1
|
Negi KS, Das N, Khan T, Sen P. Osmolyte induced protein stabilization: modulation of associated water dynamics might be a key factor. Phys Chem Chem Phys 2023; 25:32602-32612. [PMID: 38009208 DOI: 10.1039/d3cp03357k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
The mechanism of protein stabilization by osmolytes remains one of the most important and long-standing puzzles. The traditional explanation of osmolyte-induced stability through the preferential exclusion of osmolytes from the protein surface has been seriously challenged by the observations like the concentration-dependent reversal of osmolyte-induced stabilization/destabilization. The more modern explanation of protein stabilization/destabilization by osmolytes considers an indirect effect due to osmolyte-induced distortion of the water structure. It provides a general mechanism, but there are numerous examples of protein-specific effects, i.e., a particular osmolyte might stabilize one protein, but destabilize the other, that could not be rationalized through such an explanation. Herein, we hypothesized that osmolyte-induced modulation of associated water might be a critical factor in controlling protein stability in such a medium. Taking different osmolytes and papain as a protein, we proved that our proposal could explain protein stability in osmolyte media. Stabilizing osmolytes rigidify associated water structures around the protein, whereas destabilizing osmolytes make them flexible. The strong correlation between the stability and the associated water dynamics, and the fact that such dynamics are very much protein specific, established the importance of considering the modulation of associated water structures in explaining the osmolyte-induced stabilization/destabilization of proteins. More interestingly, we took another protein, bromelain, for which a traditionally stabilizing osmolyte, sucrose, acts as a stabilizer at higher concentrations but as a destabilizer at lower concentrations. Our proposal successfully explains such observations, which is probably impossible by any known mechanisms. We believe this report will trigger much research in this area.
Collapse
Affiliation(s)
- Kuldeep Singh Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, Uttar Pradesh, India.
| | - Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, Uttar Pradesh, India.
| | - Tanmoy Khan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, Uttar Pradesh, India.
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, Uttar Pradesh, India.
| |
Collapse
|
2
|
Hu K, Shirakashi R. Molecular dynamics study of water rotational relaxation in saccharide solution for the development of bioprotective agent. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
|
3
|
Roget SA, Carter-Fenk KA, Fayer MD. Water Dynamics in Aqueous Poly- N-Isopropylacrylamide Below and Through the Lower Critical Solution Temperature. J Phys Chem B 2022; 126:7066-7075. [PMID: 36067498 DOI: 10.1021/acs.jpcb.2c05506] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Poly-N-isopropylacrylamide (PNIPAM) is a thermo-responsive polymer that exhibits a reversible structural change from extended chains to aggregates in aqueous solution above its lower critical solution temperature (LCST). Using polarization-selective IR pump-probe spectroscopy, the water orientational dynamics in PNIPAM from below to above the LCST were examined and compared to those of its monomer solution, N-isopropylacrylamide (NIPAM), polyacrylamide, and an acrylamide monomer solution, which are not thermo-responsive. The OD stretch of dilute HOD in H2O is used as a vibrational probe of water orientational dynamics. Below the LCST of the polymer, NIPAM and PNIPAM solutions exhibited identical water dynamics that were significantly different from those of bulk water, containing both faster and slower components due to solute-water interactions. Therefore, there is no difference in the nature of water interactions with a single NIPAM moiety and a long polymer chain. For all systems, including PNIPAM below and above the LCST, the orientational dynamics were modeled with a bulk water component and a polymer/monomer-associated component based on previous experimental and computational findings. Above the LCST, PNIPAM showed fast water orientational relaxation but much slower long-time dynamics compared to those of NIPAM. The slow component in PNIPAM, which was too slow to be accurately measured due to the limited OD vibrational lifetime, is ascribed to water confined in small voids (<2 nm in diameter) of PNIPAM globules. These results highlight important details about thermo-responsive polymers and the dynamics of their solvation water as they undergo a significant structural change.
Collapse
Affiliation(s)
- Sean A Roget
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | | | - Michael D Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
4
|
Caporaletti F, Bonn D, Woutersen S. Lifetime-Associated Two-Dimensional Infrared Spectroscopy Reveals the Hydrogen-Bond Structure of Supercooled Water in Soft Confinement. J Phys Chem Lett 2021; 12:5951-5956. [PMID: 34157231 PMCID: PMC8256423 DOI: 10.1021/acs.jpclett.1c01595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
We demonstrate a method to address the problem of spectral overlap in multidimensional vibrational spectroscopy and use it to investigate supercooled aqueous sorbitol solutions. The absence of crystallization in these solutions has been attributed to "soft" confinement of water in subnanometer voids in the sorbitol matrix, but the details of the hydrogen-bond structure are still largely unknown. 2D-IR spectroscopy of the OH-stretch mode is an excellent tool to investigate hydrogen bonding, but in this case it seems difficult because of the overlapping water and sorbitol contributions to the 2D-IR spectrum. Using the difference in OH-stretch lifetimes of water and sorbitol we can cleanly separate these contributions. Surprisingly, the separated 2D-IR spectra show that the hydrogen-bond disorder of soft-confined water is independent of temperature and decoupled from its orientational order. We believe the approach we use to separate overlapping 2D-IR spectra will enhance the applicability of 2D-IR spectroscopy to study multicomponent systems.
Collapse
Affiliation(s)
- Federico Caporaletti
- Van
der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098XH Amsterdam, The Netherlands
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Daniel Bonn
- Van
der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Sander Woutersen
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| |
Collapse
|
5
|
Cota R, van Dam EP, Woutersen S, Bakker HJ. Slowing Down of the Molecular Reorientation of Water in Concentrated Alkaline Solutions. J Phys Chem B 2020; 124:8309-8316. [PMID: 32841025 PMCID: PMC7520889 DOI: 10.1021/acs.jpcb.0c03614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is generally accepted that the hydroxide ion (OH-) is a strong hydrogen bond acceptor and that its anomalously high diffusion constant in water results from a Grotthuss-like structural diffusion mechanism. However, the spatial extent over which OH- ions influence the dynamics of the hydrogen-bond network of water remained largely unclear. Here, we measure the ultrafast dynamics of OH groups of HDO molecules interacting with the deuterated hydroxide ion OD-. For solutions with OD- concentrations up to 4 M, we find that HDO molecules that are not directly interacting with the ions have a reorientation time constant of ∼2.7 ps, similar to that of pure liquid water. When the concentration of OD- ions is increased, the reorientation time constant increases, indicating a strong slowing down of the structural dynamics of the solution.
Collapse
Affiliation(s)
- Roberto Cota
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands.,AMOLF, Science Park 104, 1098 XG Amsterdam, Netherlands
| | | | - Sander Woutersen
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Huib J Bakker
- AMOLF, Science Park 104, 1098 XG Amsterdam, Netherlands
| |
Collapse
|
6
|
van Dam EP, Giubertoni G, Burla F, Koenderink GH, Bakker HJ. Hyaluronan biopolymers release water upon pH-induced gelation. Phys Chem Chem Phys 2020; 22:8667-8671. [DOI: 10.1039/d0cp00215a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We measure the reorientation dynamics of water in hyaluronan solutions, and find that, upon pH-induced gelation, these biopolymers release water.
Collapse
Affiliation(s)
| | | | | | - Gijsje H. Koenderink
- AMOLF
- 1098 XG Amsterdam
- The Netherlands
- Department of Bionanoscience
- Kavli Institute of Nanoscience Delft
| | | |
Collapse
|
7
|
Discharging behavior of confined bipolar electrodes: Coupled electrokinetic and electrochemical dynamics. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2019.135275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
8
|
Kundu A, Verma PK, Cho M. Water Structure and Dynamics in the Stern Layer of Micelles: Femtosecond Mid-Infrared Pump-Probe Spectroscopy Study. J Phys Chem B 2019; 123:5238-5245. [PMID: 31145621 DOI: 10.1021/acs.jpcb.9b03183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular-level understanding of the water structure and dynamics in the Stern layer of micelles is important to elucidate the active role of water in biological processes on membrane surfaces. Micelles and reverse micelles are considered to be excellent membrane model systems. Here, to address the question of whether or not the spatial confinement effect on water in reverse micelles and nanometric water pool systems plays a role in modulating water dynamics, we consider four different aqueous micelle solutions and study the water dynamics in the Stern layer of micelles using a femtosecond mid-infrared pump-probe spectroscopy technique. Vibrational energy relaxation and rotational dynamics of the O?D stretch mode of HDO and the azido stretch mode of hydrazoic acid are critically dependent on the charge, polarity, and chemical structure of the surfactant head group. In particular, water molecules in the Stern layer of micelles, which are not in spatially confined environments, are notably different from those in bulk water. This finding clearly indicates that changes in the vibrational and rotational dynamics of water molecules, even in spatially confined systems, are mainly induced by surface effects instead of spatial confinement effects. We believe that the present experimental results are of importance for understanding water-involved biochemical processes on biological membranes.
Collapse
Affiliation(s)
- Achintya Kundu
- Center for Molecular Spectroscopy and Dynamics , Institute for Basic Science (IBS) , Seoul 02841 , Republic of Korea.,Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
| | - Pramod Kumar Verma
- Center for Molecular Spectroscopy and Dynamics , Institute for Basic Science (IBS) , Seoul 02841 , Republic of Korea.,Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics , Institute for Basic Science (IBS) , Seoul 02841 , Republic of Korea.,Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
| |
Collapse
|
9
|
Heid E, Honegger P, Braun D, Szabadi A, Stankovic T, Steinhauser O, Schröder C. Computational spectroscopy of trehalose, sucrose, maltose, and glucose: A comprehensive study of TDSS, NQR, NOE, and DRS. J Chem Phys 2019; 150:175102. [DOI: 10.1063/1.5095058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Esther Heid
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
| | - Philipp Honegger
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
| | - Daniel Braun
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - András Szabadi
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
| | - Toda Stankovic
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
| | - Othmar Steinhauser
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
| | - Christian Schröder
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
| |
Collapse
|
10
|
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).
Collapse
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
| |
Collapse
|
11
|
Choi JH, Lee H, Choi HR, Cho M. Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions. Annu Rev Phys Chem 2018; 69:125-149. [DOI: 10.1146/annurev-physchem-050317-020915] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jun-Ho Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Current affiliation: Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Hochan Lee
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Hyung Ran Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| |
Collapse
|
12
|
Kurniawan N, van Kempen THS, Sonneveld S, Rosalina TT, Vos BE, Jansen KA, Peters GWM, van de Vosse FN, Koenderink GH. Buffers Strongly Modulate Fibrin Self-Assembly into Fibrous Networks. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6342-6352. [PMID: 28558246 PMCID: PMC5489959 DOI: 10.1021/acs.langmuir.7b00527] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/27/2017] [Indexed: 05/20/2023]
Abstract
Fibrin is a plasma protein with a central role in blood clotting and wound repair. Upon vascular injury, fibrin forms resilient fibrillar networks (clots) via a multistep self-assembly process, from monomers, to double-stranded protofibrils, to a branched network of thick fibers. In vitro, fibrin self-assembly is sensitive to physicochemical conditions like the solution pH and ionic strength, which tune the strength of the noncovalent driving forces. Here we report a surprising finding that the buffer-which is necessary to control the pH and is typically considered to be inert-also significantly influences fibrin self-assembly. We show by confocal microscopy and quantitative light scattering that various common buffering agents have no effect on the initial assembly of fibrin monomers into protofibrils but strongly hamper the subsequent lateral association of protofibrils into thicker fibers. We further find that the structural changes are independent of the molecular structure of the buffering agents as well as of the activation mechanism and even occur in fibrin networks formed from platelet-poor plasma. This buffer-mediated decrease in protofibril bundling results in a marked reduction in the permeability of fibrin networks but only weakly influences the elastic modulus of fibrin networks, providing a useful tuning parameter to independently control the elastic properties and the permeability of fibrin networks. Our work raises the possibility that fibrin assembly in vivo may be regulated by variations in the acute-phase levels of bicarbonate and phosphate, which act as physiological buffering agents of blood pH. Moreover, our findings add a new example of buffer-induced effects on biomolecular self-assembly to recent findings for a range of proteins and lipids.
Collapse
Affiliation(s)
- Nicholas
A. Kurniawan
- Department
of Systems Biophysics, AMOLF, Amsterdam 1009 DB, The Netherlands
- Department of Biomedical
Engineering & Institute for Complex
Molecular Systems, and Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Thomas H. S. van Kempen
- Department of Biomedical
Engineering & Institute for Complex
Molecular Systems, and Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Stijn Sonneveld
- Department
of Systems Biophysics, AMOLF, Amsterdam 1009 DB, The Netherlands
| | - Tilaï T. Rosalina
- Department of Biomedical
Engineering & Institute for Complex
Molecular Systems, and Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Bart E. Vos
- Department
of Systems Biophysics, AMOLF, Amsterdam 1009 DB, The Netherlands
| | - Karin A. Jansen
- Department
of Systems Biophysics, AMOLF, Amsterdam 1009 DB, The Netherlands
| | - Gerrit W. M. Peters
- Department of Biomedical
Engineering & Institute for Complex
Molecular Systems, and Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Frans N. van de Vosse
- Department of Biomedical
Engineering & Institute for Complex
Molecular Systems, and Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Gijsje H. Koenderink
- Department
of Systems Biophysics, AMOLF, Amsterdam 1009 DB, The Netherlands
- E-mail:
| |
Collapse
|
13
|
Groot CCM, Meister K, DeVries AL, Bakker HJ. Dynamics of the Hydration Water of Antifreeze Glycoproteins. J Phys Chem Lett 2016; 7:4836-4840. [PMID: 27934047 DOI: 10.1021/acs.jpclett.6b02483] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Antifreeze glycoproteins (AFGPs) are unique proteins that inhibit the growth of ice by a mechanism that is still unclear. We study the dynamics of water in aqueous solutions of small and large isoforms of AFGPs using polarization-resolved femtosecond infrared spectroscopy. We find that a fraction of the water molecules is strongly slowed down by the interaction with the antifreeze glycoprotein surface. The fraction of slow water molecules scales with the size and concentration of AFGP, and is similar to the fraction of slow water observed for nonantifreeze proteins, both at room temperature and close to biologically relevant working temperatures. We observe that inhibiting AFGP antifreeze activity using borate buffer induces no changes in the dynamics of water hydrating the AFGP. Our findings support a mechanism in which the sugar unit of AFGP forms the active ice-binding site.
Collapse
Affiliation(s)
- Carien C M Groot
- FOM Institute AMOLF , Science Park 104, 1098 XG, Amsterdam, The Netherlands
| | - Konrad Meister
- FOM Institute AMOLF , Science Park 104, 1098 XG, Amsterdam, The Netherlands
| | - Arthur L DeVries
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huib J Bakker
- FOM Institute AMOLF , Science Park 104, 1098 XG, Amsterdam, The Netherlands
| |
Collapse
|
14
|
Heid E, Schröder C. Computational solvation dynamics of oxyquinolinium betaine linked to trehalose. J Chem Phys 2016; 145:164507. [DOI: 10.1063/1.4966189] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Esther Heid
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstraße 19, A-1090 Vienna, Austria
| | - Christian Schröder
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstraße 19, A-1090 Vienna, Austria
| |
Collapse
|
15
|
Lee H, Choi JH, Verma PK, Cho M. Computational Vibrational Spectroscopy of HDO in Osmolyte–Water Solutions. J Phys Chem A 2016; 120:5874-86. [DOI: 10.1021/acs.jpca.6b06305] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hochan Lee
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science and ‡Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Ho Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science and ‡Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Pramod Kumar Verma
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science and ‡Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science and ‡Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
- L Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | | | | | | | | | | |
Collapse
|
17
|
Lee H, Choi JH, Verma PK, Cho M. Spectral Graph Analyses of Water Hydrogen-Bonding Network and Osmolyte Aggregate Structures in Osmolyte-Water Solutions. J Phys Chem B 2015; 119:14402-12. [PMID: 26473387 DOI: 10.1021/acs.jpcb.5b08029] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, it was shown that the spectral graph theory is exceptionally useful for understanding not only morphological structural differences in ion aggregates but also similarities between an ion network and a water H-bonding network in highly concentrated salt solutions. Here, we present spectral graph analysis results on osmolyte aggregates and water H-bonding network structures in aqueous renal osmolyte solutions. The quantitative analyses of the adjacency matrices that are graph-theoretical representations of aggregates of osmolyte molecules and water H-bond structures provide the ensemble average eigenvalue spectra and degree distribution. We show that urea molecules form quite different morphological structures compared to other protecting renal osmolyte molecules in water, particularly sorbitol and trimethylglycine, which are well-known protecting osmolytes, and at high concentrations exhibit a strong propensity to form morphological structures that are graph-theoretically similar to that of the water H-bond network. Conversely, urea molecules, even at similarly high concentrations, form separated clusters instead of extended osmolyte-osmolyte networks. This difference in morphological structure of osmolyte-osmolyte aggregates between protecting and destabilizing osmolytes is considered to be an important observation that led us to propose a hypothesis on the osmolyte aggregate growth mechanism via either osmolyte network formation or segregated osmolyte cluster formation. We anticipate that the present spectral graph analyses of osmolyte aggregate structures and their interplay with the water H-bond network structure in highly concentrated renal osmolyte solutions could provide important information on the osmolyte effects of not only water structures but also protein stability in biologically relevant osmolyte solutions.
Collapse
Affiliation(s)
- Hochan Lee
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) , Seoul 136-701, Republic of Korea.,Department of Chemistry, Korea University , Seoul 136-713, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Korea University , Seoul 136-713, Republic of Korea
| | - Pramod Kumar Verma
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) , Seoul 136-701, Republic of Korea.,Department of Chemistry, Korea University , Seoul 136-713, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) , Seoul 136-701, Republic of Korea.,Department of Chemistry, Korea University , Seoul 136-713, Republic of Korea
| |
Collapse
|
18
|
Verma PK, Lee H, Park JY, Lim JH, Maj M, Choi JH, Kwak KW, Cho M. Modulation of the Hydrogen Bonding Structure of Water by Renal Osmolytes. J Phys Chem Lett 2015; 6:2773-2779. [PMID: 26266862 DOI: 10.1021/acs.jpclett.5b01087] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Osmolytes are an integral part of living organism, e.g., the kidney uses sorbitol, trimethylglycine, taurine and myo-inositol to counter the deleterious effects of urea and salt. Therefore, knowing that the osmolytes' act either directly to the protein or mediated through water is of great importance. Our experimental and computational results show that protecting osmolytes, e.g., trimethylglycine and sorbitol, significantly modulate the water H-bonding network structure, although the magnitude and spatial extent of osmolyte-induced perturbation greatly vary. In contrast, urea behaves neutrally toward local water H-bonding network. Protecting osmolytes studied here show strong concentration-dependent behaviors (vibrational frequencies and lifetimes of two different infrared (IR) probes), while denaturant does not. The H-bond donor and/or acceptor (OH/NH) in a given osmolyte molecule play a critical role in defining their action. Our findings highlight the significance of the alteration of H-bonding network of water under biologically relevant environment, often encountered in real biological systems.
Collapse
Affiliation(s)
- Pramod Kumar Verma
- †Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 136-701, Republic of Korea
- ‡Department of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| | - Hochan Lee
- †Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 136-701, Republic of Korea
- ‡Department of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| | - Joon-Young Park
- †Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 136-701, Republic of Korea
- ‡Department of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| | - Joon-Hyung Lim
- †Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 136-701, Republic of Korea
- ‡Department of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| | - Michał Maj
- †Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 136-701, Republic of Korea
- ‡Department of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| | - Jun-Ho Choi
- †Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 136-701, Republic of Korea
| | - Kyung-Won Kwak
- §Department of Chemistry, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Minhaeng Cho
- †Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 136-701, Republic of Korea
- ‡Department of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| |
Collapse
|