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Laurent H, Youngs TGA, Headen TF, Soper AK, Dougan L. The ability of trimethylamine N-oxide to resist pressure induced perturbations to water structure. Commun Chem 2022; 5:116. [PMID: 36697784 PMCID: PMC9814673 DOI: 10.1038/s42004-022-00726-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/19/2022] [Indexed: 01/28/2023] Open
Abstract
Trimethylamine N-oxide (TMAO) protects organisms from the damaging effects of high pressure. At the molecular level both TMAO and pressure perturb water structure but it is not understood how they act in combination. Here, we use neutron scattering coupled with computational modelling to provide atomistic insight into the structure of water under pressure at 4 kbar in the presence and absence of TMAO. The data reveal that TMAO resists pressure-induced perturbation to water structure, particularly in retaining a clear second solvation shell, enhanced hydrogen bonding between water molecules and strong TMAO - water hydrogen bonds. We calculate an 'osmolyte protection' ratio at which pressure and TMAO-induced energy changes effectively cancel out. Remarkably this ratio translates across scales to the organism level, matching the observed concentration dependence of TMAO in the muscle tissue of organisms as a function of depth. Osmolyte protection may therefore offer a molecular mechanism for the macroscale survival of life in extreme environments.
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Affiliation(s)
- Harrison Laurent
- grid.9909.90000 0004 1936 8403School of Physics and Astronomy, University of Leeds, Leeds, UK
| | - Tristan G. A. Youngs
- grid.76978.370000 0001 2296 6998ISIS Facility, STFC Rutherford Appleton Laboratory, Didcot, UK
| | - Thomas F. Headen
- grid.76978.370000 0001 2296 6998ISIS Facility, STFC Rutherford Appleton Laboratory, Didcot, UK
| | - Alan K. Soper
- grid.76978.370000 0001 2296 6998ISIS Facility, STFC Rutherford Appleton Laboratory, Didcot, UK
| | - Lorna Dougan
- grid.9909.90000 0004 1936 8403School of Physics and Astronomy, University of Leeds, Leeds, UK ,grid.9909.90000 0004 1936 8403Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
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Boosting the kinetic efficiency of formate dehydrogenase by combining the effects of temperature, high pressure and co-solvent mixtures. Colloids Surf B Biointerfaces 2021; 208:112127. [PMID: 34626897 DOI: 10.1016/j.colsurfb.2021.112127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
The application of co-solvents and high pressure has been shown to be an efficient means to modify the kinetics of enzyme-catalyzed reactions without compromising enzyme stability, which is often limited by temperature modulation. In this work, the high-pressure stopped-flow methodology was applied in conjunction with fast UV/Vis detection to investigate kinetic parameters of formate dehydrogenase reaction (FDH), which is used in biotechnology for cofactor recycling systems. Complementary FTIR spectroscopic and differential scanning fluorimetric studies were performed to reveal pressure and temperature effects on the structure and stability of the FDH. In neat buffer solution, the kinetic efficiency increases by one order of magnitude by increasing the temperature from 25° to 45 °C and the pressure from ambient up to the kbar range. The addition of particular co-solvents further doubled the kinetic efficiency of the reaction, in particular the compatible osmolyte trimethylamine-N-oxide and its mixtures with the macromolecular crowding agent dextran. The thermodynamic model PC-SAFT was successfully applied within a simplified activity-based Michaelis-Menten framework to predict the effects of co-solvents on the kinetic efficiency by accounting for interactions involving substrate, co-solvent, water, and FDH. Especially mixtures of the co-solvents at high concentrations were beneficial for the kinetic efficiency and for the unfolding temperature.
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Kolling I, Hölzl C, Imoto S, Alfarano SR, Vondracek H, Knake L, Sebastiani F, Novelli F, Hoberg C, Brubach JB, Roy P, Forbert H, Schwaab G, Marx D, Havenith M. Aqueous TMAO solution under high hydrostatic pressure. Phys Chem Chem Phys 2021; 23:11355-11365. [PMID: 33972970 DOI: 10.1039/d1cp00703c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trimethylamine N-oxide (TMAO) is a well known osmolyte in nature, which is used by deep sea fish to stabilize proteins against High Hydrostatic Pressure (HHP). We present a combined ab initio molecular dynamics, force field molecular dynamics, and THz absorption study of TMAO in water up to 12 kbar to decipher its solvation properties upon extreme compression. On the hydrophilic oxygen side of TMAO, AIMD simulations at 1 bar and 10 kbar predict a change of the coordination number from a dominating TMAO·(H2O)3 complex at ambient conditions towards an increased population of a TMAO·(H2O)4 complex at HHP conditions. This increase of the TMAO-oxygen coordination number goes in line with a weakening of the local hydrogen bond network, spectroscopic shifts and intensity changes of the corresponding intermolecular THz bands. Using a pressure-dependent HHP force field, FFMD simulations predict a significant increase of hydrophobic hydration from 1 bar up to 4-5 kbar, which levels off at higher pressures up to 10 kbar. THz spectroscopic data reveal two important pressure regimes with spectroscopic inflection points of the dominant intermolecular modes: The first regime (1.5-2 kbar) is barely recognizable in the simulation data. However, it relates well with the observation that the apparent molar volume of solvated TMAO is nearly constant in the biologically relevant pressure range up to 1 kbar as found in the deepest habitats on Earth in the ocean. The second inflection point around 4-5 kbar is related to the amount of hydrophobic hydration as predicted by the FFMD simulations. In particular, the blueshift of the intramolecular CNC bending mode of TMAO at about 390 cm-1 is the spectroscopic signature of increasingly pronounced pressure-induced changes in the solvation shell of TMAO. Thus, the CNC bend can serve as local pressure sensor in the multi-kbar pressure regime.
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Affiliation(s)
- Inga Kolling
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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Ganguly P, Polák J, van der Vegt NFA, Heyda J, Shea JE. Protein Stability in TMAO and Mixed Urea–TMAO Solutions. J Phys Chem B 2020; 124:6181-6197. [DOI: 10.1021/acs.jpcb.0c04357] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
| | - Jakub Polák
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, United States
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Knierbein M, Wangler A, Luong TQ, Winter R, Held C, Sadowski G. Combined co-solvent and pressure effect on kinetics of a peptide hydrolysis: an activity-based approach. Phys Chem Chem Phys 2019; 21:22224-22229. [PMID: 31576857 DOI: 10.1039/c9cp03868j] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The application of co-solvents and high pressure has been reported to be an efficient means to tune the kinetics of enzyme-catalyzed reactions. Co-solvents and pressure can lead to increased reaction rates without sacrificing enzyme stability, while temperature and pH operation windows are generally very narrow. Quantitative prediction of co-solvent and pressure effects on enzymatic reactions has not been successfully addressed in the literature. Herein, we are introducing a thermodynamic approach that is based on molecular interactions in the form of activity coefficients of substrate and of enzyme in the multi-component solution. This allowed us to quantitatively predict the combined effect of co-solvent and pressure on the kinetic constants, i.e. the Michaelis constant KM and the catalytic constant kcat, of an α-CT-catalyzed peptide hydrolysis reaction. The reaction was studied in the presence of different types of co-solvents and at pressures up to 2 kbar, and quantitative predictions could be obtained for KM, kcat, and finally even primary Michaelis-Menten plots using activity coefficients provided by the thermodynamic model PC-SAFT.
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Affiliation(s)
- Michael Knierbein
- Laboratory of Thermodynamics, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany.
| | - Anton Wangler
- Laboratory of Thermodynamics, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany.
| | - Trung Quan Luong
- Physical Chemistry I, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Christoph Held
- Laboratory of Thermodynamics, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany.
| | - Gabriele Sadowski
- Laboratory of Thermodynamics, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany.
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Hölzl C, Kibies P, Imoto S, Noetzel J, Knierbein M, Salmen P, Paulus M, Nase J, Held C, Sadowski G, Marx D, Kast SM, Horinek D. Structure and thermodynamics of aqueous urea solutions from ambient to kilobar pressures: From thermodynamic modeling, experiments, and first principles simulations to an accurate force field description. Biophys Chem 2019; 254:106260. [PMID: 31522071 DOI: 10.1016/j.bpc.2019.106260] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/29/2019] [Accepted: 08/29/2019] [Indexed: 12/17/2022]
Abstract
Molecular simulations based on classical force fields are a powerful method for shedding light on the complex behavior of biomolecules in solution. When cosolutes are present in addition to water and biomolecules, subtle balances of weak intermolecular forces have to be accounted for. This imposes high demands on the quality of the underlying force fields, and therefore force field development for small cosolutes is still an active field. Here, we present the development of a new urea force field from studies of urea solutions at ambient and elevated hydrostatic pressures based on a combination of experimental and theoretical approaches. Experimental densities and solvation shell properties from ab initio molecular dynamics simulations at ambient conditions served as the target properties for the force field optimization. Since urea is present in many marine life forms, elevated hydrostatic pressure was rigorously addressed: densities at high pressure were measured by vibrating tube densitometry up to 500 bar and by X-ray absorption up to 5 kbar. Densities were determined by the perturbed-chain statistical associating fluid theory equation of state. Solvation properties were determined by embedded cluster integral equation theory and ab initio molecular dynamics. Our new force field is able to capture the properties of urea solutions at high pressures without further high-pressure adaption, unlike trimethylamine-N-oxide, for which a high-pressure adaption is necessary.
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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
| | - Jan Noetzel
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Michael Knierbein
- Laboratory of Thermodynamics, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Paul Salmen
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Michael Paulus
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Julia Nase
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Christoph Held
- Laboratory of Thermodynamics, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Gabriele Sadowski
- Laboratory of Thermodynamics, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, 44227 Dortmund, Germany.
| | - Dominik Horinek
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany.
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