1
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Kansari M, Idiris F, Szurmant H, Kubař T, Schug A. Mechanism of activation and autophosphorylation of a histidine kinase. Commun Chem 2024; 7:196. [PMID: 39227740 PMCID: PMC11371814 DOI: 10.1038/s42004-024-01272-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/06/2024] [Indexed: 09/05/2024] Open
Abstract
Histidine kinases (HK) are one of the main prokaryotic signaling systems. Two structurally conserved catalytic domains inside the HK enable autokinase, phosphotransfer, and phosphatase activities. Here, we focus on a detailed mechanistic understanding of the functional cycle of the WalK HK by a multi-scale simulation approach, consisting of classical as well as hybrid QM/MM molecular dynamics simulation. Strikingly, a conformational transition induced solely in DHp leads to the correct activated conformation in CA crucial for autophosphorylation. This finding explains how variable sensor domains induce the transition from inactive to active state. The subsequent autophosphorylation inside DHp proceeds via a penta-coordinated transition state to a protonated phosphohistidine intermediate. This intermediate is consequently deprotonated by a suitable nearby base. The reaction energetics are controlled by the final proton acceptor and presence of a magnesium cation. The slow rates of the process result from the high energy barrier of the conformational transition between inactive and active states. The phosphorylation step exhibits a lower barrier and down-the-hill energetics. Thus, our work suggests a detailed mechanistic model for HK autophosphorylation.
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Affiliation(s)
- Mayukh Kansari
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Fathia Idiris
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Hendrik Szurmant
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, USA
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alexander Schug
- Jülich Supercomputing Centre, Forschungszentrum Jülich, Jülich, Germany.
- Faculty of Biology, University of Duisburg/Essen, Essen, Germany.
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2
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Pederson JP, McDaniel JG. PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics. J Chem Phys 2024; 161:034103. [PMID: 39007371 DOI: 10.1063/5.0219851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM/MM/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM/MM/PME and alternative QM/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100 ps QM/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule's electron density.
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Affiliation(s)
- John P Pederson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Jesse G McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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3
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Solov’yov AV, Verkhovtsev AV, Mason NJ, Amos RA, Bald I, Baldacchino G, Dromey B, Falk M, Fedor J, Gerhards L, Hausmann M, Hildenbrand G, Hrabovský M, Kadlec S, Kočišek J, Lépine F, Ming S, Nisbet A, Ricketts K, Sala L, Schlathölter T, Wheatley AEH, Solov’yov IA. Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment. Chem Rev 2024; 124:8014-8129. [PMID: 38842266 PMCID: PMC11240271 DOI: 10.1021/acs.chemrev.3c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.
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Affiliation(s)
| | | | - Nigel J. Mason
- School
of Physics and Astronomy, University of
Kent, Canterbury CT2 7NH, United
Kingdom
| | - Richard A. Amos
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Ilko Bald
- Institute
of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gérard Baldacchino
- Université
Paris-Saclay, CEA, LIDYL, 91191 Gif-sur-Yvette, France
- CY Cergy Paris Université,
CEA, LIDYL, 91191 Gif-sur-Yvette, France
| | - Brendan Dromey
- Centre
for Light Matter Interactions, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Martin Falk
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Juraj Fedor
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
- Faculty
of Engineering, University of Applied Sciences
Aschaffenburg, Würzburger
Str. 45, 63743 Aschaffenburg, Germany
| | | | - Stanislav Kadlec
- Eaton European
Innovation Center, Bořivojova
2380, 25263 Roztoky, Czech Republic
| | - Jaroslav Kočišek
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Franck Lépine
- Université
Claude Bernard Lyon 1, CNRS, Institut Lumière
Matière, F-69622, Villeurbanne, France
| | - Siyi Ming
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew Nisbet
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Kate Ricketts
- Department
of Targeted Intervention, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Leo Sala
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Thomas Schlathölter
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
- University
College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
| | - Andrew E. H. Wheatley
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
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4
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Sarngadharan P, Holtkamp Y, Kleinekathöfer U. Protein Effects on the Excitation Energies and Exciton Dynamics of the CP24 Antenna Complex. J Phys Chem B 2024; 128:5201-5217. [PMID: 38756003 PMCID: PMC11145653 DOI: 10.1021/acs.jpcb.4c01637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024]
Abstract
In this study, the site energy fluctuations, energy transfer dynamics, and some spectroscopic properties of the minor light-harvesting complex CP24 in a membrane environment were determined. For this purpose, a 3 μs-long classical molecular dynamics simulation was performed for the CP24 complex. Furthermore, using the density functional tight binding/molecular mechanics molecular dynamics (DFTB/MM MD) approach, we performed excited state calculations for the chlorophyll a and chlorophyll b molecules in the complex starting from five different positions of the MD trajectory. During the extended simulations, we observed variations in the site energies of the different sets as a result of the fluctuating protein environment. In particular, a water coordination to Chl-b 608 occurred only after about 1 μs in the simulations, demonstrating dynamic changes in the environment of this pigment. From the classical and the DFTB/MM MD simulations, spectral densities and the (time-dependent) Hamiltonian of the complex were determined. Based on these results, three independent strongly coupled chlorophyll clusters were revealed within the complex. In addition, absorption and fluorescence spectra were determined together with the exciton relaxation dynamics, which reasonably well agrees with experimental time scales.
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Affiliation(s)
- Pooja Sarngadharan
- School of Science, Constructor
University, Campus Ring
1, 28759 Bremen, Germany
| | - Yannick Holtkamp
- School of Science, Constructor
University, Campus Ring
1, 28759 Bremen, Germany
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5
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Giese TJ, York DM. Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations. J Chem Phys 2023; 158:174105. [PMID: 37125722 PMCID: PMC10154067 DOI: 10.1063/5.0147218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/17/2023] [Indexed: 05/02/2023] Open
Abstract
We use the modified Bigeleisen-Mayer equation to compute kinetic isotope effect values for non-enzymatic phosphoryl transfer reactions from classical and path integral molecular dynamics umbrella sampling. The modified form of the Bigeleisen-Mayer equation consists of a ratio of imaginary mode vibrational frequencies and a contribution arising from the isotopic substitution's effect on the activation free energy, which can be computed from path integral simulation. In the present study, we describe a practical method for estimating the frequency ratio correction directly from umbrella sampling in a manner that does not require normal mode analysis of many geometry optimized structures. Instead, the method relates the frequency ratio to the change in the mass weighted coordinate representation of the minimum free energy path at the transition state induced by isotopic substitution. The method is applied to the calculation of 16/18O and 32/34S primary kinetic isotope effect values for six non-enzymatic phosphoryl transfer reactions. We demonstrate that the results are consistent with the analysis of geometry optimized transition state ensembles using the traditional Bigeleisen-Mayer equation. The method thus presents a new practical tool to enable facile calculation of kinetic isotope effect values for complex chemical reactions in the condensed phase.
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Affiliation(s)
- Timothy J. Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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6
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Clemente CM, Capece L, Martí MA. Best Practices on QM/MM Simulations of Biological Systems. J Chem Inf Model 2023; 63:2609-2627. [PMID: 37100031 DOI: 10.1021/acs.jcim.2c01522] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
During the second half of the 20th century, following structural biology hallmark works on DNA and proteins, biochemists shifted their questions from "what does this molecule look like?" to "how does this process work?". Prompted by the theoretical and practical developments in computational chemistry, this led to the emergence of biomolecular simulations and, along with the 2013 Nobel Prize in Chemistry, to the development of hybrid QM/MM methods. QM/MM methods are necessary whenever the problem we want to address involves chemical reactivity and/or a change in the system's electronic structure, with archetypal examples being the studies of an enzyme's reaction mechanism and a metalloprotein's active site. In the last decades QM/MM methods have seen an increasing adoption driven by their incorporation in widely used biomolecular simulation software. However, properly setting up a QM/MM simulation is not an easy task, and several issues need to be properly addressed to obtain meaningful results. In the present work, we describe both the theoretical concepts and practical issues that need to be considered when performing QM/MM simulations. We start with a brief historical perspective on the development of these methods and describe when and why QM/MM methods are mandatory. Then we show how to properly select and analyze the performance of the QM level of theory, the QM system size, and the position and type of the boundaries. We show the relevance of performing prior QM model system (or QM cluster) calculations in a vacuum and how to use the corresponding results to adequately calibrate those derived from QM/MM. We also discuss how to prepare the starting structure and how to select an adequate simulation strategy, including those based on geometry optimizations as well as free energy methods. In particular, we focus on the determination of free energy profiles using multiple steered molecular dynamics (MSMD) combined with Jarzynski's equation. Finally, we describe the results for two illustrative and complementary examples: the reaction performed by chorismate mutase and the study of ligand binding to hemoglobins. Overall, we provide many practical recommendations (or shortcuts) together with important conceptualizations that we hope will encourage more and more researchers to incorporate QM/MM studies into their research projects.
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Affiliation(s)
- Camila M Clemente
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química de los Materiales, Ambiente y Energía (INQUIMAE) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
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7
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Zlobin A, Belyaeva J, Golovin A. Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms. J Chem Inf Model 2023; 63:546-560. [PMID: 36633836 DOI: 10.1021/acs.jcim.2c01071] [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: 01/13/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) simulations fuel discoveries in many fields of science including computational biochemistry and enzymology. Development of more convenient tools leads to an increase in the number of works in which mechanical insights into enzymes' mode of operation are obtained. Most commonly, these tools feature hydrogen-capping (link atom) approach to provide coupling between QM and MM subsystems across a covalent bond. Extensive studies were conducted to provide a solid foundation for the correctness of such an approach when a bond to a nonpolar MM atom is considered. However, not every task may be accomplished this way. Certain scenarios of using QM/MM in computational enzymology encourage or even necessitate the incorporation of backbone atoms into the QM region. Two out of three backbone atoms are polar, and in QM/MM with electrostatic embedding, a neighboring link atom will be hyperpolarized. Several schemes to mitigate this effect were previously proposed alongside a rigorous assessment of quantitative effects on model systems. However, it was not clear whether they may translate into qualitatively different results and how link atom hyperpolarization may manifest itself in a real-life enzymological scenario. Here, we show that the consequences of such an artifact may be severe and may completely overturn the conclusions drawn from the simulations. Our case advocates for the use of charge redistribution schemes whenever intra-backbone QM/MM boundaries are considered. Moreover, we addressed how different boundary types and charge redistribution schemes influence backbone dynamics. We showed that the results are heavily dependent on which boundary MM terms are retained, with charge alteration being of secondary importance. In the worst case, only three intra-backbone boundaries may be used with relative confidence in the adequacy of resulting simulations, irrespective of the hyperpolarization mitigation scheme. Thus, advances in the field are certainly needed to fuel new discoveries. As of now, we believe that issues raised in this work might encourage authors in the field to report what boundaries, boundary MM terms, and charge redistribution schemes they are using, so their results may be correctly interpreted.
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Affiliation(s)
- Alexander Zlobin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Julia Belyaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Andrey Golovin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
- Sirius University of Science and Technology, 354340 Sochi, Russia
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8
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Giese TJ, Zeng J, York DM. Multireference Generalization of the Weighted Thermodynamic Perturbation Method. J Phys Chem A 2022; 126:8519-8533. [PMID: 36301936 PMCID: PMC9771595 DOI: 10.1021/acs.jpca.2c06201] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe the generalized weighted thermodynamic perturbation (gwTP) method for estimating the free energy surface of an expensive "high-level" potential energy function from the umbrella sampling performed with multiple inexpensive "low-level" reference potentials. The gwTP method is a generalization of the weighted thermodynamic perturbation (wTP) method developed by Li and co-workers [J. Chem. Theory Comput. 2018, 14, 5583-5596] that uses a single "low-level" reference potential. The gwTP method offers new possibilities in model design whereby the sampling generated from several low-level potentials may be combined (e.g., specific reaction parameter models that might have variable accuracy at different stages of a multistep reaction). The gwTP method is especially well suited for use with machine learning potentials (MLPs) that are trained against computationally expensive ab initio quantum mechanical/molecular mechanical (QM/MM) energies and forces using active learning procedures that naturally produce multiple distinct neural network potentials. Simulations can be performed with greater sampling using the fast MLPs and then corrected to the ab initio level using gwTP. The capabilities of the gwTP method are demonstrated by creating reference potentials based on the MNDO/d and DFTB2/MIO semiempirical models supplemented with the "range-corrected deep potential" (DPRc). The DPRc parameters are trained to ab initio QM/MM data, and the potentials are used to calculate the free energy surface of stepwise mechanisms for nonenzymatic RNA 2'-O-transesterification model reactions. The extended sampling made possible by the reference potentials allows one to identify unequilibrated portions of the simulations that are not always evident from the short time scale commonly used with ab initio QM/MM potentials. We show that the reference potential approach can yield more accurate ab initio free energy predictions than the wTP method or what can be reasonably afforded from explicit ab initio QM/MM sampling.
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Affiliation(s)
- Timothy J. Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Jinzhe Zeng
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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9
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Electrostatic and steric effects underlie acetylation-induced changes in ubiquitin structure and function. Nat Commun 2022; 13:5435. [PMID: 36114200 PMCID: PMC9481602 DOI: 10.1038/s41467-022-33087-1] [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] [Received: 11/02/2021] [Accepted: 08/26/2022] [Indexed: 12/29/2022] Open
Abstract
Covalent attachment of ubiquitin (Ub) to proteins is a highly versatile posttranslational modification. Moreover, Ub is not only a modifier but itself is modified by phosphorylation and lysine acetylation. However, the functional consequences of Ub acetylation are poorly understood. By generation and comprehensive characterization of all seven possible mono-acetylated Ub variants, we show that each acetylation site has a particular impact on Ub structure. This is reflected in selective usage of the acetylated variants by different E3 ligases and overlapping but distinct interactomes, linking different acetylated variants to different cellular pathways. Notably, not only electrostatic but also steric effects contribute to acetylation-induced changes in Ub structure and, thus, function. Finally, we provide evidence that p300 acts as a position-specific Ub acetyltransferase and HDAC6 as a general Ub deacetylase. Our findings provide intimate insights into the structural and functional consequences of Ub acetylation and highlight the general importance of Ub acetylation. Ubiquitin is not only a posttranslational modifier but itself is subject to modifications, such as acetylation. Characterization of distinct acetylated ubiquitin variants reveals that each acetylation site has a particular impact on ubiquitin structure and its protein-protein interaction properties.
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10
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Cofer-Shabica DV, Menger MFSJ, Ou Q, Shao Y, Subotnik JE, Faraji S. INAQS, a Generic Interface for Nonadiabatic QM/MM Dynamics: Design, Implementation, and Validation for GROMACS/Q-CHEM simulations. J Chem Theory Comput 2022; 18:4601-4614. [PMID: 35901266 DOI: 10.1021/acs.jctc.2c00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The accurate description of large molecular systems in complex environments remains an ongoing challenge for the field of computational chemistry. This problem is even more pronounced for photoinduced processes, as multiple excited electronic states and their corresponding nonadiabatic couplings must be taken into account. Multiscale approaches such as hybrid quantum mechanics/molecular mechanics (QM/MM) offer a balanced compromise between accuracy and computational burden. Here, we introduce an open-source software package (INAQS) for nonadiabatic QM/MM simulations that bridges the sampling capabilities of the GROMACS MD package and the excited-state infrastructure of the Q-CHEM electronic structure software. The interface is simple and can be adapted easily to other MD codes. The code supports a variety of different trajectory-based molecular dynamics, ranging from Born-Oppenheimer to surface hopping dynamics. To illustrate the power of this combination, we simulate electronic absorption spectra, free-energy surfaces along a reaction coordinate, and the excited-state dynamics of 1,3-cyclohexadiene in solution.
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Affiliation(s)
- D Vale Cofer-Shabica
- Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Cret Wing 141D, Philadelphia, Pennsylvania 19104-6243, United States
| | - Maximilian F S J Menger
- Zernike Institute for Advanced Materials, Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Qi Ou
- AI for Science Institute, Beijing 100080, China
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Joseph E Subotnik
- Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Cret Wing 141D, Philadelphia, Pennsylvania 19104-6243, United States
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
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11
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Giese TJ, Zeng J, Ekesan Ş, York DM. Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions. J Chem Theory Comput 2022; 18:4304-4317. [PMID: 35709391 PMCID: PMC9283286 DOI: 10.1021/acs.jctc.2c00151] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a fast, accurate, and robust approach for determination of free energy profiles and kinetic isotope effects for RNA 2'-O-transphosphorylation reactions with inclusion of nuclear quantum effects. We apply a deep potential range correction (DPRc) for combined quantum mechanical/molecular mechanical (QM/MM) simulations of reactions in the condensed phase. The method uses the second-order density-functional tight-binding method (DFTB2) as a fast, approximate base QM model. The DPRc model modifies the DFTB2 QM interactions and applies short-range corrections to the QM/MM interactions to reproduce ab initio DFT (PBE0/6-31G*) QM/MM energies and forces. The DPRc thus enables both QM and QM/MM interactions to be tuned to high accuracy, and the QM/MM corrections are designed to smoothly vanish at a specified cutoff boundary (6 Å in the present work). The computational speed-up afforded by the QM/MM+DPRc model enables free energy profiles to be calculated that include rigorous long-range QM/MM interactions under periodic boundary conditions and nuclear quantum effects through a path integral approach using a new interface between the AMBER and i-PI software. The approach is demonstrated through the calculation of free energy profiles of a native RNA cleavage model reaction and reactions involving thio-substitutions, which are important experimental probes of the mechanism. The DFTB2+DPRc QM/MM free energy surfaces agree very closely with the PBE0/6-31G* QM/MM results, and it is vastly superior to the DFTB2 QM/MM surfaces with and without weighted thermodynamic perturbation corrections. 18O and 34S primary kinetic isotope effects are compared, and the influence of nuclear quantum effects on the free energy profiles is examined.
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Affiliation(s)
- Timothy J. Giese
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Jinzhe Zeng
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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12
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Sarngadharan P, Maity S, Kleinekathöfer U. Spectral densities and absorption spectra of the core antenna complex CP43 from photosystem II. J Chem Phys 2022; 156:215101. [DOI: 10.1063/5.0091005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Besides absorbing light, the core antenna complex CP43 of photosystem II is of great importance in transferring excitation energy from the antenna complexes to the reaction center. Excitation energies, spectral densities, and linear absorption spectra of the complex have been evaluated by a multiscale approach. In this scheme, quantum mechanics/molecular mechanics molecular dynamics simulations are performed employing the parameterized density functional tight binding (DFTB) while the time-dependent long-range-corrected DFTB scheme is applied for the excited state calculations. The obtained average spectral density of the CP43 complex shows a very good agreement with experimental results. Moreover, the excitonic Hamiltonian of the system along with the computed site-dependent spectral densities was used to determine the linear absorption. While a Redfield-like approximation has severe shortcomings in dealing with the CP43 complex due to quasi-degenerate states, the non-Markovian full second-order cumulant expansion formalism is able to overcome the drawbacks. Linear absorption spectra were obtained, which show a good agreement with the experimental counterparts at different temperatures. This study once more emphasizes that by combining diverse techniques from the areas of molecular dynamics simulations, quantum chemistry, and open quantum systems, it is possible to obtain first-principle results for photosynthetic complexes, which are in accord with experimental findings.
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Affiliation(s)
- Pooja Sarngadharan
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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13
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Yusef Buey M, Mineva T, Rapacioli M. Coupling density functional based tight binding with class 1 force fields in a hybrid QM/MM scheme. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02878-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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inanlou S, Cortés-Mejía R, Özdemir AD, Höfener S, Klopper W, Wenzel W, Xie W, Elstner M. Understanding excited state properties of host materials in OLEDs: simulation of absorption spectrum of amorphous 4,4-bis(carbazol-9-yl)-2,2-biphenyl (CBP). Phys Chem Chem Phys 2022; 24:4576-4587. [DOI: 10.1039/d1cp04293a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
4,4-bis(carbazol-9-yl)-2,2-biphenyl (CBP) is widely used as a host material in phosphorescent organic light-emitting diodes (PhOLEDs). In the present study, we simulate the absorption spectra of CBP in gas and condensed...
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15
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Maag D, Putzu M, Gómez-Flores CL, Gräter F, Elstner M, Kubař T. Electrostatic interactions contribute to the control of intramolecular thiol-disulfide isomerization in a protein. Phys Chem Chem Phys 2021; 23:26366-26375. [PMID: 34792054 DOI: 10.1039/d1cp03129e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The roles of structural factors and of electrostatic interactions with the environment on the outcome of thiol-disulfide exchange reactions were investigated in a mutated immunoglobulin domain (I27*) under mechanical stress. An extensive ensemble of molecular dynamics trajectories was generated by means of QM/MM simulations for a total sampling of 5.7 μs. A significant number of thiol-disulfide exchanges were observed, and the Cys32 thiolate preferred to attack Cys55 over Cys24, in agreement with previous experimental and computational studies. The structural features as well as electronic structures of the thiol-disulfide system along the reaction were analyzed, as were the electrostatic interactions with the environment. The previous findings of better accessibility of Cys55 were confirmed. Additionally, the reaction was found to be directed by the electrostatic interactions of the involved sulfur atoms with the molecular environment. The relationships of atomic charges, which stem from the electrostatic interactions, lead to the kinetic preference of the attack on Cys55. Further, QM/MM metadynamics simulations of thiol-disulfide exchange in a small model system with varied artificial external electric potentials revealed changes in reaction kinetics of the same magnitude as in I27*. Therefore, the electrostatic interactions are confirmed to play a role in the regioselectivity of the thiol-disulfide exchange reactions in the protein.
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Affiliation(s)
- Denis Maag
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany.
| | - Marina Putzu
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany.
| | - Claudia L Gómez-Flores
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany.
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany. .,Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany.
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16
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Maag D, Mast T, Elstner M, Cui Q, Kubař T. O to bR transition in bacteriorhodopsin occurs through a proton hole mechanism. Proc Natl Acad Sci U S A 2021; 118:e2024803118. [PMID: 34561302 PMCID: PMC8488608 DOI: 10.1073/pnas.2024803118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 12/27/2022] Open
Abstract
Extensive classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations are used to establish the structural features of the O state in bacteriorhodopsin (bR) and its conversion back to the bR ground state. The computed free energy surface is consistent with available experimental data for the kinetics and thermodynamics of the O to bR transition. The simulation results highlight the importance of the proton release group (PRG, consisting of Glu194/204) and the conserved arginine 82 in modulating the hydration level of the protein cavity. In particular, in the O state, deprotonation of the PRG and downward rotation of Arg82 lead to elevated hydration level and a continuous water network that connects the PRG to the protonated Asp85. Proton exchange through this water network is shown by ∼0.1-μs semiempirical QM/MM free energy simulations to occur through the generation and propagation of a proton hole, which is relayed by Asp212 and stabilized by Arg82. This mechanism provides an explanation for the observation that the D85S mutant of bacteriorhodopsin pumps chloride ions. The electrostatics-hydration coupling mechanism and the involvement of all titration states of water are likely applicable to many biomolecules involved in bioenergetic transduction.
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Affiliation(s)
- Denis Maag
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Thilo Mast
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Institute for Biological Interfaces, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, MA 02215
- Department of Physics, Boston University, Boston, MA 02215
- Department of Biomedical Engineering, Boston University, Boston, MA 02215
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany;
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17
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Maity S, Sarngadharan P, Daskalakis V, Kleinekathöfer U. Time-dependent atomistic simulations of the CP29 light-harvesting complex. J Chem Phys 2021; 155:055103. [PMID: 34364345 DOI: 10.1063/5.0053259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Light harvesting as the first step in photosynthesis is of prime importance for life on earth. For a theoretical description of photochemical processes during light harvesting, spectral densities are key quantities. They serve as input functions for modeling the excitation energy transfer dynamics and spectroscopic properties. Herein, a recently developed procedure is applied to determine the spectral densities of the pigments in the minor antenna complex CP29 of photosystem II, which has recently gained attention because of its active role in non-photochemical quenching processes in higher plants. To this end, the density functional-based tight binding (DFTB) method has been employed to enable simulation of the ground state dynamics in a quantum-mechanics/molecular mechanics (QM/MM) scheme for each chlorophyll pigment. Subsequently, the time-dependent extension of the long-range corrected DFTB approach has been used to obtain the excitation energy fluctuations along the ground-state trajectories also in a QM/MM setting. From these results, the spectral densities have been determined and compared for different force fields and to spectral densities from other light-harvesting complexes. In addition, time-dependent and time-independent excitonic Hamiltonians of the system have been constructed and applied to the determination of absorption spectra as well as exciton dynamics.
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Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Pooja Sarngadharan
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str. 3603, Limassol, Cyprus
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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18
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Watanabe HC, Yamada M, Suzuki Y. Proton transfer in bulk water using the full adaptive QM/MM method: integration of solute- and solvent-adaptive approaches. Phys Chem Chem Phys 2021; 23:8344-8360. [PMID: 33875999 DOI: 10.1039/d1cp00116g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The quantum mechanical/molecular mechanical (QM/MM) method is a hybrid molecular simulation technique that increases the accessibility of local electronic structures of large systems. The technique combines the benefit of accuracy found in the QM method and that of cost efficiency found in the MM method. However, it is difficult to directly apply the QM/MM method to the dynamics of solution systems, particularly for proton transfer. As explained in the Grotthuss mechanism, proton transfer is a structural interconversion between hydronium ions and solvent water molecules. Hence, when the QM/MM method is applied, an adaptive treatment, namely on-the-fly revisions on molecular definitions, is required for both the solute and solvent. Although several solvent-adaptive methods have been proposed, a full adaptive framework, which is an approach that also considers adaptation for solutes, remains untapped. In this paper, we propose a new numerical expression for the coordinates of the excess proton and its control algorithm. Furthermore, we confirm that this method can stably and accurately simulate proton transfer dynamics in bulk water.
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Affiliation(s)
- Hiroshi C Watanabe
- Quantum Computing Center, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
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19
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Maity S, Daskalakis V, Elstner M, Kleinekathöfer U. Multiscale QM/MM molecular dynamics simulations of the trimeric major light-harvesting complex II. Phys Chem Chem Phys 2021; 23:7407-7417. [PMID: 33876100 DOI: 10.1039/d1cp01011e] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photosynthetic processes are driven by sunlight. Too little of it and the photosynthetic machinery cannot produce the reductive power to drive the anabolic pathways. Too much sunlight and the machinery can get damaged. In higher plants, the major Light-Harvesting Complex (LHCII) efficiently absorbs the light energy, but can also dissipate it when in excess (quenching). In order to study the dynamics related to the quenching process but also the exciton dynamics in general, one needs to accurately determine the so-called spectral density which describes the coupling between the relevant pigment modes and the environmental degrees of freedom. To this end, Born-Oppenheimer molecular dynamics simulations in a quantum mechanics/molecular mechanics (QM/MM) fashion utilizing the density functional based tight binding (DFTB) method have been performed for the ground state dynamics. Subsequently, the time-dependent extension of the long-range-corrected DFTB scheme has been employed for the excited state calculations of the individual chlorophyll-a molecules in the LHCII complex. The analysis of this data resulted in spectral densities showing an astonishing agreement with the experimental counterpart in this rather large system. This consistency with an experimental observable also supports the accuracy, robustness, and reliability of the present multi-scale scheme. To the best of our knowledge, this is the first theoretical attempt on this large complex system is ever made to accurately simulate the spectral density. In addition, the resulting spectral densities and site energies were used to determine the exciton transfer rate within a special pigment pair consisting of a chlorophyll-a and a carotenoid molecule which is assumed to play a role in the balance between the light harvesting and quenching modes.
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Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
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20
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Pan X, Nam K, Epifanovsky E, Simmonett AC, Rosta E, Shao Y. A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations. J Chem Phys 2021; 154:024115. [PMID: 33445891 DOI: 10.1063/5.0038120] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In a previous work [Pan et al., Molecules 23, 2500 (2018)], a charge projection scheme was reported, where outer molecular mechanical (MM) charges [>10 Å from the quantum mechanical (QM) region] were projected onto the electrostatic potential (ESP) grid of the QM region to accurately and efficiently capture long-range electrostatics in ab initio QM/MM calculations. Here, a further simplification to the model is proposed, where the outer MM charges are projected onto inner MM atom positions (instead of ESP grid positions). This enables a representation of the long-range MM electrostatic potential via augmentary charges (AC) on inner MM atoms. Combined with the long-range electrostatic correction function from Cisneros et al. [J. Chem. Phys. 143, 044103 (2015)] to smoothly switch between inner and outer MM regions, this new QM/MM-AC electrostatic model yields accurate and continuous ab initio QM/MM electrostatic energies with a 10 Å cutoff between inner and outer MM regions. This model enables efficient QM/MM cluster calculations with a large number of MM atoms as well as QM/MM calculations with periodic boundary conditions.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, Oklahoma 73019, USA
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Andrew C Simmonett
- National Institutes of Health-National Heart, Lung and Blood Institute, Laboratory of Computational Biology, Bethesda, Maryland 20892, USA
| | - Edina Rosta
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, Oklahoma 73019, USA
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21
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Golovin AV, Devred F, Yatoui D, Roman AY, Zalevsky AO, Puppo R, Lebrun R, Guerlesquin F, Tsvetkov PO. Zinc Binds to RRM2 Peptide of TDP-43. Int J Mol Sci 2020; 21:E9080. [PMID: 33260324 PMCID: PMC7730363 DOI: 10.3390/ijms21239080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022] Open
Abstract
Transactive response DNA and RNA binding protein 43 kDa (TDP-43) is a highly conserved heterogeneous nuclear ribonucleoprotein (hnRNP), which is involved in several steps of protein production including transcription and splicing. Its aggregates are frequently observed in motor neurons from amyotrophic lateral sclerosis patients and in the most common variant of frontotemporal lobar degeneration. Recently it was shown that TDP-43 is able to bind Zn2+ by its RRM domain. In this work, we have investigated Zn2+ binding to a short peptide 256-264 from C-terminus of RRM2 domain using isothermal titration calorimetry, electrospray ionization mass spectrometry, QM/MM simulations, and NMR spectroscopy. We have found that this peptide is able to bind zinc ions with a Ka equal to 1.6 × 105 M-1. Our findings suggest the existence of a zinc binding site in the C-terminal region of RRM2 domain. Together with the existing structure of the RRM2 domain of TDP-43 we propose a model of its complex with Zn2+ which illustrates how zinc might regulate DNA/RNA binding.
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Affiliation(s)
- Andrey V. Golovin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russian; (A.V.G.); (A.O.Z.)
- Sirius University of Science and Technology, 354340 Sochi, Russian
- Faculty of Computer Science, National Research University Higher School of Economics, 101000 Moscow, Russian
| | - Francois Devred
- Inst Neurophysiopathol, CNRS, INP, Aix Marseille Université, 13385 Marseille, France; (F.D.); (D.Y.); (A.Y.R.)
| | - Dahbia Yatoui
- Inst Neurophysiopathol, CNRS, INP, Aix Marseille Université, 13385 Marseille, France; (F.D.); (D.Y.); (A.Y.R.)
| | - Andrei Yu. Roman
- Inst Neurophysiopathol, CNRS, INP, Aix Marseille Université, 13385 Marseille, France; (F.D.); (D.Y.); (A.Y.R.)
- Institute of Physiologically Active Compounds, RAS, 142432 Chernogolovka, Russian
| | - Arthur O. Zalevsky
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russian; (A.V.G.); (A.O.Z.)
- Sirius University of Science and Technology, 354340 Sochi, Russian
| | - Remy Puppo
- Plate-forme Protéomique, Institut de Microbiologie de la Méditerranée (IMM), CNRS FR 3479, Aix-Marseille Université, Marseille Protéomique (MaP), 13009 Marseille, France; (R.P.); (R.L.)
| | - Regine Lebrun
- Plate-forme Protéomique, Institut de Microbiologie de la Méditerranée (IMM), CNRS FR 3479, Aix-Marseille Université, Marseille Protéomique (MaP), 13009 Marseille, France; (R.P.); (R.L.)
| | - Francoise Guerlesquin
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, UMR 7255, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, 13009 Marseille, France;
| | - Philipp O. Tsvetkov
- Inst Neurophysiopathol, CNRS, INP, Aix Marseille Université, 13385 Marseille, France; (F.D.); (D.Y.); (A.Y.R.)
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22
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Terekhov SS, Mokrushina YA, Nazarov AS, Zlobin A, Zalevsky A, Bourenkov G, Golovin A, Belogurov A, Osterman IA, Kulikova AA, Mitkevich VA, Lou HJ, Turk BE, Wilmanns M, Smirnov IV, Altman S, Gabibov AG. A kinase bioscavenger provides antibiotic resistance by extremely tight substrate binding. SCIENCE ADVANCES 2020; 6:eaaz9861. [PMID: 32637600 PMCID: PMC7314540 DOI: 10.1126/sciadv.aaz9861] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities are self-controlled by repertoires of lethal agents, the antibiotics. In their turn, these antibiotics are regulated by bioscavengers that are selected in the course of evolution. Kinase-mediated phosphorylation represents one of the general strategies for the emergence of antibiotic resistance. A new subfamily of AmiN-like kinases, isolated from the Siberian bear microbiome, inactivates antibiotic amicoumacin by phosphorylation. The nanomolar substrate affinity defines AmiN as a phosphotransferase with a unique catalytic efficiency proximal to the diffusion limit. Crystallographic analysis and multiscale simulations revealed a catalytically perfect mechanism providing phosphorylation exclusively in the case of a closed active site that counteracts substrate promiscuity. AmiN kinase is a member of the previously unknown subfamily representing the first evidence of a specialized phosphotransferase bioscavenger.
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Affiliation(s)
- Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Yuliana A. Mokrushina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Anton S. Nazarov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Alexander Zlobin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Arthur Zalevsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, Russia
| | | | - Andrey Golovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, Russia
| | - Alexey Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Ilya A. Osterman
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Alexandra A. Kulikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir A. Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | | | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Sidney Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Arizona State University, Tempe, AZ, USA
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Department of Life Sciences, Higher School of Economics, Moscow, Russia
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23
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Spiegelman F, Tarrat N, Cuny J, Dontot L, Posenitskiy E, Martí C, Simon A, Rapacioli M. Density-functional tight-binding: basic concepts and applications to molecules and clusters. ADVANCES IN PHYSICS: X 2020; 5:1710252. [PMID: 33154977 PMCID: PMC7116320 DOI: 10.1080/23746149.2019.1710252] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023] Open
Abstract
The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.
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Affiliation(s)
- Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Nathalie Tarrat
- CEMES, Université de Toulouse (UPS), CNRS, UPR8011, Toulouse, Toulouse, France
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Leo Dontot
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Evgeny Posenitskiy
- Laboratoire Collisions Agrégats et Réactivité LCAR/IRSAMC, UMR5589, Université de Toulouse (UPS) and CNRS, Toulouse, France
| | - Carles Martí
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
- Laboratoire de Chimie, UMR5182, Ecole Normale Supérieure de Lyon, Université de Lyon and CNRS, Lyon, France
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
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24
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Bold BM, Sokolov M, Maity S, Wanko M, Dohmen PM, Kranz JJ, Kleinekathöfer U, Höfener S, Elstner M. Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes. Phys Chem Chem Phys 2020; 22:10500-10518. [PMID: 31950960 DOI: 10.1039/c9cp05753f] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The chromophores of rhodopsins (Rh) and light-harvesting (LH) complexes still represent a major challenge for a quantum chemical description due to their size and complex electronic structure. Since gradient corrected and hybrid density functional approaches have been shown to fail for these systems, only range-separated functionals seem to be a promising alternative to the more time consuming post-Hartree-Fock approaches. For extended sampling of optical properties, however, even more approximate approaches are required. Recently, a long-range corrected (LC) functional has been implemented into the efficient density functional tight binding (DFTB) method, allowing to sample the excited states properties of chromophores embedded into proteins using quantum mechanical/molecular mechanical (QM/MM) with the time-dependent (TD) DFTB approach. In the present study, we assess the accuracy of LC-TD-DFT and LC-TD-DFTB for rhodopsins (bacteriorhodopsin (bR) and pharaonis phoborhodopsin (ppR)) and LH complexes (light-harvesting complex II (LH2) and Fenna-Matthews-Olson (FMO) complex). This benchmark study shows the improved description of the color tuning parameters compared to standard DFT functionals. In general, LC-TD-DFTB can exhibit a similar performance as the corresponding LC functionals, allowing a reliable description of excited states properties at significantly reduced cost. The two chromophores investigated here pose complementary challenges: while huge sensitivity to external field perturbation (color tuning) and charge transfer excitations are characteristic for the retinal chromophore, the multi-chromophoric character of the LH complexes emphasizes a correct description of inter-chromophore couplings, giving less importance to color tuning. None of the investigated functionals masters both systems simultaneously with satisfactory accuracy. LC-TD-DFTB, at the current stage, although showing a systematic improvement compared to TD-DFTB cannot be recommended for studying color tuning in retinal proteins, similar to some of the LC-DFT functionals, because the response to external fields is still too weak. For sampling of LH-spectra, however, LC-TD-DFTB is a viable tool, allowing to efficiently sample absorption energies, as shown for three different LH complexes. As the calculations indicate, geometry optimization may overestimate the importance of local minima, which may be averaged over when using trajectories. Fast quantum chemical approaches therefore may allow for a direct sampling of spectra in the near future.
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Affiliation(s)
- Beatrix M Bold
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, 76131 Karlsruhe, Germany.
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25
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Schmidt-Engler JM, Blankenburg L, Błasiak B, van Wilderen LJGW, Cho M, Bredenbeck J. Vibrational Lifetime of the SCN Protein Label in H 2O and D 2O Reports Site-Specific Solvation and Structure Changes During PYP's Photocycle. Anal Chem 2019; 92:1024-1032. [PMID: 31769286 DOI: 10.1021/acs.analchem.9b03997] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The application of vibrational labels such as thiocyanate (-S-C≡N) for studying protein structure and dynamics is thriving. Absorption spectroscopy is usually employed to obtain wavenumber and line shape of the label. An observable of great significance might be the vibrational lifetime, which can be obtained by pump probe or 2D-IR spectroscopy. Due to the insulating effect of the heavy sulfur atom in the case of the SCN label, the lifetime of the C≡N oscillator is expected to be particularly sensitive to its surrounding as it is not dominated by through-bond relaxation. We therefore investigate the vibrational lifetime of the SCN label at various positions in the blue light sensor protein Photoactive Yellow Protein (PYP) in the ground state and signaling state of the photoreceptor. We find that the vibrational lifetime of the C≡N stretching mode is strongly affected both by its protein environment and by the degree of exposure to the solvent. Even for label positions where the line shape and wavenumber observed by FTIR are barely changing upon activation of the photoreceptor, we find that the lifetime can change considerably. To obtain an unambiguous measure for the solvent exposure of the labeled site, we show that it is imperative to compare the lifetimes in H2O and D2O. Importantly, the lifetimes shorten in H2O as compared to D2O for water exposed labels, while they stay largely the same for buried labels. We quantify this effect by defining a solvent exclusion coefficient (SEC). The response of the label's vibrational lifetime to its solvent exposure renders it a suitable universal probe for protein investigations. This applies even to systems that are otherwise hard to address, such as transient or short-lived states, which could be created during a protein's working cycle (as here in PYP) or during protein folding. It is also applicable to flexible systems (intrinsically disordered proteins), protein-protein and protein-membrane interactions.
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Affiliation(s)
- Julian M Schmidt-Engler
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
| | - Larissa Blankenburg
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
| | - Bartosz Błasiak
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
| | - Luuk J G W van Wilderen
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
| | - Minhaeng Cho
- Institute of Basic Science , Center of Molecular Spectroscopy and Dynamics , 145 Anam-ro , Seongbuk-gu , Seoul 02841 , Republic of Korea.,Korea University , Department of Chemistry , 145 Anam-ro , Seongbuk-gu , Seoul 02841 , Republic of Korea
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
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26
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Watanabe HC, Cui Q. Quantitative Analysis of QM/MM Boundary Artifacts and Correction in Adaptive QM/MM Simulations. J Chem Theory Comput 2019; 15:3917-3928. [DOI: 10.1021/acs.jctc.9b00180] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hiroshi C. Watanabe
- Quantum Computing Center, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- Japan Science and Technology Agency, PRESTO, 4-18, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Qiang Cui
- Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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27
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Balogh G, Muszbek L, Komáromi I. First Step of the Transglutaminase Reaction Catalyzed by Activated Factor XIII Subunit A, Hybrid Quantum Chemistry/Molecular Mechanics Calculations. J Phys Chem B 2019; 123:3887-3897. [DOI: 10.1021/acs.jpcb.9b00542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Gábor Balogh
- Division of Clinical Laboratory Sciences, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - László Muszbek
- Division of Clinical Laboratory Sciences, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - István Komáromi
- Division of Clinical Laboratory Sciences, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
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Tsvetkov PO, Roman AY, Baksheeva VE, Nazipova AA, Shevelyova MP, Vladimirov VI, Buyanova MF, Zinchenko DV, Zamyatnin AA, Devred F, Golovin AV, Permyakov SE, Zernii EY. Functional Status of Neuronal Calcium Sensor-1 Is Modulated by Zinc Binding. Front Mol Neurosci 2018; 11:459. [PMID: 30618610 PMCID: PMC6302015 DOI: 10.3389/fnmol.2018.00459] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/28/2018] [Indexed: 11/29/2022] Open
Abstract
Neuronal calcium sensor-1 (NCS-1) protein is abundantly expressed in the central nervous system and retinal neurons, where it regulates many vital processes such as synaptic transmission. It coordinates three calcium ions by EF-hands 2-4, thereby transducing Ca2+ signals to a wide range of protein targets, including G protein-coupled receptors and their kinases. Here, we demonstrate that NCS-1 also has Zn2+-binding sites, which affect its structural and functional properties upon filling. Fluorescence and circular dichroism experiments reveal the impact of Zn2+ binding on NCS-1 secondary and tertiary structure. According to atomic absorption spectroscopy and isothermal titration calorimetry studies, apo-NCS-1 has two high-affinity (4 × 106 M-1) and one low-affinity (2 × 105 M-1) Zn2+-binding sites, whereas Mg2+-loaded and Ca2+-loaded forms (which dominate under physiological conditions) bind two zinc ions with submicromolar affinity. Metal competition analysis and circular dichroism studies suggest that Zn2+-binding sites of apo- and Mg2+-loaded NCS-1 overlap with functional EF-hands of the protein. Consistently, high Zn2+ concentrations displace Mg2+ from the EF-hands and decrease the stoichiometry of Ca2+ binding. Meanwhile, one of the EF-hands of Zn2+-saturated NCS-1 exhibits a 14-fold higher calcium affinity, which increases the overall calcium sensitivity of the protein. Based on QM/MM molecular dynamics simulations, Zn2+ binding to Ca2+-loaded NCS-1 could occur at EF-hands 2 and 4. The high-affinity zinc binding increases the thermal stability of Ca2+-free NCS-1 and favours the interaction of its Ca2+-loaded form with target proteins, such as dopamine receptor D2R and GRK1. In contrast, low-affinity zinc binding promotes NCS-1 aggregation accompanied by the formation of twisted rope-like structures. Altogether, our findings suggest a complex interplay between magnesium, calcium and zinc binding to NCS-1, leading to the appearance of multiple conformations of the protein, in turn modulating its functional status.
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Affiliation(s)
- Philipp O Tsvetkov
- Aix-Marseille University, CNRS, INP, Institute of Neurophysiopathology, Faculty of Pharmacy, Marseille, France
| | - Andrei Yu Roman
- Institute of Physiologically Active Compounds (RAS), Chernogolovka, Russia
| | - Viktoriia E Baksheeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aliya A Nazipova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Russia
| | - Marina P Shevelyova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Russia
| | - Vasiliy I Vladimirov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
| | - Michelle F Buyanova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry V Zinchenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
| | - Andrey A Zamyatnin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - François Devred
- Aix-Marseille University, CNRS, INP, Institute of Neurophysiopathology, Faculty of Pharmacy, Marseille, France
| | - Andrey V Golovin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow, Russia
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Russia
| | - Evgeni Yu Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
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29
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Gillet N, Elstner M, Kubař T. Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer. J Chem Phys 2018; 149:072328. [PMID: 30134697 DOI: 10.1063/1.5027100] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a new concept of free energy calculations of chemical reactions by means of extended sampling molecular dynamics simulations. Biasing potentials are applied on partial atomic charges, which may be combined with atomic coordinates either in a single collective variable or in multi-dimensional biasing simulations. The necessary additional gradients are obtained by solving coupled-perturbed equations within the approximative density-functional tight-binding method. The new computational scheme was implemented in a combination of Gromacs and Plumed. As a prospective application, proton-coupled electron transfer in a model molecular system is studied. Two collective variables are introduced naturally, one for the proton transfer and the other for the electron transfer. The results are in qualitative agreement with the extended free simulations performed for reference. Free energy minima as well as the mechanism of the process are identified correctly, while the topology of the transition region and the height of the energy barrier are only reproduced qualitatively. The application also illustrates possible difficulties with the new methodology. These may be inefficient sampling of spatial coordinates when atomic charges are biased exclusively and a decreased stability of the simulations. Still, the new approach represents a viable alternative for free energy calculations of a certain class of chemical reactions, for instance a proton-coupled electron transfer in proteins.
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Affiliation(s)
- Natacha Gillet
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
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30
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Zlobin A, Mokrushina Y, Terekhov S, Zalevsky A, Bobik T, Stepanova A, Aliseychik M, Kartseva O, Panteleev S, Golovin A, Belogurov A, Gabibov A, Smirnov I. QM/MM Description of Newly Selected Catalytic Bioscavengers Against Organophosphorus Compounds Revealed Reactivation Stimulus Mediated by Histidine Residue in the Acyl-Binding Loop. Front Pharmacol 2018; 9:834. [PMID: 30123127 PMCID: PMC6085465 DOI: 10.3389/fphar.2018.00834] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/11/2018] [Indexed: 11/14/2022] Open
Abstract
Butyrylcholinesterase (BChE) is considered as an efficient stoichiometric antidote against organophosphorus (OP) poisons. Recently we utilized combination of calculations and ultrahigh-throughput screening (uHTS) to select BChE variants capable of catalytic destruction of OP pesticide paraoxon. The purpose of this study was to elucidate the molecular mechanism underlying enzymatic hydrolysis of paraoxon by BChE variants using hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. Detailed analysis of accomplished QM/MM runs revealed that histidine residues introduced into the acyl-binding loop are always located in close proximity with aspartate residue at position 70. Histidine residue acts as general base thus leading to attacking water molecule activation and subsequent SN2 inline hydrolysis resulting in BChE reactivation. This combination resembles canonical catalytic triad found in active centers of various proteases. Carboxyl group activates histidine residue by altering its pKa, which in turn promotes the activation of water molecule in terms of its nucleophilicity. Observed re-protonation of catalytic serine residue at position 198 from histidine residue at position 438 recovers initial configuration of the enzyme’s active center, facilitating next catalytic cycle. We therefore suggest that utilization of uHTS platform in combination with deciphering of molecular mechanisms by QM/MM calculations may significantly improve our knowledge of enzyme function, propose new strategies for enzyme design and open new horizons in generation of catalytic bioscavengers against OP poisons.
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Affiliation(s)
- Alexander Zlobin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Yuliana Mokrushina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Stanislav Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Arthur Zalevsky
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Bobik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya Stepanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria Aliseychik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Olga Kartseva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Sergey Panteleev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Golovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexey Belogurov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexander Gabibov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ivan Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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31
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Improvement of Performance, Stability and Continuity by Modified Size-Consistent Multipartitioning Quantum Mechanical/Molecular Mechanical Method. Molecules 2018; 23:molecules23081882. [PMID: 30060503 PMCID: PMC6222491 DOI: 10.3390/molecules23081882] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/25/2018] [Accepted: 07/25/2018] [Indexed: 11/17/2022] Open
Abstract
For condensed systems, the incorporation of quantum chemical solvent effects into molecular dynamics simulations has been a major concern. To this end, quantum mechanical/molecular mechanical (QM/MM) techniques are popular and powerful options to treat gigantic systems. However, they cannot be directly applied because of temporal and spatial discontinuity problems. To overcome these problems, in a previous study, we proposed a corrective QM/MM method, size-consistent multipartitioning (SCMP) QM/MM and successfully demonstrated that, using SCMP, it is possible to perform stable molecular dynamics simulations by effectively taking into account solvent quantum chemical effects. The SCMP method is characterized by two original features: size-consistency of a QM region among all QM/MM partitioning and partitioning update. However, in our previous study, the performance was not fully elicited compared to the theoretical upper bound and the optimal partitioning update protocol and parameters were not fully verified. To elicit the potential performance, in the present study, we simplified the theoretical framework and modified the partitioning protocol.
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32
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Muždalo A, Saalfrank P, Vreede J, Santer M. Cis-to-Trans Isomerization of Azobenzene Derivatives Studied with Transition Path Sampling and Quantum Mechanical/Molecular Mechanical Molecular Dynamics. J Chem Theory Comput 2018; 14:2042-2051. [DOI: 10.1021/acs.jctc.7b01120] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Anja Muždalo
- Department of Theory and Biosystems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Peter Saalfrank
- Department of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Jocelyne Vreede
- Computational Chemistry, Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Mark Santer
- Department of Theory and Biosystems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
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33
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Putzu M, Gräter F, Elstner M, Kubař T. On the mechanism of spontaneous thiol–disulfide exchange in proteins. Phys Chem Chem Phys 2018; 20:16222-16230. [DOI: 10.1039/c8cp01325j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Free energy surfaces from QM/MM metadynamics on model peptides will be a basis to build reactive force field for reaction in proteins.
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Affiliation(s)
- Marina Putzu
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology (KIT)
- 76131 Karlsruhe
- Germany
- Center for Functional Nanostructures
| | - Frauke Gräter
- Interdisciplinary Center for Scientific Computing (IWR)
- Heidelberg University
- 69120 Heidelberg
- Germany
- Heidelberg Institute for Theoretical Studies
| | - Marcus Elstner
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology (KIT)
- 76131 Karlsruhe
- Germany
- Institute for Biological Interfaces (IBG-2)
| | - Tomáš Kubař
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology (KIT)
- 76131 Karlsruhe
- Germany
- Center for Functional Nanostructures
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34
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Stability and properties of quasi-stable conformational states in the LH2 light-harvesting complex of Rbl. acidophilus bacteria formed by hexacoordination of bacteriochlorophyll a magnesium atom. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Mlýnský V, Bussi G. Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides. RNA (NEW YORK, N.Y.) 2017; 23:712-720. [PMID: 28202709 PMCID: PMC5393180 DOI: 10.1261/rna.060442.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/03/2017] [Indexed: 05/25/2023]
Abstract
Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural data sets for a variety of RNAs and are used to characterize conformational changes in riboswitches. However, the structural determinants that lead to differential reactivities in unpaired nucleotides have not been investigated yet. In this work, we used a combination of theoretical approaches, i.e., classical molecular dynamics simulations, multiscale quantum mechanical/molecular mechanical calculations, and enhanced sampling techniques in order to compute and interpret the differential reactivity of individual residues in several RNA motifs, including members of the most important GNRA and UNCG tetraloop families. Simulations on the multinanosecond timescale are required to converge the related free-energy landscapes. The results for uGAAAg and cUUCGg tetraloops and double helices are compared with available data from in-line probing experiments and show that the introduced technique is able to distinguish between nucleotides of the uGAAAg tetraloop based on their structural predispositions toward phosphodiester backbone cleavage. For the cUUCGg tetraloop, more advanced ab initio calculations would be required. This study is the first attempt to computationally classify chemical probing experiments and paves the way for an identification of tertiary structures based on the measured reactivity of nonreactive nucleotides.
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Affiliation(s)
- Vojtěch Mlýnský
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
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36
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Tulub AA, Stefanov VE. Hidden symmetries of DNA molecule. J Theor Biol 2017; 416:144-148. [PMID: 28077290 DOI: 10.1016/j.jtbi.2017.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 01/02/2017] [Accepted: 01/03/2017] [Indexed: 11/29/2022]
Abstract
Despite the fact that DNA molecule is studied up and down, we know very little about the role of DNA triplets in coding amino acids and stop-codons. The paper aims to fill this gap through attracting spintronic ideas and carrying out QM/MM computations on a full-turn DNA fragment. The computations reveal two hidden symmetries: the spin splitting (the Rashba effect), confined within each triplet, and the quantum "phase" link between the triplet nature (in total, 64 triplets) and the corresponding amino acid and three stop-codons. The hidden symmetries become evident upon binding the magnesium cofactor to DNA triplets in 5'-3' and 3'-5' directions.
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Affiliation(s)
- Alexander A Tulub
- Centre for Interdisciplinary Computational and Dynamical Analysis, University of Manchester, Oxford Road, Manchester M13 9PL, UK; Saint-Petersburg State University, Universitetskaya Emb. 7/9, 199034, Saint-Petersburg, RF, Russia.
| | - Vassily E Stefanov
- Saint-Petersburg State University, Universitetskaya Emb. 7/9, 199034, Saint-Petersburg, RF, Russia
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37
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Watanabe HC, Kubillus M, Kubař T, Stach R, Mizaikoff B, Ishikita H. Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method. Phys Chem Chem Phys 2017; 19:17985-17997. [DOI: 10.1039/c7cp01708a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics.
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Affiliation(s)
- Hiroshi C. Watanabe
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
- Department of Applied Chemistry
| | - Maximilian Kubillus
- Institute of Physical Chemistry and Center for Functional Nanostructures
- Karlsruhe Institute of Technology
- Karlsruhe 73131
- Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry and Center for Functional Nanostructures
- Karlsruhe Institute of Technology
- Karlsruhe 73131
- Germany
| | - Robert Stach
- Institute of Analytical Bioanalytical Chemistry
- Ulm University
- Ulm 89081
- Germany
| | - Boris Mizaikoff
- Institute of Analytical Bioanalytical Chemistry
- Ulm University
- Ulm 89081
- Germany
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
- Department of Applied Chemistry
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38
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Christensen A, Kubař T, Cui Q, Elstner M. Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chem Rev 2016; 116:5301-37. [PMID: 27074247 PMCID: PMC4867870 DOI: 10.1021/acs.chemrev.5b00584] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Indexed: 12/28/2022]
Abstract
Semiempirical (SE) methods can be derived from either Hartree-Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems.
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Affiliation(s)
- Anders
S. Christensen
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Tomáš Kubař
- Institute of Physical
Chemistry & Center for Functional Nanostructures and Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Marcus Elstner
- Institute of Physical
Chemistry & Center for Functional Nanostructures and Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
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39
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Almeida GG, Cordeiro JMM, Martín ME, Aguilar MA. Conformational Changes of the Alanine Dipeptide in Water–Ethanol Binary Mixtures. J Chem Theory Comput 2016; 12:1514-24. [DOI: 10.1021/acs.jctc.5b00952] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Glauco G. Almeida
- Faculdade de Engenharia,
Universidade Estadual Paulista “Julio de Mesquita Filho″, Ilha Solteira 15385-000, Brasil
| | - João M. M. Cordeiro
- Faculdade de Engenharia,
Universidade Estadual Paulista “Julio de Mesquita Filho″, Ilha Solteira 15385-000, Brasil
| | - M. Elena Martín
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, Edif. José Ma Viguera
Lobo, 3a planta, Badajoz 06006, Spain
| | - Manuel A. Aguilar
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, Edif. José Ma Viguera
Lobo, 3a planta, Badajoz 06006, Spain
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40
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Guo Y, Beyle FE, Bold BM, Watanabe HC, Koslowski A, Thiel W, Hegemann P, Marazzi M, Elstner M. Active site structure and absorption spectrum of channelrhodopsin-2 wild-type and C128T mutant. Chem Sci 2016; 7:3879-3891. [PMID: 30155032 PMCID: PMC6013792 DOI: 10.1039/c6sc00468g] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 02/24/2016] [Indexed: 12/25/2022] Open
Abstract
We show by extensive ground state and absorption spectra simulations that the channelrhodopsin-2 active site samples three different hydrogen-bonding patterns.
In spite of considerable interest, the active site of channelrhodopsin still lacks a detailed atomistic description, the understanding of which could strongly enhance the development of novel optogenetics tools. We present a computational study combining different state-of-the-art techniques, including hybrid quantum mechanics/molecular mechanics schemes and high-level quantum chemical methods, to properly describe the hydrogen-bonding pattern between the retinal chromophore and its counterions in channelrhodopsin-2 Wild-Type and C128T mutant. Especially, we show by extensive ground state dynamics that the active site, containing a glutamic acid (E123) and a water molecule, is highly dynamic, sampling three different hydrogen-bonding patterns. This results in a broad absorption spectrum that is representative of the different structural motifs found. A comparison with bacteriorhodopsin, characterized by a pentagonal hydrogen-bonded active site structure, elucidates their different absorption properties.
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Affiliation(s)
- Yanan Guo
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
| | - Franziska E Beyle
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
| | - Beatrix M Bold
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
| | - Hiroshi C Watanabe
- Research Center for Advanced Science and Technology , The University of Tokyo , 4-6-1 Komaba, Meguro-ku , Tokyo 153-8904 , Japan
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany
| | - Peter Hegemann
- Institute of Biology , Experimental Biophysics , Humboldt-Universität , Invalidenstraße 42 , D-10115 Berlin , Germany
| | - Marco Marazzi
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
| | - Marcus Elstner
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
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41
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Watanabe HC, Banno M, Sakurai M. An adaptive quantum mechanics/molecular mechanics method for the infrared spectrum of water: incorporation of the quantum effect between solute and solvent. Phys Chem Chem Phys 2016; 18:7318-33. [DOI: 10.1039/c5cp07136d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum effects in solute–solvent interactions, such as the many-body effect and the dipole-induced dipole, are known to be critical factors influencing the infrared spectra of species in the liquid phase.
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Affiliation(s)
- Hiroshi C. Watanabe
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Meguro-ku
- Japan
| | - Misa Banno
- Center for Biological Resources and Informatics
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics
- Tokyo Institute of Technology
- Midori-ku
- Japan
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42
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Saez DA, Vogt-Geisse S, Inostroza-Rivera R, Kubař T, Elstner M, Toro-Labbé A, Vöhringer-Martinez E. The effect of the environment on the methyl transfer reaction mechanism between trimethylsulfonium and phenolate. Phys Chem Chem Phys 2016; 18:24033-42. [DOI: 10.1039/c6cp02821g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The methyl transfer reaction mechanism in different molecular environments were studied by electronic structure methods and QM/MM molecular dynamics simulations.
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Affiliation(s)
- David Adrian Saez
- Departamento de Físico-Química
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Millenium Nucleus Chemical Processes and Catalysis (CPC)
- Chile
| | - Stefan Vogt-Geisse
- Departamento de Físico-Química
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Millenium Nucleus Chemical Processes and Catalysis (CPC)
- Chile
| | | | - Tomáš Kubař
- Center for Functional Nanomaterials
- Karlsruhe Institute of Technology
- Germany
- Institute for Physical Chemistry
- Karlsruhe Institute of Technology
| | - Marcus Elstner
- Institute for Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Alejandro Toro-Labbé
- QTC
- Facultad de Química
- Pontificia Universidad Católica de Chile
- Millenium Nucleus Chemical Processes and Catalysis (CPC)
- Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Millenium Nucleus Chemical Processes and Catalysis (CPC)
- Chile
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