1
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Reidelbach M, Bai M, Schneeberger M, Zöllner MS, Kubicek K, Kirchberg H, Bressler C, Thorwart M, Herrmann C. Solvent Dynamics of Aqueous Halides before and after Photoionization. J Phys Chem B 2023; 127:1399-1413. [PMID: 36728132 DOI: 10.1021/acs.jpcb.2c07992] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Electron transfer reactions can be strongly influenced by solvent dynamics. We study the photoionization of halides in water as a model system for such reactions. There are no internal nuclear degrees of freedom in the solute, allowing the dynamics of the solvent to be uniquely identified. We simulate the equilibrium solvent dynamics for Cl-, Br-, I-, and their respective neutral atoms in water, comparing quantum mechanical/molecular mechanical (QM/MM) and classical molecular dynamics (MD) methods. On the basis of the obtained configurations, we calculate the extended X-ray absorption fine structure (EXAFS) spectra rigorously based on the MD snapshots and compare them in detail with other theoretical and experimental results available in the literature. We find our EXAFS spectra based on QM/MM MD simulations in good agreement with their experimental counterparts for the ions. Classical MD simulations for the ions lead to EXAFS spectra that agree equally well with the experiment when it comes to the oscillatory period of the signal, even though they differ from the QM/MM radial distribution functions extracted from the MD. The amplitude is, however, considerably overestimated. This suggests that to judge the reliability of theoretical simulation methods or to elucidate fine details of the atomistic dynamics of the solvent based on EXAFS spectra, the amplitude as well as the oscillatory period need to be considered. If simulations fail qualitatively, as does the classical MD for the aqueous neutral halogen atoms, the resulting EXAFS will also be strongly affected in both oscillatory period and amplitude. The good reliability of QM/MM-based EXAFS simulations, together with clear qualitative differences in the EXAFS spectra found between halides and their atomic counterparts, suggests that a combined theory and experimental EXAFS approach is suitable for elucidating the nonequilibrium solvent dynamics in the photoionization of halides and possibly also for electron transfer reactions in more complex systems.
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Affiliation(s)
- Marco Reidelbach
- Department of Chemistry, Universität Hamburg, Harbor Bldg. 610, Luruper Chaussee 149, 22761Hamburg, Germany.,The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany
| | - Mei Bai
- The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany.,I. Institut für Theoretische Physik, Universität Hamburg, Notkestr. 9, 22607Hamburg, Germany
| | - Michaela Schneeberger
- Department of Chemistry, Universität Hamburg, Harbor Bldg. 610, Luruper Chaussee 149, 22761Hamburg, Germany.,The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany
| | - Martin Sebastian Zöllner
- Department of Chemistry, Universität Hamburg, Harbor Bldg. 610, Luruper Chaussee 149, 22761Hamburg, Germany.,The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany
| | - Katharina Kubicek
- The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany.,Department of Physics, Universität Hamburg, Notkestr. 85, 22607Hamburg, Germany.,European XFEL, Holzkoppel 4, 22869Schenefeld, Germany
| | - Henning Kirchberg
- The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany.,I. Institut für Theoretische Physik, Universität Hamburg, Notkestr. 9, 22607Hamburg, Germany
| | - Christian Bressler
- The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany.,Department of Physics, Universität Hamburg, Notkestr. 85, 22607Hamburg, Germany.,European XFEL, Holzkoppel 4, 22869Schenefeld, Germany
| | - Michael Thorwart
- The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany.,I. Institut für Theoretische Physik, Universität Hamburg, Notkestr. 9, 22607Hamburg, Germany
| | - Carmen Herrmann
- Department of Chemistry, Universität Hamburg, Harbor Bldg. 610, Luruper Chaussee 149, 22761Hamburg, Germany.,The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany
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2
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Conformational Heterogeneity and Frustration of the Tumor Suppressor p53 as Tuned by Punctual Mutations. Int J Mol Sci 2022; 23:ijms232012636. [PMID: 36293489 PMCID: PMC9604312 DOI: 10.3390/ijms232012636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 12/02/2022] Open
Abstract
The conformational heterogeneity of the p53 tumor suppressor, the wild-type (p53wt) and mutated forms, was investigated by a computational approach, including the modeling and all atoms of the molecular dynamics (MD) simulations. Four different punctual mutations (p53R175H, p53R248Q, p53R273H, and p53R282W) which are known to affect the DNA binding and belong to the most frequent hot-spot mutations in human cancers, were taken into consideration. The MD trajectories of the wild-type and mutated p53 forms were analyzed by essential dynamics to extract the relevant collective motions and by the frustration method to evaluate the degeneracy of the energy landscape. We found that p53 is characterized by wide collective motions and its energy landscape exhibits a rather high frustration level, especially in the regions involved in the binding to physiological ligands. Punctual mutations give rise to a modulation of both the collective motions and the frustration of p53, with different effects depending on the mutation. The regions of p53wt and of the mutated forms characterized by a high frustration level are also largely involved in the collective motions. Such a correlation is discussed also in connection with the intrinsic disordered character of p53 and with its central functional role.
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3
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Raskar T, Niebling S, Devos JM, Yorke BA, Härtlein M, Huse N, Forsyth VT, Seydel T, Pearson AR. Structure and diffusive dynamics of aspartate α-decarboxylase (ADC) liganded with D-serine in aqueous solution. Phys Chem Chem Phys 2022; 24:20336-20347. [PMID: 35980136 PMCID: PMC9429672 DOI: 10.1039/d2cp02063g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Incoherent neutron spectroscopy, in combination with dynamic light scattering, was used to investigate the effect of ligand binding on the center-of-mass self-diffusion and internal diffusive dynamics of Escherichia coli aspartate α-decarboxylase (ADC). The X-ray crystal structure of ADC in complex with the d-serine inhibitor was also determined, and molecular dynamics simulations were used to further probe the structural rearrangements that occur as a result of ligand binding. These experiments reveal that d-serine forms hydrogen bonds with some of the active site residues, that higher order oligomers of the ADC tetramer exist on ns–ms time-scales, and also show that ligand binding both affects the ADC internal diffusive dynamics and appears to further increase the size of the higher order oligomers. Neutron spectroscopy, dynamic light scattering, X-ray diffraction, and MD-simulations were used to investigate the effect of ligand binding on the structure and diffusive dynamics of Escherichia coli aspartate alpha-decarboxylase.![]()
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Affiliation(s)
- Tushar Raskar
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France. .,Partnership for Structural Biology, 71 Avenue des Martyrs, Grenoble 38000, France.,Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany.
| | - Stephan Niebling
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany. .,European Molecular Biology Laboratory, Hamburg, Notkestr. 85, 22607 Hamburg, Germany
| | - Juliette M Devos
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France. .,Partnership for Structural Biology, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Briony A Yorke
- School of Chemistry and Bioscience, University of Bradford, Bradford, BD7 1DP, UK
| | - Michael Härtlein
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France. .,Partnership for Structural Biology, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Nils Huse
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany.
| | - V Trevor Forsyth
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France. .,Partnership for Structural Biology, 71 Avenue des Martyrs, Grenoble 38000, France.,Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France.
| | - Arwen R Pearson
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany.
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4
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Töpfer K, Käser S, Meuwly M. Double proton transfer in hydrated formic acid dimer: Interplay of spatial symmetry and solvent-generated force on reactivity. Phys Chem Chem Phys 2022; 24:13869-13882. [PMID: 35620978 PMCID: PMC9176184 DOI: 10.1039/d2cp01583h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The double proton transfer (DPT) reaction in the hydrated formic acid dimer (FAD) is investigated at molecular-level detail. For this, a global and reactive machine learned (ML) potential energy surface (PES) is developed to run extensive (more than 100 ns) mixed ML/MM molecular dynamics (MD) simulations in explicit molecular mechanics (MM) solvent at MP2-quality for the solute. Simulations with fixed – as in a conventional empirical force field – and conformationally fluctuating – as available from the ML-based PES – charge models for FAD show a significant impact on the competition between DPT and dissociation of FAD into two formic acid monomers. With increasing temperature the barrier height for DPT in solution changes by about 10% (∼1 kcal mol−1) between 300 K and 600 K. The rate for DPT is largest, ∼1 ns−1, at 350 K and decreases for higher temperatures due to destabilisation and increased probability for dissociation of FAD. The water solvent is found to promote the first proton transfer by exerting a favourable solvent-induced Coulomb force along the O–H⋯O hydrogen bond whereas the second proton transfer is significantly controlled by the O–O separation and other conformational degrees of freedom. Double proton transfer in hydrated FAD is found to involve a subtle interplay and balance between structural and electrostatic factors. Simulation of double proton transfer in formic acid dimer by reactive ML potential in explicit molecular mechanics water solvent.![]()
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Affiliation(s)
- Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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5
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Siani P, Di Valentin C. Effect of dopamine-functionalization, charge and pH on protein corona formation around TiO 2 nanoparticles. NANOSCALE 2022; 14:5121-5137. [PMID: 35302136 PMCID: PMC8969454 DOI: 10.1039/d1nr07647g] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Inorganic nanoparticles (NPs) are gaining increasing attention in nanomedicine because of their stimuli responsiveness, which allows combining therapy with diagnosis. However, little information is known about their interaction with intracellular or plasma proteins when they are introduced in a biological environment. Here we present atomistic molecular dynamics (MD) simulations investigating the case study of dopamine-functionalized TiO2 nanoparticles and two proteins that are overexpressed in cancer cells, i.e. PARP1 and HSP90, since experiments proved them to be the main components of the corona in cell cultures. The mechanism and the nature of the interaction (electrostatic, van der Waals, H-bonds, etc.) is unravelled by defining the protein residues that are more frequently in contact with the NPs, the extent of contact surface area and the variations in the protein secondary structures, at different pH and ionic strength conditions of the solution where they are immersed to simulate a realistic biological environment. The effects of the NP surface functionalization and charge are also considered. Our MD results suggest that less acidic intracellular pH conditions in the presence of cytosolic ionic strength enhance PARP1 interaction with the nanoparticle, whereas the HSP90 contribution is partly weakened, providing a rational explanation to existing experimental observations.
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Affiliation(s)
- Paulo Siani
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 55, 20125 Milano, Italy.
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 55, 20125 Milano, Italy.
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6
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Käser S, Meuwly M. Transfer learned potential energy surfaces: accurate anharmonic vibrational dynamics and dissociation energies for the formic acid monomer and dimer. Phys Chem Chem Phys 2021; 24:5269-5281. [PMID: 34792523 PMCID: PMC8890265 DOI: 10.1039/d1cp04393e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vibrational dynamics of the formic acid monomer (FAM) and dimer (FAD) is investigated from machine-learned potential energy surfaces at the MP2 (PESMP2) and transfer-learned (PESTL) to the CCSD(T) levels of theory. The normal mode (MAEs of 17.6 and 25.1 cm−1) and second order vibrational perturbation theory (VPT2, MAEs of 6.7 and 17.1 cm−1) frequencies from PESTL for all modes below 2000 cm−1 for FAM and FAD agree favourably with experiment. For the OH stretch mode the experimental frequencies are overestimated by more than 150 cm−1 for both FAM and FAD from normal mode calculations. Conversely, VPT2 calculations on PESTL for FAM reproduce the experimental OH frequency to within 22 cm−1. For FAD the VPT2 calculations find the high-frequency OH stretch at 3011 cm−1, compared with an experimentally reported, broad (∼100 cm−1) absorption band with center frequency estimated at ∼3050 cm−1. In agreement with earlier reports, MD simulations at higher temperature shift the position of the OH-stretch in FAM to the red, consistent with improved sampling of the anharmonic regions of the PES. However, for FAD the OH-stretch shifts to the blue and for temperatures higher than 1000 K the dimer partly or fully dissociates using PESTL. Including zero-point energy corrections from diffusion Monte Carlo simulations for FAM and FAD and corrections due to basis set superposition and completeness errors yields a dissociation energy of D0 = −14.23 ± 0.08 kcal mol−1 compared with an experimentally determined value of −14.22 ± 0.12 kcal mol−1. Neural network based PESs are constructed for formic acid monomer and dimer at the MP2 and transfer learned to the CCSD(T) level of theory. The PESs are used to study the vibrational dynamics and dissociation energy of the molecules.![]()
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Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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7
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Kübel J, Westenhoff S, Maj M. Giving voice to the weak: Application of active noise reduction in transient infrared spectroscopy. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.139059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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8
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Bacellar C, Kinschel D, Cannelli O, Sorokin B, Katayama T, Mancini GF, Rouxel JR, Obara Y, Nishitani J, Ito H, Ito T, Kurahashi N, Higashimura C, Kudo S, Cirelli C, Knopp G, Nass K, Johnson PJM, Wach A, Szlachetko J, Lima FA, Milne CJ, Yabashi M, Suzuki T, Misawa K, Chergui M. Femtosecond X-ray spectroscopy of haem proteins. Faraday Discuss 2021; 228:312-328. [PMID: 33565544 DOI: 10.1039/d0fd00131g] [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
We discuss our recently reported femtosecond (fs) X-ray emission spectroscopy results on the ligand dissociation and recombination in nitrosylmyoglobin (MbNO) in the context of previous studies on ferrous haem proteins. We also present a preliminary account of femtosecond X-ray absorption studies on MbNO, pointing to the presence of more than one species formed upon photolysis.
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Affiliation(s)
- Camila Bacellar
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Dominik Kinschel
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Oliviero Cannelli
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Boris Sorokin
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Tetsuo Katayama
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1, Kouto, Sayo-cho Sayo-gun, Hyogo 679-5198, Japan
| | - Giulia F Mancini
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Jeremy R Rouxel
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Yuki Obara
- Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Junichi Nishitani
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Hironori Ito
- Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Terumasa Ito
- Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Naoya Kurahashi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Kioicho, 7-1, Chiyoda, 102-8554 Tokyo, Japan
| | - Chika Higashimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Shotaro Kudo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Claudio Cirelli
- SwissFEL, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland
| | - Gregor Knopp
- SwissFEL, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland
| | - Karol Nass
- SwissFEL, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland
| | | | - Anna Wach
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Krakow, Poland
| | - Jakub Szlachetko
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Krakow, Poland
| | | | | | - Makina Yabashi
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1, Kouto, Sayo-cho Sayo-gun, Hyogo 679-5198, Japan
| | - Toshinori Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Kazuhiko Misawa
- Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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9
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Turan HT, Meuwly M. Spectroscopy, Dynamics, and Hydration of S-Nitrosylated Myoglobin. J Phys Chem B 2021; 125:4262-4273. [PMID: 33724027 DOI: 10.1021/acs.jpcb.0c10353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
S-Nitrosylation, the covalent addition of NO to the thiol side chain of cysteine, is an important post-transitional modification that can alter the function of various proteins. The structural dynamics and vibrational spectroscopy of S-nitrosylation in the condensed phase are investigated for the methyl-capped cysteine model system and for myoglobin. Using conventional point charge and physically more realistic multipolar force fields for the -SNO group, it is found that the SN- and NO-stretch and the SNO-bend vibrations can be located and distinguished from the other protein modes for simulations of MbSNO at 50 K. The finding of stable cis- and trans-MbSNO agrees with experimental findings on other proteins as is the observation of buried -SNO. For MbSNO the observed relocation of the EF loop in the simulations by ∼3 Å is consistent with the available X-ray structure, and the conformations adopted by the -SNO label are in good overall agreement with the X-ray structure. Despite the larger size of the -SNO group compared with -SH, MbSNO recruits more water molecules in the first two hydration shells due to stronger electrostatic interactions. Similarly, when comparing the hydration between the A- and H-helices, they differ by up to 30% between WT and MbSNO. This suggests that local hydration can also be significantly modulated through nitrosylation.
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Affiliation(s)
- Haydar Taylan Turan
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel, Switzerland
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10
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Siani P, Motta S, Ferraro L, Dohn AO, Di Valentin C. Dopamine-Decorated TiO 2 Nanoparticles in Water: A QM/MM vs an MM Description. J Chem Theory Comput 2020; 16:6560-6574. [PMID: 32880452 PMCID: PMC7735700 DOI: 10.1021/acs.jctc.0c00483] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
Nanoparticle functionalization
is a modern strategy in nanotechnology
to build up devices for several applications. Modeling fully decorated
metal oxide nanoparticles of realistic size (few nanometers) in an
aqueous environment is a challenging task. In this work, we present
a case study relevant for solar-light exploitation and for biomedical
applications, i.e., a dopamine-functionalized TiO2 nanoparticle
(1700 atoms) in bulk water, for which we have performed an extensive
comparative investigation with both MM and QM/MM approaches of the
structural properties and of the conformational dynamics. We have
used a combined multiscale protocol for a more efficient exploration
of the complex conformational space. On the basis of the results of
this study and of some QM and experimental data, we have defined strengths
and limitations of the existing force field parameters. Our findings
will be useful for an improved modeling and simulation of many other
similar hybrid bioinorganic nanosystems in an aqueous environment
that are pivotal in a broad range of nanotechnological applications.
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Affiliation(s)
- Paulo Siani
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 55, 20125 Milano, Italy
| | - Stefano Motta
- Dipartimento di Scienze dell'Ambiente e della Terra, Università di Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Lorenzo Ferraro
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 55, 20125 Milano, Italy
| | - Asmus O Dohn
- Department of Physics, Technical University of Denmark, DK-2800 Lyngby, Denmark.,Faculty of Physical Sciences and Science Institute, University of Iceland, 107 Reykjavík, Iceland
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 55, 20125 Milano, Italy
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11
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Adjieufack AI, Nana CN, Ketcha-Mbadcam J, Mbouombouo Ndassa I, Andrés J, Oliva M, Safont VS. Deciphering the Curly Arrow Representation and Electron Flow for the 1,3-Dipolar Rearrangement between Acetonitrile Oxide and (1 S,2 R,4 S)-2-Cyano-7-oxabicyclo[2.2.1]hept-5-en-2-yl Acetate Derivatives. ACS OMEGA 2020; 5:22215-22225. [PMID: 32923779 PMCID: PMC7482254 DOI: 10.1021/acsomega.0c02371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
This study is focused on describing the molecular mechanism beyond the molecular picture provided by the evolution of molecular orbitals, valence bond structures along the reaction progress, or conceptual density functional theory. Using bonding evolution theory (BET) analysis, we have deciphered the mechanism of the 1,3-dipolar rearrangement between acetonitrile oxide and (1S,2R,4S)-2-cyano-7-oxabicyclo[2.2.1]hept-5-en-2-yl acetate derivatives. The BET study revealed that the formation of the C-C bond takes place via a usual sharing model before the O-C one that is also formed in the halogenated species through a not very usual sharing model. The mechanism includes depopulation of the electron density at the N-C triple bond and creation of the V(N) and V(C) monosynaptic basins, depopulation of the former C-C double bond with the creation of V(C,C) basins, and final formation of the V(O,C) basin associated with the O-C bond. The topological changes along the reaction pathway take place in a highly synchronous way. BET provides a convenient quantitative method for deriving curly arrows and electron flow representation to unravel molecular mechanisms.
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Affiliation(s)
- Abel Idrice Adjieufack
- Physical
and Theoretical Chemistry Laboratory and Computational Chemistry Laboratory,
High Teacher Training College, University
of Yaoundé 1, P.O. Box 47 Yaoundé, Cameroon
| | - Cyrille Nouhou Nana
- Physical
and Theoretical Chemistry Laboratory and Computational Chemistry Laboratory,
High Teacher Training College, University
of Yaoundé 1, P.O. Box 47 Yaoundé, Cameroon
| | - Joseph Ketcha-Mbadcam
- Physical
and Theoretical Chemistry Laboratory, University
of Yaoundé 1, P. O. Box 812 Yaoundé, Cameroon
| | - Ibrahim Mbouombouo Ndassa
- Computational
Chemistry Laboratory, High Teacher Training College, University of Yaoundé 1, P.O.
Box 47 Yaoundé, Cameroon
| | - Juan Andrés
- Departament
de Química Física i Analítica, Universitat Jaume I, Avda. Sos Baynat s/n, 12071 Castelló, Spain
| | - Mónica Oliva
- Departament
de Química Física i Analítica, Universitat Jaume I, Avda. Sos Baynat s/n, 12071 Castelló, Spain
| | - Vicent Sixte Safont
- Departament
de Química Física i Analítica, Universitat Jaume I, Avda. Sos Baynat s/n, 12071 Castelló, Spain
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12
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Unke OT, Koner D, Patra S, Käser S, Meuwly M. High-dimensional potential energy surfaces for molecular simulations: from empiricism to machine learning. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2020. [DOI: 10.1088/2632-2153/ab5922] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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13
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Mazal H, Haran G. Single-molecule FRET methods to study the dynamics of proteins at work. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019; 12:8-17. [PMID: 31989063 PMCID: PMC6984960 DOI: 10.1016/j.cobme.2019.08.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Feynman commented that "Everything that living things do can be understood in terms of the jiggling and wiggling of atoms". Proteins can jiggle and wiggle large structural elements such as domains and subunits as part of their functional cycles. Single-molecule fluorescence resonance energy transfer (smFRET) is an excellent tool to study conformational dynamics and decipher coordinated large-scale motions within proteins. smFRET methods introduced in recent years are geared toward understanding the time scales and amplitudes of function-related motions. This review discusses the methodology for obtaining and analyzing smFRET temporal trajectories that provide direct dynamic information on transitions between conformational states. It also introduces correlation methods that are useful for characterizing intramolecular motions. This arsenal of techniques has been used to study multiple molecular systems, from membrane proteins through molecular chaperones, and we examine some of these studies here. Recent exciting methodological novelties permit revealing very fast, submillisecond dynamics, whose relevance to protein function is yet to be fully grasped.
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Affiliation(s)
- Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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14
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Desmond JL, Koner D, Meuwly M. Probing the Differential Dynamics of the Monomeric and Dimeric Insulin from Amide-I IR Spectroscopy. J Phys Chem B 2019; 123:6588-6598. [PMID: 31318551 DOI: 10.1021/acs.jpcb.9b04628] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The monomer-dimer equilibrium for insulin is one of the essential steps in forming the receptor-binding competent monomeric form of the hormone. Despite this importance, the thermodynamic stability, in particular for modified insulins, is quite poorly understood, in part, due to experimental difficulties. This work explores one- and two-dimensional infrared spectroscopy in the range of the amide-I band for the hydrated monomeric and dimeric wild-type hormone. It is found that for the monomer the frequency fluctuation correlation function (FFCF) and the one-dimensional infrared spectra are position sensitive. The spectra of the -CO probes at the dimerization interface (residues Phe24, Phe25, and Tyr26) split and indicate an asymmetry despite the overall (formal) point symmetry of the dimer structure. Also, the decay times of the FFCF for the same -CO probe in the monomer and the dimer can differ by up to 1 order of magnitude, for example, for residue PheB24, which is solvent exposed for the monomer but at the interface for the dimer. The spectroscopic shifts correlate approximately with the average number of hydration waters and the magnitude of the FFCF at time zero. However, this correlation is only qualitative due to the heterogeneous and highly dynamical environment. Based on density functional theory calculations, the dominant contribution for solvent-exposed -CO is found to arise from the surrounding water (∼75%), whereas the protein environment contributes considerably less. The results suggest that infrared spectroscopy is a positionally sensitive probe of insulin dimerization, in particular in conjunction with isotopic labeling of the probe.
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Affiliation(s)
- Jasmine L Desmond
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , 4056 Basel , Switzerland
| | - Debasish Koner
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , 4056 Basel , Switzerland
| | - Markus Meuwly
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , 4056 Basel , Switzerland
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15
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Salehi SM, Koner D, Meuwly M. Vibrational Spectroscopy of N 3- in the Gas and Condensed Phase. J Phys Chem B 2019; 123:3282-3290. [PMID: 30830786 DOI: 10.1021/acs.jpcb.8b11430] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Azido-derivatized amino acids are potentially useful, positionally resolved spectroscopic probes for studying the structural dynamics of proteins and macromolecules in solution. To this end, a computational model for the vibrational modes of N3- based on accurate electronic structure calculations and a reproducing kernel Hilbert space representation of the potential energy surface for the internal degrees of freedom is developed. Fully dimensional quantum bound state calculations yield the antisymmetric stretch vibration at 1974 cm-1 compared with 1986 cm-1 from experiment. This mode shifts by 64 cm-1 (from the frequency distribution) and 74 cm-1 (from the IR line shape) to the blue, respectively, compared with 61 cm-1 from experiment for N3- in water. The decay time of the frequency fluctuation correlation function is 1.1 ps, which is in good agreement with experiment (1.2-1.3 ps) and the full width at half maximum of the asymmetric stretch in solution is 18.5 cm-1 compared with 25.2 cm-1 from experiment. A computationally more efficient analysis based on instantaneous normal modes is shown to provide comparable, albeit somewhat less quantitative results compared to solving the three-dimensional Schrödinger equation for the fundamental vibrations.
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Affiliation(s)
- Seyedeh Maryam Salehi
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , CH-4056 Basel , Switzerland
| | - Debasish Koner
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , CH-4056 Basel , Switzerland
| | - Markus Meuwly
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , CH-4056 Basel , Switzerland
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Abstract
The exchange of vibrational energy in proteins is crucial for their function. Here, we establish a connection between quantities related to it with geometry-based properties such as the proteins' residues coordination number. This relation is proven by molecular simulation in a neuro-pharmacologically relevant transmembrane receptor. The connection demonstrated here paves the way to studies of protein allostery and conformational changes based solely on protein structure.
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Affiliation(s)
- L Maggi
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - P Carloni
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
- Institute for Neuroscience and Medicine INM-11 , Forschungszentrum Jülich , 52428 Jülich , Germany
- Department of Physics , RWTH Aachen University , 52078 Aachen , Germany
- Department of Neurology , University Hospital Aachen , 52078 Aachen , Germany
| | - G Rossetti
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
- Division Computational Science - Simulation Laboratory Biology, Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH , 52428 Jülich , Germany
- Department of Oncology, Hematology and Stem Cell Transplantation, University Hospital Aachen , RWTH Aachen University , 52074 Aachen , Germany
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17
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Meuwly M. Reactive molecular dynamics: From small molecules to proteins. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1386] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Markus Meuwly
- Department of Chemistry University of Basel Basel Switzerland
- Department of Chemistry Brown University Providence Rhode Island
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Abela R, Beaud P, van Bokhoven JA, Chergui M, Feurer T, Haase J, Ingold G, Johnson SL, Knopp G, Lemke H, Milne CJ, Pedrini B, Radi P, Schertler G, Standfuss J, Staub U, Patthey L. Perspective: Opportunities for ultrafast science at SwissFEL. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061602. [PMID: 29376109 PMCID: PMC5758366 DOI: 10.1063/1.4997222] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 10/17/2017] [Indexed: 05/03/2023]
Abstract
We present the main specifications of the newly constructed Swiss Free Electron Laser, SwissFEL, and explore its potential impact on ultrafast science. In light of recent achievements at current X-ray free electron lasers, we discuss the potential territory for new scientific breakthroughs offered by SwissFEL in Chemistry, Biology, and Materials Science, as well as nonlinear X-ray science.
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Affiliation(s)
- Rafael Abela
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Paul Beaud
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Jeroen A van Bokhoven
- Laboratory for Catalysis and Sustainable Chemistry, Paul-Scherrer Institute, 5232 Villigen PSI, and Department of Chemistry, ETH-Zürich, 8093 Zürich, Switzerland
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide (LSU) and Lausanne Centre for Ultrafast Science (LACUS), Ecole Polytechnique Fédérale de Lausanne (EPFL), ISIC-FSB, Station 6, 1015 Lausanne, Switzerland
| | - Thomas Feurer
- Institute of Applied Physics, University of Bern, Bern, Switzerland
| | - Johannes Haase
- Laboratory for Catalysis and Sustainable Chemistry, Paul-Scherrer Institute, 5232 Villigen PSI, and Department of Chemistry, ETH-Zürich, 8093 Zürich, Switzerland
| | - Gerhard Ingold
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Steven L Johnson
- Institute for Quantum Electronics, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zurich, Switzerland
| | - Gregor Knopp
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Henrik Lemke
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Chris J Milne
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Bill Pedrini
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Peter Radi
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | | | - Jörg Standfuss
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Urs Staub
- Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Luc Patthey
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
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