1
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Pouliquen DL. The biophysics of water in cell biology: perspectives on a keystone for both marine sciences and cancer research. Front Cell Dev Biol 2024; 12:1403037. [PMID: 38803391 PMCID: PMC11128620 DOI: 10.3389/fcell.2024.1403037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
The biophysics of water, has been debated over more than a century. Although its importance is still underestimated, significant breakthroughs occurred in recent years. The influence of protein condensation on water availability control was documented, new findings on water-transport proteins emerged, and the way water molecules rearrange to minimize free energy at interfaces was deciphered, influencing membrane thermodynamics. The state of knowledge continued to progress in the field of deep-sea marine biology, highlighting unknown effects of high hydrostatic pressure and/or temperature on interactions between proteins and ligands in extreme environments, and membrane structure adaptations. The role of osmolytes in protein stability control under stress is also discussed here in relation to fish egg hydration/buoyancy. The complexity of water movements within the cell is updated, all these findings leading to a better view of their impact on many cellular processes. The way water flow and osmotic gradients generated by ion transport work together to produce the driving force behind cell migration is also relevant to both marine biology and cancer research. Additional common points concern water dynamic changes during the neoplastic transformation of cells and tissues, or embryo development. This could improve imaging techniques, early cancer diagnosis, and understanding of the molecular and physiological basis of buoyancy for many marine species.
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Affiliation(s)
- Daniel L. Pouliquen
- Inserm, CNRS, CRCINA, Nantes Université, University of Angers, Angers, France
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2
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Imamura K, Yokogawa D, Sato H. Recent developments and applications of reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED): A hybrid model of quantum chemistry and integral equation theory of molecular liquids. J Chem Phys 2024; 160:050901. [PMID: 38341702 DOI: 10.1063/5.0190116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/04/2024] [Indexed: 02/13/2024] Open
Abstract
The significance of solvent effects in electronic structure calculations has long been noted, and various methods have been developed to consider this effect. The reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED) is a hybrid model that combines the integral equation theory of molecular liquids with quantum chemistry. This method can consider the statistically convergent solvent distribution at a significantly lower cost than molecular dynamics simulations. Because the RISM theory explicitly considers the solvent structure, it performs well for systems where hydrogen bonds are formed between the solute and solvent molecules, which is a challenge for continuum solvent models. Taking advantage of being founded on the variational principle, theoretical developments have been made in calculating various properties and incorporating electron correlation effects. In this review, we organize the theoretical aspects of RISM-SCF-cSED and its distinctions from other hybrid methods involving integral equation theories. Furthermore, we carefully present its progress in terms of theoretical developments and recent applications.
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Affiliation(s)
- Kosuke Imamura
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Daisuke Yokogawa
- Graduate School of Arts and Science, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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3
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Hachuła B, Włodarczyk P, Jurkiewicz K, Grelska J, Scelta D, Fanetti S, Paluch M, Pawlus S, Kamiński K. Pressure-Induced Aggregation of Associating Liquids as a Driving Force Enhancing Hydrogen Bond Cooperativity. J Phys Chem Lett 2024; 15:127-135. [PMID: 38147681 DOI: 10.1021/acs.jpclett.3c03037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
The behavior of hydrogen bonds under extreme pressure is still not well understood. Until now, the shift of the stretching vibration band of the X-H group (X = the donor atom) in infrared spectra has been attributed to the variation in the length of the covalent X-H bond. Herein, we combined infrared spectroscopy and X-ray diffraction experimental studies of two H-bonded liquid hexane derivatives, i.e., 2-ethyl-1-hexanol and 2-ethyl-1-hexylamine, in diamond anvil cells at pressures up to the GPa level, with molecular dynamics simulations covering similar thermodynamic conditions. Our findings revealed that the observed changes in the X-H stretching vibration bands under compression are not primarily due to H-bond shortening resulting from increased density but mainly due to cooperative enhancement of H-bonds caused by intensified molecular clustering. This sheds new light on the nature of H-bond interactions and the structure of liquid molecular systems under compression.
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Affiliation(s)
- Barbara Hachuła
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia in Katowice, Szkolna 9, 40-007 Katowice, Poland
| | - Patryk Włodarczyk
- Lukasiewicz Research Network─Institute of Non-Ferrous Metals, 5 Sowinskiego, 44-100 Gliwice, Poland
| | - Karolina Jurkiewicz
- Institute of Physics, Faculty of Science and Technology, University of Silesia in Katowice, 75 Pulku Piechoty 1, 41-500 Chorzow, Poland
| | - Joanna Grelska
- Institute of Physics, Faculty of Science and Technology, University of Silesia in Katowice, 75 Pulku Piechoty 1, 41-500 Chorzow, Poland
| | - Demetrio Scelta
- LENS, European Laboratory for Non-linear Spectroscopy, Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- ICCOM-CNR, Institute of Chemistry of OrganoMetallic Compounds, National Research Council of Italy, Via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Samuele Fanetti
- LENS, European Laboratory for Non-linear Spectroscopy, Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- ICCOM-CNR, Institute of Chemistry of OrganoMetallic Compounds, National Research Council of Italy, Via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Marian Paluch
- Institute of Physics, Faculty of Science and Technology, University of Silesia in Katowice, 75 Pulku Piechoty 1, 41-500 Chorzow, Poland
| | - Sebastian Pawlus
- Institute of Physics, Faculty of Science and Technology, University of Silesia in Katowice, 75 Pulku Piechoty 1, 41-500 Chorzow, Poland
| | - Kamil Kamiński
- Institute of Physics, Faculty of Science and Technology, University of Silesia in Katowice, 75 Pulku Piechoty 1, 41-500 Chorzow, Poland
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4
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Peters J, Oliva R, Caliò A, Oger P, Winter R. Effects of Crowding and Cosolutes on Biomolecular Function at Extreme Environmental Conditions. Chem Rev 2023; 123:13441-13488. [PMID: 37943516 DOI: 10.1021/acs.chemrev.3c00432] [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: 11/10/2023]
Abstract
The extent of the effect of cellular crowding and cosolutes on the functioning of proteins and cells is manifold and includes the stabilization of the biomolecular systems, the excluded volume effect, and the modulation of molecular dynamics. Simultaneously, it is becoming increasingly clear how important it is to take the environment into account if we are to shed light on biological function under various external conditions. Many biosystems thrive under extreme conditions, including the deep sea and subseafloor crust, and can take advantage of some of the effects of crowding. These relationships have been studied in recent years using various biophysical techniques, including neutron and X-ray scattering, calorimetry, FTIR, UV-vis and fluorescence spectroscopies. Combining knowledge of the structure and conformational dynamics of biomolecules under extreme conditions, such as temperature, high hydrostatic pressure, and high salinity, we highlight the importance of considering all results in the context of the environment. Here we discuss crowding and cosolute effects on proteins, nucleic acids, membranes, and live cells and explain how it is possible to experimentally separate crowding-induced effects from other influences. Such findings will contribute to a better understanding of the homeoviscous adaptation of organisms and the limits of life in general.
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Affiliation(s)
- Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, 140 rue de la physique, 38400 St Martin d'Hères, France
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France
- Institut Universitaire de France, 75005 Paris, France
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Antonino Caliò
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Philippe Oger
- INSA Lyon, Universite Claude Bernard Lyon1, CNRS, UMR5240, 69621 Villeurbanne, France
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Dortmund, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
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5
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Schienbein P. Spectroscopy from Machine Learning by Accurately Representing the Atomic Polar Tensor. J Chem Theory Comput 2023; 19:705-712. [PMID: 36695707 PMCID: PMC9933433 DOI: 10.1021/acs.jctc.2c00788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Vibrational spectroscopy is a key technique to elucidate microscopic structure and dynamics. Without the aid of theoretical approaches, it is, however, often difficult to understand such spectra at a microscopic level. Ab initio molecular dynamics has repeatedly proved to be suitable for this purpose; however, the computational cost can be daunting. Here, the E(3)-equivariant neural network e3nn is used to fit the atomic polar tensor of liquid water a posteriori on top of existing molecular dynamics simulations. Notably, the introduced methodology is general and thus transferable to any other system as well. The target property is most fundamental and gives access to the IR spectrum, and more importantly, it is a highly powerful tool to directly assign IR spectral features to nuclear motion─a connection which has been pursued in the past but only using severe approximations due to the prohibitive computational cost. The herein introduced methodology overcomes this bottleneck. To benchmark the machine learning model, the IR spectrum of liquid water is calculated, indeed showing excellent agreement with the explicit reference calculation. In conclusion, the presented methodology gives a new route to calculate accurate IR spectra from molecular dynamics simulations and will facilitate the understanding of such spectra on a microscopic level.
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6
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Hsieh CM, Grabbet B, Zeller F, Benter S, Scheele T, Sieroka N, Neudecker T. Can a Finite Chain of Hydrogen Cyanide Molecules Model a Crystal? Chemphyschem 2022; 23:e202200414. [PMID: 35946306 PMCID: PMC10087120 DOI: 10.1002/cphc.202200414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/09/2022] [Indexed: 01/05/2023]
Abstract
When calculating structural or spectroscopic properties of molecular crystals, the question arises whether it is sufficient to simulate only a single molecule or a small molecular cluster or whether the simulation of the entire crystal is indispensable. In this work we juxtapose calculations on the high-pressure structural properties of the (periodic) HCN crystal and chains of HCN molecules of finite length. We find that, in most cases, the behavior of the crystal can be reproduced by computational methods simulating only around 15 molecules. The pressure-induced lengthening of the C-H bond in HCN found in calculations on both the periodic and finite material are explained in terms of orbital interaction. Our results pave the way for a more thorough understanding of high-pressure structural properties of materials and give incentives for the design of materials that expand under pressure. In addition, they shed light on the complementarity between calculations on periodic materials and systems of finite size.
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Affiliation(s)
- Chieh-Min Hsieh
- University of Bremen, Institute for Physical and Theoretical Chemistry, Leobener Straße NW2, D-28359, Bremen, Germany
| | - Björn Grabbet
- University of Bremen, Institute for Physical and Theoretical Chemistry, Leobener Straße NW2, D-28359, Bremen, Germany.,Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Felix Zeller
- University of Bremen, Institute for Physical and Theoretical Chemistry, Leobener Straße NW2, D-28359, Bremen, Germany
| | - Sanna Benter
- University of Bremen, Institute for Physical and Theoretical Chemistry, Leobener Straße NW2, D-28359, Bremen, Germany.,Present address: Bergische Universität Wuppertal, Gaußstraße 20, D-42119, Wuppertal, Germany
| | - Tarek Scheele
- University of Bremen, Institute for Physical and Theoretical Chemistry, Leobener Straße NW2, D-28359, Bremen, Germany
| | - Norman Sieroka
- University of Bremen, Theoretical Philosophy, Enrique-Schmidt-Straße 7, D-28359, Bremen, Germany
| | - Tim Neudecker
- University of Bremen, Institute for Physical and Theoretical Chemistry, Leobener Straße NW2, D-28359, Bremen, Germany.,Bremen Center for Computational Materials Science, Am Fallturm 1, D-28359, Bremen, Germany.,MAPEX Center for Materials and Processes, Bibliothekstraße 1, D-28359, Bremen, Germany
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7
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Folberth A, van der Vegt NFA. Influence of TMAO and Pressure on the Folding Equilibrium of TrpCage. J Phys Chem B 2022; 126:8374-8380. [PMID: 36251479 DOI: 10.1021/acs.jpcb.2c04034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Trimethylamine-N-oxide (TMAO) is an osmolyte known for its ability to counteract the pressure denaturation of proteins. Computational studies addressing the molecular mechanisms of TMAO's osmolyte action have however focused exclusively on its protein-stabilizing properties at ambient pressure, neglecting the changes that may occur under high-pressure conditions where TMAO's hydration structure changes to that of increased water binding. Here, we present the first study on the combined effect of pressure and TMAO on a mini-protein, TrpCage. The results showed that at high pressures, nonpolar residues packed less tightly and the salt bridge of TrpCage was destabilized. This effect was mitigated by TMAO which was found to be strongly depleted from the protein/water interface at 1 kbar than at 1 bar ambient pressure, thus counterbalancing the thermodynamically unfavorable effect of elevated pressure in the free energy of folding. TMAO was depleted from charged groups, like the salt bridge-forming ones, and accumulated around hydrophobic groups. Still, it stabilized both kinds of interactions. Furthermore, enthalpically favorable TrpCage-water hydrogen bonds were reduced in the presence of TMAO, causing a stronger destabilization of the unfolded state than the folded state. This shifted the protein-folding equilibrium toward the folded state. Therefore, TMAO showed stabilizing effects on different kinds of groups, which were partially enhanced at high pressures.
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Affiliation(s)
- Angelina Folberth
- Eduard-Zintl-Institut Fuer Anorganische und Physikalische Chemie, Technical University of Darmstadt, Alarich-Weiss-Strasse 10, 64287 Darmstadt, Germany
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut Fuer Anorganische und Physikalische Chemie, Technical University of Darmstadt, Alarich-Weiss-Strasse 10, 64287 Darmstadt, Germany
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8
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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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9
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Muñoz-Santiburcio D. Accurate diffusion coefficients of the excess proton and hydroxide in water via extensive ab initio simulations with different schemes. J Chem Phys 2022; 157:024504. [PMID: 35840376 DOI: 10.1063/5.0093958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite its simple molecular formula, obtaining an accurate in silico description of water is far from straightforward. Many of its very peculiar properties are quite elusive, and in particular, obtaining good estimations of the diffusion coefficients of the solvated proton and hydroxide at a reasonable computational cost has been an unsolved challenge until now. Here, I present extensive results of several unusually long ab initio molecular dynamics (MD) simulations employing different combinations of the Born-Oppenheimer and second-generation Car-Parrinello MD propagation methods with different ensembles (NVE and NVT) and thermostats, which show that these methods together with the RPBE-D3 functional provide a very accurate estimation of the diffusion coefficients of the solvated H3O+ and OH- ions, together with an extremely accurate description of several properties of neutral water (such as the structure of the liquid and its diffusion and shear viscosity coefficients). In addition, I show that the estimations of DH3O+ and DOH- depend dramatically on the simulation length, being necessary to reach timescales in the order of hundreds of picoseconds to obtain reliable results.
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Affiliation(s)
- Daniel Muñoz-Santiburcio
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, 20018 San Sebastián, Spain and Instituto de Fusión Nuclear "Guillermo Velarde," Universidad Politécnica de Madrid, C/ José Gutiérrez Abascal 2, 28006 Madrid, Spain
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10
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Noetzel J, Schienbein P, Forbert H, Marx D. Solvation of Small Gold Clusters in Supercritical Water. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Ganyecz Á, Kállay M. Implementation and Optimization of the Embedded Cluster Reference Interaction Site Model with Atomic Charges. J Phys Chem A 2022; 126:2417-2429. [PMID: 35394778 PMCID: PMC9036516 DOI: 10.1021/acs.jpca.1c07904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In this work, we
implemented the embedded cluster reference interaction
site model (EC-RISM) originally developed by Kloss, Heil, and Kast
(J. Phys. Chem. B2008, 112, 4337–4343).
This method combines quantum mechanical calculations with the 3D reference
interaction site model (3D-RISM). Numerous options, such as buffer,
grid space, basis set, charge model, water model, closure relation,
and so forth, were investigated to find the best settings. Additionally,
the small point charges, which are derived from the solvent distribution
from the 3D-RISM solution to represent the solvent in the QM calculation,
were neglected to reduce the overhead without the loss of accuracy.
On the MNSOL[a], MNSOL, and FreeSolv databases, our implemented and
optimized method provides solvation free energies in water with 5.70,
6.32, and 6.44 kJ/mol root-mean-square deviations, respectively, but
with different settings, 5.22, 6.08, and 6.63 kJ/mol can also be achieved.
Only solvent models containing fitting parameters, like COSMO-RS and
EC-RISM with universal correction and directly used electrostatic
potential, perform better than our EC-RISM implementation with atomic
charges.
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Affiliation(s)
- Ádám Ganyecz
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest P.O. Box 91, H-1521 Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest P.O. Box 91, H-1521 Hungary
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12
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Śmiechowski M. The influence of intermolecular correlations on the infrared spectrum of liquid dimethyl sulfoxide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119869. [PMID: 34015747 DOI: 10.1016/j.saa.2021.119869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/09/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Dimethyl sulfoxide (DMSO) is routinely applied as an excellent, water-miscible solvent and chemical reagent. Some of the most important data concerning its liquid structure were obtained using infrared (IR) spectroscopy. However, the actual extent of intermolecular correlations that connect the isolated monomer spectrum to the IR response of the bulk liquid is poorly studied thus far. Using ab initio molecular dynamics (AIMD) simulations, IR spectra of liquid DMSO are obtained here from first principles and further analyzed using an array of sophisticated spectral decomposition techniques. The calculated spectra when unfolded in space reveal non-trivial spatial correlations underlying the IR response of liquid DMSO. It is unequivocally demonstrated that some of the fundamental vibrations visible in the intramolecular limit are effectively suppressed by the solvation environment due to symmetry reasons and thus disappear in the bulk limit, escaping experimental detection. Overall, DMSO as an aprotic solvent with dominant dipole-dipole interactions displays strong intermolecular correlations that contribute significantly to the IR spectra, on par with the situation observed in strongly associated liquids, such as water.
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Affiliation(s)
- Maciej Śmiechowski
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland.
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13
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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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14
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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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15
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Stasiulewicz M, Panuszko A, Śmiechowski M, Bruździak P, Maszota P, Stangret J. Effect of urea and glycine betaine on the hydration sphere of model molecules for the surface features of proteins. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.115090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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16
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Scheurer M, Dreuw A, Epifanovsky E, Head-Gordon M, Stauch T. Modeling Molecules under Pressure with Gaussian Potentials. J Chem Theory Comput 2021; 17:583-597. [PMID: 33350311 DOI: 10.1021/acs.jctc.0c01212] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The computational modeling of molecules under high pressure is a growing research area that augments experimental high-pressure chemistry. Here, a new electronic structure method for modeling atoms and molecules under pressure, Gaussians On Surface Tesserae Simulate HYdrostatic Pressure (GOSTSHYP) approach, is introduced. In this method, a set of Gaussian potentials is distributed evenly on the van der Waals surface of the investigated chemical system, leading to a compression of the electron density and the atomic scaffold. Since no parameters other than pressure need to be specified, GOSTSHYP allows straightforward geometry optimizations and ab initio molecular dynamics simulations of chemical systems under pressure for nonexpert users. Calculated energies, bond lengths, and dipole moments under pressure fall within the range of established computational methods for high-pressure chemistry. A Diels-Alder reaction and the cyclotrimerization of acetylene showcase the ability of GOSTSHYP to model pressure-induced chemical reactions. The connection to mechanochemistry is pointed out.
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Affiliation(s)
- Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Heidelberg University, D-69120 Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Heidelberg University, D-69120 Heidelberg, Germany
| | - Evgeny Epifanovsky
- Q-Chem Inc., 6601 Owens Dr, Suite 105, Pleasanton, California 94588, United States
| | - Martin Head-Gordon
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, South Dr, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, California 94720, United States
| | - Tim Stauch
- Institute for Physical and Theoretical Chemistry, University of Bremen, Leobener Str. NW2, D-28359 Bremen, Germany.,Bremen Center for Computational Materials Science, University of Bremen, Am Fallturm 1, D-28359 Bremen, Germany.,MAPEX Center for Materials and Processes, University of Bremen, Bibliothekstr. 1, D-28359 Bremen, Germany
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17
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Stauch T. A mechanochemical model for the simulation of molecules and molecular crystals under hydrostatic pressure. J Chem Phys 2020; 153:134503. [PMID: 33032415 DOI: 10.1063/5.0024671] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A novel mechanochemical method for the simulation of molecules and molecular crystals under hydrostatic pressure, the eXtended Hydrostatic Compression Force Field (X-HCFF) approach, is introduced. In contrast to comparable methods, the desired pressure can be adjusted non-iteratively and molecules of general shape retain chemically reasonable geometries even at high pressure. The implementation of the X-HCFF approach is straightforward, and the computational cost is practically the same as for regular geometry optimization. Pressure can be applied by using any desired electronic structure method for which a nuclear gradient is available. The results of the X-HCFF for pressure-dependent intramolecular structural changes in the investigated molecules and molecular crystals as well as a simple pressure-induced dimerization reaction are chemically intuitive and fall within the range of other established computational methods. Experimental spectroscopic data of a molecular crystal under pressure are reproduced accurately.
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Affiliation(s)
- Tim Stauch
- University of Bremen, Institute for Physical and Theoretical Chemistry, Leobener Straße NW2, D-28359 Bremen, Germany; Bremen Center for Computational Materials Science, University of Bremen, Am Fallturm 1, D-28359 Bremen, Germany; and MAPEX Center for Materials and Processes, University of Bremen, Bibliothekstraße 1, D-28359 Bremen, Germany
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18
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Imoto S, Marx D. How Can Protons Migrate in Extremely Compressed Liquid Water? PHYSICAL REVIEW LETTERS 2020; 125:086001. [PMID: 32909792 DOI: 10.1103/physrevlett.125.086001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/24/2020] [Indexed: 06/11/2023]
Abstract
Compression of liquid water up to multi-kbar pressures is known to perturb dramatically its local structure required for charge defects to migrate as topological defects in the hydrogen-bonded network. Our ab initio simulations show that the migration of excess protons is not much affected at 10 kbar, whereas that of proton holes is significantly reduced. Non-Markovian analyses show that this is not due to modifying the free energy barriers of both charge transfer and migration. It is rather pressure-induced modifications of the population of activated states, depending on interstitial water, which rules charge migration at extreme compression.
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Affiliation(s)
- Sho Imoto
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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19
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Jaworek MW, Ruggiero A, Graziano G, Winter R, Vitagliano L. On the extraordinary pressure stability of the Thermotoga maritima arginine binding protein and its folded fragments - a high-pressure FTIR spectroscopy study. Phys Chem Chem Phys 2020; 22:11244-11248. [PMID: 32400824 DOI: 10.1039/d0cp01618g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The arginine binding protein from T. maritima (ArgBP) exhibits several distinctive biophysical and structural properties. Here we show that ArgBP is also endowed with a ramarkable pressure stability as it undergoes minor structural changes only, even at 10 kbar. A similar stability is also observed for its folded fragments (truncated monomer and individual domains). A survey of literature data on the pressure stability of proteins highlights the uncommon behavior of ArgBP.
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Affiliation(s)
- Michel W Jaworek
- Faculty of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn Str. 4a, D-44227 Dortmund, Germany.
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20
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Pongratz T, Kibies P, Eberlein L, Tielker N, Hölzl C, Imoto S, Beck Erlach M, Kurrmann S, Schummel PH, Hofmann M, Reiser O, Winter R, Kremer W, Kalbitzer HR, Marx D, Horinek D, Kast SM. Pressure-dependent electronic structure calculations using integral equation-based solvation models. Biophys Chem 2020; 257:106258. [DOI: 10.1016/j.bpc.2019.106258] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 08/25/2019] [Indexed: 12/18/2022]
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21
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Tielker N, Tomazic D, Eberlein L, Güssregen S, Kast SM. The SAMPL6 challenge on predicting octanol-water partition coefficients from EC-RISM theory. J Comput Aided Mol Des 2020; 34:453-461. [PMID: 31981015 PMCID: PMC7125249 DOI: 10.1007/s10822-020-00283-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/08/2020] [Indexed: 12/14/2022]
Abstract
Results are reported for octanol–water partition coefficients (log P) of the neutral states of drug-like molecules provided during the SAMPL6 (Statistical Assessment of Modeling of Proteins and Ligands) blind prediction challenge from applying the “embedded cluster reference interaction site model” (EC-RISM) as a solvation model for quantum-chemical calculations. Following the strategy outlined during earlier SAMPL challenges we first train 1- and 2-parameter water-free (“dry”) and water-saturated (“wet”) models for n-octanol solvation Gibbs energies with respect to experimental values from the “Minnesota Solvation Database” (MNSOL), yielding a root mean square error (RMSE) of 1.5 kcal mol−1 for the best-performing 2-parameter wet model, while the optimal water model developed for the pKa part of the SAMPL6 challenge is kept unchanged (RMSE 1.6 kcal mol−1 for neutral compounds from a model trained on both neutral and ionic species). Applying these models to the blind prediction set yields a log P RMSE of less than 0.5 for our best model (2-parameters, wet). Further analysis of our results reveals that a single compound is responsible for most of the error, SM15, without which the RMSE drops to 0.2. Since this is the only compound in the challenge dataset with a hydroxyl group we investigate other alcohols for which Gibbs energy of solvation data for both water and n-octanol are available in the MNSOL database to demonstrate a systematic cause of error and to discuss strategies for improvement.
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Affiliation(s)
- Nicolas Tielker
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Daniel Tomazic
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Lukas Eberlein
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Stefan Güssregen
- Sanofi-Aventis Deutschland GmbH, R&D Integrated Drug Discovery, 65926, Frankfurt am Main, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
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22
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Schienbein P, Marx D. Assessing the properties of supercritical water in terms of structural dynamics and electronic polarization effects. Phys Chem Chem Phys 2020; 22:10462-10479. [DOI: 10.1039/c9cp05610f] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Evolution of water's structural dynamics from ambient liquid to supercritical dense liquid-like and dilute gas-like conditions.
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Affiliation(s)
- Philipp Schienbein
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
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23
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Alfarano SR, Vondracek H, Sebastiani F, Novelli F, Hoberg C, Kolling I, Brubach JB, Roy P, Schwaab G, Havenith M. Does hydrated glycine act as solidification nucleus at multi-kilobar conditions? Biophys Chem 2019; 253:106215. [DOI: 10.1016/j.bpc.2019.106215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/29/2019] [Accepted: 06/29/2019] [Indexed: 11/16/2022]
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24
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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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25
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Kumar N, Marx D. How do ribozymes accommodate additional water molecules upon hydrostatic compression deep into the kilobar pressure regime? Biophys Chem 2019; 252:106192. [DOI: 10.1016/j.bpc.2019.106192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/23/2019] [Accepted: 05/23/2019] [Indexed: 12/19/2022]
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26
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Vondracek H, Imoto S, Knake L, Schwaab G, Marx D, Havenith M. Hydrogen-Bonding in Liquid Water at Multikilobar Pressures. J Phys Chem B 2019; 123:7748-7753. [PMID: 31419128 DOI: 10.1021/acs.jpcb.9b06821] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-precision THz (30 to 360 cm-1) spectra of bulk liquid water are presented from ambient conditions up to hydrostatic pressures of 10 kbar. In concert with ab initio simulations, this allows us to characterize the molecular-level changes of the H-bond network under solvent stress conditions. Both the experimental and theoretical THz spectra reveal a blue shift in the intermolecular translational mode at 180 cm-1 by 40 cm-1 at 10 kbar and a blue shift together with an intensity increase in the relaxation mode. These changes can be traced back to a pressure-induced increase of the population of so-called short H-bond double donor configurations at the expense of those with longer such intermolecular bonds. Distinct electronic polarization effects are critical to capture the characteristic intensity changes of the THz line shape function. These advances in high-pressure THz spectroscopy open the door to investigate the pressure response of solvation shells and solute-solvent couplings.
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Affiliation(s)
- Hendrik Vondracek
- Lehrstuhl für Physikalische Chemie II , Ruhr-Universität Bochum , 44780 Bochum , Germany
| | - Sho Imoto
- Lehrstuhl für Theoretische Chemie , Ruhr-Universität Bochum , 44780 Bochum , Germany
| | - Lukas Knake
- Lehrstuhl für Physikalische Chemie II , Ruhr-Universität Bochum , 44780 Bochum , Germany
| | - Gerhard Schwaab
- Lehrstuhl für Physikalische Chemie II , Ruhr-Universität Bochum , 44780 Bochum , Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie , Ruhr-Universität Bochum , 44780 Bochum , Germany
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II , Ruhr-Universität Bochum , 44780 Bochum , Germany
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27
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Cinar H, Fetahaj Z, Cinar S, Vernon RM, Chan HS, Winter RHA. Temperature, Hydrostatic Pressure, and Osmolyte Effects on Liquid-Liquid Phase Separation in Protein Condensates: Physical Chemistry and Biological Implications. Chemistry 2019; 25:13049-13069. [PMID: 31237369 DOI: 10.1002/chem.201902210] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/23/2019] [Indexed: 01/04/2023]
Abstract
Liquid-liquid phase separation (LLPS) of proteins and other biomolecules play a critical role in the organization of extracellular materials and membrane-less compartmentalization of intra-organismal spaces through the formation of condensates. Structural properties of such mesoscopic droplet-like states were studied by spectroscopy, microscopy, and other biophysical techniques. The temperature dependence of biomolecular LLPS has been studied extensively, indicating that phase-separated condensed states of proteins can be stabilized or destabilized by increasing temperature. In contrast, the physical and biological significance of hydrostatic pressure on LLPS is less appreciated. Summarized here are recent investigations of protein LLPS under pressures up to the kbar-regime. Strikingly, for the cases studied thus far, LLPSs of both globular proteins and intrinsically disordered proteins/regions are typically more sensitive to pressure than the folding of proteins, suggesting that organisms inhabiting the deep sea and sub-seafloor sediments, under pressures up to 1 kbar and beyond, have to mitigate this pressure-sensitivity to avoid unwanted destabilization of their functional biomolecular condensates. Interestingly, we found that trimethylamine-N-oxide (TMAO), an osmolyte upregulated in deep-sea fish, can significantly stabilize protein droplets under pressure, pointing to another adaptive advantage for increased TMAO concentrations in deep-sea organisms besides the osmolyte's stabilizing effect against protein unfolding. As life on Earth might have originated in the deep sea, pressure-dependent LLPS is pertinent to questions regarding prebiotic proto-cells. Herein, we offer a conceptual framework for rationalizing the recent experimental findings and present an outline of the basic thermodynamics of temperature-, pressure-, and osmolyte-dependent LLPS as well as a molecular-level statistical mechanics picture in terms of solvent-mediated interactions and void volumes.
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Affiliation(s)
- Hasan Cinar
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Zamira Fetahaj
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Süleyman Cinar
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Robert M Vernon
- Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Hue Sun Chan
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Ontario, M5S 1A8, Canada.,Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Ontario, M5S 1A8, Canada
| | - Roland H A Winter
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
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28
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Hata H, Nishiyama M, Kitao A. Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics. Biochim Biophys Acta Gen Subj 2019; 1864:129395. [PMID: 31302180 DOI: 10.1016/j.bbagen.2019.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Molecular dynamics (MD) simulation is well-recognized as a powerful tool to investigate protein structure, function, and thermodynamics. MD simulation is also used to investigate high pressure effects on proteins. For conducting better MD simulation under high pressure, the main issues to be addressed are: (i) protein force fields and water models were originally developed to reproduce experimental properties obtained at ambient pressure; and (ii) the timescale to observe the pressure effect is often much longer than that of conventional MD simulations. SCOPE OF REVIEW First, we describe recent developments in MD simulation methodologies for studying the high-pressure structure and dynamics of protein molecules. These developments include force fields for proteins and water molecules, and enhanced simulation techniques. Then, we summarize recent studies of MD simulations of proteins in water under high pressure. MAJOR CONCLUSIONS Recent MD simulations of proteins in solution under pressure have reproduced various phenomena identified by experiments using high pressure, such as hydration, water penetration, conformational change, helix stabilization, and molecular stiffening. GENERAL SIGNIFICANCE MD simulations demonstrate differences in the properties of proteins and water molecules between ambient and high-pressure conditions. Comparing the results obtained by MD calculations with those obtained experimentally could reveal the mechanism by which biological molecular machines work well in collaboration with water molecules.
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Affiliation(s)
- Hiroaki Hata
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama, 2-12-1 Meguro-ku, Tokyo 152-8550, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Kindai University, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama, 2-12-1 Meguro-ku, Tokyo 152-8550, Japan.
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29
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Knierbein M, Venhuis M, Held C, Sadowski G. Thermodynamic properties of aqueous osmolyte solutions at high-pressure conditions. Biophys Chem 2019; 253:106211. [PMID: 31280070 DOI: 10.1016/j.bpc.2019.106211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/20/2019] [Indexed: 12/25/2022]
Abstract
Living organisms can be encountered in nature under extreme conditions. At the seabed, pressure may reach 1000 bar. Yet microorganisms can be found that still function under these conditions. On the one hand, it is known that high pressure even has a positive effect on piezophile enzymes increasing their activity. On the other hand, such microorganisms might contain up to very high concentrations of osmolytes that counteract osmotic stress. To better understand high-pressure influences on biochemical systems, fundamental knowledge about pressure effects on thermodynamic properties of such osmolytes is important. However, literature data is scarce and experiments at high-pressure conditions are challenging. Hence, new high-pressure density data of aqueous osmolyte solutions were measured in this work at temperatures between 298.15 K and 318.15 K and at osmolyte concentrations up to 3 mol/kg water. Further, the thermodynamic model PC-SAFT has been applied recently to successfully model vapor pressures of water and density of water up to 10 kbar [M. Knierbein et al., Density variations of TMAO solutions in the kilobar range: experiments, PC-SAFT predictions, and molecular dynamics simulations, Biophysical chemistry, (2019)]. This allowed accurately predicting effects of temperature and osmolyte concentration on thermodynamic properties (especially mixture densities) up to very high pressures. Common osmolytes (trimethylamine-N-oxide, urea, ectoine, glycerol, glycine) as well as the dipeptides acetyl-N-methylglycine amide, acetyl-N-methylalanine amide, and acetyl-N-methylleucine amide were under investigation.
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Affiliation(s)
| | | | - Christoph Held
- Laboratory of Thermodynamics, TU Dortmund, 44227 Dortmund, Germany
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30
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Winter R. Interrogating the Structural Dynamics and Energetics of Biomolecular Systems with Pressure Modulation. Annu Rev Biophys 2019; 48:441-463. [DOI: 10.1146/annurev-biophys-052118-115601] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High hydrostatic pressure affects the structure, dynamics, and stability of biomolecular systems and is a key parameter in the context of the exploration of the origin and the physical limits of life. This review lays out the conceptual framework for exploring the conformational fluctuations, dynamical properties, and activity of biomolecular systems using pressure perturbation. Complementary pressure-jump relaxation studies are useful tools to study the kinetics and mechanisms of biomolecular phase transitions and structural transformations, such as membrane fusion or protein and nucleic acid folding. Finally, the advantages of using pressure to explore biomolecular assemblies and modulate enzymatic reactions are discussed.
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Affiliation(s)
- Roland Winter
- Faculty of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44227 Dortmund, Germany
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31
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Cinar S, Cinar H, Chan HS, Winter R. Pressure-Sensitive and Osmolyte-Modulated Liquid–Liquid Phase Separation of Eye-Lens γ-Crystallins. J Am Chem Soc 2019; 141:7347-7354. [DOI: 10.1021/jacs.8b13636] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Süleyman Cinar
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Hasan Cinar
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Hue Sun Chan
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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32
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Schummel PH, Anders C, Jaworek MW, Winter R. Cosolvent and Crowding Effects on the Temperature- and Pressure-Dependent Dissociation Process of the α/β-Tubulin Heterodimer. Chemphyschem 2019; 20:1098-1109. [PMID: 30829441 DOI: 10.1002/cphc.201900115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/01/2019] [Indexed: 11/09/2022]
Abstract
Tubulin is one of the main components of the cytoskeleton of eukaryotic cells. The formation of microtubules depends strongly on environmental and solution conditions, and has been found to be among the most pressure sensitive processes in vivo. We explored the effects of different types of cosolvents, such as trimethylamine-N-oxide (TMAO), sucrose and urea, and crowding agents to mimic cell-like conditions, on the temperature and pressure stability of the building block of microtubules, i. e. the α/β-tubulin heterodimer. To this end, fluorescence and FTIR spectroscopy, differential scanning and pressure perturbation calorimetry as well as fluorescence anisotropy and correlation spectroscopies were applied. The pressure and temperature of dissociation of α/β-tubulin as well as the underlying thermodynamic parameters upon dissociation, such as volume and enthalpy changes, have been determined for the different solution conditions. The temperature and pressure of dissociation of the α/β-tubulin heterodimer and hence its stability increases dramatically in the presence of TMAO and the nanocrowder sucrose. We show that by adjusting the levels of compatible cosolutes and crowders, cells are able to withstand deteriorating effects of pressure even up to the kbar-range.
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Affiliation(s)
- Paul Hendrik Schummel
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Christian Anders
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Michel W Jaworek
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
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Xie WJ, Cha S, Ohto T, Mizukami W, Mao Y, Wagner M, Bonn M, Hunger J, Nagata Y. Large Hydrogen-Bond Mismatch between TMAO and Urea Promotes Their Hydrophobic Association. Chem 2018. [DOI: 10.1016/j.chempr.2018.08.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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34
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Tielker N, Eberlein L, Güssregen S, Kast SM. The SAMPL6 challenge on predicting aqueous pKa values from EC-RISM theory. J Comput Aided Mol Des 2018; 32:1151-1163. [DOI: 10.1007/s10822-018-0140-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 07/28/2018] [Indexed: 12/15/2022]
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35
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Julius K, Weine J, Berghaus M, König N, Gao M, Latarius J, Paulus M, Schroer MA, Tolan M, Winter R. Water-Mediated Protein-Protein Interactions at High Pressures are Controlled by a Deep-Sea Osmolyte. PHYSICAL REVIEW LETTERS 2018; 121:038101. [PMID: 30085800 DOI: 10.1103/physrevlett.121.038101] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Indexed: 06/08/2023]
Abstract
The influence of natural cosolvent mixtures on the pressure-dependent structure and protein-protein interaction potential of dense protein solutions is studied and analyzed using small-angle X-ray scattering in combination with a liquid-state theoretical approach. The deep-sea osmolyte trimethylamine-N-oxide is shown to play a crucial and singular role in its ability to not only guarantee sustainability of the native protein's folded state under harsh environmental conditions, but it also controls water-mediated intermolecular interactions at high pressure, thereby preventing contact formation and hence aggregation of proteins.
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Affiliation(s)
- Karin Julius
- Faculty of Physics/DELTA, TU Dortmund University, 44221 Dortmund, Germany
| | - Jonathan Weine
- Faculty of Physics/DELTA, TU Dortmund University, 44221 Dortmund, Germany
| | - Melanie Berghaus
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Nico König
- Faculty of Physics/DELTA, TU Dortmund University, 44221 Dortmund, Germany
| | - Mimi Gao
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Jan Latarius
- Faculty of Physics/DELTA, TU Dortmund University, 44221 Dortmund, Germany
| | - Michael Paulus
- Faculty of Physics/DELTA, TU Dortmund University, 44221 Dortmund, Germany
| | - Martin A Schroer
- European Molecular Biology Laboratory (EMBL) Hamburg c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Metin Tolan
- Faculty of Physics/DELTA, TU Dortmund University, 44221 Dortmund, Germany
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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36
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Jaworek MW, Schuabb V, Winter R. The effects of glycine, TMAO and osmolyte mixtures on the pressure dependent enzymatic activity of α-chymotrypsin. Phys Chem Chem Phys 2018; 20:1347-1354. [DOI: 10.1039/c7cp06042d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different natural osmolytes modulate the pressure dependent enzyme kinetics in different ways.
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Affiliation(s)
- Michel W. Jaworek
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- Technical University Dortmund
- 44227 Dortmund
- Germany
| | - Vitor Schuabb
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- Technical University Dortmund
- 44227 Dortmund
- Germany
| | - Roland Winter
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- Technical University Dortmund
- 44227 Dortmund
- Germany
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37
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Imoto S, Forbert H, Marx D. Aqueous TMAO solutions as seen by theoretical THz spectroscopy: hydrophilic versus hydrophobic water. Phys Chem Chem Phys 2018; 20:6146-6158. [DOI: 10.1039/c7cp07003a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
All THz resonances of aqueous TMAO solutions are computed and assigned based on ab initio molecular dynamics simulations.
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Affiliation(s)
- Sho Imoto
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Harald Forbert
- Center for Solvation Science ZEMOS
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
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38
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Schienbein P, Marx D. Liquid–Vapor Phase Diagram of RPBE-D3 Water: Electronic Properties along the Coexistence Curve and in the Supercritical Phase. J Phys Chem B 2017; 122:3318-3329. [DOI: 10.1021/acs.jpcb.7b09761] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Philipp Schienbein
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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39
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Visualizing spatially decomposed intermolecular correlations in the infrared spectra of aprotic liquids. J Mol Graph Model 2017; 78:148-157. [DOI: 10.1016/j.jmgm.2017.09.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 01/10/2023]
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40
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Beck Erlach M, Koehler J, Crusca E, Munte CE, Kainosho M, Kremer W, Kalbitzer HR. Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH 2. JOURNAL OF BIOMOLECULAR NMR 2017; 69:53-67. [PMID: 28913741 DOI: 10.1007/s10858-017-0134-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of 13C chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx, one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of a number of nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The size of the polynomial pressure coefficients B 1 and B 2 is dependent on the type of atom and amino acid studied. For HN, N and Cα the first order pressure coefficient B 1 is also correlated to the chemical shift at atmospheric pressure. The first and second order pressure coefficients of a given type of carbon atom show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure also are weakly correlated. The downfield shifts of the methyl resonances suggest that gauche conformers of the side chains are not preferred with pressure. The valine and leucine methyl groups in the model peptides were assigned using stereospecifically 13C enriched amino acids with the pro-R carbons downfield shifted relative to the pro-S carbons.
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Affiliation(s)
- Markus Beck Erlach
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Joerg Koehler
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Edson Crusca
- Institute of Chemistry, São Paulo State University (UNESP), Araraquara, 14800-060, Brazil
| | - Claudia E Munte
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
- Physics Institute of São Carlos, University of São Paulo, São Carlos, 13566-590, Brazil
| | - Masatsune Kainosho
- Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Werner Kremer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Hans Robert Kalbitzer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany.
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41
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Gao M, Held C, Patra S, Arns L, Sadowski G, Winter R. Crowders and Cosolvents-Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses. Chemphyschem 2017; 18:2951-2972. [DOI: 10.1002/cphc.201700762] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/15/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Mimi Gao
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Christoph Held
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Satyajit Patra
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Loana Arns
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Gabriele Sadowski
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Roland Winter
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
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Heyden M, Ebbinghaus S, Winter R. Das Innere der Zelle: Ein komplexes Lösungsmittel. CHEM UNSERER ZEIT 2017. [DOI: 10.1002/ciuz.201700777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Śmiechowski M, Krakowiak J, Bruździak P, Stangret J. Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent. Phys Chem Chem Phys 2017; 19:9270-9280. [DOI: 10.1039/c6cp08799j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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