1
|
Calcagno F, Maryasin B, Garavelli M, Avagliano D, Rivalta I. Modeling solvent effects and convergence of 31P-NMR shielding calculations with COBRAMM. J Comput Chem 2024; 45:1562-1575. [PMID: 38514234 DOI: 10.1002/jcc.27338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
Solvent effects on 31P-NMR parameters for triphenylphosphine oxide and triphenylphosphine in chloroform have been extensively investigated by testing different solvation models. The solvent is described implicitly, mixed implicitly/explicitly, and using full explicit models. Polarizable continuum model (PCM), molecular dynamic (MD) simulations, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations are used to disclose the effects of solute/solvent interactions and, more generally, the role of the embedding in NMR simulations. The results show the beneficial effect of carrying out QM/MM optimizations on top of geometries directly extracted from classical MD simulations, used to ensure representative conformational sampling. The nuclear shielding convergence has been tested against a different number of snapshots and with the inclusion of solvent shells into the QM region. An automated MD//QM/MM//GIAO protocol, implemented in the COBRAMM package, is here proposed and tested on trimethyl phosphite showing that our approach boosts the convergence of nuclear shielding satisfactorily. The present work aims to be a stepping-stone to assess proper QM/MM computational strategies in simulating chemical shifts in non-homogeneous systems like supramolecular and biological systems.
Collapse
Affiliation(s)
- Francesco Calcagno
- Department of Industrial Chemistry "Toso Montanari", University of Bologna, Bologna, Italy
- Center for Chemical Catalysis - C3, University of Bologna, Bologna, Italy
| | - Boris Maryasin
- Institute of Organic Chemistry, University of Vienna, Vienna, Austria
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Marco Garavelli
- Department of Industrial Chemistry "Toso Montanari", University of Bologna, Bologna, Italy
| | - Davide Avagliano
- Department of Industrial Chemistry "Toso Montanari", University of Bologna, Bologna, Italy
| | - Ivan Rivalta
- Department of Industrial Chemistry "Toso Montanari", University of Bologna, Bologna, Italy
- Center for Chemical Catalysis - C3, University of Bologna, Bologna, Italy
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, Lyon, France
| |
Collapse
|
2
|
Nochebuena J, Liu S, Cisneros GA. Relative cooperativity in neutral and charged molecular clusters using QM/MM calculations. J Chem Phys 2024; 160:134301. [PMID: 38557841 DOI: 10.1063/5.0203020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
QM/MM methods have been used to study electronic structure properties and chemical reactivity in complex molecular systems where direct electronic structure calculations are not feasible. In our previous work, we showed that non-polarizable force fields, by design, describe intermolecular interactions through pairwise interactions, overlooking many-body interactions involving three or more particles. In contrast, polarizable force fields account partially for many-body effects through polarization, but still handle van der Waals and permanent electrostatic interactions pairwise. We showed that despite those limitations, polarizable and non-polarizable force fields can reproduce relative cooperativity achieved using density functional theory due to error compensation mechanisms. In this contribution, we assess the performance of QM/MM methods in reproducing these phenomena. Our study highlights the significance of the QM region size and force field choice in QM/MM calculations, emphasizing the importance of parameter validation to obtain accurate interaction energy predictions.
Collapse
Affiliation(s)
- Jorge Nochebuena
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - G Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, USA
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, USA
| |
Collapse
|
3
|
Szántó JK, Dietschreit JCB, Shein M, Schütz AK, Ochsenfeld C. Systematic QM/MM Study for Predicting 31P NMR Chemical Shifts of Adenosine Nucleotides in Solution and Stages of ATP Hydrolysis in a Protein Environment. J Chem Theory Comput 2024; 20:2433-2444. [PMID: 38497488 DOI: 10.1021/acs.jctc.3c01280] [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: 03/19/2024]
Abstract
NMR (nuclear magnetic resonance) spectroscopy allows for important atomistic insights into the structure and dynamics of biological macromolecules; however, reliable assignments of experimental spectra are often difficult. Herein, quantum mechanical/molecular mechanical (QM/MM) calculations can provide crucial support. A major problem for the simulations is that experimental NMR signals are time-averaged over much longer time scales, and since computed chemical shifts are highly sensitive to local changes in the electronic and structural environment, sufficiently large averages over representative structural ensembles are essential. This entails high computational demands for reliable simulations. For NMR measurements in biological systems, a nucleus of major interest is 31P since it is both highly present (e.g., in nucleic acids) and easily observable. The focus of our present study is to develop a robust and computationally cost-efficient framework for simulating 31P NMR chemical shifts of nucleotides. We apply this scheme to study the different stages of the ATP hydrolysis reaction catalyzed by p97. Our methodology is based on MM molecular dynamics (MM-MD) sampling, followed by QM/MM structure optimizations and NMR calculations. Overall, our study is one of the most comprehensive QM-based 31P studies in a protein environment and the first to provide computed NMR chemical shifts for multiple nucleotide states in a protein environment. This study sheds light on a process that is challenging to probe experimentally and aims to bridge the gap between measured and calculated NMR spectroscopic properties.
Collapse
Affiliation(s)
- Judit Katalin Szántó
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Johannes C B Dietschreit
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mikhail Shein
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 5-13, D-81377 München, Germany
| | - Anne K Schütz
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 5-13, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Max Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
| |
Collapse
|
4
|
Maste S, Sharma B, Pongratz T, Grabe B, Hiller W, Erlach MB, Kremer W, Kalbitzer HR, Marx D, Kast SM. The accuracy limit of chemical shift predictions for species in aqueous solution. Phys Chem Chem Phys 2024; 26:6386-6395. [PMID: 38315169 DOI: 10.1039/d3cp05471c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Interpreting NMR experiments benefits from first-principles predictions of chemical shifts. Reaching the accuracy limit of theory is relevant for unambiguous structural analysis and dissecting theoretical approximations. Since accurate chemical shift measurements are based on using internal reference compounds such as trimethylsilylpropanesulfonate (DSS), a detailed comparison of experimental with theoretical data requires simultaneous consideration of both target and reference species ensembles in the same solvent environment. Here we show that ab initio molecular dynamics simulations to generate liquid-state ensembles of target and reference compounds, including explicitly their short-range solvation environments and combined with quantum-mechanical solvation models, allows for predicting highly accurate 1H (∼0.1-0.5 ppm) and aliphatic 13C (∼1.5 ppm) chemical shifts for aqueous solutions of the model compounds trimethylamine N-oxide (TMAO) and N-methylacetamide (NMA), referenced to DSS without any system-specific adjustments. This encompasses the two peptide bond conformations of NMA identified by NMR. The results are used to derive a general-purpose guideline set for predictive NMR chemical shift calculations of NMA in the liquid state and to identify artifacts of force field models. Accurate predictions are only obtained if a sufficient number of explicit water molecules is included in the quantum-mechanical calculations, disproving a purely electrostatic model of the solvent effect on chemical shifts.
Collapse
Affiliation(s)
- Stefan Maste
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Bikramjit Sharma
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Tim Pongratz
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Bastian Grabe
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Wolf Hiller
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Markus Beck Erlach
- Fakultät für Biologie und Vorklinische Medizin, Universität Regensburg, 93040 Regensburg, Germany
| | - Werner Kremer
- Fakultät für Biologie und Vorklinische Medizin, Universität Regensburg, 93040 Regensburg, Germany
| | - Hans Robert Kalbitzer
- Fakultät für Biologie und Vorklinische Medizin, Universität Regensburg, 93040 Regensburg, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Stefan M Kast
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| |
Collapse
|
5
|
Brandt F, Jacob CR. Efficient automatic construction of atom-economical QM regions with point-charge variation analysis. Phys Chem Chem Phys 2023; 25:14484-14495. [PMID: 37190855 DOI: 10.1039/d3cp01263h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The setup of QM/MM calculations is not trivial since many decisions have to be made by the simulation scientist to achieve reasonable and consistent results. The main challenge to be tackled is the construction of the QM region to make sure to take into account all important parts of the adjacent environment and exclude less important ones. In our previous work [F. Brandt and Ch. R. Jacob, Systematic QM Region Construction in QM/MM Calculations Based on Uncertainty Quantification, J. Chem. Theory Comput., 2022, 18, 2584-2596.], we introduced the point charge variation analysis (PCVA) as a simple and reliable tool to systematically construct QM regions based on the sensitivity of the reaction energy with respect to variations of the MM point charges. Here, we assess several simplified variants of this PCVA approach for the example of catechol O-methyltransferase and apply PCVA for another system, the triosephosphate isomerase. Furthermore, we extend its scope by applying it to a DNA system. Our results indicate that PCVA offers an efficient and versatile approach of the automatic construction of atom-economical QM regions, but also identify possible pitfalls and limitations.
Collapse
Affiliation(s)
- Felix Brandt
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany.
| | - Christoph R Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany.
| |
Collapse
|
6
|
Kubař T, Elstner M, Cui Q. Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines. Annu Rev Biophys 2023; 52:525-551. [PMID: 36791746 PMCID: PMC10810093 DOI: 10.1146/annurev-biophys-111622-091140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become indispensable tools for the study of biomolecules. In this article, we briefly review the basic methodological details of QM/MM approaches and discuss their applications to various energy transduction problems in biomolecular machines, such as long-range proton transports, fast electron transfers, and mechanochemical coupling. We highlight the particular importance for these applications of balancing computational efficiency and accuracy. Using several recent examples, we illustrate the value and limitations of QM/MM methodologies for both ground and excited states, as well as strategies for calibrating them in specific applications. We conclude with brief comments on several areas that can benefit from further efforts to make QM/MM analyses more quantitative and applicable to increasingly complex biological problems.
Collapse
Affiliation(s)
- T Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - M Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - Q Cui
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
- Department of Physics, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Bramley GA, Beynon OT, Stishenko PV, Logsdail AJ. The application of QM/MM simulations in heterogeneous catalysis. Phys Chem Chem Phys 2023; 25:6562-6585. [PMID: 36810655 DOI: 10.1039/d2cp04537k] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The QM/MM simulation method is provenly efficient for the simulation of biological systems, where an interplay of extensive environment and delicate local interactions drives a process of interest through a funnel on a complex energy landscape. Recent advances in quantum chemistry and force-field methods present opportunities for the adoption of QM/MM to simulate heterogeneous catalytic processes, and their related systems, where similar intricacies exist on the energy landscape. Herein, the fundamental theoretical considerations for performing QM/MM simulations, and the practical considerations for setting up QM/MM simulations of catalytic systems, are introduced; then, areas of heterogeneous catalysis are explored where QM/MM methods have been most fruitfully applied. The discussion includes simulations performed for adsorption processes in solvent at metallic interfaces, reaction mechanisms within zeolitic systems, nanoparticles, and defect chemistry within ionic solids. We conclude with a perspective on the current state of the field and areas where future opportunities for development and application exist.
Collapse
Affiliation(s)
- Gabriel Adrian Bramley
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, CF10 3AT, UK.
| | - Owain Tomos Beynon
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, CF10 3AT, UK.
| | | | - Andrew James Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, CF10 3AT, UK.
| |
Collapse
|
9
|
Csizi K, Reiher M. Universal
QM
/
MM
approaches for general nanoscale applications. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Markus Reiher
- Laboratorium für Physikalische Chemie ETH Zürich Zürich Switzerland
| |
Collapse
|
10
|
Pérez-Barcia Á, Cárdenas G, Nogueira JJ, Mandado M. Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis. J Chem Inf Model 2023; 63:882-897. [PMID: 36661314 PMCID: PMC9930123 DOI: 10.1021/acs.jcim.2c01184] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Herein, an Energy Decomposition Analysis (EDA) scheme extended to the framework of QM/MM calculations in the context of electrostatic embeddings (QM/MM-EDA) including atomic charges and dipoles is applied to assess the effect of the QM region size on the convergence of the different interaction energy components, namely, electrostatic, Pauli, and polarization, for cationic, anionic, and neutral systems interacting with a strong polar environment (water). Significant improvements are found when the bulk solvent environment is described by a MM potential in the EDA scheme as compared to pure QM calculations that neglect bulk solvation. The predominant electrostatic interaction requires sizable QM regions. The results reported here show that it is necessary to include a surprisingly large number of water molecules in the QM region to obtain converged values for this energy term, contrary to most cluster models often employed in the literature. Both the improvement of the QM wave function by means of a larger basis set and the introduction of polarization into the MM region through a polarizable force field do not translate to a faster convergence with the QM region size, but they lead to better results for the different interaction energy components. The results obtained in this work provide insight into the effect of each energy component on the convergence of the solute-solvent interaction energy with the QM region size. This information can be used to improve the MM FFs and embedding schemes employed in QM/MM calculations of solvated systems.
Collapse
Affiliation(s)
- Álvaro Pérez-Barcia
- Department
of Physical Chemistry, University of Vigo, Lagoas-Marcosende s\n, ES-36310-Vigo, Galicia, Spain
| | - Gustavo Cárdenas
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049, Madrid, Spain
| | - Juan J. Nogueira
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049, Madrid, Spain,Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049Madrid, Spain,E-mail:
| | - Marcos Mandado
- Department
of Physical Chemistry, University of Vigo, Lagoas-Marcosende s\n, ES-36310-Vigo, Galicia, Spain,E-mail:
| |
Collapse
|
11
|
Jiang Y, Stull SL, Shao Q, Yang ZJ. Convergence in determining enzyme functional descriptors across Kemp eliminase variants. ELECTRONIC STRUCTURE (BRISTOL, ENGLAND) 2022; 4:044007. [PMID: 37425623 PMCID: PMC10327861 DOI: 10.1088/2516-1075/acad51] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Molecular simulations have been extensively employed to accelerate biocatalytic discoveries. Enzyme functional descriptors derived from molecular simulations have been leveraged to guide the search for beneficial enzyme mutants. However, the ideal active-site region size for computing the descriptors over multiple enzyme variants remains untested. Here, we conducted convergence tests for dynamics-derived and electrostatic descriptors on 18 Kemp eliminase variants across six active-site regions with various boundary distances to the substrate. The tested descriptors include the root-mean-square deviation of the active-site region, the solvent accessible surface area ratio between the substrate and active site, and the projection of the electric field (EF) on the breaking C-H bond. All descriptors were evaluated using molecular mechanics methods. To understand the effects of electronic structure, the EF was also evaluated using quantum mechanics/molecular mechanics methods. The descriptor values were computed for 18 Kemp eliminase variants. Spearman correlation matrices were used to determine the region size condition under which further expansion of the region boundary does not substantially change the ranking of descriptor values. We observed that protein dynamics-derived descriptors, including RMSDactive_site and SASAratio, converge at a distance cutoff of 5 Å from the substrate. The electrostatic descriptor, EFC-H, converges at 6 Å using molecular mechanics methods with truncated enzyme models and 4 Å using quantum mechanics/molecular mechanics methods with whole enzyme model. This study serves as a future reference to determine descriptors for predictive modeling of enzyme engineering.
Collapse
Affiliation(s)
- Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Sebastian L Stull
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Zhongyue J Yang
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, United States of America
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States of America
- Data Science Institute, Vanderbilt University, Nashville, TN 37235, United States of America
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, United States of America
| |
Collapse
|
12
|
Ritacca AG, Rovaletti A, Moro G, Cosentino U, Ryde U, Sicilia E, Greco C. Unraveling the Reaction Mechanism of Mo/Cu CO Dehydrogenase Using QM/MM Calculations. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alessandra G. Ritacca
- Department of Chemistry and Chemical Technologies, University of Calabria, Via P. Bucci, Rende 87036, Italy
| | - Anna Rovaletti
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, Milan 20126, Italy
| | - Giorgio Moro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milan 20126, Italy
| | - Ugo Cosentino
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, Milan 20126, Italy
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, Lund SE-221 00, Sweden
| | - Emilia Sicilia
- Department of Chemistry and Chemical Technologies, University of Calabria, Via P. Bucci, Rende 87036, Italy
| | - Claudio Greco
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, Milan 20126, Italy
| |
Collapse
|
13
|
Brandt F, Jacob CR. Systematic QM Region Construction in QM/MM Calculations Based on Uncertainty Quantification. J Chem Theory Comput 2022; 18:2584-2596. [PMID: 35271768 DOI: 10.1021/acs.jctc.1c01093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
While QM/MM studies of enzymatic reactions are widely used in computational chemistry, the results of such studies are subject to numerous sources of uncertainty, and the effect of different choices by the simulation scientist that are required when setting up QM/MM calculations is often unclear. In particular, the selection of the QM region is crucial for obtaining accurate and reliable results. Simply including amino acids by their distance to the active site is mostly not sufficient as necessary residues are missing or unimportant residues are included without evidence. Here, we take a first step toward quantifying uncertainties in QM/MM calculations by assessing the sensitivity of QM/MM reaction energies with respect to variations of the MM point charges. We show that such a point charge variation analysis (PCVA) can be employed to judge the accuracy of QM/MM reaction energies obtained with a selected QM region and devise a protocol to systematically construct QM regions that minimize this uncertainty. We apply such a PCVA to the example of catechol O-methyltransferase and demonstrate that it provides a simple and reliable approach for the construction of the QM region. Our PCVA-based scheme is computationally efficient and requires only calculations for a system with a minimal QM region. Our work highlights the promise of applying methods of uncertainty quantification in computational chemistry.
Collapse
Affiliation(s)
- Felix Brandt
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106 Braunschweig, Germany
| |
Collapse
|
14
|
Demapan D, Kussmann J, Ochsenfeld C, Cui Q. Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition. J Chem Theory Comput 2022; 18:2530-2542. [PMID: 35226489 PMCID: PMC9652774 DOI: 10.1021/acs.jctc.1c00714] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To analyze the impact of various technical details on the results of quantum mechanical (QM)/molecular mechanical (MM) enzyme simulations, including the QM region size, catechol-O-methyltransferase (COMT) is studied as a model system using an approximate QM/MM method (DFTB3/CHARMM). The results show that key equilibrium and kinetic properties for methyl transfer in COMT exhibit limited variations with respect to the size of the QM region, which ranges from ∼100 to ∼500 atoms in this study. With extensive sampling, local and global structural characteristics of the enzyme are largely conserved across the studied QM regions, while the nature of the transition state (e.g., secondary kinetic isotope effect) and reaction exergonicity are largely maintained. Deviations in the free energy profile with different QM region sizes are similar in magnitude to those observed with changes in other simulation protocols, such as different initial enzyme conformations and boundary conditions. Electronic structural properties, such as the covariance matrix of residual charge fluctuations, appear to exhibit rather long-range correlations, especially when the peptide backbone is included in the QM region; this observation holds when a range-separated DFT approach is used as the QM region, suggesting that delocalization error is unlikely the origin. Overall, the analyses suggest that multiple simulation details determine the results of QM/MM enzyme simulations with comparable contributions.
Collapse
Affiliation(s)
- Darren Demapan
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany.,Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jörg Kussmann
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| |
Collapse
|
15
|
Rovaletti A, Moro G, Cosentino U, Ryde U, Greco C. Can water act as a nucleophile in CO oxidation catalysed by Mo/Cu CO-dehydrogenase? Answers from theory. Chemphyschem 2022; 23:e202200053. [PMID: 35170169 PMCID: PMC9310835 DOI: 10.1002/cphc.202200053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/14/2022] [Indexed: 11/14/2022]
Abstract
The aerobic CO dehydrogenase from Oligotropha carboxidovorans is an environmentally crucial bacterial enzyme for maintenance of subtoxic concentration of CO in the lower atmosphere, as it allows for the oxidation of CO to CO2 which takes place at its Mo−Cu heterobimetallic active site. Despite extensive experimental and theoretical efforts, significant uncertainties still concern the reaction mechanism for the CO oxidation. In this work, we used the hybrid quantum mechanical/molecular mechanical approach to evaluate whether a water molecule present in the active site might act as a nucleophile upon formation of the new C−O bond, a hypothesis recently suggested in the literature. Our study shows that activation of H2O can be favoured by the presence of the Mo=Oeq group. However, overall our results suggest that mechanisms other than the nucleophilic attack by Mo=Oeq to the activated carbon of the CO substrate are not likely to constitute reactive channels for the oxidation of CO by the enzyme.
Collapse
Affiliation(s)
- Anna Rovaletti
- University of Milano-Bicocca: Universita degli Studi di Milano-Bicocca, Department of Earth and Environmental Sciences, ITALY
| | - Giorgio Moro
- University of Milano-Bicocca: Universita degli Studi di Milano-Bicocca, Department of Biotechnology and Biosciences, ITALY
| | - Ugo Cosentino
- University of Milano-Bicocca: Universita degli Studi di Milano-Bicocca, Department of Earth and Environmental Sciences, ITALY
| | - Ulf Ryde
- Lund University: Lunds Universitet, Department of Theoretical Chemistry, ITALY
| | - Claudio Greco
- Università degli Studi di Milano-Bicocca: Universita degli Studi di Milano-Bicocca, earth and environmental sciences, Piazza della Scienza 1, 20126, Milan, ITALY
| |
Collapse
|
16
|
Harder, better, faster, stronger: Large-scale QM and QM/MM for predictive modeling in enzymes and proteins. Curr Opin Struct Biol 2021; 72:9-17. [PMID: 34388673 DOI: 10.1016/j.sbi.2021.07.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/25/2021] [Accepted: 07/05/2021] [Indexed: 11/23/2022]
Abstract
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have reduced the cost of high-accuracy models. Tradeoffs between sampling and accuracy have motivated modeling with molecular mechanics (MM) in a multiscale QM/MM or iterative approach. Limitations to both conventional density-functional theory and classical MM force fields remain for describing noncovalent interactions in comparison to experiment or wavefunction theory. Because predictions of enzyme action (i.e. electrostatics), free energy barriers, and mechanisms are sensitive to the protocol and embedding method in QM/MM, convergence tests and systematic methods for quantifying QM-level interactions are a needed, active area of development.
Collapse
|
17
|
Hix MA, Leddin EM, Cisneros GA. Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations. J Chem Theory Comput 2021; 17:4524-4537. [PMID: 34087064 PMCID: PMC8477969 DOI: 10.1021/acs.jctc.1c00313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Selection of residues and other molecular fragments for inclusion in the quantum mechanics (QM) region for QM/molecular mechanics (MM) simulations is an important step for these calculations. Here, we present an approach that combines protein sequence/structure evolution and electron localization function (ELF) analyses. The combination of these two analyses allows the determination of whether a residue needs to be included in the QM subsystem or can be represented by the MM environment. We have applied this approach on two systems previously investigated by QM/MM simulations, 4-oxalocrotonate tautomerase (4OT) and ten-eleven translocation-2 (TET2), that provide examples where fragments may or may not need to be included in the QM subsystem. Subsequently, we present the use of this approach to determine the appropriate QM subsystem to calculate the minimum energy path (MEP) for the reaction catalyzed by human DNA polymerase λ (Polλ) with a third cation in the active site. Our results suggest that the combination of protein evolutionary and ELF analyses provides insights into residue/molecular fragment selection for QM/MM simulations.
Collapse
Affiliation(s)
- Mark A Hix
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Emmett M Leddin
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| |
Collapse
|
18
|
Brunken C, Reiher M. Automated Construction of Quantum–Classical Hybrid Models. J Chem Theory Comput 2021; 17:3797-3813. [DOI: 10.1021/acs.jctc.1c00178] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Christoph Brunken
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| |
Collapse
|
19
|
Rovaletti A, Greco C, Ryde U. QM/MM study of the binding of H 2 to MoCu CO dehydrogenase: development and applications of improved H 2 van der Waals parameters. J Mol Model 2021; 27:68. [PMID: 33538901 PMCID: PMC7862525 DOI: 10.1007/s00894-020-04655-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/20/2020] [Indexed: 11/28/2022]
Abstract
The MoCu CO dehydrogenase enzyme not only transforms CO into CO2 but it can also oxidise H2. Even if its hydrogenase activity has been known for decades, a debate is ongoing on the most plausible mode for the binding of H2 to the enzyme active site and the hydrogen oxidation mechanism. In the present work, we provide a new perspective on the MoCu-CODH hydrogenase activity by improving the in silico description of the enzyme. Energy refinement—by means of the BigQM approach—was performed on the intermediates involved in the dihydrogen oxidation catalysis reported in our previously published work (Rovaletti, et al. “Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase.” Inorganics 7 (2019) 135). A suboptimal description of the H2–HN(backbone) interaction was observed when the van der Waals parameters described in previous literature for H2 were employed. Therefore, a new set of van der Waals parameters is developed here in order to better describe the hydrogen–backbone interaction. They give rise to improved binding modes of H2 in the active site of MoCu CO dehydrogenase. Implications of the resulting outcomes for a better understanding of hydrogen oxidation catalysis mechanisms are proposed and discussed.
Collapse
Affiliation(s)
- Anna Rovaletti
- Department of Earth and Environmental Sciences, Milano-Bicocca University, Piazza della Scienza 1, 20126, Milan, Italy
| | - Claudio Greco
- Department of Earth and Environmental Sciences, Milano-Bicocca University, Piazza della Scienza 1, 20126, Milan, Italy.
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00, Lund, Sweden.
| |
Collapse
|
20
|
Abstract
QM/MM simulations have become an indispensable tool in many chemical and biochemical investigations. Considering the tremendous degree of success, including recognition by a 2013 Nobel Prize in Chemistry, are there still "burning challenges" in QM/MM methods, especially for biomolecular systems? In this short Perspective, we discuss several issues that we believe greatly impact the robustness and quantitative applicability of QM/MM simulations to many, if not all, biomolecules. We highlight these issues with observations and relevant advances from recent studies in our group and others in the field. Despite such limited scope, we hope the discussions are of general interest and will stimulate additional developments that help push the field forward in meaningful directions.
Collapse
Affiliation(s)
- Qiang Cui
- Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Tanmoy Pal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Luke Xie
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| |
Collapse
|
21
|
Hashem S, Cupellini L, Lipparini F, Mennucci B. A polarisable QM/MM description of NMR chemical shifts of a photoreceptor protein. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1771449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Shaima Hashem
- Department of Chemistry, University of Pisa, Pisa, Italy
| | | | | | | |
Collapse
|
22
|
Unzueta PA, Beran GJO. Polarizable continuum models provide an effective electrostatic embedding model for fragment-based chemical shift prediction in challenging systems. J Comput Chem 2020; 41:2251-2265. [PMID: 32748418 DOI: 10.1002/jcc.26388] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/04/2020] [Accepted: 07/04/2020] [Indexed: 12/25/2022]
Abstract
Ab initio nuclear magnetic resonance chemical shift prediction provides an important tool for interpreting and assigning experimental spectra, but it becomes computationally prohibitive in large systems. The computational costs can be reduced considerably by fragmentation of the large system into a series of contributions from many smaller subsystems. However, the presence of charged functional groups and the need to partition the system across covalent bonds create complications in biomolecules that typically require the use of large fragments and careful descriptions of the electrostatic environment. The present work shows how a model that combines chemical shielding contributions from non-overlapping monomer and dimer fragments embedded in a polarizable continuum model provides a simple, easy-to-implement, and computationally inexpensive approach for predicting chemical shifts in complex systems. The model's performance proves rather insensitive to the continuum dielectric constant, making the selection of the optimal embedding dielectric less critical. The PCM-embedded fragment model is demonstrated to perform well across systems ranging from molecular crystals to proteins.
Collapse
Affiliation(s)
- Pablo A Unzueta
- Department of Chemistry, Univeristy of California, Riverside, California, USA
| | - Gregory J O Beran
- Department of Chemistry, Univeristy of California, Riverside, California, USA
| |
Collapse
|
23
|
Dietschreit JCB, Wagner A, Le TA, Klein P, Schindelin H, Opatz T, Engels B, Hellmich UA, Ochsenfeld C. Predicting
19
F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase–Inhibitor Complex. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Johannes C. B. Dietschreit
- Theoretical Chemistry Department of Chemistry University of Munich (LMU) Butenandtstr. 7 81377 Munich Germany
| | - Annika Wagner
- Dept. Chemistry Section Biochemistry Johannes Gutenberg-Universität Mainz 55128 Mainz Germany
- Centre for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue Str. 9 60438 Frankfurt Germany
| | - T. Anh Le
- Institute for Physical and Theoretical Chemistry University of Würzburg Emil-Fischer-Straße 42 97074 Würzburg Germany
| | - Philipp Klein
- Dept. Chemistry Section Organic Chemistry Johannes Gutenberg-Universität Mainz 55128 Mainz Germany
| | - Hermann Schindelin
- Institute of Structural Biology Rudolf Virchow Center for Experimental Biomedicine University of Würzburg 97080 Würzburg Germany
| | - Till Opatz
- Dept. Chemistry Section Organic Chemistry Johannes Gutenberg-Universität Mainz 55128 Mainz Germany
| | - Bernd Engels
- Institute for Physical and Theoretical Chemistry University of Würzburg Emil-Fischer-Straße 42 97074 Würzburg Germany
| | - Ute A. Hellmich
- Dept. Chemistry Section Biochemistry Johannes Gutenberg-Universität Mainz 55128 Mainz Germany
- Centre for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue Str. 9 60438 Frankfurt Germany
| | - Christian Ochsenfeld
- Theoretical Chemistry Department of Chemistry University of Munich (LMU) Butenandtstr. 7 81377 Munich Germany
- Max Planck Institute for Solid State Research 70569 Stuttgart Germany
| |
Collapse
|
24
|
Dietschreit JCB, Wagner A, Le TA, Klein P, Schindelin H, Opatz T, Engels B, Hellmich UA, Ochsenfeld C. Predicting 19 F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase-Inhibitor Complex. Angew Chem Int Ed Engl 2020; 59:12669-12673. [PMID: 32239740 PMCID: PMC7496126 DOI: 10.1002/anie.202000539] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/22/2020] [Indexed: 02/02/2023]
Abstract
The absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor-protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable 19 F chemical-shift predictions to deduce ligand-binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the 19 F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleeping sickness. We include many protein-inhibitor conformations as well as monomeric and dimeric inhibitor-protein complexes, thus rendering it the largest computational study on chemical shifts of 19 F nuclei in a biological context to date. Our predicted shifts agree well with those obtained experimentally and pave the way for future work in this area.
Collapse
Affiliation(s)
| | - Annika Wagner
- Dept. ChemistrySection BiochemistryJohannes Gutenberg-Universität Mainz55128MainzGermany
- Centre for Biomolecular Magnetic Resonance (BMRZ)Goethe-University FrankfurtMax-von-Laue Str. 960438FrankfurtGermany
| | - T. Anh Le
- Institute for Physical and Theoretical ChemistryUniversity of WürzburgEmil-Fischer-Straße 4297074WürzburgGermany
| | - Philipp Klein
- Dept. ChemistrySection Organic ChemistryJohannes Gutenberg-Universität Mainz55128MainzGermany
| | - Hermann Schindelin
- Institute of Structural BiologyRudolf Virchow Center for Experimental BiomedicineUniversity of Würzburg97080WürzburgGermany
| | - Till Opatz
- Dept. ChemistrySection Organic ChemistryJohannes Gutenberg-Universität Mainz55128MainzGermany
| | - Bernd Engels
- Institute for Physical and Theoretical ChemistryUniversity of WürzburgEmil-Fischer-Straße 4297074WürzburgGermany
| | - Ute A. Hellmich
- Dept. ChemistrySection BiochemistryJohannes Gutenberg-Universität Mainz55128MainzGermany
- Centre for Biomolecular Magnetic Resonance (BMRZ)Goethe-University FrankfurtMax-von-Laue Str. 960438FrankfurtGermany
| | - Christian Ochsenfeld
- Theoretical ChemistryDepartment of ChemistryUniversity of Munich (LMU)Butenandtstr. 781377MunichGermany
- Max Planck Institute for Solid State Research70569StuttgartGermany
| |
Collapse
|
25
|
Imamura K, Yamazaki T, Yokogawa D, Higashi M, Sato H. Nuclear magnetic shielding of molecule in solution based on reference interaction site model self-consistent field with spatial electron density distribution. J Chem Phys 2020; 152:194102. [DOI: 10.1063/5.0008903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Kosuke Imamura
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Takeshi Yamazaki
- 1QB Information Technologies (1QBit), 200-1285 West Pender Street, Vancouver, British Columbia V6E 4B1, Canada
| | - Daisuke Yokogawa
- Graduate School of Arts and Science, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Masahiro Higashi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto 615-8520, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto 615-8520, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| |
Collapse
|
26
|
Mehmood R, Kulik HJ. Both Configuration and QM Region Size Matter: Zinc Stability in QM/MM Models of DNA Methyltransferase. J Chem Theory Comput 2020; 16:3121-3134. [PMID: 32243149 DOI: 10.1021/acs.jctc.0c00153] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Quantum-mechanical/molecular-mechanical (QM/MM) methods are essential to the study of metalloproteins, but the relative importance of sampling and degree of QM treatment in achieving quantitative predictions is poorly understood. We study the relative magnitude of configurational and QM-region sensitivity of energetic and electronic properties in a representative Zn2+ metal binding site of a DNA methyltransferase. To quantify property variations, we analyze snapshots extracted from 250 ns of molecular dynamics simulation. To understand the degree of QM-region sensitivity, we perform analysis using QM regions ranging from a minimal 49-atom region consisting only of the Zn2+ metal and its four coordinating Cys residues up to a 628-atom QM region that includes residues within 12 Å of the metal center. Over the configurations sampled, we observe that illustrative properties (e.g., rigid Zn2+ removal energy) exhibit large fluctuations that are well captured with even minimal QM regions. Nevertheless, for both energetic and electronic properties, we observe a slow approach to asymptotic limits with similarly large changes in absolute values that converge only with larger (ca. 300-atom) QM region sizes. For the smaller QM regions, the electronic description of Zn2+ binding is incomplete: the metal binds too tightly and is too stabilized by the strong electrostatic potential of MM point charges, and the Zn-S bond covalency is overestimated. Overall, this work suggests that efficient sampling with QM/MM in small QM regions is an effective method to explore the influence of enzyme structure on target properties. At the same time, accurate descriptions of electronic and energetic properties require a larger QM region than the minimal metal-coordinating residues in order to converge treatment of both metal-local bonding and the overall electrostatic environment.
Collapse
Affiliation(s)
- Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
27
|
Saura P, Röpke M, Gamiz-Hernandez AP, Kaila VRI. Quantum Chemical and QM/MM Models in Biochemistry. Methods Mol Biol 2020; 2022:75-104. [PMID: 31396900 DOI: 10.1007/978-1-4939-9608-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Quantum chemical (QC) calculations provide a basis for deriving a microscopic understanding of enzymes and photobiological systems. Here we describe how QC models can be used to explore the electronic structure, dynamics, and energetics of biomolecules. We introduce the hybrid quantum mechanics/classical mechanics (QM/MM) approach, where a quantum mechanically described system of interest is embedded in a classically described force field representation of the biochemical surroundings. We also discuss the QM cluster model approach, as well as embedding theories, that provide complementary methodologies to model quantum mechanical effects in biomolecules. The chapter also provides some practical guides for building quantum biochemical models using the quinone reduction catalysis in respiratory complex I and a model reaction in solution as examples.
Collapse
Affiliation(s)
- Patricia Saura
- Department Chemie, Technische Universität München, Garching, Germany
| | - Michael Röpke
- Department Chemie, Technische Universität München, Garching, Germany
| | | | - Ville R I Kaila
- Department Chemie, Technische Universität München, Garching, Germany.
| |
Collapse
|
28
|
Simm GN, Türtscher PL, Reiher M. Systematic microsolvation approach with a cluster-continuum scheme and conformational sampling. J Comput Chem 2020; 41:1144-1155. [PMID: 32027384 DOI: 10.1002/jcc.26161] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 01/11/2020] [Accepted: 01/16/2020] [Indexed: 12/12/2022]
Abstract
Solvation is a notoriously difficult and nagging problem for the rigorous theoretical description of chemistry in the liquid phase. Successes and failures of various approaches ranging from implicit solvation modeling through dielectric continuum embedding and microsolvated quantum chemical modeling to explicit molecular dynamics highlight this situation. Here, we focus on quantum chemical microsolvation and discuss an explicit conformational sampling ansatz to make this approach systematic. For this purpose, we introduce an algorithm for rolling and automated microsolvation of solutes. Our protocol takes conformational sampling and rearrangements in the solvent shell into account. Its reliability is assessed by monitoring the evolution of the spread and average of the observables of interest.
Collapse
Affiliation(s)
- Gregor N Simm
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Paul L Türtscher
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| |
Collapse
|
29
|
A benchmark for the size of the QM system required for accurate hybrid QM/MM calculations on the metal site of the protein copper, zinc superoxide dismutase. J Mol Model 2019; 25:176. [PMID: 31154525 DOI: 10.1007/s00894-019-4066-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/14/2019] [Indexed: 12/12/2022]
Abstract
The protein superoxide dismutase 1 (SOD1) is a copper and zinc-binding protein that has been implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS). The Zn(II) binding to SOD1 is critical for the stability of the protein, and has been by itself implicated in ALS pathogenesis. Hence, the quantum mechanical (QM) study of the Zn(II)-site of SOD1 is relevant for understanding ALS. The hybrid QM-molecular mechanics (QM/MM) approach commonly employed for the QM study of proteins is highly dependent on the size of the sub-system treated quantum-mechanically. The size of the QM system also determines the computational feasibility of a given method. In the present work, we compare optimized geometries for the metal site and Zn(II) dissociation energies obtained with a QM/MM methodology employing different sizes for the QM sub-system. We find that geometries converge rapidly to RMSDs of around 0.3 Å, and fails to converge further, while a QM system of 480 atoms was required for converging the Zn(II) interaction energy of SOD1 to within 5 kcal*mol-1, and a 611-atoms QM system for a 1 kcal*mol-1 convergence with respect to our reference, 1280 QM-atoms system. Graphical Abstract The size of the QM system is critical for both the accuracy and the computational cost of a QM/MM calculation. We have identified a optimum balance for the study of the active site of the coppper, zinc superoxide dismutase.
Collapse
|
30
|
Ranaghan KE, Shchepanovska D, Bennie SJ, Lawan N, Macrae SJ, Zurek J, Manby FR, Mulholland AJ. Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution. J Chem Inf Model 2019; 59:2063-2078. [PMID: 30794388 DOI: 10.1021/acs.jcim.8b00940] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly widely utilized in studies of reactions in enzymes and other large systems. Here, we apply a range of QM/MM methods to investigate the Claisen rearrangement of chorismate to prephenate, in solution, and in the enzyme chorismate mutase. Using projector-based embedding in a QM/MM framework, we apply treatments up to the CCSD(T) level. We test a range of density functional QM/MM methods and QM region sizes. The results show that the calculated reaction energetics are significantly more sensitive to the choice of density functional than they are to the size of the QM region in these systems. Projector-based embedding of a wave function method in DFT reduced the 13 kcal/mol spread in barrier heights calculated at the DFT/MM level to a spread of just 0.3 kcal/mol, essentially eliminating dependence on the functional. Projector-based embedding of correlated ab initio methods provides a practical method for achieving high accuracy for energy profiles derived from DFT and DFT/MM calculations for reactions in condensed phases.
Collapse
Affiliation(s)
- Kara E Ranaghan
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Darya Shchepanovska
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Simon J Bennie
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Narin Lawan
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Stephen J Macrae
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Jolanta Zurek
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| |
Collapse
|
31
|
Yuan M, Zhang Y, Qu Z, Xiao Y, Liu W. Sublinear scaling quantum chemical methods for magnetic shieldings in large molecules. J Chem Phys 2019; 150:154113. [DOI: 10.1063/1.5083193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Minghong Yuan
- Beijing National Center for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yong Zhang
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao 266237, China
| | - Zhi Qu
- Beijing National Center for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yunlong Xiao
- Beijing National Center for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao 266237, China
| |
Collapse
|
32
|
A thiocarbonate sink on the enzymatic energy landscape of aerobic CO oxidation? Answers from DFT and QM/MM models of Mo Cu CO-dehydrogenases. J Catal 2019. [DOI: 10.1016/j.jcat.2019.02.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
33
|
Yang Z, Mehmood R, Wang M, Qi HW, Steeves AH, Kulik HJ. Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation. REACT CHEM ENG 2019; 4:298-315. [PMID: 31572618 PMCID: PMC6768422 DOI: 10.1039/c8re00213d] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzymes have evolved to facilitate challenging reactions at ambient conditions with specificity seldom matched by other catalysts. Computational modeling provides valuable insight into catalytic mechanism, and the large size of enzymes mandates multi-scale, quantum mechanical-molecular mechanical (QM/MM) simulations. Although QM/MM plays an essential role in balancing simulation cost to enable sampling with full QM treatment needed to understand electronic structure in enzyme active sites, the relative importance of these two strategies for understanding enzyme mechanism is not well known. We explore challenges in QM/MM for studying the reactivity and stability of three diverse enzymes: i) Mg2+-dependent catechol O-methyltransferase (COMT), ii) radical enzyme choline trimethylamine lyase (CutC), and iii) DNA methyltransferase (DNMT1), which has structural Zn2+ binding sites. In COMT, strong non-covalent interactions lead to long range coupling of electronic structure properties across the active site, but the more isolated nature of the metallocofactor in DNMT1 leads to faster convergence of some properties. We quantify these effects in COMT by computing covariance matrices of by-residue electronic structure properties during dynamics and along the reaction coordinate. In CutC, we observe spontaneous bond cleavage following initiation events, highlighting the importance of sampling and dynamics. We use electronic structure analysis to quantify the relative importance of CHO and OHO non-covalent interactions in imparting reactivity. These three diverse cases enable us to provide some general recommendations regarding QM/MM simulation of enzymes.
Collapse
Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mengyi Wang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Helena W. Qi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Adam H. Steeves
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| |
Collapse
|
34
|
Wei WJ, Qian HX, Wang WJ, Liao RZ. Computational Understanding of the Selectivities in Metalloenzymes. Front Chem 2018; 6:638. [PMID: 30622942 PMCID: PMC6308299 DOI: 10.3389/fchem.2018.00638] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/07/2018] [Indexed: 01/26/2023] Open
Abstract
Metalloenzymes catalyze many different types of biological reactions with high efficiency and remarkable selectivity. The quantum chemical cluster approach and the combined quantum mechanics/molecular mechanics methods have proven very successful in the elucidation of the reaction mechanism and rationalization of selectivities in enzymes. In this review, recent progress in the computational understanding of various selectivities including chemoselectivity, regioselectivity, and stereoselectivity, in metalloenzymes, is discussed.
Collapse
Affiliation(s)
| | | | | | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
35
|
Do Better Quality Embedding Potentials Accelerate the Convergence of QM/MM Models? The Case of Solvated Acid Clusters. Molecules 2018; 23:molecules23102466. [PMID: 30261616 PMCID: PMC6222911 DOI: 10.3390/molecules23102466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 09/22/2018] [Accepted: 09/24/2018] [Indexed: 12/28/2022] Open
Abstract
This study examines whether the use of more accurate embedding potentials improves the convergence of quantum mechanics/molecular mechanics (QM/MM) models with respect to the size of the QM region. In conjunction with density functional theory calculations using the ωB97X-D functional, various embedding potentials including the TIP3P water model, the effective fragment potential (EFP), and semi-empirical methods (PM6, PM7, and DFTB) were used to simulate the deprotonation energies of solvated acid clusters. The calculations were performed on solvated neutral (HA) and cationic (HB⁺) acids clusters containing 160 and 480 water molecules using configurations sampled from molecular dynamics simulations. Consistently, the ωB97X-D/EFP model performed the best when using a minimal QM region size. The performance for the other potentials appears to be highly sensitive to the charge character of the acid/base pair. Neutral acids display the expected trend that semi-empirical methods generally perform better than TIP3P; however, an opposite trend was observed for the cationic acids. Additionally, electronic embedding provided an improvement over mechanical embedding for the cationic systems, but not the neutral acids. For the best performing ωB97X-D/EFP model, a QM region containing about 6% of the total number of solvent molecules is needed to approach within 10 kJ mol-1 of the pure QM result if the QM region was chosen based on the distance from the reaction centre.
Collapse
|
36
|
Roston D, Lu X, Fang D, Demapan D, Cui Q. Analysis of Phosphoryl-Transfer Enzymes with QM/MM Free Energy Simulations. Methods Enzymol 2018; 607:53-90. [PMID: 30149869 DOI: 10.1016/bs.mie.2018.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We discuss the application of quantum mechanics/molecular mechanics (QM/MM) free energy simulations to the analysis of phosphoryl transfers catalyzed by two enzymes: alkaline phosphatase and myosin. We focus on the nature of the transition state and the issue of mechanochemical coupling, respectively, in the two enzymes. The results illustrate unique insights that emerged from the QM/MM simulations, especially concerning the interpretation of experimental data regarding the nature of enzymatic transition states and coupling between global structural transition and catalysis in the active site. We also highlight a number of technical issues worthy of attention when applying QM/MM free energy simulations, and comment on a number of technical and mechanistic issues that require further studies.
Collapse
Affiliation(s)
- Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Dong Fang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Darren Demapan
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States.
| |
Collapse
|
37
|
Kulik HJ. Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer. Phys Chem Chem Phys 2018; 20:20650-20660. [PMID: 30059109 PMCID: PMC6085747 DOI: 10.1039/c8cp03871f] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations provide key insights into enzyme structure-function relationships. Numerous studies have demonstrated that large QM regions are needed to systematically converge ground state, zero temperature properties with electrostatic embedding QM/MM. However, it is not well known if ab initio QM/MM free energy simulations have this same dependence, in part due to the hundreds of thousands of energy evaluations required for free energy estimations that in turn limit QM region size. Here, we leverage recent advances in electronic structure efficiency and accuracy to carry out range-separated hybrid density functional theory free energy simulations in a representative methyltransferase. By studying 200 ps of ab initio QM/MM dynamics for each of five QM regions from minimal (64 atoms) to one-sixth of the protein (544 atoms), we identify critical differences between large and small QM region QM/MM in charge transfer between substrates and active site residues as well as in geometric structure and dynamics that coincide with differences in predicted free energy barriers. Distinct geometric and electronic structure features in the largest QM region indicate that important aspects of enzymatic rate enhancement in methyltransferases are identified with large-scale electronic structure.
Collapse
Affiliation(s)
- Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
38
|
Nogueira JJ, Roßbach S, Ochsenfeld C, González L. Effect of DNA Environment on Electronically Excited States of Methylene Blue Evaluated by a Three-Layered QM/QM/MM ONIOM Scheme. J Chem Theory Comput 2018; 14:4298-4308. [DOI: 10.1021/acs.jctc.8b00185] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan J. Nogueira
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, A-1090 Wien, Austria
| | - Sven Roßbach
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 7, D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 7, D-81377 Munich, Germany
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, A-1090 Wien, Austria
| |
Collapse
|
39
|
Caprasecca S, Cupellini L, Jurinovich S, Loco D, Lipparini F, Mennucci B. A polarizable QM/MM description of environment effects on NMR shieldings: from solvated molecules to pigment–protein complexes. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2264-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
40
|
Jin X, Zhu T, Zhang JZH, He X. Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes. Front Chem 2018; 6:150. [PMID: 29868556 PMCID: PMC5952040 DOI: 10.3389/fchem.2018.00150] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/16/2018] [Indexed: 01/13/2023] Open
Abstract
In this study, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method was applied for NMR chemical shift calculations of protein-ligand complexes. In the AF-QM/MM approach, the protein binding pocket is automatically divided into capped fragments (within ~200 atoms) for density functional theory (DFT) calculations of NMR chemical shifts. Meanwhile, the solvent effect was also included using the Poission-Boltzmann (PB) model, which properly accounts for the electrostatic polarization effect from the solvent for protein-ligand complexes. The NMR chemical shifts of neocarzinostatin (NCS)-chromophore binding complex calculated by AF-QM/MM accurately reproduce the large-sized system results. The 1H chemical shift perturbations (CSP) between apo-NCS and holo-NCS predicted by AF-QM/MM are also in excellent agreement with experimental results. Furthermore, the DFT calculated chemical shifts of the chromophore and residues in the NCS binding pocket can be utilized as molecular probes to identify the correct ligand binding conformation. By combining the CSP of the atoms in the binding pocket with the Glide scoring function, the new scoring function can accurately distinguish the native ligand pose from decoy structures. Therefore, the AF-QM/MM approach provides an accurate and efficient platform for protein-ligand binding structure prediction based on NMR derived information.
Collapse
Affiliation(s)
- Xinsheng Jin
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
| | - Tong Zhu
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
| | - John Z. H. Zhang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
- Department of Chemistry, New York University, New York, NY, United States
| | - Xiao He
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
- National Engineering Research Centre for Nanotechnology, Shanghai, China
| |
Collapse
|
41
|
Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| |
Collapse
|
42
|
|
43
|
Parrish RM, Thompson KC, Martínez TJ. Large-Scale Functional Group Symmetry-Adapted Perturbation Theory on Graphical Processing Units. J Chem Theory Comput 2018; 14:1737-1753. [DOI: 10.1021/acs.jctc.7b01053] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Robert M. Parrish
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Keiran C. Thompson
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Todd J. Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| |
Collapse
|
44
|
How reliable are Minnesota density functionals for modeling phosphorus–hydrogen NMR spin–spin coupling constants? Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2182-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
45
|
Nåbo LJ, Olsen JMH, Martínez TJ, Kongsted J. The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein. J Chem Theory Comput 2017; 13:6230-6236. [DOI: 10.1021/acs.jctc.7b00528] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lina J. Nåbo
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Todd J. Martínez
- Department
of Chemistry and PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94305, United States
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| |
Collapse
|
46
|
Provorse Long MR, Isborn CM. Combining Explicit Quantum Solvent with a Polarizable Continuum Model. J Phys Chem B 2017; 121:10105-10117. [DOI: 10.1021/acs.jpcb.7b06693] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Christine M. Isborn
- Chemistry
and Chemical Biology, University of California Merced, Merced, California 95343, United States
| |
Collapse
|
47
|
Zhao D, Song R, Li W, Ma J, Dong H, Li S. Accurate Prediction of NMR Chemical Shifts in Macromolecular and Condensed-Phase Systems with the Generalized Energy-Based Fragmentation Method. J Chem Theory Comput 2017; 13:5231-5239. [DOI: 10.1021/acs.jctc.7b00380] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dongbo Zhao
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
- Kuang
Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Ruiheng Song
- Kuang
Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Wei Li
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Jing Ma
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Hao Dong
- Kuang
Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Shuhua Li
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| |
Collapse
|
48
|
Nørby MS, Olsen JMH, Steinmann C, Kongsted J. Modeling Electronic Circular Dichroism within the Polarizable Embedding Approach. J Chem Theory Comput 2017; 13:4442-4451. [DOI: 10.1021/acs.jctc.7b00712] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Morten S. Nørby
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | | | - Casper Steinmann
- Department
of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| |
Collapse
|
49
|
Mao Y, Shao Y, Dziedzic J, Skylaris CK, Head-Gordon T, Head-Gordon M. Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis. J Chem Theory Comput 2017; 13:1963-1979. [PMID: 28430427 DOI: 10.1021/acs.jctc.7b00089] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH3, NH4+, CN-) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model ( Dziedzic et al. J. Chem. Phys. 2016 , 145 , 124106 ). The implications of these results for further refinement of this model are also discussed.
Collapse
Affiliation(s)
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K.,Faculty of Applied Physics and Mathematics, Gdańsk University of Technology , Gdańsk 80-233, Poland
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | | | - Martin Head-Gordon
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
50
|
Milanese JM, Provorse MR, Alameda E, Isborn CM. Convergence of Computed Aqueous Absorption Spectra with Explicit Quantum Mechanical Solvent. J Chem Theory Comput 2017; 13:2159-2171. [DOI: 10.1021/acs.jctc.7b00159] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel M. Milanese
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Makenzie R. Provorse
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Enrique Alameda
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| |
Collapse
|