1
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Baruah I, Borgohain G. Temperature dependent molecular dynamics simulation study to understand the stabilizing effect of NADES on the protein β-Lactoglobulin. J Mol Graph Model 2023; 125:108582. [PMID: 37595383 DOI: 10.1016/j.jmgm.2023.108582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 08/20/2023]
Abstract
The thermal stability of a protein is an important concern for its practical application in food processing industries. In this study, we have carried out classical molecular dynamics simulations to systematically investigate the effect of NADES (natural deep eutectic solvent) on the stabilization of the protein β-Lactoglobulin (BLG) at different temperatures. This study sheds light on the very aspects of NADES composed of betaine and sorbitol on the stability of the protein. NADES provides better stability to the protein up to a temperature of 400 K than in water. It is observed that the protein starts to unfold above temperature 400 K in spite of the presence of NADES which is quiet evident from the root mean square deviation (RMSD) and radius of gyration (Rg) plots. The decreasing average solvent accessible surface area (SASA) values and increasing intra-protein hydrogen bonds indicate better stability of the protein in NADES medium than in water at temperatures 300 K and 400 K. At high temperatures viz. 450 K and 500 K the number and distribution of solvent species (betaine and sorbitol) around the protein surface show an increment that are evident from the calculations of solvation shell, radial and spatial distribution functions. Increased number of betaine molecules that interact with the protein through electrostatic interaction may lead to destabilization of the protein at these temperatures. This study suggests that NADES could be used as an ideal medium for thermal stability of the protein BLG up to a temperature of 400 K. Beyond this temperature, NADES used for this study fails to exert stabilization effect on the protein.
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Affiliation(s)
- Indrani Baruah
- Department of Chemistry, Cotton University, Guwahati, Assam, 781001, India
| | - Gargi Borgohain
- Department of Chemistry, Cotton University, Guwahati, Assam, 781001, India.
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2
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Monhemi H, Hoang HN, Standley DM, Matsuda T, Housaindokht MR. The protein-stabilizing effects of TMAO in aqueous and non-aqueous conditions. Phys Chem Chem Phys 2022; 24:21178-21187. [PMID: 36039911 DOI: 10.1039/d2cp01279k] [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
We present a new water-dependent molecular mechanism for the widely-used protein stabilizing osmolyte, trimethylamine N-oxide (TMAO), whose mode of action has remained controversial. Classical interpretations, such as osmolyte exclusion from the vicinity of protein, cannot adequately explain the behavior of this osmolyte and were challenged by recent data showing the direct interactions of TMAO with proteins, mainly via hydrophobic binding. Solvent effect theories also fail to propose a straightforward mechanism. To explore the role of water and the hydrophobic association, we disabled osmolyte-protein hydrophobic interactions by replacing water with hexane and using lipase enzyme as an anhydrous-stable protein. Biocatalysis experiments showed that under this non-aqueous condition, TMAO does not act as a stabilizer, but strongly deactivates the enzyme. Molecular dynamics (MD) simulations reveal that TMAO accumulates near the enzyme and makes many hydrogen bonds with it, like denaturing osmolytes. Some TMAO molecules even reach the active site and interact strongly with the catalystic traid. In aqueous solvent, the enzyme functions well: the extent of TMAO interactions is reduced and can be divided into both polar and non-polar terms. Structural analysis shows that in water, some TMAO molecules bind to the enzyme surface like a surfactant. We show that these interactions limit water-protein hydrogen bonds and unfavorable water-hydrophobic surface contacts. Moreover, a more hydrophobic environment is formed in the solvation layer, which reduces water dynamics and subsequently, rigidifies the backbone in aqueous solution. We show that osmolyte amphiphilicity and protein surface heterogeneity can address the weaknesses of exclusion and solvent effect theories about the TMAO mechanism.
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Affiliation(s)
- Hassan Monhemi
- Department of Chemistry, University of Neyshabur, Neyshabur, Iran. .,Research and Technology Center of Biomolecules, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hai Nam Hoang
- Department of Food Technology, Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Vietnam.,Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Daron M Standley
- Laboratory of Systems Immunology, WPI Immunology Frontier Research Center Osaka University, Osaka 565-0871, Japan
| | - Tomoko Matsuda
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Mohammad Reza Housaindokht
- Research and Technology Center of Biomolecules, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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3
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Baruah I, Borgohain G. Structural and functional changes of the protein β-lactoglobulin under thermal and electrical processing conditions. Biophys Chem 2020; 267:106479. [PMID: 33027745 DOI: 10.1016/j.bpc.2020.106479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022]
Abstract
In the present study we have tried to explore the effect of static external electric field of strength 3.0 V/nm on the conformational changes adopted by the protein β-lactoglobulin. We have chosen different temperatures viz. 300 K, 400 K and 450 K to evaluate the temperature dependent effect of electric field. We have observed that combined effect of high temperature and static external electric field show significant changes on the structural conformation of the protein which in turn may affect the functional properties of the protein. Calculations of root mean square deviations reveal that both helical and β-sheet regions of the protein are noticeably affected at high temperature. We have used solvent accessible surface area (SASA) and dipole moment values to explain that there is changes in hydrophobicity of the protein surface due to presence of external electric field. The study reveals that electric field in combination with high temperature can be used to alter the conformation of the protein and the effect of external electric field is more pronounced at high temperature than that of low temperature. The study provides a better understanding of the conformational changes adopted by the protein under the stress of external electric field and high temperature and provide guidance to choose optimum conditions for processing without loss of nutritional properties.
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Affiliation(s)
- Indrani Baruah
- Department of Chemistry, Cotton University, Guwahati, Assam 781001, India
| | - Gargi Borgohain
- Department of Chemistry, Cotton University, Guwahati, Assam 781001, India.
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4
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Gawrys-Kopczynska M, Konop M, Maksymiuk K, Kraszewska K, Derzsi L, Sozanski K, Holyst R, Pilz M, Samborowska E, Dobrowolski L, Jaworska K, Mogilnicka I, Ufnal M. TMAO, a seafood-derived molecule, produces diuresis and reduces mortality in heart failure rats. eLife 2020; 9:57028. [PMID: 32510330 PMCID: PMC7334024 DOI: 10.7554/elife.57028] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/07/2020] [Indexed: 02/06/2023] Open
Abstract
Trimethylamine-oxide (TMAO) is present in seafood which is considered to be beneficial for health. Deep-water animals accumulate TMAO to protect proteins, such as lactate dehydrogenase (LDH), against hydrostatic pressure stress (HPS). We hypothesized that TMAO exerts beneficial effects on the circulatory system and protects cardiac LDH exposed to HPS produced by the contracting heart. Male, Sprague-Dawley and Spontaneously-Hypertensive-Heart-Failure (SHHF) rats were treated orally with either water (control) or TMAO. In vitro, LDH with or without TMAO was exposed to HPS and was evaluated using fluorescence correlation spectroscopy. TMAO-treated rats showed higher diuresis and natriuresis, lower arterial pressure and plasma NT-proBNP. Survival in SHHF-control was 66% vs 100% in SHHF-TMAO. In vitro, exposure of LDH to HPS with or without TMAO did not affect protein structure. In conclusion, TMAO reduced mortality in SHHF, which was associated with diuretic, natriuretic and hypotensive effects. HPS and TMAO did not affect LDH protein structure. Heart failure is a common cause of death in industrialized countries with aging populations. Japan, however, has lower rates of heart failure and fewer deaths linked to this disease than the United States or Europe, despite having the highest proportion of elderly people in the world. Dietary differences between these regions may explain the lower rate of heart failure in Japan. The Japanese diet is rich in seafood, which contains nutrients that promote heart health, such as omega-3 fatty acids. Seafood also contains other compounds, including trimethylamine oxide (TMAO). Fish that live in deep waters undergo high pressures, which can damage their proteins, but TMAO seems to protect the proteins from harm. In humans, eating seafood increases TMAO levels in the blood and urine, but it is unclear what effects this has on heart health. Increased levels of TMAO in the blood are associated with cardiovascular diseases, but scientists are not sure whether TMAO itself harms the heart. A toxic byproduct of gut bacteria called TMA is converted in TMAO in the body, so it is possible that TMA rather than TMAO is to blame. To assess the effects of dietary TMAO on heart failure, Gawrys-Kopczynska et al. fed the compound to healthy rats and rats with heart failure for one year. TMAO had no effects on the healthy rats. Of the rats with heart failure that were fed TMAO, all of them survived the year, while one third of rats with heart failure that were not fed TMAO died. TMAO-treated rats with heart failure had lower blood pressure and urinated more than untreated rats with the condition. The experiments suggest that dietary TMAO may mimic the effects of heart failure treatments, which remove excess water and salt and lower pressure on the heart. More studies are needed to confirm whether TMAO has this same effect on humans.
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Affiliation(s)
- Marta Gawrys-Kopczynska
- Department of Experimental Physiology and Pathophysiology, Laboratory of the Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Marek Konop
- Department of Experimental Physiology and Pathophysiology, Laboratory of the Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Klaudia Maksymiuk
- Department of Experimental Physiology and Pathophysiology, Laboratory of the Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Katarzyna Kraszewska
- Department of Experimental Physiology and Pathophysiology, Laboratory of the Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Ladislav Derzsi
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Krzysztof Sozanski
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Robert Holyst
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Marta Pilz
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Emilia Samborowska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Leszek Dobrowolski
- Department of Renal and Body Fluid Physiology, M. Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Kinga Jaworska
- Department of Experimental Physiology and Pathophysiology, Laboratory of the Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Izabella Mogilnicka
- Department of Experimental Physiology and Pathophysiology, Laboratory of the Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Ufnal
- Department of Experimental Physiology and Pathophysiology, Laboratory of the Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
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5
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Teng X, Ichiye T. Dynamical Model for the Counteracting Effects of Trimethylamine N-Oxide on Urea in Aqueous Solutions under Pressure. J Phys Chem B 2020; 124:1978-1986. [PMID: 32059113 DOI: 10.1021/acs.jpcb.9b10844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Of cosolutes found in living cells, urea denatures and trimethylamine N-oxide (TMAO) stabilizes proteins; furthermore, these effects cancel at a 2:1 ratio of urea to TMAO. Interestingly, cartilaginous fish use urea and TMAO as osmolytes at similar ratios at the ocean surface but with increasing fractions of TMAO at increasing depths. Here, molecular dynamics simulations of aqueous solutions with different urea:TMAO ratios show that the diffusion coefficients of water in the solutions vary with pressure if the urea:TMAO ratio is constant, but strikingly, they are almost pressure independent at the ratio found in these fish as a function of depth. This suggests that this ratio may be maintaining a homeostasis of water dynamics. In addition, diffusion is determined by hydrogen-bond lifetimes of the different species in the solution. Based on these observations, a dynamical model in terms of hydrogen-bond lifetimes is developed for the hydrogen bonding propensities of cosolutes and water in an aqueous solution to proteins. This model provides an explanation for both the counteracting effects of TMAO on urea denaturation and the depth-dependent urea:TMAO ratio found in cartilaginous fish.
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Affiliation(s)
- Xiaojing Teng
- Department of Chemistry, Georgetown University, Washington, D.C. 20057, United States
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, D.C. 20057, United States
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6
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Plamitzer L, Bouř P. Pressure dependence of vibrational optical activity of model biomolecules. A computational study. Chirality 2020; 32:710-721. [PMID: 32150771 DOI: 10.1002/chir.23216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 11/07/2022]
Abstract
Change of molecular properties with pressure is an attracting means to regulate molecular reactivity or biological activity. However, the effect is usually small and so far explored rather scarcely. To obtain a deeper insight and estimate the sensitivity of vibrational optical activity spectra to pressure-induced conformational changes, we investigate small model molecules. The Ala-Ala dipeptide, isomaltose disaccharide and adenine-uracil dinucleotide were chosen to represent three different biomolecular classes. The pressure effects were modeled by molecular dynamics and density functional theory simulations. The dinucleotide was found to be the most sensitive to the pressure, whereas for the disaccharide the smallest changes are predicted. Pressure-induced relative intensity changes in vibrational circular dichroism and Raman optical activity spectra are predicted to be 2-3-times larger than for non-polarized IR and Raman techniques.
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Affiliation(s)
- Luboš Plamitzer
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, Prague 6, 166 10, Czech Republic.,Faculty of Mathematics and Physics, Charles University, Ke Karlovu 2027/3, Prague 2, 121 16, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, Prague 6, 166 10, Czech Republic
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7
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Paul S, Paul S. Molecular dynamics simulation study on the inhibitory effects of choline-O-sulfate on hIAPP protofibrilation. J Comput Chem 2019; 40:1957-1968. [PMID: 31062393 DOI: 10.1002/jcc.25851] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 04/10/2019] [Accepted: 04/16/2019] [Indexed: 11/06/2022]
Abstract
Type 2 diabetes mellitus (T2Dm) is a neurodegenerative disease, which occurs due to the self-association of human islet amyloid polypeptide (hIAPP), also known as human amylin. It was reported experimentally that choline-O-sulfate (COS), a small organic molecule having a tertiary amino group and sulfate group, can prevent the aggregation of human amylin without providing the mechanism of the action of COS in the inhibition process. In this work, we investigate the influence of COS on the full-length hIAPP peptide by performing 500 ns classical molecular dynamics simulations. From pure water simulation (without COS), we have identified the residues 11-20 and 23-36 that mainly participate in the fibril formation, but in the presence of 1.07 M COS these residues become totally free of β-sheet conformation. Our results also show that the sulfate oxygen of COS directly interacts with the peptide backbone, which leads to the local disruption of peptide-peptide interaction. Moreover, the presence of favorable peptide-COS vdW interaction energy and high coordination number of COS molecules in the first solvation shell of the peptide indicates the hydrophobic solvation of the peptide residues by COS molecules, which also play a crucial role in the prevention of β-sheet formation. Finally, from the potential of mean force (PMFs) calculations, we observe that the free energy between two peptides is more negative in the absence of COS and with increasing concentration of COS, it becomes unfavorable significantly indicating that the peptide dimer formation is most stable in pure water, which becomes less favorable in the presence of COS. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India 781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India 781039
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8
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Paul S, Paul S. Inhibitory Effect of Choline-O-sulfate on Aβ16–22 Peptide Aggregation: A Molecular Dynamics Simulation Study. J Phys Chem B 2019; 123:3475-3489. [DOI: 10.1021/acs.jpcb.9b02727] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India 781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India 781039
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9
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Paul S, Paul S. How Does Aqueous Choline-O-Sulfate Solution Nullify the Action of Urea in Protein Denaturation? J Chem Inf Model 2018; 58:1858-1869. [DOI: 10.1021/acs.jcim.8b00395] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India−781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India−781039
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10
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Borgohain G, Paul S. Atomistic level understanding of the stabilization of protein Trp cage in denaturing and mixed osmolyte solutions. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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11
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The opposing effect of urea and high pressure on the conformation of the protein β-hairpin: A molecular dynamics simulation study. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.12.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Banik D, Bhattacharya S, Datta PK, Sarkar N. Anomalous Dynamics in tert-Butyl Alcohol-Water and Trimethylamine N-Oxide-Water Binary Mixtures: A Femtosecond Transient Absorption Study. ACS OMEGA 2018; 3:383-392. [PMID: 31457899 PMCID: PMC6641418 DOI: 10.1021/acsomega.7b01595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/27/2017] [Indexed: 05/17/2023]
Abstract
In this article, we have investigated the unusual dynamics of tert-butyl alcohol (TBA)-water and trimethylamine N-oxide (TMAO)-water binary mixtures using solvation dynamics as a tool. For this purpose, femtosecond transient absorption spectroscopy has been employed. Although these two molecules are isosteres to each other, a significant difference in water dynamics has been observed. The solvation times in TBA-water binary mixtures are found to be between 1.5 and 15.5 ps. On the contrary, we have observed very fast dynamics in TMAO-water binary mixtures (between 210 and 600 fs). Interestingly, unusual retardation in dynamics is observed at 0.10 mole fraction of TBA and TMAO in both the binary mixtures.
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Affiliation(s)
- Debasis Banik
- Department
of Chemistry and Department of Physics, Indian Institute
of Technology, Kharagpur 721302, West Bengal, India
| | - Sayantan Bhattacharya
- Department
of Chemistry and Department of Physics, Indian Institute
of Technology, Kharagpur 721302, West Bengal, India
| | - Prasanta Kumar Datta
- Department
of Chemistry and Department of Physics, Indian Institute
of Technology, Kharagpur 721302, West Bengal, India
- E-mail: (P.K.D.)
| | - Nilmoni Sarkar
- Department
of Chemistry and Department of Physics, Indian Institute
of Technology, Kharagpur 721302, West Bengal, India
- E-mail: . Phone: +91-3222-283332. Fax: 91-3222-255303 (N.S.)
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13
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Markthaler D, Zeman J, Baz J, Smiatek J, Hansen N. Validation of Trimethylamine-N-oxide (TMAO) Force Fields Based on Thermophysical Properties of Aqueous TMAO Solutions. J Phys Chem B 2017; 121:10674-10688. [DOI: 10.1021/acs.jpcb.7b07774] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Daniel Markthaler
- Institute of Thermodynamics and Thermal Process Engineering and ‡Institute for Computational
Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Johannes Zeman
- Institute of Thermodynamics and Thermal Process Engineering and ‡Institute for Computational
Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Jörg Baz
- Institute of Thermodynamics and Thermal Process Engineering and ‡Institute for Computational
Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Jens Smiatek
- Institute of Thermodynamics and Thermal Process Engineering and ‡Institute for Computational
Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering and ‡Institute for Computational
Physics, University of Stuttgart, D-70569 Stuttgart, Germany
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14
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15
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16
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Trimethylamine N-oxide stabilizes proteins via a distinct mechanism compared with betaine and glycine. Proc Natl Acad Sci U S A 2017; 114:2479-2484. [PMID: 28228526 DOI: 10.1073/pnas.1614609114] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report experimental and computational studies investigating the effects of three osmolytes, trimethylamine N-oxide (TMAO), betaine, and glycine, on the hydrophobic collapse of an elastin-like polypeptide (ELP). All three osmolytes stabilize collapsed conformations of the ELP and reduce the lower critical solution temperature (LSCT) linearly with osmolyte concentration. As expected from conventional preferential solvation arguments, betaine and glycine both increase the surface tension at the air-water interface. TMAO, however, reduces the surface tension. Atomically detailed molecular dynamics (MD) simulations suggest that TMAO also slightly accumulates at the polymer-water interface, whereas glycine and betaine are strongly depleted. To investigate alternative mechanisms for osmolyte effects, we performed FTIR experiments that characterized the impact of each cosolvent on the bulk water structure. These experiments showed that TMAO red-shifts the OH stretch of the IR spectrum via a mechanism that was very sensitive to the protonation state of the NO moiety. Glycine also caused a red shift in the OH stretch region, whereas betaine minimally impacted this region. Thus, the effects of osmolytes on the OH spectrum appear uncorrelated with their effects upon hydrophobic collapse. Similarly, MD simulations suggested that TMAO disrupts the water structure to the least extent, whereas glycine exerts the greatest influence on the water structure. These results suggest that TMAO stabilizes collapsed conformations via a mechanism that is distinct from glycine and betaine. In particular, we propose that TMAO stabilizes proteins by acting as a surfactant for the heterogeneous surfaces of folded proteins.
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17
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Smolin N, Voloshin VP, Anikeenko AV, Geiger A, Winter R, Medvedev NN. TMAO and urea in the hydration shell of the protein SNase. Phys Chem Chem Phys 2017; 19:6345-6357. [DOI: 10.1039/c6cp07903b] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We performed all-atom MD simulations of the protein SNase in aqueous solution and in the presence of two major osmolytes, trimethylamine-N-oxide (TMAO) and urea, as cosolvents at various concentrations and compositions and at different pressures and temperatures.
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Affiliation(s)
- Nikolai Smolin
- Department of Cell and Molecular Physiology
- Loyola University Chicago
- Maywood
- USA
| | | | - Alexey V. Anikeenko
- Institute of Chemical Kinetics and Combustion
- 630090 Novosibirsk
- Russia
- Novosibirsk State University
- 630090 Novosibirsk
| | - Alfons Geiger
- Physikalische Chemie
- Fakultät für Chemie und Chemische Biologie
- Technische Universität Dortmund
- 44221 Dortmund
- Germany
| | - Roland Winter
- Physikalische Chemie
- Fakultät für Chemie und Chemische Biologie
- Technische Universität Dortmund
- 44221 Dortmund
- Germany
| | - Nikolai N. Medvedev
- Institute of Chemical Kinetics and Combustion
- 630090 Novosibirsk
- Russia
- Novosibirsk State University
- 630090 Novosibirsk
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18
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Ghosh S, Dey S, Patel M, Chakrabarti R. Can an ammonium-based room temperature ionic liquid counteract the urea-induced denaturation of a small peptide? Phys Chem Chem Phys 2017; 19:7772-7787. [DOI: 10.1039/c6cp08842b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The folding/unfolding equilibrium of proteins in aqueous medium can be altered by adding small organic molecules generally termed as co-solvents.
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Affiliation(s)
- Soumadwip Ghosh
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
| | - Souvik Dey
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
| | - Mahendra Patel
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
| | - Rajarshi Chakrabarti
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
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19
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Borgohain G, Mandal B, Paul S. Molecular dynamics approach to understand the denaturing effect of a millimolar concentration of dodine on a λ-repressor and counteraction by trehalose. Phys Chem Chem Phys 2017; 19:13160-13171. [DOI: 10.1039/c6cp08289k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Here, we use a molecular dynamics approach to calculate the spatial distribution function of the ternary water–dodine–trehalose (1.0 M) system.
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Affiliation(s)
- Gargi Borgohain
- Department of Chemistry
- Indian Institute of Technology
- Guwahati
- India
| | | | - Sandip Paul
- Department of Chemistry
- Indian Institute of Technology
- Guwahati
- India
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20
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Fedotova MV, Kruchinin SE, Chuev GN. Hydration structure of osmolyte TMAO: concentration/pressure-induced response. NEW J CHEM 2017. [DOI: 10.1039/c6nj03296f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of solute concentration/pressure on the TMAO hydration structure was studied to understand its protective action under abiotic stressors.
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Affiliation(s)
- Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry
- The Russian Academy of Sciences
- Ivanovo
- Russia
| | - Sergey E. Kruchinin
- G.A. Krestov Institute of Solution Chemistry
- The Russian Academy of Sciences
- Ivanovo
- Russia
| | - Gennady N. Chuev
- Institute of Theoretical and Experimental Biophysics
- The Russian Academy of Sciences
- Pushchino
- Russia
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21
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Borgohain G, Paul S. Temperature-mediated switching of protectant-denaturant behavior of trimethylamine-N-oxide and consequences on protein stability from a replica exchange molecular dynamics simulation study. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1233546] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Gargi Borgohain
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, India
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22
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Rodríguez-Ropero F, Rötzscher P, van der Vegt NFA. Comparison of Different TMAO Force Fields and Their Impact on the Folding Equilibrium of a Hydrophobic Polymer. J Phys Chem B 2016; 120:8757-67. [DOI: 10.1021/acs.jpcb.6b04100] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francisco Rodríguez-Ropero
- Eduard-Zintl-Institut für
Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287, Darmstadt, Germany
| | - Philipp Rötzscher
- Eduard-Zintl-Institut für
Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287, Darmstadt, Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für
Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287, Darmstadt, Germany
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23
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Hölzl C, Kibies P, Imoto S, Frach R, Suladze S, Winter R, Marx D, Horinek D, Kast SM. Design principles for high–pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures. J Chem Phys 2016; 144:144104. [DOI: 10.1063/1.4944991] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Christoph Hölzl
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Patrick Kibies
- Physikalische Chemie III, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Sho Imoto
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Roland Frach
- Physikalische Chemie III, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Saba Suladze
- Physikalische Chemie I, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Roland Winter
- Physikalische Chemie I, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Horinek
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Stefan M. Kast
- Physikalische Chemie III, Technische Universität Dortmund, 44227 Dortmund, Germany
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24
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Borgohain G, Paul S. Model Dependency of TMAO’s Counteracting Effect Against Action of Urea: Kast Model versus Osmotic Model of TMAO. J Phys Chem B 2016; 120:2352-61. [DOI: 10.1021/acs.jpcb.5b10968] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gargi Borgohain
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, India
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25
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Yang Y, Mu Y, Li W. Microscopic significance of hydrophobic residues in the protein-stabilizing effect of trimethylamine N-oxide (TMAO). Phys Chem Chem Phys 2016; 18:22081-8. [DOI: 10.1039/c6cp01205a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteins with a higher hydrophobic content are better protected by TMAO against the deleterious effect of urea.
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Affiliation(s)
- Yanmei Yang
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou
- China
| | - Yuguang Mu
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Weifeng Li
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou
- China
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26
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Paul S, Paul S. Investigating the Counteracting Effect of Trehalose on Urea-Induced Protein Denaturation Using Molecular Dynamics Simulation. J Phys Chem B 2015; 119:10975-88. [DOI: 10.1021/acs.jpcb.5b01457] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Subrata Paul
- Department
of Chemistry, Indian Institute of Technology, Guwahati, Assam India-781039
| | - Sandip Paul
- Department
of Chemistry, Indian Institute of Technology, Guwahati, Assam India-781039
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27
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Paul S, Paul S. Molecular Insights into the Role of Aqueous Trehalose Solution on Temperature-Induced Protein Denaturation. J Phys Chem B 2015; 119:1598-610. [DOI: 10.1021/jp510423n] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Subrata Paul
- Department
of Chemistry, Indian Institute of Technology, Guwahati, Assam India-781039
| | - Sandip Paul
- Department
of Chemistry, Indian Institute of Technology, Guwahati, Assam India-781039
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28
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Bandyopadhyay D, Mohan S, Ghosh SK, Choudhury N. Molecular Dynamics Simulation of Aqueous Urea Solution: Is Urea a Structure Breaker? J Phys Chem B 2014; 118:11757-68. [DOI: 10.1021/jp505147u] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dibyendu Bandyopadhyay
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Sadhana Mohan
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Swapan K. Ghosh
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Niharendu Choudhury
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
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