration of the hydrogen-bond (H-bond) network by trehalose is acknowledged as a bioprotective agent. However, most studies exploring the hydration superiority of the trehalose structure are limited structure are limited by the computational cost or a narrow-range spectrum. In the present study, the structural and dynamical behaviors of the H-bond network of trehalose and maltose solutions were observed and compared with a broadband dielectric spectrum (100 MHz-18 THz) to investigate the influence of the trehalose structure on the bioprotective function. From the relaxation time, the reorientation cooperativity, resonant frequency, and damping constant of water-water vibration, the symmetric structure of trehalose allowed a more significant H-bond strengthening effect and homogeneous aqueous environment. In contrast, the difference in the hydration number between trehalose and maltose was negligible. Thus, the enhanced H-bond strengthening effect and homogeneous aqueous environment owing to the symmetric structure are the essential factors that contribute to the remarkable bioprotective effect of trehalose.
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Affiliation(s)
- Junru Hu
- Department of Electrical Engineering and Information Systems, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Zhiqiang Liao
- Department of Electrical Engineering and Information Systems, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yasuo Yano
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroyasu Yamahara
- Department of Electrical Engineering and Information Systems, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hitoshi Tabata
- Department of Electrical Engineering and Information Systems, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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8
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Suzuki Y, Takeya S. Transformation process of ice crystallized from a glassy dilute trehalose aqueous solution. Phys Chem Chem Phys 2022; 24:26659-26667. [DOI: 10.1039/d2cp02712g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Crystal growth of ice Isd occurring after crystallization of a glassy dilute trehalose aqueous solution is slower than that of ice Isd in a dilute glycerol solution and pure ice Isd, and ice Isd in trehalose aqueous solution survives to ∼230 K.
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Affiliation(s)
- Yoshiharu Suzuki
- Research Center for Advanced Measurement and Characterization, National Institute for Materials Science (NIMS), Namiki 1-1, Tsukuba, Ibaraki, 305-0044, Japan
| | - Satoshi Takeya
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Central 5, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8565, Japan
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Gao S, Zhu K, Zhang Q, Niu Q, Chong J, Ren L, Yuan X. Development of Icephilic ACTIVE Glycopeptides for Cryopreservation of Human Erythrocytes. Biomacromolecules 2021; 23:530-542. [PMID: 34965723 DOI: 10.1021/acs.biomac.1c01372] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ice formation and recrystallization exert severe impairments to cellular cryopreservation. In light of cell-damaging washing procedures in the current glycerol approach, many researches have been devoted to the development of biocompatible cryoprotectants for optimal bioprotection of human erythrocytes. Herein, we develop a novel ACTIVE glycopeptide of saccharide-grafted ε-poly(L-lysine), that can be credited with adsorption on membrane surfaces, cryopreservation with trehalose, and icephilicity for validity of human erythrocytes. Then, by Borch reductive amination or amidation, glucose, lactose, maltose, maltotriose, or trehalose was tethered to ε-polylysine. The synthesized ACTIVE glycopeptides with intrinsic icephilicity could localize on the membrane surface of human erythrocytes and improve cryopreservation with trehalose, so that remarkable post-thaw cryosurvival of human erythrocytes was achieved with a slight variation in cell morphology and functions. Human erythrocytes (∼50% hematocrit) in cryostores could maintain high cryosurvival above 74%, even after plunged in liquid nitrogen for 6 months. Analyses of differential scanning calorimetry, Raman spectroscopy, and dynamic ice shaping suggested that this cryopreservation protocol combined with the ACTIVE glycopeptide and trehalose could enhance the hydrogen bond network in nonfrozen solutions, resulting in inhibition of recrystallization and growth of ice. Therefore, the ACTIVE glycopeptide can be applied as a trehalose-associated "chaperone", providing a new way to serve as a candidate in glycerol-free human erythrocyte cryopreservation.
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Affiliation(s)
- Shuhui Gao
- School of Materials Science and Engineering, Tianjin Key Laboratory of Composite and Functional Materials, Tianjin University, Tianjin 300350, China
| | - Kongying Zhu
- Analysis and Measurement Center, Tianjin University, Tianjin 300072, China
| | - Qifa Zhang
- School of Materials Science and Engineering, Tianjin Key Laboratory of Composite and Functional Materials, Tianjin University, Tianjin 300350, China
| | - Qingjing Niu
- School of Materials Science and Engineering, Tianjin Key Laboratory of Composite and Functional Materials, Tianjin University, Tianjin 300350, China
| | | | - Lixia Ren
- School of Materials Science and Engineering, Tianjin Key Laboratory of Composite and Functional Materials, Tianjin University, Tianjin 300350, China
| | - Xiaoyan Yuan
- School of Materials Science and Engineering, Tianjin Key Laboratory of Composite and Functional Materials, Tianjin University, Tianjin 300350, China
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11
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Relationships between Molecular Structure of Carbohydrates and Their Dynamic Hydration Shells Revealed by Terahertz Time-Domain Spectroscopy. Int J Mol Sci 2021; 22:ijms222111969. [PMID: 34769399 PMCID: PMC8584907 DOI: 10.3390/ijms222111969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/26/2021] [Accepted: 11/03/2021] [Indexed: 11/17/2022] Open
Abstract
Despite more than a century of research on the hydration of biomolecules, the hydration of carbohydrates is insufficiently studied. An approach to studying dynamic hydration shells of carbohydrates in aqueous solutions based on terahertz time-domain spectroscopy assay is developed in the current work. Monosaccharides (glucose, galactose, galacturonic acid) and polysaccharides (dextran, amylopectin, polygalacturonic acid) solutions were studied. The contribution of the dissolved carbohydrates was subtracted from the measured dielectric permittivities of aqueous solutions based on the corresponding effective medium models. The obtained dielectric permittivities of the water phase were used to calculate the parameters describing intermolecular relaxation and oscillatory processes in water. It is established that all of the analyzed carbohydrates lead to the increase of the binding degree of water. Hydration shells of monosaccharides are characterized by elevated numbers of hydrogen bonds and their mean energies compared to undisturbed water, as well as by elevated numbers and the lifetime of free water molecules. The axial orientation of the OH(4) group of sugar facilitates a wider distribution of hydrogen bond energies in hydration shells compared to equatorial orientation. The presence of the carboxylic group affects water structure significantly. The hydration of polysaccharides is less apparent than that of monosaccharides, and it depends on the type of glycosidic bonds.
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Lopes ES, Leal Silva JF, Nascimento LAD, Bohórquez JFC, Lopes MS, Tovar LP, Maciel Filho R. Feasibility of the Conversion of Sugarcane Molasses to Levulinic Acid: Reaction Optimization and Techno-Economic Analysis. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.1c02550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emília Savioli Lopes
- School of Chemical Engineering, University of Campinas, 13083-852 Campinas, SP, Brazil
| | | | | | | | - Melina Savioli Lopes
- Department of Chemical Engineering, Federal University of Alfenas, 37715-400 Poços de Caldas, MG, Brazil
| | - Laura Plazas Tovar
- Department of Chemical Engineering, Federal University of São Paulo, 09913-030 Diadema, SP, Brazil
| | - Rubens Maciel Filho
- School of Chemical Engineering, University of Campinas, 13083-852 Campinas, SP, Brazil
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13
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Li D, Zhu Z, Sun DW. Quantification of hydrogen bonding strength of water in saccharide aqueous solutions by confocal Raman microscopy. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117498] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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14
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Katyal N, Sharma S, Deep S. Delving into controversial dichotomy of direct and indirect mechanisms of Trehalose: In search of unanimous consensus. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Nie Y, Li Y, Liu L, Ren S, Tian Y, Yang F. Molecular mechanism underlying modulation of TRPV1 heat activation by polyols. J Biol Chem 2021; 297:100806. [PMID: 34022223 PMCID: PMC8214097 DOI: 10.1016/j.jbc.2021.100806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 11/30/2022] Open
Abstract
Sensing noxiously high temperatures is crucial for living organisms to avoid heat-induced injury. The TRPV1 channel has long been known as a sensor for noxious heat. However, the mechanism of how this channel is activated by heat remains elusive. Here we found that a series of polyols including sucrose, sorbitol, and hyaluronan significantly elevate the heat activation threshold temperature of TRPV1. The modulatory effects of these polyols were only observed when they were perfused extracellularly. Interestingly, mutation of residues E601 and E649 in the outer pore region of TRPV1 largely abolished the effects of these polyols. We further observed that intraplantar injection of polyols into the hind paws of rats reduced their heat-induced pain response. Our observations not only suggest that the extracellular regions of TRPV1 are critical for the modulation of heat activation by polyols, but also indicate a potential role of polyols in reducing heat-induced pain sensation.
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Affiliation(s)
- Yingying Nie
- Department of Pharmacology, School of Pharmacy, Qingdao University Medical College, Qingdao, China
| | - Yanxin Li
- Department of Pharmacology, School of Pharmacy, Qingdao University Medical College, Qingdao, China
| | - Lei Liu
- Department of Pharmacology, School of Pharmacy, Qingdao University Medical College, Qingdao, China
| | - Shouyan Ren
- Department of Otorhinolaryngology, The Affiliated Hospital of Qingdao University, Qingdao, Shangdong, China
| | - Yuhua Tian
- Department of Pharmacology, School of Pharmacy, Qingdao University Medical College, Qingdao, China.
| | - Fan Yang
- Department of Biophysics, and Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.
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16
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Sachar HS, Chava BS, Pial TH, Das S. All-Atom Molecular Dynamics Simulations of the Temperature Response of Densely Grafted Polyelectrolyte Brushes. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Harnoor Singh Sachar
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Bhargav Sai Chava
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Turash Haque Pial
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Siddhartha Das
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
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17
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Alam MM, Mahbub S, Alfakeer M, Hoque MA, Mustafa SK, Ahmad MA, Kabir SE. The Assembly of the Mixture of Two Ionic Surfactants in Polyols Media at Variable Temperatures: Combined Conductivity and Theoretical Investigations. J SURFACTANTS DETERG 2021. [DOI: 10.1002/jsde.12528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Md. Masud Alam
- Department of Chemistry Jahangirnagar University Savar Dhaka 1342 Bangladesh
- Department of Chemistry Mawlana Bhashani Science and Technology University Santosh Tangail 1902 Bangladesh
| | - Shamim Mahbub
- Department of Chemistry and Physics Gono Bishwabidyalay Savar Dhaka 1344 Bangladesh
| | - M. Alfakeer
- Chemistry Department, Faculty of Science Princess Nourah bint Abdulrahman University Riyadh 11671 Kingdom of Saudi Arabia
| | - Md. Anamul Hoque
- Department of Chemistry Jahangirnagar University Savar Dhaka 1342 Bangladesh
| | - Syed Khalid Mustafa
- Department of Chemistry, Faculty of Science University of Tabuk Tabuk 71491 Kingdom of Saudi Arabia
| | - M. Ayaz Ahmad
- Department of Physics, Faculty of Science University of Tabuk Tabuk 71491 Kingdom of Saudi Arabia
| | - Shariff E. Kabir
- Department of Chemistry Jahangirnagar University Savar Dhaka 1342 Bangladesh
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18
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Camisasca G, De Marzio M, Gallo P. Effect of trehalose on protein cryoprotection: Insights into the mechanism of slowing down of hydration water. J Chem Phys 2021; 153:224503. [PMID: 33317300 DOI: 10.1063/5.0033526] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study, with molecular dynamics simulations, a lysozyme protein immersed in a water-trehalose solution upon cooling. The aim is to understand the cryoprotectant role played by this disaccharide through the modifications that it induces on the slow dynamics of protein hydration water with its presence. The α-relaxation shows a fragile to strong crossover about 20° higher than that in the bulk water phase and 15° higher than that in lysozyme hydration water without trehalose. The protein hydration water without trehalose was found to show a second slower relaxation exhibiting a strong to strong crossover coupled with the protein dynamical transition. This slower relaxation time importantly appears enormously slowed down in our cryoprotectant solution. On the other hand, this long-relaxation in the presence of trehalose is also connected with a stronger damping of the protein structural fluctuations than that found when the protein is in contact with the pure hydration water. Therefore, this appears to be the mechanism through which trehalose manifests its cryoprotecting function.
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Affiliation(s)
- Gaia Camisasca
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
| | - Margherita De Marzio
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
| | - Paola Gallo
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
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19
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Renzetti S, van den Hoek IA, van der Sman RG. Amino acids, polyols and soluble fibres as sugar replacers in bakery applications: Egg white proteins denaturation controlled by hydrogen bond density of solutions. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2020.106034] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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20
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Brender JR, Kishimoto S, Eaton GR, Eaton SS, Saida Y, Mitchell J, Krishna MC. Trehalose as an alternative to glycerol as a glassing agent for in vivo DNP MRI. Magn Reson Med 2020; 85:42-48. [PMID: 32697878 DOI: 10.1002/mrm.28405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/12/2020] [Accepted: 06/09/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE In dynamic nuclear polarization (DNP), the solution needs to form a glass to attain significant levels of polarization in reasonable time periods. Molecules that do not form glasses by themselves are often mixed with glass forming excipients. Although glassing agents are often essential in DNP studies, they have the potential to perturb the metabolic measurements that are being studied. Glycerol, the glassing agent of choice for in vivo DNP studies, is effective in reducing ice crystal formation during freezing, but is rapidly metabolized, potentially altering the redox and adenosine triphosphate balance of the system. METHODS DNP buildup curves of 13 C urea and alanine with OX063 in the presence of trehalose, glycerol, and other polyol excipients were measured as a function of concentration. T1 and Tm relaxation times for OX063 in the presence of trehalose were measured by EPR. RESULTS Approximately 15-20 wt% trehalose gives a glass that polarizes samples more rapidly than the commonly used 60%-wt formulation of glycerol and yields similar polarization levels within clinically relevant timeframes. CONCLUSIONS Trehalose may be an attractive biologically inert alternative to glycerol for situations where there may be concerns about glycerol's glucogenic potential and possible alteration of the adenosine triphosphate/adenosine diphosphate and redox balance.
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Affiliation(s)
- Jeffrey R Brender
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shun Kishimoto
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gareth R Eaton
- Department of Chemistry & Biochemistry, University of Denver, Denver, CO, USA
| | - Sandra S Eaton
- Department of Chemistry & Biochemistry, University of Denver, Denver, CO, USA
| | - Yu Saida
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James Mitchell
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Murali C Krishna
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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21
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Franzè S, Selmin F, Rocco P, Colombo G, Casiraghi A, Cilurzo F. Preserving the Integrity of Liposomes Prepared by Ethanol Injection upon Freeze-Drying: Insights from Combined Molecular Dynamics Simulations and Experimental Data. Pharmaceutics 2020; 12:pharmaceutics12060530. [PMID: 32526935 PMCID: PMC7356173 DOI: 10.3390/pharmaceutics12060530] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 11/17/2022] Open
Abstract
The freeze-drying of complex formulations, such as liposomes, is challenging, particularly if dispersions contain residual organic solvents. This work aimed to investigate the effects of possible protectants, namely sucrose, trehalose and/or poly(vinyl pyrrolidone) (PVP), on the main features of the dried product using a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC)-based liposomal dispersion prepared by ethanol injection and containing ethanol up to 6%, as a model. The interactions among vesicles and protectants were preliminary screened by Molecular Dynamics (MD) simulations, which have been proved useful in rationalizing the selection of protectant(s). The freeze-drying protocol was based on calorimetric results. Overall data suggested a stronger cryo-protectant effect of trehalose, compared with sucrose, due to stronger interactions with the DPPC bilayer and the formation of highly ordered clusters around the lipids. The effect further improved in the presence of PVP. Differently from the other tested protectants, the selected trehalose/PVP combination allows to preserve liposome size, even in the presence of 6% ethanol, as demonstrated by Nanoparticle Tracking Analysis (NTA). Nevertheless, it should be also underlined that cakes blew out at an ethanol concentration higher than 1% v/v, probably due to the poor cohesion within the cake and solvent vapour pressure upon sublimation.
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Affiliation(s)
- Silvia Franzè
- Department of Pharmaceutical Sciences, University of Milan, Via G. Colombo 71, 20133 Milan, Italy; (S.F.); (P.R.); (A.C.); (F.C.)
| | - Francesca Selmin
- Department of Pharmaceutical Sciences, University of Milan, Via G. Colombo 71, 20133 Milan, Italy; (S.F.); (P.R.); (A.C.); (F.C.)
- Correspondence: ; Tel.: +39-02-503-24645
| | - Paolo Rocco
- Department of Pharmaceutical Sciences, University of Milan, Via G. Colombo 71, 20133 Milan, Italy; (S.F.); (P.R.); (A.C.); (F.C.)
| | | | - Antonella Casiraghi
- Department of Pharmaceutical Sciences, University of Milan, Via G. Colombo 71, 20133 Milan, Italy; (S.F.); (P.R.); (A.C.); (F.C.)
| | - Francesco Cilurzo
- Department of Pharmaceutical Sciences, University of Milan, Via G. Colombo 71, 20133 Milan, Italy; (S.F.); (P.R.); (A.C.); (F.C.)
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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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23
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Jahan I, Nayeem SM. Effect of Osmolytes on Conformational Behavior of Intrinsically Disordered Protein α-Synuclein. Biophys J 2019; 117:1922-1934. [PMID: 31699336 DOI: 10.1016/j.bpj.2019.09.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/21/2019] [Accepted: 09/30/2019] [Indexed: 11/20/2022] Open
Abstract
α-Synuclein is an intrinsically disordered protein whose function in a healthy brain is poorly understood. It is genetically and neuropathologically linked to Parkinson's disease (PD). PD is manifested after the accumulation of plaques of α-synuclein aggregates in the brain cells. Aggregates of α-synuclein are very toxic and lead to the disruption of cellular homeostasis and neuronal death. α-Synuclein can also contribute to disease propagation as it may exert noxious effects on neighboring cells. Understanding the mechanism of α-synuclein aggregation will facilitate the problem of dealing with neurodegenerative diseases in general and that of PD in particular. Here, we have used molecular dynamics simulations to investigate the behavior of α-synuclein at various temperatures and in different concentrations of urea and trimethyl amine oxide. The residue region from 61 to 95 of α-synuclein is experimentally known as amyloidogenic. In our study, we have identified some other regions, which also have the propensity to form an aggregate besides this known sequence. Urea being a denaturant interacts more with these regions of α-synuclein through hydrogen bond formation and inhibits the β-sheet formation, whereas trimethyl amine oxide itself does not interact much with the protein and stabilizes the protein by preferentially distributing water molecules on the surface of the protein.
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Affiliation(s)
- Ishrat Jahan
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Shahid M Nayeem
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
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24
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Iorio A, Camisasca G, Rovere M, Gallo P. Characterization of hydration water in supercooled water-trehalose solutions: The role of the hydrogen bonds network. J Chem Phys 2019; 151:044507. [PMID: 31370561 DOI: 10.1063/1.5108579] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The structural and dynamical properties of hydration water in aqueous solutions of trehalose are studied with molecular dynamics simulation. We simulate the systems in the supercooled region to investigate how the interaction with the trehalose molecules modifies the hydrogen bond network, the structural relaxation, and the diffusion properties of hydration water. The analysis is performed by considering the radial distribution functions, the residence time of water molecules in the hydration shell, the two body excess entropy, and the hydrogen bond water-water and water-trehalose correlations of the hydration water. The study of the two body excess entropy shows the presence of a fragile to strong crossover in supercooled hydration water also found in the relaxation time of the water-water hydrogen bond correlation function, and this is in agreement with predictions of the mode coupling theory and of previous studies of the oxygen-oxygen density correlators [A. Iorio et al., J. Mol. Liq. 282, 617 (2019); Sci. China: Phys., Mech. Astron. 62, 107011 (2019)]. The water-trehalose hydrogen bond correlation function instead evidences a strong to strong crossover in the relaxation time, and this crossover is related to a trehalose dynamical transition. This signals the role that the strong interplay between the soluted molecules and the surrounding solvent has in determining the dynamical transition common to both components of the system that happens upon cooling and that is similar to the well known protein dynamical transition. We connect our results with the cryoprotecting role of trehalose molecules.
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Affiliation(s)
- A Iorio
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - G Camisasca
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91 Stockholm, Sweden
| | - M Rovere
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - P Gallo
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
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25
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Messnaoui B, Mounir A, Dinane A, Samaouali A, Mounir B. Determination of water activity, osmotic coefficients, activity coefficients, solubility and excess Gibbs free energies of NaCl-sucrose-H2O mixture at 298.15 K. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.03.156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Iorio A, Camisasca G, Gallo P. Slow dynamics of hydration water and the trehalose dynamical transition. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.088] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Kinetic pH Titration to Predict the Acid and Hydrothermal Conditions for the Hydrolysis of Disaccharides: Use of a Microcapillary System. J CHEM-NY 2019. [DOI: 10.1155/2019/3985915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The hydrolysis of disaccharides was conducted using a microcapillary system under hydrothermal conditions (up to 190°C at 10 MPa and pH 4–11). The hydrolysis reaction showed a sigmoidal progression with time, especially under alkaline conditions. Analysis using a kinetic model yielded the reaction induction period. The specific pH value (pHamb) at the induction time, which is the pH value corresponding to the progression of disaccharide hydrolysis, was peculiar to each disaccharide. Finally, the calculation of the electron density around the oxygen atom of the glycosidic bond between saccharides was found to roughly predict the pHamb value required for the progression of hydrolysis.
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29
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Weng L, Stott SL, Toner M. Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation. Annu Rev Biomed Eng 2018; 21:1-31. [PMID: 30525930 DOI: 10.1146/annurev-bioeng-060418-052130] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Successful stabilization and preservation of biological materials often utilize low temperatures and dehydration to arrest molecular motion. Cryoprotectants are routinely employed to help the biological entities survive the physicochemical and mechanical stresses induced by cold or dryness. Molecular interactions between biomolecules, cryoprotectants, and water fundamentally determine the outcomes of preservation. The optimization of assays using the empirical approach is often limited in structural and temporal resolution, whereas classical molecular dynamics simulations can provide a cost-effective glimpse into the atomic-level structure and interaction of individual molecules that dictate macroscopic behavior. Computational research on biomolecules, cryoprotectants, and water has provided invaluable insights into the development of new cryoprotectants and the optimization of preservation methods. We describe the rapidly evolving state of the art of molecular simulations of these complex systems, summarize the molecular-scale protective and stabilizing mechanisms, and discuss the challenges that motivate continued innovation in this field.
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Affiliation(s)
- Lindong Weng
- Center for Engineering in Medicine and BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA; , , .,Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Shannon L Stott
- Center for Engineering in Medicine and BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA; , , .,Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Mehmet Toner
- Center for Engineering in Medicine and BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA; , , .,Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Shriners Hospital for Children, Boston, Massachusetts 02114, USA
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30
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Paul S, Paul S. How Does Aqueous Choline-O-Sulfate Solution Nullify the Action of Urea in Protein Denaturation? J Chem Inf Model 2018; 58:1858-1869. [DOI: 10.1021/acs.jcim.8b00395] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India−781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India−781039
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31
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Shiraga K, Adachi A, Nakamura M, Tajima T, Ajito K, Ogawa Y. Characterization of the hydrogen-bond network of water around sucrose and trehalose: Microwave and terahertz spectroscopic study. J Chem Phys 2018; 146:105102. [PMID: 28298096 DOI: 10.1063/1.4978232] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Modification of the water hydrogen bond network imposed by disaccharides is known to serve as a bioprotective agent in living organisms, though its comprehensive understanding is still yet to be reached. In this study, aiming to characterize the dynamical slowing down and destructuring effect of disaccharides, we performed broadband dielectric spectroscopy, ranging from 0.5 GHz to 12 THz, of sucrose and trehalose aqueous solutions. The destructuring effect was examined in two ways (the hydrogen bond fragmentation and disordering) and our result showed that both sucrose and trehalose exhibit an obvious destructuring effect with a similar strength, by fragmenting hydrogen bonds and distorting the tetrahedral-like structure of water. This observation strongly supports a chaotropic (structure-breaking) aspect of disaccharides on the water structure. At the same time, hydration water was found to exhibit slower dynamics and a greater reorientational cooperativity than bulk water because of the strengthened hydrogen bonds. These results lead to the conclusion that strong disaccharide-water hydrogen bonds structurally incompatible with native water-water bonds lead to the rigid but destructured hydrogen bond network around disaccharides. Another important finding in this study is that the greater dynamical slowing down of trehalose was found compared with that of sucrose, at variance with the destructuring effect where no solute dependent difference was observed. This discovery suggests that the exceptionally greater bioprotective impact especially of trehalose among disaccharides is mainly associated with the dynamical slowing down (rather than the destructuring effect).
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Affiliation(s)
- Keiichiro Shiraga
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Aya Adachi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masahito Nakamura
- NTT Device Technology Labs, NTT Corporation, Morinosato Wakamiya, Atsugi-shi, Kanagawa 243-0198, Japan
| | - Takuro Tajima
- NTT Device Technology Labs, NTT Corporation, Morinosato Wakamiya, Atsugi-shi, Kanagawa 243-0198, Japan
| | - Katsuhiro Ajito
- NTT Device Technology Labs, NTT Corporation, Morinosato Wakamiya, Atsugi-shi, Kanagawa 243-0198, Japan
| | - Yuichi Ogawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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32
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Katyal N, Agarwal M, Sen R, Kumar V, Deep S. Paradoxical Effect of Trehalose on the Aggregation of α-Synuclein: Expedites Onset of Aggregation yet Reduces Fibril Load. ACS Chem Neurosci 2018; 9:1477-1491. [PMID: 29601727 DOI: 10.1021/acschemneuro.8b00056] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Aggregation of α-synuclein is closely connected to the pathology of Parkinson's disease. The phenomenon involves multiple steps, commenced by partial misfolding and eventually leading to mature amyloid fibril formation. Trehalose, a widely accepted osmolyte, has been shown previously to inhibit aggregation of various globular proteins owing to its ability to prevent the initial unfolding of protein. In this study, we have examined if it behaves in a similar fashion with intrinsically disordered protein α-synuclein and possesses the potential to act as therapeutic agent against Parkinson's disease. It was observed experimentally that samples coincubated with trehalose fibrillate faster compared to the case in its absence. Molecular dynamics simulations suggested that this initial acceleration is manifestation of trehalose's tendency to perturb the conformational transitions between different conformers of monomeric protein. It stabilizes the aggregation prone "extended" conformer of α-synuclein, by binding to its exposed acidic residues of the C terminus. It also favors the β-rich oligomers once formed. Interestingly, the total fibrils formed are still promisingly less since it accelerates the competing pathway toward formation of amorphous aggregates.
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Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Manish Agarwal
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Raktim Sen
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Vinay Kumar
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
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33
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Dahanayake JN, Mitchell-Koch KR. Entropy connects water structure and dynamics in protein hydration layer. Phys Chem Chem Phys 2018; 20:14765-14777. [PMID: 29780979 PMCID: PMC6005386 DOI: 10.1039/c8cp01674g] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The enzyme Candida Antarctica lipase B (CALB) serves here as a model for understanding connections among hydration layer dynamics, solvation shell structure, and protein surface structure. The structure and dynamics of water molecules in the hydration layer were characterized for regions of the CALB surface, divided around each α-helix, β-sheet, and loop structure. Heterogeneous hydration dynamics were observed around the surface of the enzyme, in line with spectroscopic observations of other proteins. Regional differences in the structure of the biomolecular hydration layer were found to be concomitant with variations in dynamics. In particular, it was seen that regions of higher density exhibit faster water dynamics. This is analogous to the behavior of bulk water, where dynamics (diffusion coefficients) are connected to water structure (density and tetrahedrality) by excess (or pair) entropy, detailed in the Rosenfeld scaling relationship. Additionally, effects of protein surface topology and hydrophobicity on water structure and dynamics were evaluated using multiregression analysis, showing that topology has a somewhat larger effect on hydration layer structure-dynamics. Concave and hydrophobic protein surfaces favor a less dense and more tetrahedral solvation layer, akin to a more ice-like structure, with slower dynamics. Results show that pairwise entropies of local hydration layers, calculated from regional radial distribution functions, scale logarithmically with local hydration dynamics. Thus, the Rosenfeld relationship describes the heterogeneous structure-dynamics of the hydration layer around the enzyme CALB. These findings raise the question of whether this may be a general principle for understanding the structure-dynamics of biomolecular solvation.
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34
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Elola MD, Rodriguez J. Influence of Cholesterol on the Dynamics of Hydration in Phospholipid Bilayers. J Phys Chem B 2018; 122:5897-5907. [PMID: 29742895 DOI: 10.1021/acs.jpcb.8b00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the dynamics of interfacial waters in dipalmitoylphosphatidylcholine (DPPC) bilayers upon the addition of cholesterol, by molecular dynamics simulations. Our data reveal that the inclusion of cholesterol modifies the membrane aqueous interfacial dynamics: waters diffuse faster, their rotational decay time is shorter, and the DPPC/water hydrogen bond dynamics relaxes faster than in the pure DPPC membrane. The observed acceleration of the translational water dynamics agrees with recent experimental results, in which, by means of NMR techniques, an increment of the surface water diffusivity is measured upon the addition of cholesterol. A microscopic analysis of the lipid/water hydrogen bond network at the interfacial region suggests that the mechanism underlying the observed water mobility enhancement is given by the rupture of a fraction of interlipid water bridge hydrogen bonds connecting two different DPPC molecules, concomitant to the formation of new lipid/solvent bonds, whose dynamics is faster than that of the former. The consideration of a simple two-state model for the decay of the hydrogen bond correlation function yielded excellent results, obtaining two well-separated characteristic time scales: a slow one (∼250 ps) associated with bonds linking two DPPC molecules, and a fast one (∼15 ps), related to DPPC/solvent bonds.
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Affiliation(s)
- M Dolores Elola
- Departamento de Física , Comisión Nacional de Energía Atómica , Av Libertador 8250, 1429 Buenos Aires , Argentina
| | - Javier Rodriguez
- Departamento de Física , Comisión Nacional de Energía Atómica , Av Libertador 8250, 1429 Buenos Aires , Argentina.,ECyT , UNSAM , Martín de Irigoyen 3100, 1650 San Martín, Provincia de Buenos Aires , Argentina
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35
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Katyal N, Deep S. Inhibition of GNNQQNY prion peptide aggregation by trehalose: a mechanistic view. Phys Chem Chem Phys 2018; 19:19120-19138. [PMID: 28702592 DOI: 10.1039/c7cp02912h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Deposition of amyloid fibrils is the seminal event in the pathogenesis of numerous neurodegenerative diseases. The formation of this amyloid assembly is the manifestation of a cascade of structural transitions including toxic oligomer formation in the early stages of aggregation. Thus a viable therapeutic strategy involves the use of small molecular ligands to interfere with this assembly. In this perspective, we have explored the kinetics of aggregate formation of the fibril forming GNNQQNY peptide fragment from the yeast prion protein SUP35 using multiple all atom MD simulations with explicit solvent and provided mechanistic insights into the way trehalose, an experimentally known aggregation inhibitor, modulates the aggregation pathway. The results suggest that the assimilation process is impeded by different barriers at smaller and larger oligomeric sizes: the initial one being easily surpassed at higher temperatures and peptide concentrations. The kinetic profile demonstrates that trehalose delays the aggregation process by increasing both these activation barriers, specifically the latter one. It increases the sampling of small-sized aggregates that lack the beta sheet conformation. Analysis reveals that the barrier in the growth of larger stable oligomers causes the formation of multiple stable small oligomers which then fuse together bimolecularly. The PCA of 26 properties was carried out to deconvolute the events within the temporary lag phases, which suggested dynamism in lags involving an increase in interchain contacts and burial of SASA. The predominant growth route is monomer addition, which changes to condensation on account of a large number of depolymerisation events in the presence of trehalose. The favourable interaction of trehalose specifically with the sidechain of the peptide promotes crowding of trehalose molecules in its vicinity - the combination of both these factors imparts the observed behaviour. Furthermore, increasing trehalose concentration leads to faster expulsion of water molecules than interpeptide interactions. These expelled water molecules have larger translational movement, suggesting an entropy factor to favor the assembly process. Different conformations observed under this condition suggest the role of water molecules in guiding the morphology of the aggregates as well. A similar scenario exists on increasing peptide concentration.
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Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauzkhas, New Delhi, India.
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauzkhas, New Delhi, India.
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36
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Arsiccio A, Pisano R. Water entrapment and structure ordering as protection mechanisms for protein structural preservation. J Chem Phys 2018; 148:055102. [DOI: 10.1063/1.5012884] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. Arsiccio
- Department of Applied Science and Technology, Politecnico di Torino, 24 Corso Duca Degli Abruzzi, Torino 10129, Italy
| | - R. Pisano
- Department of Applied Science and Technology, Politecnico di Torino, 24 Corso Duca Degli Abruzzi, Torino 10129, Italy
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37
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Tomobe K, Yamamoto E, Yasui M, Yasuoka K. Effects of temperature, concentration, and isomer on the hydration structure in monosaccharide solutions. Phys Chem Chem Phys 2018; 19:15239-15246. [PMID: 28569306 DOI: 10.1039/c7cp02392h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Water-monosaccharide coupled interactions are essential for the function, stability, and dynamics of all glycans. Using molecular dynamics simulations, we investigated the effects of temperature, concentration, and monosaccharide isomer on the hydration structure and water dynamics in the hydration shell of monosaccharides in solution. We found that perturbations of the hydrogen-bond (H-bond) network in the first hydration shell around each monosaccharide molecule can be separated into two regions: one rich in water molecules with donor H-bonds (in the 2.4-2.8 Å region) and the other rich in water molecules with abundant acceptor H-bonds (in the 2.8-3.3 Å region). Moreover, we investigated the dependencies of clustering and conversion of the conformers of the monosaccharides on temperature and concentration. Increasing the concentration enhances monosaccharide clustering in all the monosaccharide solutions, while cluster formation does not depend on temperature. In the clusters, some water molecules in the hydration shell are replaced with monosaccharide oxygen atoms, which contributes to the shrinkage of the hydration shell with increasing monosaccharide concentration. The monosaccharides basically adopt one of two conformers, the stable chair or the unstable boat conformer. We revealed that the hydration structures of the boat and chair conformers were dramatically different. As the temperature increases, the content of the chair conformer decreases. Thus, the conversion of conformers strongly affects the hydration structure around the monosaccharide. These results are critical to understand the important roles of the hydration structure in glycan solutions.
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Affiliation(s)
- Katsufumi Tomobe
- Department of Mechanical Engineering, Keio University, Yokohama, 223-8522, Japan.
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Lv J, Ren K, Chen Y. CO 2 Diffusion in Various Carbonated Beverages: A Molecular Dynamics Study. J Phys Chem B 2018; 122:1655-1661. [PMID: 29314846 DOI: 10.1021/acs.jpcb.7b10469] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbonated beverages are widely enjoyed in spare time, yet there remain many physical and chemical processes clouded at the molecular level. In this report, we employ molecular dynamics simulations to estimate the diffusion coefficients of CO2 and the molecular origin of its variations in three model systems with characteristic features of champagnes, sugar-based cola drinks, and club sodas. The computed diffusion coefficients of CO2 are in good agreement with experimental data. Analyses of hydrogen bonding and the solvent's structural and dynamic properties reveal that the change of CO2 diffusion coefficient is closely associated with the diffusional behavior of the solvent water itself, as a result of changes in the number and strength of hydrogen bonding interactions among the species and solvent.
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Affiliation(s)
- Ji Lv
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun, Jilin Province 130023, People's Republic of China.,Department of Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Kaixin Ren
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun, Jilin Province 130023, People's Republic of China
| | - Yakun Chen
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun, Jilin Province 130023, People's Republic of China
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39
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Singh SK. Sucrose and Trehalose in Therapeutic Protein Formulations. CHALLENGES IN PROTEIN PRODUCT DEVELOPMENT 2018. [DOI: 10.1007/978-3-319-90603-4_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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40
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Characterization of the hydrogen-bond network of water around sucrose and trehalose: H-O-H bending analysis. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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41
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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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42
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Giuffrida S, Cottone G, Cordone L. The water association band as a marker of hydrogen bonds in trehalose amorphous matrices. Phys Chem Chem Phys 2017; 19:4251-4265. [DOI: 10.1039/c6cp06848k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The water association band is a suitable marker of residual water behavior in bioprotective trehalose matrices.
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Affiliation(s)
- Sergio Giuffrida
- Dipartimento di Fisica e Chimica
- Università degli Studi di Palermo
- Palermo
- Italy
| | - Grazia Cottone
- Dipartimento di Fisica e Chimica
- Università degli Studi di Palermo
- Palermo
- Italy
- School of Physics
| | - Lorenzo Cordone
- Dipartimento di Fisica e Chimica
- Università degli Studi di Palermo
- Palermo
- Italy
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43
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Olsson C, Jansson H, Youngs T, Swenson J. Structure of Aqueous Trehalose Solution by Neutron Diffraction and Structural Modeling. J Phys Chem B 2016; 120:12669-12678. [DOI: 10.1021/acs.jpcb.6b10556] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Tristan Youngs
- ISIS
Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Harwell Campus, Oxon, OX11 0QX, Oxfordshire, U.K
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44
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Wiebenga-Sanford BP, DiVerdi J, Rithner CD, Levinger NE. Nanoconfinement's Dramatic Impact on Proton Exchange between Glucose and Water. J Phys Chem Lett 2016; 7:4597-4601. [PMID: 27779880 DOI: 10.1021/acs.jpclett.6b01651] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Glucose nanoconfined by solubilization in water-containing AOT (sodium bis(2-ethylhexyl) sulfosuccinate) reverse micelles has been investigated using 1H NMR. NMR spectra reveal well-defined signals for the glucose hydroxyl groups that suggest slow chemical exchange between them and the water hydroxyl groups. Using the EXSY (ZZ-exchange) method, the chemical exchange rate from water to glucose hydroxyl groups was measured for glucose in reverse micelles as a function of size (water pool diameter of ∼1-5 nm) at 25 °C. The chemical exchange rates observed in the nanoconfined interior are dramatically slower (5-20 times) than those observed for glucose in bulk aqueous solution at the same concentration as the micelle interior. Exchange rate constants are calculated via a mechanism that accounts for these observations, and implications of these results are presented and discussed.
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Affiliation(s)
| | - Joseph DiVerdi
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80523-1872, United States
| | - Christopher D Rithner
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80523-1872, United States
| | - Nancy E Levinger
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80523-1872, United States
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45
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Sekine Y, Endo H, Iwase H, Takeda S, Mukai SA, Fukazawa H, Littrell KC, Sasaki Y, Akiyoshi K. Nanoscopic Structural Investigation of Physically Cross-Linked Nanogels Formed from Self-Associating Polymers. J Phys Chem B 2016; 120:11996-12002. [DOI: 10.1021/acs.jpcb.6b06795] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yurina Sekine
- Materials Sciences
Research Center, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Hitoshi Endo
- Neutron Science
Laboratory, High Energy Accelerator Research Organization, 203-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
- Department
of Materials Structure Science, The Graduate University for Advanced Studies (SOKENDAI), 203-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Hiroki Iwase
- Comprehensive Research Organization for Science and Society, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Shigeo Takeda
- Department
of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Sada-atsu Mukai
- Department
of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO
Bio-Nanotransporter
Project, Japan Science and Technology Agency (JST), Kyoto University, Kastura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hiroshi Fukazawa
- Materials Sciences
Research Center, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Kenneth C. Littrell
- Neutron
Science Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6393, United States
| | - Yoshihiro Sasaki
- Department
of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO
Bio-Nanotransporter
Project, Japan Science and Technology Agency (JST), Kyoto University, Kastura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazunari Akiyoshi
- Department
of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO
Bio-Nanotransporter
Project, Japan Science and Technology Agency (JST), Kyoto University, Kastura, Nishikyo-ku, Kyoto 615-8510, Japan
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46
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Sonoda MT, Dolores Elola M, Skaf MS. Molecular dynamics simulations of the dielectric properties of fructose aqueous solutions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:414018. [PMID: 27546528 DOI: 10.1088/0953-8984/28/41/414018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The static dielectric permittivity and dielectric relaxation properties of fructose aqueous solutions of different concentrations ranging from 1.0 to 4.0 mol l(-1) are investigated by means of molecular dynamics simulations. The contributions from intra- and interspecies molecular correlations were computed individually for both the static and frequency-dependent dielectric properties, and the results were compared with the available experimental data. Simulation results in the time- and frequency-domains were analyzed and indicate that the presence of fructose has little effect on the position of the fast, high-frequency (>500 cm(-1)) components of the dielectric response spectrum. The low-frequency (<0.1 cm(-1)) components, however, are markedly influenced by sugar concentration. Our analysis indicates that fructose-fructose and fructose-water interactions strongly affect the rotational-diffusion regime of molecular motions in the solutions. Increasing fructose concentration not only enhances sugar-sugar and sugar-water low frequency contributions to the dielectric loss spectrum but also slows down the reorientational dynamics of water molecules. These results are consistent with previous computer simulations carried out for other disaccharide aqueous solutions.
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Affiliation(s)
- Milton T Sonoda
- Universidade Federal do Triângulo Mineiro Av. Frei Paulino, 30 Uberaba, MG 38025-180 Brazil
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47
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Indra S, Biswas R. How Heterogeneous Are Trehalose/Glycerol Cryoprotectant Mixtures? A Combined Time-Resolved Fluorescence and Computer Simulation Investigation. J Phys Chem B 2016; 120:11214-11228. [PMID: 27723334 DOI: 10.1021/acs.jpcb.6b06511] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Heterogeneity and molecular motions in representative cryoprotectant mixtures made of trehalose and glycerol are investigated in the temperature range 298 ≤ T (K) ≤ 353, via time-resolved fluorescence Stokes shift and anisotropy measurements, and molecular dynamics simulations of four-point density-time correlations and H-bond relaxations. Mixtures containing 5 and 20 wt % of trehalose along with neat glycerol are studied. Viscosity coefficients for these systems lie in the range 0.30 < η (P) < 23. Measured solute (Coumarin 153) rotation and solvation times reveal a substantial departure from the hydrodynamic viscosity dependence, suggesting the strong microheterogeneous nature of these systems. Fluorescence anisotropy decays are highly nonexponential, reflecting a non-Markovian character of the medium friction. A complete missing of the Stokes shift dynamics in these systems at 298 K but partial detection of it at other higher temperatures (shift magnitude being ∼400-600 cm-1) indicates rigid solute environments. An amorphous solid-like feature emerges in the simulated radial distribution functions at these temperatures. Analyses of mean squared displacements reveal rattling-in-a-cage motion, non-Gaussian displacement distributions, and strong dynamic heterogeneity features. Simulated dynamic structure factors and four-point correlations hint, respectively, at very long α-relaxation and correlated time scales at 298 K. This explains the long solute rotation times (∼80-200 ns) measured at 298 K. Stretched exponential decay of the simulated H-bond relaxations with long time scales further highlights the strong temporal heterogeneity and slow dynamics inherent to these systems. In summary, this work provides the first insight into the molecular motions and interspecies interaction in a representative cryoprotectant mixture, and stimulates further study to investigate the interconnection between cryoprotection and dynamic heterogeneity.
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Affiliation(s)
- Sandipa Indra
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block-JD, Salt Lake, Sector-III, Kolkata 700106, India
| | - Ranjit Biswas
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block-JD, Salt Lake, Sector-III, Kolkata 700106, India
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48
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Evaluation of ReaxFF-lg force fields for use in molecular dynamics simulations of sucrose. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1973-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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49
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Comez L, Paolantoni M, Sassi P, Corezzi S, Morresi A, Fioretto D. Molecular properties of aqueous solutions: a focus on the collective dynamics of hydration water. SOFT MATTER 2016; 12:5501-5514. [PMID: 27280176 DOI: 10.1039/c5sm03119b] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
When a solute is dissolved in water, their mutual interactions determine the molecular properties of the solute on one hand, and the structure and dynamics of the surrounding water particles (the so-called hydration water) on the other. The very existence of soft matter and its peculiar properties are largely due to the wide variety of possible water-solute interactions. In this context, water is not an inert medium but rather an active component, and hydration water plays a crucial role in determining the structure, stability, dynamics, and function of matter. This review focuses on the collective dynamics of hydration water in terms of retardation with respect to the bulk, and of the number of molecules whose dynamics is perturbed. Since water environments are in a dynamic equilibrium, with molecules continuously exchanging from around the solute towards the bulk and vice versa, we examine the ability of different techniques to measure the water dynamics on the basis of the explored time scales and exchange rates. Special emphasis is given to the collective dynamics probed by extended depolarized light scattering and we discuss whether and to what extent the results obtained in aqueous solutions of small molecules can be extrapolated to the case of large biomacromolecules. In fact, recent experiments performed on solutions of increasing complexity clearly indicate that a reductionist approach is not adequate to describe their collective dynamics. We conclude this review by presenting current ideas that are being developed to describe the dynamics of water interacting with macromolecules.
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Affiliation(s)
- L Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
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50
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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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