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Robertson H, Gresham IJ, Nelson ARJ, Gregory KP, Johnson EC, Willott JD, Prescott SW, Webber GB, Wanless EJ. Solvent-Modulated Specific Ion Effects: Poly( N-isopropylacrylamide) Brushes in Nonaqueous Electrolytes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:335-347. [PMID: 38117209 PMCID: PMC10910595 DOI: 10.1021/acs.langmuir.3c02596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023]
Abstract
Pertinent to cryopreservation as well as energy storage and batteries, nonaqueous electrolytes and their mixtures with water were investigated. In particular, specific ion-induced effects on the modulation of a poly(N-isopropylacrylamide) (PNIPAM) brush were investigated in various dimethyl sulfoxide (DMSO)-water solvent mixtures. Spectroscopic ellipsometry and neutron reflectometry were employed to probe changes in brush swelling and structure, respectively. In water-rich solvents (i.e., pure water and 6 mol % DMSO), PNIPAM undergoes a swollen to collapsed thermotransition with increasing temperature, whereby a forward Hofmeister series was noted; K+ and Li+ electrolytes composed of SCN- and I- salted-in (stabilized) PNIPAM chains, and electrolytes of Cl- and Br- salted-out (destabilized) the polymer. The cation was seen to play a lesser role than that of the anion, merely modulating the magnitude of the anion effect. In 70 mol % DMSO, a collapsed to swollen thermotransition was noted for PNIPAM. Here, concentration-dependent specific ion effects were observed; a forward series was observed in 0.2 mol % electrolytes, whereas increasing the electrolyte concentration to 0.9 mol % led to a series reversal. While no thermotransition was observed in pure DMSO, a solvent-induced specific ion series reversal was noted; SCN- destabilized the brush and Cl- stabilized the brush. Both series reversals are attributed to the delicate balance of interactions between the solvent, solute (ion), and substrate (brush). Namely, the stability of the solvent clusters was hypothesized to drive polymer solvation.
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Affiliation(s)
- Hayden Robertson
- College
of Science, Engineering and Environment, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Isaac J. Gresham
- School
of Chemistry, University of Sydney, Sydney 2052, Australia
| | - Andrew R. J. Nelson
- Australian
Centre for Neutron Scattering, ANSTO, Locked Bag 2001, Kirrawee DC, New South Wales 2232, Australia
| | - Kasimir P. Gregory
- Division
of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital
Territory 0200, Australia
| | - Edwin C. Johnson
- Department
of Chemistry, University of Sheffield, Dainton Building, Brook Hill, Sheffield S3 7HF, U.K.
| | - Joshua D. Willott
- College
of Science, Engineering and Environment, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Stuart W. Prescott
- School of
Chemical Engineering, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Grant B. Webber
- College
of Science, Engineering and Environment, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Erica J. Wanless
- College
of Science, Engineering and Environment, University of Newcastle, Callaghan, New South Wales 2308, Australia
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2
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Vahidi SH, Monhemi H, Hassani Sabzevar B, Eftekhari M. Electrostatic interactions of enzymes in non-aqueous conditions: insights from molecular dynamics simulations. J Biomol Struct Dyn 2023:1-14. [PMID: 37965802 DOI: 10.1080/07391102.2023.2280775] [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: 05/29/2023] [Accepted: 11/01/2023] [Indexed: 11/16/2023]
Abstract
Electrostatic interactions of enzymes and their effects on enzyme activity and stability are poorly understood in non-aqueous conditions. Here, we investigate the contribution of the electrostatic interactions on the stability and activity of enzymes in the non-aqueous environment using molecular dynamics simulations. Lipase was selected as active and lysozyme as inactive model enzymes in non-aqueous media. Hexane was used as a common non-aqueous solvent model. In agreement with the previous experiments, simulations show that lysozyme has more structural instabilities than lipase in hexane. The number of hydrogen bonds and salt bridges of both enzymes is dramatically increased in hexane. In contrast to the other opinions, we show that the increase of the electrostatic interactions in non-aqueous media is not so favorable for enzymatic function and stability. In this condition, the newly formed hydrogen bonds and salt bridges can partially denature the local structure of the enzymes. For lysozyme, the changes in electrostatic interactions occur in all domains including the active site cleft, which leads to enzyme inactivation and destabilization. Interestingly, most of the changes in electrostatic interactions of lipase occur far from the active site regions. Therefore, the active site entrance regions remain functional in hexane. The results of this study reveal how the changes in electrostatic interactions can affect enzyme stability and activity in non-aqueous conditions. Moreover, we show for the first time how some enzymes, such as lipase, remain active in a non-aqueous environment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Hooman Vahidi
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Hassan Monhemi
- Department of Chemistry, Faculty of Sciences, University of Neyshabur, Neyshabur, Iran
| | | | - Mohammad Eftekhari
- Department of Chemistry, Faculty of Sciences, University of Neyshabur, Neyshabur, Iran
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3
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Di Mino C, Clancy AJ, Sella A, Howard CA, Headen TF, Seel AG, Skipper NT. Weak Interactions in Dimethyl Sulfoxide (DMSO)-Tertiary Amide Solutions: The Versatility of DMSO as a Solvent. J Phys Chem B 2023; 127:1357-1366. [PMID: 36752593 PMCID: PMC9940205 DOI: 10.1021/acs.jpcb.2c07155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The structures of equimolar mixtures of the commonly used polar aprotic solvents dimethylformamide (DMF) and dimethylacetamide (DMAc) in dimethyl sulfoxide (DMSO) have been investigated via neutron diffraction augmented by extensive hydrogen/deuterium isotopic substitution. Detailed 3-dimensional structural models of these solutions have been derived from the neutron data via Empirical Potential Structure Refinement (EPSR). The intermolecular center-of-mass (CoM) distributions show that the first coordination shell of the amides comprises ∼13-14 neighbors, of which approximately half are DMSO. In spite of this near ideal coordination shell mixing, the changes to the amide-amide structure are found to be relatively subtle when compared to the pure liquids. Analysis of specific intermolecular atom-atom correlations allows quantitative interpretation of the competition between weak interactions in the solution. We find a hierarchy of formic and methyl C-H···O hydrogen bonds forms the dominant local motifs, with peak positions in the range of 2.5-3.0 Å. We also observe a rich variety of steric and dispersion interactions, including those involving the O═C-N amide π-backbones. This detailed insight into the structural landscape of these important liquids demonstrates the versatility of DMSO as a solvent and the remarkable sensitivity of neutron diffraction, which is critical for understanding weak intermolecular interactions at the nanoscale and thereby tailoring solvent properties to specific applications.
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Affiliation(s)
- Camilla Di Mino
- Department
of Physics and Astronomy, University College
London, Gower Street, LondonWC1E
6BT, U.K.
| | - Adam J. Clancy
- Department
of Chemistry, University College London, 20 Gordon Street, LondonWC1H 0AJ, U.K.
| | - Andrea Sella
- Department
of Chemistry, University College London, 20 Gordon Street, LondonWC1H 0AJ, U.K.
| | - Christopher A. Howard
- Department
of Physics and Astronomy, University College
London, Gower Street, LondonWC1E
6BT, U.K.
| | - Thomas F. Headen
- ISIS
Neutron and Muon Source, Science and Technology
Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, DidcotOX11 0QX, U.K.
| | - Andrew G. Seel
- ISIS
Neutron and Muon Source, Science and Technology
Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, DidcotOX11 0QX, U.K.,E-mail: . Phone: +44 (0)1793 547500
| | - Neal T. Skipper
- Department
of Physics and Astronomy, University College
London, Gower Street, LondonWC1E
6BT, U.K.,E-mail: . Phone: +44 (0)207 679 3526
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4
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Robertson H, Nelson ARJ, Prescott SW, Webber GB, Wanless EJ. Cosolvent effects on the structure and thermoresponse of a polymer brush: PNIPAM in DMSO–water mixtures. Polym Chem 2023. [DOI: 10.1039/d2py01487d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Structural characterisation of thermoresponsive polymer brushes in binary DMSO–water mixtures reveals both LCST and UCST behaviour.
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Affiliation(s)
- Hayden Robertson
- College of Science, Engineering and Environment, University of Newcastle, Callaghan, Australia
| | | | | | - Grant B. Webber
- College of Science, Engineering and Environment, University of Newcastle, Callaghan, Australia
| | - Erica J. Wanless
- College of Science, Engineering and Environment, University of Newcastle, Callaghan, Australia
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5
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Toh EC, Liu KL, Tsai S, Lin C. Cryopreservation and Cryobanking of Cells from 100 Coral Species. Cells 2022; 11:cells11172668. [PMID: 36078076 PMCID: PMC9454506 DOI: 10.3390/cells11172668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/17/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
When coral species become extinct, their genetic resources cannot be recovered. Coral cryobanks can be employed to preserve coral samples and thereby maintain the availability of the samples and increase their potential to be restocked. In this study, we developed a procedure to determine coral species-specific requirements for cryobank freezing through determining suitable cryoprotective agents (CPAs), CPA concentrations, equilibration times, holding durations, viability rates, and cell amounts for banked coral cells, and we established the first ever coral cell cryobank. Coral cells, including supporting and gland cells, epidermal nematocysts, Symbiodiniaceae and symbiotic endoderm cells (SEC) were found from the extracted protocol. Approximately half of the corals from the experimental corals consisted of spindle and cluster cells. Gastrodermal nematocysts were the least common. The overall concentration of Symbiodiniaceae in the coral cells was 8.6%. Freezing using DMSO as a CPA was suitable for approximately half of the corals, and for the other half of species, successful cell cryopreservation was achieved using MeOH and EG. EG and DMSO had similar suitabilities for Acanthastrea, Euphyllia, Favites, Lobophyllia, Pavona, Seriatopora, and Turbinaria, as did EG and MeOH for Acropora, Echinopyllia, and Sinularia and MeOH and DMSO for Platygyra after freezing. At least 14 straws from each species of coral were cryobanked in this study, totaling more than 1884 straws (0.5 mL) with an average concentration of 6.4 × 106 per mL. The results of this study may serve as a framework for cryobanks worldwide and contribute to the long-term conservation of coral reefs.
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Affiliation(s)
- En-Chun Toh
- Institute of Marine Biology, National Dong Hwa University, Pingtung 944401, Taiwan
| | - Kuan-Lin Liu
- Institute of Marine Biology, National Dong Hwa University, Pingtung 944401, Taiwan
| | - Sujune Tsai
- Department of Post Modern Agriculture, Mingdao University, Peetow, Changhua 52345, Taiwan
- Correspondence: (S.T.); (C.L.); Tel.: +886-925750025 (S.T.); +886-08-88825036 (C.L.)
| | - Chiahsin Lin
- Institute of Marine Biology, National Dong Hwa University, Pingtung 944401, Taiwan
- National Museum of Marine Biology & Aquarium, Checheng, Pingtung 944, Taiwan
- Correspondence: (S.T.); (C.L.); Tel.: +886-925750025 (S.T.); +886-08-88825036 (C.L.)
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6
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Franco LR, Toledo KCF, Matias TA, Benavides PA, Cezar HM, Araujo CM, Coutinho K, Araki K. Unraveling the acid-base characterization and solvent effects on the structural and electronic properties of a bis-bidentate bridging ligand. Phys Chem Chem Phys 2022; 24:10222-10240. [PMID: 35420602 DOI: 10.1039/d1cp03912a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the interactions and the solvent effects on the distribution of several species in equilibrium and how it can influence the 1H-NMR properties, spectroscopy (UV-vis absorption), and the acid-base equilibria can be especially challenging. This is the case of a bis-bidentate bridging ligand bis(2-pyridyl)-benzo-bis(imidazole), where the two pyridyl and four imidazolyl nitrogen atoms can be protonated in different ways, depending on the solvent, generating many isomeric/tautomeric species. Herein, we report a combined theoretical-experimental approach based on a sequential quantum mechanics/molecular mechanics procedure that was successfully applied to describe in detail the acid-base characterization and its effects on the electronic properties of such a molecule in solution. The calculated free-energies allowed the identification of the main species present in solution as a function of the solvent polarity, and its effects on the magnetic shielding of protons (1H-NMR chemical shifts), the UV-vis absorption spectra, and the acid-base equilibrium constants (pKas) in aqueous solution. Three acid-base equilibrium constants were experimentally/theoretically determined (pKa1 = 1.3/1.2, pKa2 = 2.1/2.2 and pKa5 = 10.1/11.3) involving mono-deprotonated and mono-protonated cis and trans species. Interestingly, other processes with pKa3 = 3.7 and pKa4 = 6.0 were also experimentally determined and assigned to the protonation and deprotonation of dimeric species. The dimerization of the most stable neutral species was investigated by Monte Carlo simulations and its electronic effects were considered for the elucidation of the UV-vis absorption bands, revealing transitions mainly with the charge-transfer characteristic and involving both the monomeric species and the dimeric species. The good matching of the theoretical and experimental results provides an atomistic insight into the solvent effects on the electronic properties of this bis-bidentate bridging ligand.
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Affiliation(s)
- Leandro Rezende Franco
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, 05508-090 São Paulo, SP, Brazil. .,Department of Engineering and Physics, Karlstad University, 65188 Karlstad, Sweden
| | | | - Tiago Araujo Matias
- Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, Butantã, 05508-000 São Paulo, SP, Brazil.
| | - Paola Andrea Benavides
- Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, Butantã, 05508-000 São Paulo, SP, Brazil.
| | - Henrique Musseli Cezar
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, 05508-090 São Paulo, SP, Brazil.
| | - C Moyses Araujo
- Department of Engineering and Physics, Karlstad University, 65188 Karlstad, Sweden.,Materials Theory Division, Department of Physics and Astronomy, Ångström Laboratory, Uppsala University, 75120 Uppsala, Sweden
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, 05508-090 São Paulo, SP, Brazil.
| | - Koiti Araki
- Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, Butantã, 05508-000 São Paulo, SP, Brazil.
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7
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Takamuku T, Tashiro A, Kawano M, Ando M, Ogawa A, Sadakane K, Iwase H, Shirota H. Anion Effects on the Mixing States of 1-Methyl-3-octylimidazolium Tetrafluoroborate and Bis(trifluoromethylsulfonyl)amide with Methanol, Acetonitrile, and Dimethyl Sulfoxide on the Meso- and Microscopic Scales. J Phys Chem B 2021; 125:13896-13907. [PMID: 34913705 DOI: 10.1021/acs.jpcb.1c08001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mixing states of two imidazolium-based ionic liquids (ILs) with different anions, 1-methyl-3-octylimidazolium tetrafluoroborate (C8mimBF4) and bis(trifluoromethylsulfonyl)amide (C8mimTFSA), with three molecular liquids (MLs), methanol (MeOH), acetonitrile (AN), and dimethyl sulfoxide (DMSO), have been investigated on both mesoscopic and microscopic scales using small-angle neutron scattering (SANS), infrared (IR), and 1H and 13C nuclear magnetic resonance (NMR) spectroscopy. Additionally, molecular dynamics (MD) simulations have been conducted on the six combinations of ILs and MLs to observe the states of their mixtures on the atomic level. The SANS profiles of the IL-ML mixtures suggested that MeOH molecules only form clusters in both C8mimBF4 and C8mimTFSA, whereas AN and DMSO were homogeneously mixed with ILs on the SANS scale. MeOH clusters are more enhanced in BF4--IL than TFSA--IL. The microscopic interactions among IL cations, anions, and MLs should contribute to the mesoscopic mixing states of the IL-ML mixtures. In fact, the IL cation-anion, cation-ML, anion-ML, and ML-ML interactions observed by IR, NMR, and MD simulations clarified the reasons for the mixing states of the IL-ML binary solutions observed by the SANS experiments. In neat ILs, the imidazolium ring of the IL cation more strongly interacts with BF4- than TFSA- due to the higher charge density of the former. The interaction of anions with the imidazolium ring is more easily loosened on adding MLs to ILs in the order of DMSO > MeOH > AN. It does not significantly depend on the anions. However, the replacement of the anion on the imidazolium ring by an ML depends on the anions; the replacement is more proceeded in the order of MeOH > DMSO > AN in BF4--IL, while DMSO > MeOH > AN in TFSA--IL. On the other hand, the solvation of both anions by MLs is stronger in the order of MeOH > DMSO ≈ AN. Despite the stronger interactions of MeOH with both cations and anions, MeOH molecules are heterogeneously mixed with both ILs to form clusters in the mixtures. Therefore, the self-hydrogen bonding among MeOH molecules most markedly governs the mixing state of the binary solutions among the abovementioned interactions.
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Affiliation(s)
- Toshiyuki Takamuku
- Faculty of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Atsuya Tashiro
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Masahiro Kawano
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Masatoshi Ando
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
| | - Akira Ogawa
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Koichiro Sadakane
- Faculty of Life and Medical Sciences, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto 610-0394, Japan
| | - Hiroki Iwase
- Comprehensive Research Organization for Science and Society (CROSS), 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Hideaki Shirota
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
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8
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Stape THS, Mutluay MM, Tjäderhane L, Uurasjärvi E, Koistinen A, Tezvergil-Mutluay A. The pursuit of resin-dentin bond durability: Simultaneous enhancement of collagen structure and polymer network formation in hybrid layers. Dent Mater 2021; 37:1083-1095. [PMID: 33863568 DOI: 10.1016/j.dental.2021.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/28/2021] [Accepted: 03/28/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Imperfect polymer formation as well as collagen's susceptibility to enzymatic degradation increase the vulnerability of hybrid layers over time. This study investigated the effect of new dimethyl sulfoxide (DMSO)-containing pretreatments on long-term bond strength, hybrid layer quality, monomer conversion and collagen structure. METHODS H3PO4-etched mid-coronal dentin surfaces from extracted human molars (n = 8) were randomly treated with aqueous and ethanolic DMSO solutions or following the ethanol-wet bonding technique. Dentin bonding was performed with a three-step etch-and-rinse adhesive. Resin-dentin beams (0.8 mm2) were stored in artificial saliva at 37 °C for 24 h and 2.5 years, submitted to microtensile bond strength testing at 0.5 mm/min and semi-quantitative SEM nanoleakage analysis (n = 8). Micro-Raman spectroscopy was used to determine the degree of conversion at different depths in the hybrid layer (n = 6). Changes in the apparent modulus of elasticity of demineralized collagen beams measuring 0.5 × 1.7 × 7 mm (n = 10) and loss of dry mass (n = 10) after 30 days were calculated via three-point bending and precision weighing, respectively. RESULTS DMSO-containing pretreatments produced higher bond strengths, which did not change significantly over time presenting lower incidence of water-filled zones. Higher uniformity in monomer conversion across the hybrid layer occurred for all pretreatments. DMSO-induced collagen stiffening was reversible in water, but with lower peptide solubilization. SIGNIFICANCE Improved polymer formation and higher stability of the collagen-structure can be attributed to DMSO's unique ability to simultaneously modify both biological and resin components within the hybrid layer. Pretreatments composed of DMSO/ethanol may be a viable-effective alternative to extend the longevity of resin-dentin bonds.
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Affiliation(s)
- Thiago Henrique Scarabello Stape
- Department of Restorative Dentistry and Cariology, Adhesive Dentistry Research Group, Institute of Dentistry, University of Turku, Turku, Finland; Turku University Hospital, TYKS, University of Turku, Turku, Finland.
| | - Mustafa Murat Mutluay
- Department of Restorative Dentistry and Cariology, Adhesive Dentistry Research Group, Institute of Dentistry, University of Turku, Turku, Finland; Department of Prosthodontics and Clinical Dentistry, Institute of Dentistry, University of Eastern Finland, Kuopio, Finland.
| | - Leo Tjäderhane
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland and Helsinki University Hospital, Helsinki, Finland; Research Unit of Oral Health Sciences and Medical Research Center Oulu (MRC Oulu), Oulu University Hospital and University of Oulu, Oulu, Finland.
| | | | - Arto Koistinen
- University of Eastern Finland, SIB Labs, Kuopio, Finland.
| | - Arzu Tezvergil-Mutluay
- Department of Restorative Dentistry and Cariology, Adhesive Dentistry Research Group, Institute of Dentistry, University of Turku, Turku, Finland; Turku University Hospital, TYKS, University of Turku, Turku, Finland.
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9
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Ando M, Kawano M, Tashiro A, Takamuku T, Shirota H. Low-Frequency Spectra of 1-Methyl-3-octylimidazolium Tetrafluoroborate Mixtures with Methanol, Acetonitrile, and Dimethyl Sulfoxide: A Combined Study of Femtosecond Raman-Induced Kerr Effect Spectroscopy and Molecular Dynamics Simulations. J Phys Chem B 2020; 124:7857-7871. [DOI: 10.1021/acs.jpcb.0c04870] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masatoshi Ando
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
| | - Masahiro Kawano
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Atsuya Tashiro
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Toshiyuki Takamuku
- Faculty of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Hideaki Shirota
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
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10
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Casier R, Duhamel J. Effect of Like Charges on the Conformation and Internal Dynamics of Polypeptides Probed by Pyrene Excimer Fluorescence. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00836] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Remi Casier
- Institute for Polymer Research, Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo N2L3G1, Ontario, Canada
| | - Jean Duhamel
- Institute for Polymer Research, Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo N2L3G1, Ontario, Canada
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11
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Ramos TN, Silva DL, Cabral BJ, Canuto S. On the spectral line width broadening for simulation of the two-photon absorption cross-section of para-Nitroaniline in liquid environment. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Application of the 3D-RISM-KH molecular solvation theory for DMSO as solvent. J Comput Aided Mol Des 2019; 33:905-912. [PMID: 31637566 DOI: 10.1007/s10822-019-00238-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/14/2019] [Indexed: 12/16/2022]
Abstract
The molecular solvation theory in the form of the Three-Dimensional Reference Interaction Site Model (3D-RISM) with Kovalenko-Hirata (KH) closure relation is benchmarked for use with dimethyl sulfoxide (DMSO) as solvent for (bio)-chemical simulation within the framework of integral equation formalism. Several force field parameters have been tested to correctly reproduce solvation free energy in DMSO, ion solvation in DMSO, and DMSO coordination prediction. Our findings establish a united atom (UA) type parameterization as the best model of DMSO for use in 3D-RISM-KH theory based calculations.
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13
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Cyclodextrin glucosyltransferase immobilization on polydopamine-coated Fe3O4 nanoparticles in the presence of polyethyleneimine for efficient β-cyclodextrin production. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107264] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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14
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Zou Z, Alibiglou H, Mate DM, Davari MD, Jakob F, Schwaneberg U. Directed sortase A evolution for efficient site-specific bioconjugations in organic co-solvents. Chem Commun (Camb) 2018; 54:11467-11470. [PMID: 30255876 DOI: 10.1039/c8cc06017g] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Directed sortase A evolution yielded the variants R159G and D165Q/D186G/K196V with increased resistance (2.2-fold) and catalytic efficiency (6.3-fold) in 45% (v/v) dimethylsulfoxide. Interestingly, D165Q/D186G/K196V also showed an up to 4.7-fold increased activity for the conjugation of hydrophobic peptides/amines in co-solvents. MD simulations revealed that conformational mobilities are important for the gained resistance.
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Affiliation(s)
- Zhi Zou
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraβe 50, 52056 Aachen, Germany
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15
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Stachura SS, Malajczuk CJ, Mancera RL. Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field. J Mol Model 2018; 24:174. [DOI: 10.1007/s00894-018-3720-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/12/2018] [Indexed: 12/23/2022]
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16
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Sedov IA, Magsumov TI. Molecular dynamics study of unfolding of lysozyme in water and its mixtures with dimethyl sulfoxide. J Mol Graph Model 2017; 76:466-474. [PMID: 28797927 DOI: 10.1016/j.jmgm.2017.07.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/28/2017] [Accepted: 07/30/2017] [Indexed: 11/17/2022]
Abstract
All-atom explicit solvent molecular dynamics was used to study the process of unfolding of hen egg white lysozyme in water and mixtures of water with dimethyl sulfoxide at different compositions. We have determined the kinetic parameters of unfolding at a constant temperature 450K. For each run, the time of disruption of the tertiary structure of lysozyme tu was defined as the moment when a certain structural criterion computed from the trajectory reaches its critical value. A good agreement is observed between the results obtained using several different criteria. The secondary structure according to DSSP calculations is found to be partially unfolded to the moment of disruption of tertiary structure, but some of its elements keep for a long time after that. The values of tu averaged over ten 30ns-long trajectories for each solvent composition are shown to decrease very rapidly with addition of dimethyl sulfoxide, and rather small amounts of dimethyl sulfoxide are found to change the pathway of unfolding. In pure water, despite the loss of tertiary contacts and disruption of secondary structure elements, the protein preserves its compact globular state at least over 130ns of simulation, while even at 5mol percents of dimethyl sulfoxide it loses its compactness within 30ns. The proposed methodology is a generally applicable tool to quantify the rate of protein unfolding in simulation studies.
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Affiliation(s)
- Igor A Sedov
- Chemical Institute, Kazan Federal University, 420008, Kremlevskaya 18, Kazan, Russia.
| | - Timur I Magsumov
- Chemical Institute, Kazan Federal University, 420008, Kremlevskaya 18, Kazan, Russia
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17
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Mehtälä P, Pashley D, Tjäderhane L. Effect of dimethyl sulfoxide on dentin collagen. Dent Mater 2017; 33:915-922. [DOI: 10.1016/j.dental.2017.04.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 02/16/2017] [Accepted: 04/25/2017] [Indexed: 11/28/2022]
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18
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Srivastava KR, Goyal B, Kumar A, Durani S. Scrutiny of electrostatic-driven conformational ordering of polypeptide chains in DMSO: a study with a model oligopeptide. RSC Adv 2017. [DOI: 10.1039/c7ra02137b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The molecular mechanism of DMSO-induced stabilisation of β-sheets is attributed to the combination of polar electrostatic interactions among side chains, and backbone desolvation through bulky side chains which promotes backbone hydrogen bonding.
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Affiliation(s)
| | - Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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19
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Lindsay RJ, Johnson QR, Evangelista W, Nellas RB, Shen T. DMSO enhanced conformational switch of an interfacial enzyme. Biopolymers 2016; 105:864-72. [PMID: 27463323 DOI: 10.1002/bip.22924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 07/25/2016] [Indexed: 11/05/2022]
Abstract
Interfacial proteins function in unique heterogeneous solvent environments, such as water-oil interfaces. One important example is microbial lipase, which is activated in an oil-water emulsion phase and has many important enzymatic functions. A unique aprotic dipolar organic solvent, dimethyl sulfoxide (DMSO), has been shown to increase the activity of lipases, but the mechanism behind this enhancement is still unknown. Here, all-atom molecular dynamics simulations of lipase in a binary solution were performed to examine the effects of DMSO on the dynamics of the gating mechanism. The amphiphilic α5 region of the lipase was a focal point for the analysis, since the structural ordering of α5 has been shown to be important for gating under other perturbations. Compared to the closed-gorge ensemble in an aqueous environment, the conformational ensemble shifts towards open-gorge structures in the presence of DMSO solvents. Increased width of the access channel is particularly prevalent in 45% and 60% DMSO concentrations (w/w). As the amount of DMSO increases, the α5 region of the lipase becomes more α-helical, as we previously observed in studies that address water-oil interfacial and high pressure activation. We believe that the structural ordering of α5 plays an essential role on gating and lipase activity.
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Affiliation(s)
- Richard J Lindsay
- UT-ORNL Graduate School of Genome Science and Technology, Knoxville, TN, 37996.,Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830
| | - Quentin R Johnson
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830.,National Institute for Mathematical and Biological Synthesis, Knoxville, TN, 37996
| | - Wilfredo Evangelista
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830.,Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996
| | - Ricky B Nellas
- Institute of Chemistry, University of the Philippines Diliman, Quezon City, Philippines
| | - Tongye Shen
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830. .,Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996.
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20
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Tosi I, Segado Centellas M, Campioli E, Iagatti A, Lapini A, Sissa C, Baldini L, Cappelli C, Di Donato M, Sansone F, Santoro F, Terenziani F. Excitation Dynamics in Hetero-bichromophoric Calixarene Systems. Chemphyschem 2016; 17:1686-706. [PMID: 26867716 DOI: 10.1002/cphc.201501065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/22/2016] [Indexed: 11/06/2022]
Abstract
In this work, the dynamics of electronic energy transfer (EET) in bichromophoric donor-acceptor systems, obtained by functionalizing a calix[4]arene scaffold with two dyes, was experimentally and theoretically characterized. The investigated compounds are highly versatile, due to the possibility of linking the dye molecules to the cone or partial cone structure of the calix[4]arene, which directs the two active units to the same or opposite side of the scaffold, respectively. The dynamics and efficiency of the EET process between the donor and acceptor units was investigated and discussed through a combined experimental and theoretical approach, involving ultrafast pump-probe spectroscopy and density functional theory based characterization of the energetic and spectroscopic properties of the system. Our results suggest that the external medium strongly determines the particular conformation adopted by the bichromophores, with a direct effect on the extent of excitonic coupling between the dyes and hence on the dynamics of the EET process itself.
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Affiliation(s)
- Irene Tosi
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/a, 43124, Parma, Italy
| | | | - Elisa Campioli
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/a, 43124, Parma, Italy
| | - Alessandro Iagatti
- LENS (European Laboratory for Non Linear Spectroscopy), via N. Carrara 1, 50019, Sesto Fiorentino (FI), Italy.,INO (Istituto Nazionale di Ottica), Largo Fermi 6, 50125, Firenze, Italy
| | - Andrea Lapini
- LENS (European Laboratory for Non Linear Spectroscopy), via N. Carrara 1, 50019, Sesto Fiorentino (FI), Italy.,Dipartimento di Chimica "Ugo Schiff", Università di Firenze, via della Lastruccia 13, 50019, Sesto Fiorentino (FI), Italy
| | - Cristina Sissa
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/a, 43124, Parma, Italy
| | - Laura Baldini
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/a, 43124, Parma, Italy.
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy.
| | - Mariangela Di Donato
- LENS (European Laboratory for Non Linear Spectroscopy), via N. Carrara 1, 50019, Sesto Fiorentino (FI), Italy. .,INO (Istituto Nazionale di Ottica), Largo Fermi 6, 50125, Firenze, Italy. .,Dipartimento di Chimica "Ugo Schiff", Università di Firenze, via della Lastruccia 13, 50019, Sesto Fiorentino (FI), Italy.
| | - Francesco Sansone
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/a, 43124, Parma, Italy
| | - Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca via G. Moruzzi 1, I-56124, Pisa, Italy
| | - Francesca Terenziani
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/a, 43124, Parma, Italy.
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21
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Dahanayake JN, Gautam DN, Verma R, Mitchell-Koch KR. To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent. MOLECULAR SIMULATION 2016; 42:1001-1013. [PMID: 27403032 DOI: 10.1080/08927022.2016.1139108] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties. However, a common protocol for non-aqueous enzyme simulations does not exist. If you want to simulate enzymes in non-aqueous solutions, how many and which crystallographic waters do you keep? In the present work, this question is addressed by determining which crystallographic water molecules lead most quickly to an equilibrated protein structure. Five different methods of selecting and keeping crystallographic waters are used in order to discover which crystallographic waters lead the protein structure to reach an equilibrated structure more rapidly in organic solutions. It is found that buried waters contribute most to rapid equilibration in organic solvent, with slow-diffusing waters giving similar results.
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Affiliation(s)
- Jayangika N Dahanayake
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
| | - Devaki N Gautam
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
| | - Rajni Verma
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
| | - Katie R Mitchell-Koch
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
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22
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Lomas JS. (1)H NMR spectra of alcohols in hydrogen bonding solvents: DFT/GIAO calculations of chemical shifts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:28-38. [PMID: 26256675 DOI: 10.1002/mrc.4312] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/17/2015] [Indexed: 06/04/2023]
Abstract
Proton nuclear magnetic resonance (NMR) shifts of aliphatic alcohols in hydrogen bonding solvents have been computed on the basis of density functional theory by applying the gauge-including atomic orbital method to geometry-optimized alcohol/solvent complexes. The OH proton shifts and hydrogen bond distances for methanol or ethanol complexed with pyridine depend very much on the functional employed and very little on the basis set, provided it is sufficiently large to give the correct quasi-linear hydrogen bond geometry. The CH proton shifts are insensitive to both the functional and the basis set. NMR shifts for all protons in several alcohol/pyridine complexes are calculated at the Perdew, Burke and Ernzerhof PBE0/cc-pVTZ//PBE0/6-311 + G(d,p) level in the gas phase. The results correlate with the shifts for the pyridine-complexed alcohols, determined by analysing data from the NMR titration of alcohols against pyridine. More pragmatically, computed shifts for a wider range of alcohols correlate with experimental shifts in neat pyridine. Shifts for alcohols in dimethylsulfoxide, based on the corresponding complexes in the gas phase, correlate well with the experimental values, but the overall root mean square difference is high (0.23 ppm), shifts for the OH, CHOH and other CH protons being systematically overestimated, by averages of 0.42, 0.21 and 0.06 ppm, respectively. If the computed shifts are corrected accordingly, a very good correlation is obtained with a gradient of 1.00 ± 0.01, an intercept of 0.00 ± 0.02 ppm and a root mean square difference of 0.09 ppm. This is a modest improvement on the result of applying the CHARGE programme to a slightly different set of alcohols. Some alcohol complexes with acetone and acetonitrile were investigated both in the gas phase and in a continuum of the relevant solvent.
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Affiliation(s)
- John S Lomas
- ITODYS, UMR 7086, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75205, France
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23
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Hu YF, Lv WJ, Zhao S, Shang YZ, Wang HL, Liu HL. Effect of surfactant SDS on DMSO transport across water/hexane interface by molecular dynamics simulation. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2015.05.068] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Kerisit S, Vijayakumar M, Han KS, Mueller KT. Solvation structure and transport properties of alkali cations in dimethyl sulfoxide under exogenous static electric fields. J Chem Phys 2015; 142:224502. [PMID: 26071715 DOI: 10.1063/1.4921982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A combination of molecular dynamics simulations and pulsed field gradient nuclear magnetic resonance spectroscopy is used to investigate the role of exogenous electric fields on the solvation structure and dynamics of alkali ions in dimethyl sulfoxide (DMSO) and as a function of temperature. Good agreement was obtained, for select alkali ions in the absence of an electric field, between calculated and experimentally determined diffusion coefficients normalized to that of pure DMSO. Our results indicate that temperatures of up to 400 K and external electric fields of up to 1 V nm(-1) have minimal effects on the solvation structure of the smaller alkali cations (Li(+) and Na(+)) due to their relatively strong ion-solvent interactions, whereas the solvation structures of the larger alkali cations (K(+), Rb(+), and Cs(+)) are significantly affected. In addition, although the DMSO exchange dynamics in the first solvation shell differ markedly for the two groups, the drift velocities and mobilities are not significantly affected by the nature of the alkali ion. Overall, although exogenous electric fields induce a drift displacement, their presence does not significantly affect the random diffusive displacement of the alkali ions in DMSO. System temperature is found to have generally a stronger influence on dynamical properties, such as the DMSO exchange dynamics and the ion mobilities, than the presence of electric fields.
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Affiliation(s)
- Sebastien Kerisit
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - M Vijayakumar
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Kee Sung Han
- Joint Center for Energy Storage Research, Fundamental and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Karl T Mueller
- Joint Center for Energy Storage Research, Fundamental and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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25
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Wang F, Jia G. Consideration of dielectric relaxation of pure DMSO liquid in different temperatures. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.06.066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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The Role of Lid in Protein-Solvent Interaction of the Simulated Solvent Stable Thermostable Lipase fromBacillusStrain 42 in Water-Solvent Mixtures. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.2478/v10133-009-0015-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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27
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Chaban VV, Maciel C, Fileti EE. Solvent Polarity Considerations Are Unable to Describe Fullerene Solvation Behavior. J Phys Chem B 2014; 118:3378-84. [DOI: 10.1021/jp4116639] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Vitaly V. Chaban
- MEMPHYS - Center for Biomembrane Physics, Odense M, 5230, Kingdom of Denmark
| | - Cleiton Maciel
- Centro
de Ciências Naturais e Humanas, Universidade Federal do ABC, 09210-270 Santo André, São Paulo, Brazil
| | - Eudes Eterno Fileti
- Instituto
de Ciência e Tecnologia, Universidade Federal de São Paulo, 12231-280, São José dos Campos, São Paulo, Brazil
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28
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Rosenman DJ, Connors CR, Chen W, Wang C, García AE. Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach. J Mol Biol 2013; 425:3338-59. [PMID: 23811057 DOI: 10.1016/j.jmb.2013.06.021] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 05/15/2013] [Accepted: 06/12/2013] [Indexed: 12/24/2022]
Abstract
Amyloid β (Aβ) peptides are a primary component of fibrils and oligomers implicated in the etiology of Alzheimer's disease (AD). However, the intrinsic flexibility of these peptides has frustrated efforts to investigate the secondary and tertiary structure of Aβ monomers, whose conformational landscapes directly contribute to the kinetics and thermodynamics of Aβ aggregation. In this work, de novo replica exchange molecular dynamics (REMD) simulations on the microseconds-per-replica timescale are used to characterize the structural ensembles of Aβ42, Aβ40, and M35-oxidized Aβ42, three physiologically relevant isoforms with substantially different aggregation properties. J-coupling data calculated from the REMD trajectories were compared to corresponding NMR-derived values acquired through two different pulse sequences, revealing that all simulations converge on the order of hundreds of nanoseconds-per-replica toward ensembles that yield good agreement with experiment. Though all three Aβ species adopt highly heterogeneous ensembles, these are considerably more structured compared to simulations on shorter timescales. Prominent in the C-terminus are antiparallel β-hairpins between L17-A21, A30-L36, and V39-I41, similar to oligomer and fibril intrapeptide models that expose these hydrophobic side chains to solvent and may serve as hotspots for self-association. Compared to reduced Aβ42, the absence of a second β-hairpin in Aβ40 and the sampling of alternate β topologies by M35-oxidized Aβ42 may explain the reduced aggregation rates of these forms. A persistent V24-K28 bend motif, observed in all three species, is stabilized by buried backbone to side-chain hydrogen bonds with D23 and a cross-region salt bridge between E22 and K28, highlighting the role of the familial AD-linked E22 and D23 residues in Aβ monomer folding. These characterizations help illustrate the conformational landscapes of Aβ monomers at atomic resolution and provide insight into the early stages of Aβ aggregation pathways.
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Affiliation(s)
- David J Rosenman
- Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
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29
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Meng Y, Yuan Y, Zhu Y, Guo Y, Li M, Wang Z, Pu X, Jiang L. Effects of organic solvents and substrate binding on trypsin in acetonitrile and hexane media. J Mol Model 2013; 19:3749-66. [DOI: 10.1007/s00894-013-1900-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/27/2013] [Indexed: 11/29/2022]
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30
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Hu YF, Lv WJ, Shang YZ, Liu HL, Wang HL, Suh SH. DMSO Transport across Water/Hexane Interface by Molecular Dynamics Simulation. Ind Eng Chem Res 2013. [DOI: 10.1021/ie303006d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Yao-Feng Hu
- State Key
Laboratory of Chemical Engineering, Department of Chemistry, East China University of Science and Technology, Shanghai
200237, China
| | - Wen-Jie Lv
- State Environmental
Protection Key Laboratory of Environmental Risk Assessment and Control
on Chemical Process, East China University of Science and Technology, Shanghai 200237, China
| | - Ya-Zhuo Shang
- State Key
Laboratory of Chemical Engineering, Department of Chemistry, East China University of Science and Technology, Shanghai
200237, China
| | - Hong-Lai Liu
- State Key
Laboratory of Chemical Engineering, Department of Chemistry, East China University of Science and Technology, Shanghai
200237, China
| | - Hua-Lin Wang
- State Environmental
Protection Key Laboratory of Environmental Risk Assessment and Control
on Chemical Process, East China University of Science and Technology, Shanghai 200237, China
| | - Soong-Hyuck Suh
- Department of Chemical Engineering, Keimyung University, Daegu 704-701, Korea
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31
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Tretyakova T, Shushanyan M, Partskhaladze T, Makharadze M, van Eldik R, Khoshtariya DE. Simplicity within the complexity: bilateral impact of DMSO on the functional and unfolding patterns of α-chymotrypsin. Biophys Chem 2013; 175-176:17-27. [PMID: 23524288 DOI: 10.1016/j.bpc.2013.02.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 02/05/2013] [Accepted: 02/09/2013] [Indexed: 10/27/2022]
Abstract
New understanding of the fundamental links between protein stability, conformational flexibility and function, can be gained through synergic studies on their catalytic and folding/unfolding properties under the influence of stabilizing/destabilizing additives. We explored an impact of dimethyl sulfoxide (DMSO), the moderate effector of multilateral action, on the kinetic (functional) and thermodynamic (thermal unfolding) patterns of a hydrolytic enzyme, α-chymotrypsin (α-CT), over a wide range of additive concentrations, 0-70% (v/v). Both the calorimetric and kinetic data exhibited rich behavior pointing to the complex interplay of global/local stability (and flexibility) patterns. The complex action of DMSO is explained through the negative and positive preferential solvation motifs that prevail for the extreme opposite, native-like and unfolded states, respectively, implying essential stabilization of compact domains by enhancement of interfacial water networks and destabilization of a flexible active site by direct binding of DMSO to the unoccupied specific positions intended for elongated polypeptide substrates.
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Affiliation(s)
- Tatyana Tretyakova
- Institute for Biophysics and Bionanosciences at the Department of Physics, I. Javakhishvili Tbilisi State University, I. Chavchavadze Ave. 3, 0128 Tbilisi, Georgia
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32
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Xu J, Zhuang Y, Wu B, Su L, He B. Calcium-ion-induced stabilization of the protease from Bacillus cereus WQ9-2 in aqueous hydrophilic solvents: effect of calcium ion binding on the hydration shell and intramolecular interactions. J Biol Inorg Chem 2013; 18:211-221. [PMID: 23322168 DOI: 10.1007/s00775-012-0966-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 11/24/2012] [Indexed: 01/12/2023]
Abstract
The neutral protease WQ from Bacillus cereus is stable in various aqueous organic mixtures, with the exception of those containing acetonitrile (ACN) and dimethylformamide (DMF). The stability of the enzyme in aqueous hydrophilic solvents was dramatically enhanced with the addition of calcium ions, with the degree of improvement in the half-life relative to different solutions ranging from fourfold to more than 70-fold. Studies of the kinetic constants showed that calcium ions induced slight conformational changes in the active site of the enzyme in aqueous ACN. We investigated the molecular mechanisms underlying this stabilizing effect by employing a combination of biophysical techniques and molecular dynamics simulation. In aqueous ACN, the intrinsic fluorescence and circular dichroism analysis demonstrated that the addition of calcium ions induced a relatively compact conformation and maintained both the native-like microenvironment near the tryptophan residues and the secondary structure. Alternatively, homology modeling confirmed the location of four calcium-ion-binding sites in the enzyme, and molecular dynamics simulation revealed that three other calcium ions were bound to the surface of the enzyme. Calcium ions, known as a type of kosmotrope, can strongly bond with water molecules, thus aiding in the formation of the regional hydration shell required for the maintenance of enzyme activity. In addition, the introduction of calcium ions resulted in the formation of additional ionic interactions, providing propitious means for protein stabilization. Thus, the stronger intramolecular interactions were also expected to contribute partially to the enhanced stability of the enzyme in an aqueous organic solvent.
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Affiliation(s)
- Jiaxing Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Yu Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Long Su
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Bingfang He
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China.
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33
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Lousa D, Baptista AM, Soares CM. A molecular perspective on nonaqueous biocatalysis: contributions from simulation studies. Phys Chem Chem Phys 2013; 15:13723-36. [DOI: 10.1039/c3cp51761f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Wedberg R, Abildskov J, Peters GH. Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation. J Phys Chem B 2012; 116:2575-85. [DOI: 10.1021/jp211054u] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rasmus Wedberg
- Department of Chemical and Biochemical
Engineering, Technical University of Denmark, Søltofts Plads, Building 229, DTU, 2800 Kongens Lyngby, Denmark
| | - Jens Abildskov
- Department of Chemical and Biochemical
Engineering, Technical University of Denmark, Søltofts Plads, Building 229, DTU, 2800 Kongens Lyngby, Denmark
| | - Günther H. Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Building
207, DTU, 2800 Kongens Lyngby, Denmark
- MEMPHYS−Center for Biomembrane Physics
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35
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Gupta R, Chandra A. Nonideality in diffusion of ionic and neutral solutes and hydrogen bond dynamics in dimethyl sulfoxide-chloroform mixtures of varying composition. J Comput Chem 2011; 32:2679-89. [DOI: 10.1002/jcc.21849] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2010] [Revised: 04/14/2011] [Accepted: 05/10/2011] [Indexed: 12/11/2022]
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Broersen K, Jonckheere W, Rozenski J, Vandersteen A, Pauwels K, Pastore A, Rousseau F, Schymkowitz J. A standardized and biocompatible preparation of aggregate-free amyloid beta peptide for biophysical and biological studies of Alzheimer's disease. Protein Eng Des Sel 2011; 24:743-50. [DOI: 10.1093/protein/gzr020] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Srivastava KR, Kumar A, Goyal B, Durani S. Stereochemistry and Solvent Role in Protein Folding: Nuclear Magnetic Resonance and Molecular Dynamics Studies of Poly-l and Alternating-l,d Homopolypeptides in Dimethyl Sulfoxide. J Phys Chem B 2011; 115:6700-8. [DOI: 10.1021/jp200743w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Anil Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
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Cordeiro JM, Soper AK. Investigation on the structure of liquid N-methylformamide–dimethylsulfoxide mixtures. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2011.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Zhang R, Wu WJ. Structures and Intermolecular Interactions in Dimethyl Sulfoxide-Water System Studied by All-atom Molecular Simulations. CHINESE J CHEM PHYS 2010. [DOI: 10.1088/1674-0068/23/05/504-508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Bansal V, Delgado Y, Fasoli E, Ferrer A, Griebenow K, Secundo F, Barletta GL. Effect of prolonged exposure to organic solvents on the active site environment of subtilisin Carlsberg. JOURNAL OF MOLECULAR CATALYSIS. B, ENZYMATIC 2010; 64:38-44. [PMID: 20414456 PMCID: PMC2856654 DOI: 10.1016/j.molcatb.2010.01.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The potential of enzyme catalysis as a tool for organic synthesis is nowadays indisputable, as is the fact that organic solvents affect an enzyme's activity, selectivity and stability. Moreover, it was recently realized that an enzyme's initial activity is substantially decreased after prolonged exposure to organic media, an effect that further hampers their potential as catalysts for organic synthesis. Regrettably, the mechanistic reasons for these effects are still debatable. In the present study we have made an attempt to explain the reasons behind the partial loss of enzyme activity on prolonged exposure to organic solvents. Fluorescence spectroscopic studies of the serine protease subtilisin Carlsberg chemically modified with polyethylene glycol (PEG-SC) and inhibited with a Dancyl fluorophore, and dissolved in two organic solvents (acetonitrile and 1,4-dioxane) indicate that when the enzyme is initially introduced into these solvents, the active site environment is similar to that in water; however prolonged exposure to the organic medium causes this environment to resemble that of the solvent in which the enzyme is dissolved. Furthermore, kinetic studies show a reduction on both V(max) and K(M) as a result of prolonged exposure to the solvents. One interpretation of these results is that during this prolonged exposure to organic solvents the active-site fluorescent label inhibitor adopts a different binding conformation. Extrapolating this to an enzymatic reaction we argue that substrates bind in a less catalytically favorable conformation after the enzyme has been exposed to organic media for several hours.
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Affiliation(s)
- Vibha Bansal
- University of Puerto Rico at Humacao, Department of Chemistry, Humacao, Puerto Rico, 00791
| | - Yamixa Delgado
- University of Puerto Rico at Humacao, Department of Chemistry, Humacao, Puerto Rico, 00791
| | - Ezio Fasoli
- University of Puerto Rico at Humacao, Department of Chemistry, Humacao, Puerto Rico, 00791
| | - Amaris Ferrer
- University of Puerto Rico at Humacao, Department of Chemistry, Humacao, Puerto Rico, 00791
| | - Kai Griebenow
- University of Puerto Rico at Rio Piedras, Department of Chemistry, Milano, Italy
| | - Francesco Secundo
- Istituto di Chimica del Riconoscimento Molecolare, v. M. Bianco, Milano, Italy
| | - Gabriel L Barletta
- University of Puerto Rico at Humacao, Department of Chemistry, Humacao, Puerto Rico, 00791
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42
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Zalewski L, Wykes M, Brovelli S, Bonini M, Breiner T, Kastler M, Dötz F, Beljonne D, Anderson H, Cacialli F, Samorì P. A Conjugated Thiophene-Based Rotaxane: Synthesis, Spectroscopy, and Modeling. Chemistry 2010; 16:3933-41. [DOI: 10.1002/chem.200903353] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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43
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Optimisation of Dex-GMA nanoparticles prepared in modified micro-emulsion system: Physical and biologic characterization. J Biotechnol 2009; 143:268-73. [DOI: 10.1016/j.jbiotec.2009.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2008] [Revised: 07/15/2009] [Accepted: 07/17/2009] [Indexed: 11/20/2022]
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44
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Zhang Q, Zhang X, Zhao DX. Polarizable force field for water-dimethyl sulfoxide systems: II properties of mixtures by molecular dynamics simulations. J Mol Liq 2009. [DOI: 10.1016/j.molliq.2009.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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45
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Zhang Q, Zhang X, Yu L, Zhao DX. Polarizable force field for water–dimethyl sulfoxide systems: I Parameterization and gas phase test. J Mol Liq 2009. [DOI: 10.1016/j.molliq.2008.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Kobryn AE, Kovalenko A. Molecular theory of hydrodynamic boundary conditions in nanofluidics. J Chem Phys 2008; 129:134701. [DOI: 10.1063/1.2972978] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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47
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Duarte AMS, van Mierlo CPM, Hemminga MA. Molecular Dynamics Study of the Solvation of an α-Helical Transmembrane Peptide by DMSO. J Phys Chem B 2008; 112:8664-71. [DOI: 10.1021/jp076678j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Afonso M. S. Duarte
- Laboratory of Biophysics and Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Carlo P. M. van Mierlo
- Laboratory of Biophysics and Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Marcus A. Hemminga
- Laboratory of Biophysics and Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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48
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Díaz-Vergara N, Piñeiro Á. Molecular Dynamics Study of Triosephosphate Isomerase from Trypanosoma cruzi in Water/Decane Mixtures. J Phys Chem B 2008; 112:3529-39. [DOI: 10.1021/jp7102275] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Norma Díaz-Vergara
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria 04510, México D.F., Mexico
| | - Ángel Piñeiro
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria 04510, México D.F., Mexico
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Pasgreta E, Puchta R, Galle M, van Eikema Hommes N, Zahl A, van Eldik R. Ligand-Exchange Processes on Solvated Lithium Cations: DMSO and Water/DMSO Mixtures. Chemphyschem 2007; 8:1315-20. [PMID: 17525920 DOI: 10.1002/cphc.200600624] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Solutions of LiClO(4) in solvent mixtures consisting of dimethylsulfoxide (DMSO) and water, or DMSO and gamma-butyrolactone, were studied by (7)Li NMR spectroscopy (for complexation by cryptands in gamma-butyrolactone as a solvent, see: E. Pasgreta, R. Puchta, M. Galle, N. J. R. van Eikema Hommes, A. Zahl, R. van Eldik, J. Incl. Phen., 2007, 58, 81-88). Chemical shifts indicate that the Li(+) ion is coordinated by four DMSO molecules. In the binary solvent mixture of water and DMSO, no selective solvation is detected, thus indicating that on increasing the water content of the solvent mixture, DMSO is gradually displaced by water in the coordination sphere of Li(+). The ligand-exchange mechanism of Li(+) ions solvated by DMSO and water/DMSO mixtures was studied using DFT calculations. Ligand exchange on [Li(DMSO)(4)](+) was found to follow a limiting associative (A) mechanism. The displacement of coordinated H(2)O by DMSO in [Li(H(2)O)(4)](+) follows an associative interchange mechanism. The suggested mechanisms are discussed in reference to available experimental and theoretical data.
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Affiliation(s)
- Ewa Pasgreta
- Institute for Inorganic Chemistry, University of Erlangen-Nürnberg, 91058 Erlangen, Germany
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Abstract
A comprehensive study of the hydration mechanism of an enzyme in nonaqueous media was done using molecular dynamics simulations in five organic solvents with different polarities, namely, hexane, 3-pentanone, diisopropyl ether, ethanol, and acetonitrile. In these solvents, the serine protease cutinase from Fusarium solani pisi was increasingly hydrated with 12 different hydration levels ranging from 5% to 100% (w/w) (weight of water/weight of protein). The ability of organic solvents to 'strip off' water from the enzyme surface was clearly dependent on the nature of the organic solvent. The rmsd of the enzyme from the crystal structure was shown to be lower at specific hydration levels, depending on the organic solvent used. It was also shown that organic solvents determine the structure and dynamics of water at the enzyme surface. Nonpolar solvents enhance the formation of large clusters of water that are tightly bound to the enzyme, whereas water in polar organic solvents is fragmented in small clusters loosely bound to the enzyme surface. Ions seem to play an important role in the stabilization of exposed charged residues, mainly at low hydration levels. A common feature is found for the preferential localization of water molecules at particular regions of the enzyme surface in all organic solvents: water seems to be localized at equivalent regions of the enzyme surface independently of the organic solvent employed.
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Affiliation(s)
- Nuno M Micaêlo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisoba, Oeiras, Portugal
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