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Yan X, Qu C, Li Q, Zhu L, Tong HH, Liu H, Ouyang Q, Yao X. Multiscale calculations reveal new insights into the reaction mechanism between KRAS G12C and α, β-unsaturated carbonyl of covalent inhibitors. Comput Struct Biotechnol J 2024; 23:1408-1417. [PMID: 38616962 PMCID: PMC11015740 DOI: 10.1016/j.csbj.2024.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 04/16/2024] Open
Abstract
Utilizing α,β-unsaturated carbonyl group as Michael acceptors to react with thiols represents a successful strategy for developing KRASG12C inhibitors. Despite this, the precise reaction mechanism between KRASG12C and covalent inhibitors remains a subject of debate, primarily due to the absence of an appropriate residue capable of deprotonating the cysteine thiol as a base. To uncover this reaction mechanism, we first discussed the chemical reaction mechanism in solvent conditions via density functional theory (DFT) calculation. Based on this, we then proposed and validated the enzymatic reaction mechanism by employing quantum mechanics/molecular mechanics (QM/MM) calculation. Our QM/MM analysis suggests that, in biological conditions, proton transfer and nucleophilic addition may proceed through a concerted process to form an enolate intermediate, bypassing the need for a base catalyst. This proposed mechanism differs from previous findings. Following the formation of the enolate intermediate, solvent-assisted tautomerization results in the final product. Our calculations indicate that solvent-assisted tautomerization is the rate-limiting step in the catalytic cycle under biological conditions. On the basis of this reaction mechanism, the calculated kinact/ki for two inhibitors is consistent well with the experimental results. Our findings provide new insights into the reaction mechanism between the cysteine of KRASG12C and the covalent inhibitors and may provide valuable information for designing effective covalent inhibitors targeting KRASG12C and other similar targets.
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Affiliation(s)
- Xiao Yan
- Faculty of Applied Sciences, Macao Polytechnic University, Macao Special Administrative Region of China
| | - Chuanhua Qu
- College of Pharmacy, National & Local Joint Engineering Research Center of Targeted and Innovative Therapeutics, Chongqing Key Laboratory of Kinase Modulators as Innovative Medicine, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Qin Li
- Faculty of Applied Sciences, Macao Polytechnic University, Macao Special Administrative Region of China
| | - Lei Zhu
- College of Pharmacy, Third Military Medical University, Shapingba, Chongqing 400038, China
| | - Henry H.Y. Tong
- Faculty of Applied Sciences, Macao Polytechnic University, Macao Special Administrative Region of China
| | - Huanxiang Liu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao Special Administrative Region of China
| | - Qin Ouyang
- College of Pharmacy, Third Military Medical University, Shapingba, Chongqing 400038, China
| | - Xiaojun Yao
- Faculty of Applied Sciences, Macao Polytechnic University, Macao Special Administrative Region of China
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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3
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Jiang Y, Yao M, Feng J, Niu H, Qiao B, Li B, Wang B, Xiao W, Dong M, Yuan Y. Molecular Insights into Converting Hydroxide Adenosyltransferase into Halogenase. J Agric Food Chem 2024. [PMID: 38771136 DOI: 10.1021/acs.jafc.4c02581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Halogenation plays a unique role in the design of agrochemicals. Enzymatic halogenation reactions have attracted great attention due to their excellent specificity and mild reaction conditions. S-adenosyl-l-methionine (SAM)-dependent halogenases mediate the nucleophilic attack of halide ions (X-) to SAM to produce 5'-XDA. However, only 11 SAM-dependent fluorinases and 3 chlorinases have been reported, highlighting the desire for additional halogenases. SAM-dependent hydroxide adenosyltransferase (HATase) has a similar reaction mechanism as halogenases but uses water as a substrate instead of halide ions. Here, we explored a HATase from the thermophile Thermotoga maritima MSB8 and transformed it into a halogenase. We identified a key dyad W8L/V71T for the halogenation reaction. We also obtained the best performing mutants for each halogenation reaction: M1, M2 and M4 for Cl-, Br- and I-, respectively. The M4 mutant retained the thermostability of HATase in the iodination reaction at 80 °C, which surpasses the natural halogenase SalL. QM/MM revealed that these mutants bind halide ions with more suitable angles for nucleophilic attack of C5' of SAM, thus conferring halogenation capabilities. Our work achieved the halide ion specificity of halogenases and generated thermostable halogenases for the first time, which provides new opportunities to expand the halogenase repertoire from hydroxylase.
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Affiliation(s)
- Yixun Jiang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Mingdong Yao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Jianqiang Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Haoran Niu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Bingzhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Wenhai Xiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- School of Life Sciences, Faculty of Medicine, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Shenzhen 518071, China
| | - Min Dong
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
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Ali HS, de Visser SP. QM/MM Study Into the Mechanism of Oxidative C=C Double Bond Cleavage by Lignostilbene-α,β-Dioxygenase. Chemistry 2024; 30:e202304172. [PMID: 38373118 DOI: 10.1002/chem.202304172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/29/2024] [Accepted: 02/19/2024] [Indexed: 02/21/2024]
Abstract
The enzymatic biosynthesis of fragrance molecules from lignin fragments is an important reaction in biotechnology for the sustainable production of fine chemicals. In this work we investigated the biosynthesis of vanillin from lignostilbene by a nonheme iron dioxygenase using QM/MM and tested several suggested proposals via either an epoxide or dioxetane intermediate. Binding of dioxygen to the active site of the protein results in the formation of an iron(II)-superoxo species with lignostilbene cation radical. The dioxygenase mechanism starts with electrophilic attack of the terminal oxygen atom of the superoxo group on the central C=C bond of lignostilbene, and the second-coordination sphere effects in the substrate binding pocket guide the reaction towards dioxetane formation. The computed mechanism is rationalized with thermochemical cycles and valence bond schemes that explain the electron transfer processes during the reaction mechanism. Particularly, the polarity of the protein and the local electric field and dipole moments enable a facile electron transfer and an exergonic dioxetane formation pathway.
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Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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5
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Johnson S, Rothlisberger U. Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach. Chimia (Aarau) 2024; 78:243-250. [PMID: 38676618 DOI: 10.2533/chimia.2024.243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 04/29/2024] Open
Abstract
Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to explain the high detection rate in the face of numerous, small lesions. The viability of CT DNA defect detection is explored via hybrid QM/MM computational studies that leverage the accuracy of quantum mechanics (QM) for a region of interest and the descriptive power of molecularmechanics (MM) for the remainder of the system. We find that the presence of an oxidative lesion lowers theredox free energy of oxidation by approximately 1.0 eV regardless of DNA compaction (free DNA versus packed DNA in nucleosome core particles) and damage location indicating the high feasibility of a CT-based process for defect detection in DNA.
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Andrys-Olek J, Kluza A, Tataruch M, Heider J, Korecki J, Borowski T. Bacteria at Work - Experimental and Theoretical Studies Reveal the Catalytic Mechanism of Ectoine Synthase. Chemistry 2024; 30:e202304163. [PMID: 38258332 DOI: 10.1002/chem.202304163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 01/24/2024]
Abstract
Ectoine synthase (EctC) catalyses the ultimate step of ectoine biosynthesis, a kosmotropic compound produced as compatible solute by many bacteria and some archaea or eukaryotes. EctC is an Fe2+-dependent homodimeric cytoplasmic protein. Using Mössbauer spectroscopy, molecular dynamics simulations and QM/MM calculations, we determined the most likely coordination number and geometry of the Fe2+ ion and proposed a mechanism of the EctC-catalysed reaction. Most notably, we show that apart from the three amino acids binding to the iron ion (Glu57, Tyr84 and His92), one water molecule and one hydroxide ion are required as additional ligands for the reaction to occur. They fill the first coordination sphere of the Fe2+-cofactor and act as critical proton donors and acceptors during the cyclization reaction.
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Affiliation(s)
- Justyna Andrys-Olek
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Anna Kluza
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Mateusz Tataruch
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Johann Heider
- Department of Biology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Józef Korecki
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
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7
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Bonanata J. The role of the active site lysine residue on FAD reduction by NADPH in glutathione reductase. Comput Biol Chem 2024; 110:108075. [PMID: 38678729 DOI: 10.1016/j.compbiolchem.2024.108075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/01/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024]
Abstract
Glutathione reductase (GR) is a two dinucleotide binding domain flavoprotein (tDBDF) that catalyzes the reduction of glutathione disulfide to glutathione coupled to the oxidation of NADPH to NADP+. An interesting feature of GR and other tDBDFs is the presence of a lysine residue (Lys-66 in human GR) at the active site, which interacts with the flavin group, but has an unknown function. To better understand the role of this residue, the dynamics of GR was studied using molecular dynamics simulations, and the reaction mechanism of FAD reduction by NADPH was studied using QM/MM molecular modeling. The two possible protonation states of Lys-66 were considered: neutral and protonated. Molecular dynamics results suggest that the active site is more structured for neutral Lys-66 than for protonated Lys-66. QM/MM modeling results suggest that Lys-66 should be in its neutral state for a thermodynamically favorable reduction of FAD by NADPH. Since the reaction is unfavorable with protonated Lys-66, the reverse reaction (the reduction of NADP+ by FADH-) is expected to take place. A phylogenetic analysis of various tDBDFs was performed, finding that an active site lysine is present in different the tDBDFs enzymes, suggesting that it has a conserved biological role. Overall, these results suggest that the protonation state of the active site lysine determines the energetics of the reaction, controlling its reversibility.
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Affiliation(s)
- Jenner Bonanata
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Uruguay; Centro de Investigaciones Biomédicas, Universidad de la República, Uruguay.
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Frederiksen A, Aldag M, Solov’yov IA, Gerhards L. Activation of Cryptochrome 4 from Atlantic Herring. Biology (Basel) 2024; 13:262. [PMID: 38666874 PMCID: PMC11048568 DOI: 10.3390/biology13040262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/04/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
Marine fish migrate long distances up to hundreds or even thousands of kilometers for various reasons that include seasonal dependencies, feeding, or reproduction. The ability to perceive the geomagnetic field, called magnetoreception, is one of the many mechanisms allowing some fish to navigate reliably in the aquatic realm. While it is believed that the photoreceptor protein cryptochrome 4 (Cry4) is the key component for the radical pair-based magnetoreception mechanism in night migratory songbirds, the Cry4 mechanism in fish is still largely unexplored. The present study aims to investigate properties of the fish Cry4 protein in order to understand the potential involvement in a radical pair-based magnetoreception. Specifically, a computationally reconstructed atomistic model of Cry4 from the Atlantic herring (Clupea harengus) was studied employing classical molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) methods to investigate internal electron transfers and the radical pair formation. The QM/MM simulations reveal that electron transfers occur similarly to those found experimentally and computationally in Cry4 from European robin (Erithacus rubecula). It is therefore plausible that the investigated Atlantic herring Cry4 has the physical and chemical properties to form radical pairs that in turn could provide fish with a radical pair-based magnetic field compass sensor.
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Affiliation(s)
- Anders Frederiksen
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany; (A.F.); (M.A.); (I.A.S.)
| | - Mandus Aldag
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany; (A.F.); (M.A.); (I.A.S.)
| | - Ilia A. Solov’yov
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany; (A.F.); (M.A.); (I.A.S.)
- Research Centre for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky University of Oldenburg, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
| | - Luca Gerhards
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany; (A.F.); (M.A.); (I.A.S.)
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9
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López-Sosa L, Calaminici P. Cycloaddition reactions via "on water" protocol reactions: A density functional theory study. J Comput Chem 2024; 45:595-609. [PMID: 38054389 DOI: 10.1002/jcc.27268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 12/07/2023]
Abstract
In this work, the reactions of quadricyclane with dimethyl azodicarboxylate (DMAD) and of quadricyclane with diethyl azodicarboxylate (DEAD) in gas phase and in water environments were studied by a first-principles investigation within the framework of auxiliary density functional theory (ADFT). For these type of organic reactions is known that water is required to accelerate them. Since the reason of why this occur is still unknown, this work aims to gain insight into this reaction mechanism. For this investigation, the generalized gradient approximation as well as a hybrid functional were employed. The obtained optimized structures for the reactants, of the products and of the transition states are reported, together with the corresponding frequency analysis results and the reaction profiles. Along the proposed concerted reaction mechanism, a critical points search of the electron density and a charge analysis were performed. The calculated potential energy barriers of these reactions in gas phase and in water environments are compared. In agreement with experiment, the obtained results indicate that both reactions occur faster in water than in gas phase. This study shows that there is a change in the polarity of the two most important carbon atoms of the formed compounds along the reactions and that the decrease of the activation energy barrier which occurs in liquid phase in these reactions is because the structures of the main transition states are stabilized by the water environment. Therefore, the here obtained results demonstrate the important role played by the water-molecule framework into the activation energy barrier and structures of the molecules that participate in the DMAD and DEAD cycloaddition reactions.
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Affiliation(s)
- L López-Sosa
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional 2508, México, Mexico
| | - P Calaminici
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional 2508, México, Mexico
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Cabral VÁ, Govoni B, Verli H. Unravelling carbohydrate binding module 21 (CBM21) dynamics of interaction with amylose. Carbohydr Polym 2024; 330:121792. [PMID: 38368081 DOI: 10.1016/j.carbpol.2024.121792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 02/19/2024]
Abstract
The carbohydrate binding module 21 (CBM21) from Rhizopus oryzae is a dual-site CBM proposed to disrupt polysaccharide structures. Additionally, it serves as a purification tag in industry. CBM21 crystal structure features a Glc residue in an unusual 1S3 conformation, whose relevance for the CBM mechanism of action is unclear. In this context, we seek to contribute for the understanding of CBM21 mechanism of action by: i) investigating the role of the 1S3 conformation on carbohydrate recognition, and ii) characterize the protein-carbohydrate binding dynamics using molecular dynamics and metadynamics simulations at MM and QM/MM levels. Results indicate the 1S3 Glc conformation is unlikely to occur under biological conditions, being originated from the crystallographic environment. CBM21 binding to small ligands appears transient and unstable, while protein dimerization and polysaccharide chain size influence complex stability. In interactions with amylose, CBM21 exhibits a repeated unbinding followed by re-binding, while simultaneously alternating between binding sites I and II. These results suggest that CBM21 acts through transient interactions, directing carbohydrates to the catalytic center rather than forming strong and long-lasting bonds with carbohydrates. Accordingly, we expect such atomistic depiction of CBM21 mechanism could aid in CBM design targeting biotechnological applications.
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Affiliation(s)
- Vinicius Ávila Cabral
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Porto Alegre 91500-970, RS, Brazil
| | - Bruna Govoni
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Porto Alegre 91500-970, RS, Brazil
| | - Hugo Verli
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Porto Alegre 91500-970, RS, Brazil.
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11
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Freindorf M, Antonio JJ, Kraka E. Iron-histidine bonding in bishistidyl hemoproteins-A local vibrational mode study. J Comput Chem 2024; 45:574-588. [PMID: 38041830 DOI: 10.1002/jcc.27267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 12/04/2023]
Abstract
We investigated the intrinsic strength of distal and proximal FeN bonds for both ferric and ferrous oxidation states of bishistidyl hemoproteins from bacteria, animals, human, and plants, including two cytoglobins, ten hemoglobins, two myoglobins, six neuroglobins, and six phytoglobins. As a qualified measure of bond strength, we used local vibrational force constants ka (FeN) based on local mode theory developed in our group. All calculations were performed with a hybrid QM/MM ansatz. Starting geometries were taken from available x-ray structures. ka (FeN) values were correlated with FeN bond lengths and covalent bond character. We also investigated the stiffness of the axial NFeN bond angle. Our results highlight that protein effects are sensitively reflected in ka (FeN), allowing one to compare trends in diverse protein groups. Moreover, ka (NFeN) is a perfect tool to monitor changes in the axial heme framework caused by different protein environments as well as different Fe oxidation states.
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Affiliation(s)
- Marek Freindorf
- Chemistry Department, Southern Methodist University, Dallas, Texas, USA
| | - Juliana J Antonio
- Chemistry Department, Southern Methodist University, Dallas, Texas, USA
| | - Elfi Kraka
- Chemistry Department, Southern Methodist University, Dallas, Texas, USA
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12
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Jafari S, Ryde U, Irani M. QM/MM study of the catalytic reaction of aphid myrosinase. Int J Biol Macromol 2024; 262:130089. [PMID: 38360236 DOI: 10.1016/j.ijbiomac.2024.130089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/07/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
Brevicoryne brassicae, an aphid species, exclusively consumes plants from the Brassicaceae family and employs a sophisticated defense mechanism involving a myrosinase enzyme that breaks down glucosinolates obtained from its host plants. In this work, we employed combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics (MD) simulations to study the catalytic reaction of aphid myrosinase. A proper QM region to study the myrosinase reaction should contain the whole substrate, models of Gln-19, His-122, Asp-124, Asn-166, Glu-167, Lys-173, Tyr-180, Val-228, Tyr-309, Tyr-346, Ile-347, Glu-374, Glu-423, Trp-424, and a water molecule. The calculations show that Asp-124 and Glu-423 must be charged, His-122 must be protonated on NE2, and Glu-167 must be protonated on OE2. Our model reproduces the anomeric retaining characteristic of myrosinase and indicates that the deglycosylation reaction is the rate-determining step of the reaction. Based on the calculations, we propose a reaction mechanism for aphid myrosinase-mediated hydrolysis of glucosinolates with an overall barrier of 15.2 kcal/mol. According to the results, removing a proton from Arg-312 or altering it to valine or methionine increases glycosylation barriers but decreases the deglycosylation barrier.
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Affiliation(s)
- Sonia Jafari
- Department of Chemistry, University of Kurdistan, P.O. Box 66175-416, Sanandaj, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, P.O. Box 66175-416, Sanandaj, Iran.
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13
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Salvadori G, Mazzeo P, Accomasso D, Cupellini L, Mennucci B. Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response. J Mol Biol 2024; 436:168358. [PMID: 37944793 DOI: 10.1016/j.jmb.2023.168358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
In this review, we discuss the successes and challenges of the atomistic modeling of photoreceptors. Throughout our presentation, we integrate explanations of the primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples of their practical application to specific systems. To enhance the effectiveness of our analysis, our primary focus has been directed towards the examination of applications across three distinct photoreceptors. These include an example of Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, and the orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on the pivotal role played by the protein matrix in fine-tuning the initial photochemical event within the embedded chromophore. Furthermore, we will investigate how this localized perturbation initiates a cascade of events propagating from the binding pocket throughout the entire protein structure, thanks to the intricate network of interactions between the chromophore and the protein.
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Affiliation(s)
- Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Patrizia Mazzeo
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Davide Accomasso
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
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14
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Jaiswal VK, Taddei M, Nascimento DR, Garavelli M, Conti I, Nenov A. Reconciling TD-DFT and CASPT2 electronic structure methods for describing the photophysics of DNA. Photochem Photobiol 2024; 100:443-452. [PMID: 38356286 DOI: 10.1111/php.13922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024]
Abstract
Time-dependent density functional theory (TD-DFT) and multiconfigurational second-order perturbation theory (CASPT2) are two of the most widely used methods to investigate photoinduced dynamics in DNA-based systems. These methods sometimes give diverse dynamics in physiological environments usually modeled by quantum mechanics/molecular mechanics (QM/MM) protocol. In this work, we demonstrate for the uridine test case that the underlying topology of the potential energy surfaces of electronic states involved in photoinduced relaxation is similar in both electronic structure methods. This is verified by analyzing surface-hopping dynamics performed at the QM/MM level on aqueous solvated uridine at TD-DFT and CASPT2 levels. By constraining the dynamics to remain onπ π * state we observe similar fluctuations in energy and relaxation lifetimes in surface-hopping dynamics in both TD-DFT and experimentally validated CASPT2 methods. This finding calls for a systematic comparison of the ES potential energy surfaces of DNA and RNA nucleosides at the single- and multi-reference levels of theory. The anomalous long excited state lifetime at the TD-DFT level is explained byn π * trapping due to the tendency of TD-DFT in QM/MM schemes with electrostatic embedding to underestimate the energy of theπ π * state leading to a wrongπ π * / n π * energetic order. A study of the FC energetics suggests that improving the description of the surrounding environment through polarizable embedding or by the expansion of QM layer with hydrogen-bonded waters helps restore the correct state order at TD-DFT level. Thus by combining TDDFT with an accurate modeling of the environment, TD-DFT is positioned as the standout protocol to model photoinduced dynamics in DNA-based aggregates and multimers.
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Affiliation(s)
- Vishal Kumar Jaiswal
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
| | - Mario Taddei
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
| | | | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
| | - Irene Conti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
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15
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Ali HS, de Visser SP. Catalytic divergencies in the mechanism of L-arginine hydroxylating nonheme iron enzymes. Front Chem 2024; 12:1365494. [PMID: 38406558 PMCID: PMC10884159 DOI: 10.3389/fchem.2024.1365494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 01/22/2024] [Indexed: 02/27/2024] Open
Abstract
Many enzymes in nature utilize a free arginine (L-Arg) amino acid to initiate the biosynthesis of natural products. Examples include nitric oxide synthases, which generate NO from L-Arg for blood pressure control, and various arginine hydroxylases involved in antibiotic biosynthesis. Among the groups of arginine hydroxylases, several enzymes utilize a nonheme iron(II) active site and let L-Arg react with dioxygen and α-ketoglutarate to perform either C3-hydroxylation, C4-hydroxylation, C5-hydroxylation, or C4-C5-desaturation. How these seemingly similar enzymes can react with high specificity and selectivity to form different products remains unknown. Over the past few years, our groups have investigated the mechanisms of L-Arg-activating nonheme iron dioxygenases, including the viomycin biosynthesis enzyme VioC, the naphthyridinomycin biosynthesis enzyme NapI, and the streptothricin biosynthesis enzyme OrfP, using computational approaches and applied molecular dynamics, quantum mechanics on cluster models, and quantum mechanics/molecular mechanics (QM/MM) approaches. These studies not only highlight the differences in substrate and oxidant binding and positioning but also emphasize on electronic and electrostatic differences in the substrate-binding pockets of the enzymes. In particular, due to charge differences in the active site structures, there are changes in the local electric field and electric dipole moment orientations that either strengthen or weaken specific substrate C-H bonds. The local field effects, therefore, influence and guide reaction selectivity and specificity and give the enzymes their unique reactivity patterns. Computational work using either QM/MM or density functional theory (DFT) on cluster models can provide valuable insights into catalytic reaction mechanisms and produce accurate and reliable data that can be used to engineer proteins and synthetic catalysts to perform novel reaction pathways.
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Affiliation(s)
- Hafiz Saqib Ali
- Chemistry Research Laboratory, Department of Chemistry and the INEOS Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Sam P. de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, Manchester, United Kingdom
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16
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Le DPN, Hastings G, Gozem S. How Aqueous Solvation Impacts the Frequencies and Intensities of Infrared Absorption Bands in Flavin: The Quest for a Suitable Solvent Model. Molecules 2024; 29:520. [PMID: 38276598 PMCID: PMC10818357 DOI: 10.3390/molecules29020520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
FTIR spectroscopy accompanied by quantum chemical simulations can reveal important information about molecular structure and intermolecular interactions in the condensed phase. Simulations typically account for the solvent either through cluster quantum mechanical (QM) models, polarizable continuum models (PCM), or hybrid quantum mechanical/molecular mechanical (QM/MM) models. Recently, we studied the effect of aqueous solvent interactions on the vibrational frequencies of lumiflavin, a minimal flavin model, using cluster QM and PCM models. Those models successfully reproduced the relative frequencies of four prominent stretching modes of flavin's isoalloxazine ring in the diagnostic 1450-1750 cm-1 range but poorly reproduced the relative band intensities. Here, we extend our studies on this system and account for solvation through a series of increasingly sophisticated models. Only by combining elements of QM clusters, QM/MM, and PCM approaches do we obtain an improved agreement with the experiment. The study sheds light more generally on factors that can impact the computed frequencies and intensities of IR bands in solution.
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Affiliation(s)
- D. P. Ngan Le
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (D.P.N.L.); (G.H.)
| | - Gary Hastings
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (D.P.N.L.); (G.H.)
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303, USA
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (D.P.N.L.); (G.H.)
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17
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Jiang Y, Yao M, Niu H, Wang W, He J, Qiao B, Li B, Dong M, Xiao W, Yuan Y. Enzyme Engineering Renders Chlorinase the Activity of Fluorinase. J Agric Food Chem 2024; 72:1203-1212. [PMID: 38179953 DOI: 10.1021/acs.jafc.3c08185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Organofluorine compounds have attracted substantial attention owing to their wide application in agrochemistry. Fluorinase (FlA) is a unique enzyme in nature that can incorporate fluorine into an organic molecule. Chlorinase (SalL) has a similar mechanism as fluorinase and can use chloride but not fluoride as a substrate to generate 5'-chloro-deoxyadenosine (5'-ClDA) from S-adenosyl-l-methionine (SAM). Therefore, identifying the features that lead to this selectivity for halide ions is highly important. Here, we engineered SalL to gain the function of FlA. We found that residue Tyr70 plays a key role in this conversion through alanine scanning. Site-saturation mutagenesis experiments demonstrated that Y70A/C/S/T/G all exhibited obvious fluorinase activity. The G131S mutant of SalL, in which the previously thought crucial residue Ser158 for fluoride binding in FlA was introduced, did not exhibit fluorination activity. Compared with the Y70T single mutant, the double mutant Y70T/W129F increased 5'-fluoro-5-deoxyadenosine (5'-FDA) production by 76%. The quantum mechanics (QM)/molecular mechanics (MM) calculations suggested that the lower energy barriers and shorter nucleophilic distance from F- to SAM in the mutants than in the SalL wild-type may contribute to the activity. Therefore, our study not only renders SalL the activity of FlA but also sheds light on the enzyme selectivity between fluoride versus chloride.
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Affiliation(s)
- Yixun Jiang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Mingdong Yao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Haoran Niu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Wenrui Wang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jiale He
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Bingzhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Min Dong
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Wenhai Xiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Shenzhen 518071, China
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
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18
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Sepali C, Lafiosca P, Gómez S, Giovannini T, Cappelli C. Effective fully polarizable QM/MM approaches to compute Raman and Raman Optical Activity spectra in aqueous solution. Spectrochim Acta A Mol Biomol Spectrosc 2024; 305:123485. [PMID: 37827000 DOI: 10.1016/j.saa.2023.123485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/22/2023] [Accepted: 10/01/2023] [Indexed: 10/14/2023]
Abstract
Raman and Raman Optical Activity (ROA) signals are amply affected by solvent effects, especially in the presence of strongly solute-solvent interactions such as Hydrogen Bonding (HB). In this work, we extend the fully atomistic polarizable Quantum Mechanics/Molecular Mechanics approach, based on the Fluctuating Charges and Fluctuating Dipoles force field to the calculation of Raman and ROA spectra. Such an approach is able to accurately describe specific HB interactions, by also accounting for anisotropic contributions due to the inclusion of fluctuating dipoles. To highlight the potentiality of the novel approach, Raman and ROA spectra of L-Serine and L-Cysteine dissolved in aqueous solution are computed and compared both with alternative theoretical approaches and experimental measurements.
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Affiliation(s)
- Chiara Sepali
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, Pisa, 56126, Italy
| | - Piero Lafiosca
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, Pisa, 56126, Italy
| | - Sara Gómez
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, Pisa, 56126, Italy
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, Pisa, 56126, Italy.
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19
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Santos SFG, Bommareddy RR, Black GW, Singh W. Impact of the T296S mutation in P450 GcoA for aryl-O-demethylation: a QM/MM study. Front Chem 2024; 11:1327398. [PMID: 38283898 PMCID: PMC10811788 DOI: 10.3389/fchem.2023.1327398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/15/2023] [Indexed: 01/30/2024] Open
Abstract
Lignin, a complex plant cell wall component, holds promise as a renewable aromatic carbon feedstock. p-Vanillin is a key product of lignin depolymerization and a precursor of protocatechuic acid (PCA) that has tremendous potential for biofuel production. While the GcoAB enzyme, native to Amycolatopsis sp., naturally catalyzes aryl-O-demethylation toward guaiacol, recent research introduced a single mutation, T296S, into the GcoAP450 enzyme, enabling it to catalyze aryl-O-demethylation of p-vanillin. This structural modification increases the efficiency of GcoAP450 for the natural substrate while being active for p-vanillin. This study reveals the increased flexibility of p-vanillin and its ability to adapt a favorable conformation by aligning the methoxy group in close proximity to Fe(IV) = O of Cpd I in the active site of the T296S variant. The QM/MM calculations in accordance with the experimental data validated that the rate-limiting step for the oxidation of p-vanillin is hydrogen atom abstraction and provided a detailed geometric structure of stationary and saddle points for the oxidation of p-vanillin.
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Affiliation(s)
- Sonia F. G. Santos
- Hub for Biotechnology in Build Environment, Newcastle upon Tyne, United Kingdom
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Rajesh Reddy Bommareddy
- Hub for Biotechnology in Build Environment, Newcastle upon Tyne, United Kingdom
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Gary W. Black
- Hub for Biotechnology in Build Environment, Newcastle upon Tyne, United Kingdom
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Warispreet Singh
- Hub for Biotechnology in Build Environment, Newcastle upon Tyne, United Kingdom
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
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20
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Ion BF, Aboelnga MM, Gauld JW. QM/MM investigation of the discriminatory pre-transfer editing mechanism operated by Lysyl-tRNA synthetase. J Biomol Struct Dyn 2024:1-9. [PMID: 38197420 DOI: 10.1080/07391102.2023.2301054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/26/2023] [Indexed: 01/11/2024]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that remarkable facilitate the aminoacylation process during translation. With a high fidelity, the mischarged tRNA is prevented through implementing pre- and post-transfer proofreading mechanisms. For instance, Lysine-tRNA synthetase charges the native substrate, lysine, to its cognate tRNA. In spite of the great structural similarity between lysine to the noncognate and toxic ornithine, with the side chain of lysine being only one methylene group longer, LysRS is able to achieve this discrimination with a high efficiency. In this work, the hybrid quantum mechanics/molecular mechanics (QM/MM) investigation was applied to probe the pre-transfer editing mechanism catalyzed by lysyl-tRNA synthetase to reject the noncognte aminoacyl, L-ornityl (Orn), compared to the cognate substrate, L-lysyl. Particularly, the self-cyclization pre-transfer editing mechanism was explored for the two substrates. The substrate-assisted self-cyclization editing of Orn-AMP, where its phosphate moiety acts as the catalytic base, is found to be the rate-determining step with an energy barrier of 101.2 kJ mol-1. Meanwhile, the corresponding rate-limiting pathway for the native Lys-AMP lies at 140.2 kJ mol-1. This observation clearly indicated the infeasibility of this catalytic scenario in the presence of the native substrate. Interestingly, a thermodynamically favorable cyclic product of -92.9 kJ mol-1 with respect to the aminoacyl reactant complex demonstrated evidence of a successful pre-transfer editing. This reaction resulted in the discharge of the on-cognate -ornithine derivative from LysU's active site. These valuable mechanistic insights are valuable to enrich our knowledge of this extremely efficient and specific catalytic machinery of LysRS.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bogdan F Ion
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Mohamed M Aboelnga
- Chemistry Department, Faculty of Science, Damietta University, Damietta, Egypt
| | - James W Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
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21
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Li D, Shi D, Wang L. Structural insights in the permeation mechanism of an activated GIRK2 channel. Biochim Biophys Acta Biomembr 2024; 1866:184231. [PMID: 37739205 DOI: 10.1016/j.bbamem.2023.184231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/19/2023] [Accepted: 09/14/2023] [Indexed: 09/24/2023]
Abstract
G protein-gated inwardly rectifying potassium (GIRK) channels play a significant role in physiopathology by the regulation of cell excitability. This regulation depends on the K+ ion conduction induced by structural constrictions: the selectivity filters (SFs), helix bundle crossings (HBCs), and G-loop gates. To explore why no permeation occurred when the constrictions were kept in the open state, a 4-K+-related occupancy mechanism was proposed. Unfortunately, this hypothesis was neither assessed, nor was the energetic characteristics presented. To identify the permeation mechanism on an atomic level, all-atom molecular dynamic (MD) simulations and a coupled quantum mechanics and molecular mechanics (QM/MM) method were used for the GIRK2 mutant R201A. It was found that the R201A had a moderate conductive capability in the presence of PIP2. Furthermore, the 4-K+ group of ions was found to dominate the conduction through the activated HBC gate. This shielding-like mechanism was assessed by the potential energy barrier along the conduction pathway. Mutation studies did further support the assumption that E152 was responsible for the mechanism. Moreover, E152 was most probably facilitating the inflow of ions from the SF to the cavity. On the contrary, N184 had no remarkable effect on this mechanism, except for the conduction efficiency. These findings highlighted the necessity of a multi-ion distribution for the conduction to take place, and indicated that the K+ migration was not only determined by the channel conductive state in the GIRK channel. The here presented multi-ion permeation mechanism may help to provide an effective way to regulate the channelopathies.
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Affiliation(s)
- Dailin Li
- Key Laboratory of Environmental Biotechnology (XMUT), Fujian Province University, Xiamen University of Technology, Xiamen 361005, China.
| | - Dingyuan Shi
- Key Laboratory of Environmental Biotechnology (XMUT), Fujian Province University, Xiamen University of Technology, Xiamen 361005, China
| | - Lei Wang
- Key Laboratory of Environmental Biotechnology (XMUT), Fujian Province University, Xiamen University of Technology, Xiamen 361005, China
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22
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Santos SJM, Valentini A. In silico investigation of Komaroviquinone as a potential inhibitor of SARS-CoV-2 main protease (Mpro): Molecular docking, molecular dynamics, and QM/MM approaches. J Mol Graph Model 2024; 126:108662. [PMID: 37950976 DOI: 10.1016/j.jmgm.2023.108662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/13/2023]
Abstract
COVID-19 has highlighted the urgent need for new therapeutic agents to combat the spread of the virus. The main protease of SARS-CoV-2 (Mpro) has emerged as a promising target. In this study, we conducted an in silico investigation to explore the potential of Komaroviquinone, an icetexane diterpene, as a therapeutic agent against COVID-19. We employed molecular docking, molecular dynamics, and QM/MM methodologies to compare the binding affinity, molecular interactions, and stability of Komaroviquinone and the FDA-approved antiviral drug Nirmatrelvir with the SARS-CoV-2 Mpro protein. The study demonstrated that Komaroviquinone exhibits strong interaction with Mpro, with a binding energy comparable to Nirmatrelvir. The ADMET analysis revealed that Barbatusol, Brussonol, and Komaroviquinone possess superior solubility, permeability, and intestinal absorption compared to Nirmatrelvir, as well as more favorable distribution properties and lower toxicity profiles. Notably, Nirmatrelvir displayed toxicity and hepatotoxicity, which were not present in the natural compounds. Thus, it is suggested that Komaroviquinone may be a promising candidate for the development of effective and safer therapeutic agents against COVID-19. Experimental validation is necessary to confirm its potential as a treatment for the disease.
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Affiliation(s)
- Samuel J M Santos
- Federal Institute of Education, Science and Technology of Rio Grande Do Sul, 95770-000, Feliz, Rio Grande Do Sul, Brazil.
| | - Antoninho Valentini
- Department of Analytical Chemistry and Physical Chemistry, Federal University of Ceará, Campus of Pici, 60440-554, Fortaleza, Ceará, Brazil.
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23
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Luo Y, Ma X, Qiu Y, Lu Y, Shen S, Li Y, Gao H, Chen K, Zhou J, Hu T, Tu L, Zhao H, Li D, Leng F, Gao W, Jiang T, Liu C, Huang L, Wu R, Tong Y. Structural and Catalytic Insight into the Unique Pentacyclic Triterpene Synthase TwOSC. Angew Chem Int Ed Engl 2023; 62:e202313429. [PMID: 37840440 DOI: 10.1002/anie.202313429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
The oxidosqualene cyclase (OSC) catalyzed cyclization of the linear substrate (3S)-2,3-oxidosqualene to form diverse pentacyclic triterpenoid (PT) skeletons is one of the most complex reactions in nature. Friedelin has a unique PT skeleton involving a fascinating nine-step cation shuttle run (CSR) cascade rearrangement reaction, in which the carbocation formed at C2 moves to the other side of the skeleton, runs back to C3 to yield a friedelin cation, which is finally deprotonated. However, as crystal structure data of plant OSCs are lacking, it remains unknown why the CSR cascade reactions occur in friedelin biosynthesis, as does the exact catalytic mechanism of the CSR. In this study, we determined the first cryogenic electron microscopy structure of a plant OSC, friedelin synthase, from Tripterygium wilfordii Hook. f (TwOSC). We also performed quantum mechanics/molecular mechanics simulations to reveal the energy profile for the CSR cascade reaction and identify key residues crucial for PT skeleton formation. Furthermore, we semirationally designed two TwOSC mutants, which significantly improved the yields of friedelin and β-amyrin, respectively.
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Affiliation(s)
- Yunfeng Luo
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Xiaoli Ma
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yufan Qiu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yun Lu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Siyu Shen
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Yang Li
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069, China
| | - Haiyun Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Kang Chen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Media, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jiawei Zhou
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Tianyuan Hu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Lichan Tu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Huan Zhao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Dan Li
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069, China
| | - Faqiang Leng
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069, China
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Tao Jiang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Changli Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Media, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yuru Tong
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069, China
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24
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López-Sosa L, Calaminici P, Köster AM. Cartesian constraints in QM/MM optimizations. J Comput Chem 2023; 44:2358-2368. [PMID: 37635671 DOI: 10.1002/jcc.27202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023]
Abstract
With the rise of quantum mechanical/molecular mechanical (QM/MM) methods, the interest in the calculation of molecular assemblies has increased considerably. The structures and dynamics of such assemblies are usually governed to a large extend by intermolecular interactions. As a result, the corresponding potential energy surfaces are topological rich and possess many shallow minima. Therefore, local structure optimizations of QM/MM molecular assemblies can be challenging, in particular if optimization constraints are imposed. To overcome this problem, structure optimization in normal coordinate space is advocated. To do so, the external degrees of freedom of a molecule are separated from the internal ones by a projector matrix in the space of the Cartesian coordinates. Here we extend this approach to Cartesian constraints. To this end, we devise an algorithm that adds the Cartesian constraints directly to the projector matrix and in this way eliminates them from the reduced coordinate space in which the molecule is optimized. To analyze the performance and stability of the constrained optimization algorithm in normal coordinate space, we present constrained minimizations of small molecular systems and amino acids in gas phase as well as water employing QM/MM constrained optimizations. All calculations are performed in the framework of auxiliary density functional theory as implemented in the program deMon2k.
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Affiliation(s)
- L López-Sosa
- Departamento de Química, CINVESTAV, Mexico, Mexico
| | - P Calaminici
- Departamento de Química, CINVESTAV, Mexico, Mexico
| | - A M Köster
- Departamento de Química, CINVESTAV, Mexico, Mexico
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25
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Yamaguchi K, Miyagawa K, Shoji M, Kawakami T, Isobe H, Yamanaka S, Nakajima T. Theoretical elucidation of the structure, bonding, and reactivity of the CaMn 4O x clusters in the whole Kok cycle for water oxidation embedded in the oxygen evolving center of photosystem II. New molecular and quantum insights into the mechanism of the O-O bond formation. Photosynth Res 2023:10.1007/s11120-023-01053-7. [PMID: 37945776 DOI: 10.1007/s11120-023-01053-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/25/2023] [Indexed: 11/12/2023]
Abstract
This paper reviews our historical developments of broken-symmetry (BS) and beyond BS methods that are applicable for theoretical investigations of metalloenzymes such as OEC in PSII. The BS hybrid DFT (HDFT) calculations starting from high-resolution (HR) XRD structure in the most stable S1 state have been performed to elucidate structure and bonding of whole possible intermediates of the CaMn4Ox cluster (1) in the Si (i = 0 ~ 4) states of the Kok cycle. The large-scale HDFT/MM computations starting from HR XRD have been performed to elucidate biomolecular system structures which are crucial for examination of possible water inlet and proton release pathways for water oxidation in OEC of PSII. DLPNO CCSD(T0) computations have been performed for elucidation of scope and reliability of relative energies among the intermediates by HDFT. These computations combined with EXAFS, XRD, XFEL, and EPR experimental results have elucidated the structure, bonding, and reactivity of the key intermediates, which are indispensable for understanding and explanation of the mechanism of water oxidation in OEC of PSII. Interplay between theory and experiments have elucidated important roles of four degrees of freedom, spin, charge, orbital, and nuclear motion for understanding and explanation of the chemical reactivity of 1 embedded in protein matrix, indicating the participations of the Ca(H2O)n ion and tyrosine(Yz)-O radical as a one-electron acceptor for the O-O bond formation. The Ca-assisted Yz-coupled O-O bond formation mechanisms for water oxidation are consistent with recent XES and very recent time-resolved SFX XFEL and FTIR results.
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Affiliation(s)
- Kizashi Yamaguchi
- Center for Quantum Information and Quantum Biology, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan.
- SANKEN, Osaka University, Ibaraki, Osaka, 567-0047, Japan.
| | - Koichi Miyagawa
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Mitsuo Shoji
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takashi Kawakami
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Shusuke Yamanaka
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Takahito Nakajima
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
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26
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Messias A, Pasquadibisceglie A, Alonso de Armiño D, De Simone G, Polticelli F, Coletta M, Ascenzi P, Estrin DA. Nitric oxide binding to ferrous nitrobindins: A computer simulation investigation. J Inorg Biochem 2023; 248:112336. [PMID: 37572543 DOI: 10.1016/j.jinorgbio.2023.112336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/28/2023] [Accepted: 07/19/2023] [Indexed: 08/14/2023]
Abstract
Nitrobindins (Nbs) represent an evolutionary conserved all-β-barrel heme-proteins displaying a highly solvent-exposed heme-Fe(III) atom, coordinated by a proximal His residue. Interestingly, even if the distal side is exposed to the solvent, the value of the second order rate constants for ligand binding to the ferrous derivative is almost one order of magnitude lower than those reported for myoglobins (Mbs). Noteworthy, nitric oxide binding to the sixth coordination position of the heme-Fe(II)-atom causes the cleavage or the severe weakening of the proximal His-Fe(II) bond. Here, we provide a computer simulation investigation to shed light on the molecular basis of ligand binding kinetics, by dissecting the ligand binding process into the ligand migration and the bond formation steps. Classical molecular dynamics simulations were performed employing a steered molecular dynamics approach and the Jarzinski equality to obtain ligand migration free energy profiles. The formation of the heme-Fe(II)-NO bond took into consideration the iron atom displacement from the heme plane. The ligand migration is almost unhindered, and the low rate constant for NO binding is due to the large displacement of the Fe(II) atom with respect to the heme plane responsible for the barrier for the Fe(II)-NO bond formation. In addition, we investigated the weakening and breaking of the proximal His-Fe(II) bond, observed experimentally upon NO binding, by means of a combination of classical molecular dynamics simulations and quantum-classical (QM-MM) optimizations. In both human and M. tuberculosis Nbs, a stable alternative conformation of the proximal His residue interacting with a network of water molecules was observed.
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Affiliation(s)
- Andresa Messias
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | | | - Diego Alonso de Armiño
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Giovanna De Simone
- Department of Sciences, Roma Tre University, Viale G. Marconi 446, I-00146 Roma, Italy
| | - Fabio Polticelli
- Department of Sciences, Roma Tre University, Viale G. Marconi 446, I-00146 Roma, Italy
| | | | - Paolo Ascenzi
- Accademia Nazionale dei Lincei, Via della Lungara 10, 00165 Roma, Italy
| | - Darío A Estrin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina.
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27
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Zhang X, Liu T, Zhu L, Guan J, Lu Y, Keal TW, Buckeridge J, Catlow CRA, Sokol AA. Bulk and Surface Contributions to Ionisation Potentials of Metal Oxides. Angew Chem Int Ed Engl 2023; 62:e202308411. [PMID: 37503936 PMCID: PMC10953407 DOI: 10.1002/anie.202308411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 07/29/2023]
Abstract
Determining the absolute band edge positions in solid materials is crucial for optimising their performance in wide-ranging applications including photocatalysis and electronic devices. However, obtaining absolute energies is challenging, as seen in CeO2 , where experimental measurements show substantial discrepancies in the ionisation potential (IP). Here, we have combined several theoretical approaches, from classical electrostatics to quantum mechanics, to elucidate the bulk and surface contributions to the IP of metal oxides. We have determined a theoretical bulk contribution to the IP of stoichiometric CeO2 of only 5.38 eV, while surface orientation results in intrinsic IP variations ranging from 4.2 eV to 8.2 eV. Highly tuneable IPs were also found in TiO2 , ZrO2 , and HfO2 , in which surface polarisation plays a pivotal role in long-range energy level shifting. Our analysis, in addition to rationalising the observed range of experimental results, provides a firm basis for future interpretations of experimental and computational studies of oxide band structures.
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Affiliation(s)
- Xingfan Zhang
- Kathleen Lonsdale Materials ChemistryDepartment of ChemistryUniversity College LondonWC1H 0AJLondonUK
| | - Taifeng Liu
- Kathleen Lonsdale Materials ChemistryDepartment of ChemistryUniversity College LondonWC1H 0AJLondonUK
- National & Local Joint Engineering Research Center for Applied Technology of Hybrid NanomaterialsHenan University475004KaifengChina
| | - Lei Zhu
- Kathleen Lonsdale Materials ChemistryDepartment of ChemistryUniversity College LondonWC1H 0AJLondonUK
| | - Jingcheng Guan
- Kathleen Lonsdale Materials ChemistryDepartment of ChemistryUniversity College LondonWC1H 0AJLondonUK
| | - You Lu
- Scientific Computing DepartmentSTFC Daresbury LaboratoryWA4 4ADWarringtonCheshireUK
| | - Thomas W. Keal
- Scientific Computing DepartmentSTFC Daresbury LaboratoryWA4 4ADWarringtonCheshireUK
| | - John Buckeridge
- School of EngineeringLondon South Bank UniversitySE1 OAALondonUK
| | - C. Richard A. Catlow
- Kathleen Lonsdale Materials ChemistryDepartment of ChemistryUniversity College LondonWC1H 0AJLondonUK
- School of ChemistryCardiff UniversityPark PlaceCF10 1ATCardiffUK
| | - Alexey A. Sokol
- Kathleen Lonsdale Materials ChemistryDepartment of ChemistryUniversity College LondonWC1H 0AJLondonUK
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28
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Córdova JA, Palermo JC, Estrin DA, Bari SE, Capece L. Binding mechanism of disulfide species to ferric hemeproteins: The case of metmyoglobin. J Inorg Biochem 2023; 247:112313. [PMID: 37467661 DOI: 10.1016/j.jinorgbio.2023.112313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/15/2023] [Accepted: 07/01/2023] [Indexed: 07/21/2023]
Abstract
The interactions of the heme iron of hemeproteins with sulfide and disulfide compounds are of potential interest as physiological signaling processes. While the interaction with hydrogen sulfide has been described computationally and experimentally, the reaction with disulfide, and specifically the molecular mechanism for ligand binding has not been studied in detail. In this work, we study the association process for disulfane and its conjugate base disulfanide at different pH conditions. Additionally, by means of advanced sampling techniques based on multiple steered molecular dynamics, we provide free energy profiles for ligand migration for both acid/base species, showing a similar behavior to the previously reported for the related H2S/HS¯ pair. Finally, we studied the ligand interchange reaction (H2O/H2S, HS¯ and H2O/HSSH, HSS¯) by means of hybrid quantum mechanics-molecular mechanics calculations. We show that the anionic species are able to displace more efficiently the H2O bound to the iron, and that the H-bond network in the distal cavity can help the neutral species to perform the reaction. Altogether, we provide a molecular explanation for the experimental information and show that the global association process depends on a fine balance between the migration towards the active site and the ligand interchange reaction.
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Affiliation(s)
- Jonathan Alexis Córdova
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina
| | - Juan Cruz Palermo
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Darío A Estrin
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Sara E Bari
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina..
| | - Luciana Capece
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina..
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29
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Sargolzaei M, Nikoofard H. Design of prodrug for stereoisomers of omapatrilat to cross the blood-brain barrier using docking, homology modeling, MD, and QM/MM methods. J Biomol Struct Dyn 2023:1-13. [PMID: 37728537 DOI: 10.1080/07391102.2023.2259488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/09/2023] [Indexed: 09/21/2023]
Abstract
In this study, we designed a suitable ester prodrug for omapatrilat to penetrate the blood-brain barrier and treat CNS diseases. Based on the ADMET properties, the methyl carboxylate ester of omapatrilat was chosen from among several prodrug structures. Sixteen methyl carboxylate esters were constructed for omapatrilat. The structure of brain carboxylesterase was derived via homology modeling, and molecular docking was used to determine the most potent stereoisomers against brain carboxylesterase. The top three stereoisomer complexes, and the apo form of the protein, were then considered using molecular dynamics simulation and MM/GBSA analysis. Following the simulation, structural analysis was performed using RMSD, RMSF, Rg, and hydrogen bond analysis tools. Our data demonstrated that the prodrug of RSSR is a suitable structure for crossing the blood-brain barrier and binding to brain carboxylesterase. In addition, we found via QM/MM calculation that the catalytic reaction of the prodrug of RSSR against brain carboxylesterase occurs via two steps, including acylation and diacylation steps. Based on our findings, we propose a clinical trial of a methyl carboxylate ester prodrug of omapatrilat's RSSR for the treatment of brain diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohsen Sargolzaei
- Faculty of Chemistry, Shahrood University of Technology, Shahrood, Iran
| | - Hossein Nikoofard
- Faculty of Chemistry, Shahrood University of Technology, Shahrood, Iran
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Jaber Sathik Rifayee SB, Chaturvedi SS, Warner C, Wildey J, White W, Thompson M, Schofield CJ, Christov CZ. Catalysis by KDM6 Histone Demethylases - A Synergy between the Non-Heme Iron(II) Center, Second Coordination Sphere, and Long-Range Interactions. Chemistry 2023; 29:e202301305. [PMID: 37258457 PMCID: PMC10526731 DOI: 10.1002/chem.202301305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/02/2023]
Abstract
KDM6A (UTX) and KDM6B (JMJD3) are human non-heme Fe(II) and 2-oxoglutarate (2OG) dependent JmjC oxygenases that catalyze the demethylation of trimethylated lysine 27 in the N-terminal tail of histone H3, a post-translational modification that regulates transcription. A Combined Quantum Mechanics/ Molecular Mechanics (QM/MM) and Molecular Dynamics (MD) study on the catalytic mechanism of KDM6A/B reveals that the transition state for the rate-limiting hydrogen atom transfer (HAT) reaction in KDM6A catalysis is stabilized by polar (Asn217) and aromatic (Trp369)/non-polar (Pro274) residues in contrast to KDM4, KDM6B and KDM7 demethylases where charged residues (Glu, Arg, Asp) are involved. KDM6A employs both σ- and π-electron transfer pathways for HAT, whereas KDM6B employs the σ-electron pathway. Differences in hydrogen bonding of the Fe-chelating Glu252(KDM6B) contribute to the lower energy barriers in KDM6B vs. KDM6A. The study reveals a dependence of the activation barrier of the rebound hydroxylation on the Fe-O-C angle in the transition state of KDM6A. Anti-correlation of the Zn-binding domain with the active site residues is a key factor distinguishing KDM6A/B from KDM7/4s. The results reveal the importance of communication between the Fe center, second coordination sphere, and long-range interactions in catalysis by KDMs and, by implication, other 2OG oxygenases.
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Affiliation(s)
| | | | - Cait Warner
- Department of Biological Sciences, Michigan Technological University, Houghton, MI-49931, USA
| | - Jon Wildey
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI-49931, USA
| | - Walter White
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Martin Thompson
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Christopher J. Schofield
- Chemistry Research laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
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31
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Bulavko ES, Pak MA, Ivankov DN. In Silico Simulations Reveal Molecular Mechanism of Uranyl Ion Toxicity towards DNA-Binding Domain of PARP-1 Protein. Biomolecules 2023; 13:1269. [PMID: 37627334 PMCID: PMC10452222 DOI: 10.3390/biom13081269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
The molecular toxicity of the uranyl ion (UO22+) in living cells is primarily determined by its high affinity to both native and potential metal-binding sites that commonly occur in the structure of biomolecules. Recent advances in computational and experimental research have shed light on the structural properties and functional impacts of uranyl binding to proteins, organic ligands, nucleic acids, and their complexes. In the present work, we report the results of the computational investigation of the uranyl-mediated loss of DNA-binding activity of PARP-1, a eukaryotic enzyme that participates in DNA repair, cell differentiation, and the induction of inflammation. The latest experimental studies have shown that the uranyl ion directly interacts with its DNA-binding subdomains, zinc fingers Zn1 and Zn2, and alters their tertiary structure. Here, we propose an atomistic mechanism underlying this process and compute the free energy change along the suggested pathway. Our Quantum Mechanics/Molecular Mechanics (QM/MM) simulations of the Zn2-UO22+ complex indicate that the uranyl ion replaces zinc in its native binding site. However, the resulting state is destroyed due to the spontaneous internal hydrolysis of the U-Cys162 coordination bond. Despite the enthalpy of hydrolysis being +2.8 kcal/mol, the overall reaction free energy change is -0.6 kcal/mol, which is attributed to the loss of domain's native tertiary structure originally maintained by a zinc ion. The subsequent reorganization of the binding site includes the association of the uranyl ion with the Glu190/Asp191 acidic cluster and significant perturbations in the domain's tertiary structure driven by a further decrease in the free energy by 6.8 kcal/mol. The disruption of the DNA-binding interface revealed in our study is consistent with previous experimental findings and explains the loss of PARP-like zinc fingers' affinity for nucleic acids.
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Affiliation(s)
| | | | - Dmitry N. Ivankov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, Moscow 121205, Russia
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Yang W, Zhuang J, Li C, Bai C, Cheng G. Insights into the Inhibitory Mechanisms of the Covalent Drugs for DNMT3A. Int J Mol Sci 2023; 24:12652. [PMID: 37628829 PMCID: PMC10454219 DOI: 10.3390/ijms241612652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
The perturbations of DNA methyltransferase 3 alpha (DNMT3A) may cause uncontrolled gene expression, resulting in cancers and tumors. The DNMT inhibitors Azacytidine (AZA) and Zebularine (ZEB) inhibit the DNMT family with no specificities, and consequently would bring side effects during the treatment. Therefore, it is vital to understand the inhibitory mechanisms in DNMT3A to inform the new inhibitor design for DNMTs. Herein, we carried out molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) simulations to investigate the inhibitory mechanisms of the AZA and ZEB. The results were compared to the methyl transfer of cytosine. We showed how the AZA might stop the methyl transfer process, whereas the ZEB might be stuck in a methyl-transferred intermediate (IM3). The IM3 state then fails the elimination due to the unique protein dynamics that result in missing the catalytic water chain. Our results brought atomic-level insights into the mechanisms of the two drugs in DNMT3A, which could benefit the new generation of drug design for the DNMTs.
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Affiliation(s)
- Wei Yang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen 518112, China
| | - Jingyuan Zhuang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Chen Li
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia;
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Guijuan Cheng
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Shenzhen Futian Biomedical Innovation R&D Center, The Chinese University of Hong Kong, Shenzhen 518017, China
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33
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Guan J, Lu Y, Sen K, Abdul Nasir J, Desmoutier AW, Hou Q, Zhang X, Logsdail AJ, Dutta G, Beale AM, Strange RW, Yong C, Sherwood P, Senn HM, Catlow CRA, Keal TW, Sokol AA. Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems. Philos Trans A Math Phys Eng Sci 2023; 381:20220234. [PMID: 37211033 PMCID: PMC10200352 DOI: 10.1098/rsta.2022.0234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/04/2023] [Indexed: 05/23/2023]
Abstract
Vibrational spectroscopy is one of the most well-established and important techniques for characterizing chemical systems. To aid the interpretation of experimental infrared and Raman spectra, we report on recent theoretical developments in the ChemShell computational chemistry environment for modelling vibrational signatures. The hybrid quantum mechanical and molecular mechanical approach is employed, using density functional theory for the electronic structure calculations and classical forcefields for the environment. Computational vibrational intensities at chemical active sites are reported using electrostatic and fully polarizable embedding environments to achieve more realistic vibrational signatures for materials and molecular systems, including solvated molecules, proteins, zeolites and metal oxide surfaces, providing useful insight into the effect of the chemical environment on the signatures obtained from experiment. This work has been enabled by the efficient task-farming parallelism implemented in ChemShell for high-performance computing platforms. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.
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Affiliation(s)
- Jingcheng Guan
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - You Lu
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Kakali Sen
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Jamal Abdul Nasir
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | | | - Qing Hou
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Institute of Photonic Chips, University of Shanghai for Science of Technology, Shanghai 201512, People’s Republic of China
| | - Xingfan Zhang
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Andrew J. Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - Gargi Dutta
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Department of Physics, Balurghat College, Balurghat 733101, West Bengal, India
| | - Andrew M. Beale
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, UK
| | - Richard W. Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Chin Yong
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Paul Sherwood
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, UK
| | - Hans M. Senn
- School of Chemistry, University of Glasgow, Joseph Black Building, Glasgow G12 8QQ, UK
| | - C. Richard A. Catlow
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, UK
| | - Thomas W. Keal
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Alexey A. Sokol
- Department of Chemistry, University College London, London WC1H 0AJ, UK
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Beckett D, Voth GA. Unveiling the catalytic mechanism of GTP hydrolysis in microtubules. Proc Natl Acad Sci U S A 2023; 120:e2305899120. [PMID: 37364095 DOI: 10.1073/pnas.2305899120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
Microtubules (MTs) are large cytoskeletal polymers, composed of αβ-tubulin heterodimers, capable of stochastically converting from polymerizing to depolymerizing states and vice versa. Depolymerization is coupled with hydrolysis of guanosine triphosphate (GTP) within β-tubulin. Hydrolysis is favored in the MT lattice compared to a free heterodimer with an experimentally observed rate increase of 500- to 700-fold, corresponding to an energetic barrier lowering of 3.8 to 4.0 kcal/mol. Mutagenesis studies have implicated α-tubulin residues, α:E254 and α:D251, as catalytic residues completing the β-tubulin active site of the lower heterodimer in the MT lattice. The mechanism for GTP hydrolysis in the free heterodimer, however, is not understood. Additionally, there has been debate concerning whether the GTP-state lattice is expanded or compacted relative to the GDP state and whether a "compacted" GDP-state lattice is required for hydrolysis. In this work, extensive quantum mechanics/molecular mechanics simulations with transition-tempered metadynamics free-energy sampling of compacted and expanded interdimer complexes, as well as a free heterodimer, have been carried out to provide clear insight into the GTP hydrolysis mechanism. α:E254 was found to be the catalytic residue in a compacted lattice, while in the expanded lattice, disruption of a key salt bridge interaction renders α:E254 less effective. The simulations reveal a barrier decrease of 3.8 ± 0.5 kcal/mol for the compacted lattice compared to a free heterodimer, in good agreement with experimental kinetic measurements. Additionally, the expanded lattice barrier was found to be 6.3 ± 0.5 kcal/mol higher than compacted, demonstrating that GTP hydrolysis is variable with lattice state and slower at the MT tip.
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Affiliation(s)
- Daniel Beckett
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637
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35
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Mackintosh MJ, Lodowski P, Kozlowski PM. Photoproduct formation in coenzyme B 12-dependent CarH photoreceptor via a triplet pathway. J Photochem Photobiol B 2023; 245:112751. [PMID: 37441852 DOI: 10.1016/j.jphotobiol.2023.112751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/14/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023]
Abstract
CarH is a cobalamin-based photoreceptor which has attracted significant interest due to its complex mechanism involving its organometallic coenzyme-B12 chromophore. While several experimental and computational studies have sought to understand CarH's mechanism of action, there are still many aspects of the mechanism which remain unclear. While light is needed to activate the Co-C5' bond, it is not entirely clear whether reaction pathway involves singlet or triplet diradical states. A recent experimental study implicated triplet pathway and importance of intersystem crossing (ISC) as a viable mechanistic route for photoproduct formation in CarH. Herein, a combined quantum mechanics/molecular mechanics approach (QM/MM) was used to explore the involvement of triplet states in CarH. Two possibilities were explored. The first possibility involved photo-induced homolytic cleavage of the Co-C5' where the radical pair (RP) would deactivate to a triplet state (T0) on the ground state potential energy surface (PES). However, a pathway for the formation of the photoproduct, 4',5'-anhydroadenosine (anhAdo), on the triplet ground state PES was not energetically feasible. The second possibility involved exploring a manifold of low-lying triplet excited states computed using TD-DFT within the QM/MM framework. Viable crossings of triplet excited states with singlet excited states were identified using semiclassical Landau-Zener theory and the effectiveness of spin-orbit coupling by El-Sayed rules. Several candidates along both the Co-NIm potential energy curve (PEC) and Co-C5'/Co-NIm PES were identified, which appear to corroborate experimental findings and implicate the possible role of triplet states in CarH.
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Affiliation(s)
- Megan J Mackintosh
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States
| | - Piotr Lodowski
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States.
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Porwal VK, Carof A, Ingrosso F. Hydration effects on the vibrational properties of carboxylates: From continuum models to QM/MM simulations. J Comput Chem 2023. [PMID: 37300426 DOI: 10.1002/jcc.27171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 05/15/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023]
Abstract
The presence of carboxyl groups in a molecule delivers an affinity to metal cations and a sensitivity to the chemical environment, especially for an environment that can give rise to intermolecular hydrogen bonds. Carboxylate groups can also induce intramolecular interactions, such as the formation of hydrogen bonds with donor groups, leading to an impact on the conformational space of biomolecules. In the latter case, the protonation state of the amino groups plays an important role. In order to provide an accurate description of the modifications induced in a carboxylated molecule by the formation of hydrogen bonds, one needs a compromise between a quantum chemical description of the system and the necessity to take into account explicit solvent molecules. In this work, we propose a bottom-up approach to study the conformational space and the carboxylate stretching band of (bio)organic anions. Starting from the anions in a continuum solvent, we then move to calculations using a microsolvation approach including one explicit water molecule per polar group, immersed in a continuum. Finally, we run QM/MM molecular dynamics simulations to analyze the solvation properties and to explore the anions conformational space. The results thus obtained are in good agreement with the description given by the microsolvation approach and they bring a more detailed description of the solvation shell and of the intermolecular hydrogen bonds.
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Affiliation(s)
- Vishal Kumar Porwal
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques UMR 7019, Nancy, France
| | - Antoine Carof
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques UMR 7019, Nancy, France
| | - Francesca Ingrosso
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques UMR 7019, Nancy, France
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37
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Movahedi E, Razmazma H, Rezvani A, Nowroozi A, Ebrahimi A, Eigner V, Dusek M, Arjmand F. A novel Cu(II)-based DNA-intercalating agent: Structural and biological insights using biophysical and in silico techniques. Spectrochim Acta A Mol Biomol Spectrosc 2023; 293:122438. [PMID: 36758364 DOI: 10.1016/j.saa.2023.122438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 01/14/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
A new mixed-ligand Cu(II) complex formulated as [Cu(dipic)(amp)(H2O)].H2O (dipic: pyridine-2,6-dicarboxylic acid, amp: 2-amino-4-methylpyridine), was synthesized and structurally characterized by FTIR spectroscopy, CHN analysis, and the single-crystal X-ray crystallographic method. The complex crystallizes in an orthorhombic space group Pna21, and the coordination environment around the metal center was found to be a pentacoordinate CuN2O2OW distorted square-pyramidal geometry. In order to systematically explore a detailed in vitro and in silico study of the DNA binding of the title complex, various biophysical (UV-Vis absorption spectroscopy, fluorescence, competitive binding with ethidium bromide) and theoretical (DFT, molecular docking simulation, and QM/MM) methods were applied which revealed that the complex could intercalate with the insertion of the amp ligand between the DNA base pairs. The experimental thermodynamic parameters of the interaction revealed the spontaneity of the process and the domination of the hydrophobic interactions in the association and stabilization of the DNA-Cu(II) complex adduct, which was in line with the docking and QM/MM data. In vitro cytotoxic potential of the complex against the human breast adenocarcinoma (MCF-7) cells was examined using MTT assay, which indicated that cancerous cells showed inhibition in presence of the complex.
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Affiliation(s)
- Elaheh Movahedi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | - Hafez Razmazma
- Laboratory of Computational Quantum Chemistry and Drug Design, Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
| | - Alireza Rezvani
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran.
| | - Alireza Nowroozi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran.
| | - Ali Ebrahimi
- Laboratory of Computational Quantum Chemistry and Drug Design, Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
| | - Vaclav Eigner
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 18221, Prague 8, Czech Republic
| | - Michal Dusek
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 18221, Prague 8, Czech Republic
| | - Farukh Arjmand
- Department of Chemistry, Aligarh Muslim University, Aligarh, UP 202002, India
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38
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Abidi N, Steinmann SN. An Electrostatically Embedded QM/MM Scheme for Electrified Interfaces. ACS Appl Mater Interfaces 2023; 15:25009-25017. [PMID: 37163568 DOI: 10.1021/acsami.3c01430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Atomistic modeling of electrified interfaces remains a major issue for detailed insights in electrocatalysis, corrosion, electrodeposition, batteries, and related devices such as pseudocapacitors. In these domains, the use of grand-canonical density functional theory (GC-DFT) in combination with implicit solvation models has become popular. GC-DFT can be conveniently applied not only to metallic surfaces but also to semiconducting oxides and sulfides and is, furthermore, sufficiently robust to achieve a consistent description of reaction pathways. However, the accuracy of implicit solvation models for solvation effects at interfaces is in general unknown. One promising way to overcome the limitations of implicit solvents is going toward hybrid quantum mechanical (QM)/molecular mechanics (MM) models. For capturing the electrochemical potential dependence, the key quantity is the capacitance, i.e., the relation between the surface charge and the electrochemical potential. In order to retrieve the electrochemical potential from a QM/MM hybrid scheme, an electrostatic embedding is required. Furthermore, the charge of the surface and of the solvent regions has to be strictly opposite in order to consistently simulate charge-neutral unit cells in MM and in QM. To achieve such a QM/MM scheme, we present the implementation of electrostatic embedding in the VASP code. This scheme is broadly applicable to any neutral or charged solid/liquid interface. Here, we demonstrate its use in the context of GC-DFT for the hydrogen evolution reaction (HER) over a noble-metal-free electrocatalyst, MoS2. We investigate the effect of electrostatic embedding compared to the implicit solvent model for three contrasting active sites on MoS2: (i) the sulfur vacancy defect, which is rather apolar; (ii) a Mo antisite defect, where the active site is a surface bound highly polar OH group; and (iii) a reconstructed edge site, which is generally believed to be responsible for most of the catalytic activity. According to our results, the electrostatic embedding leads to almost indistinguishable results compared to the implicit solvent for the apolar system but has a significant effect on polar sites. This demonstrates the reliability of the hybrid QM/MM, electrostatically embedded solvation model for electrified interfaces.
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Affiliation(s)
- Nawras Abidi
- Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, F-69364 Lyon, France
| | - Stephan N Steinmann
- Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, F-69364 Lyon, France
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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40
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Arsenault-Escobar S, Fuentes-Galvez JF, Orellana C, Bollo S, Sierra-Rosales P, Miranda-Rojas S. Unveiling the tartrazine binding mode with ds-DNA by UV-visible spectroscopy, electrochemical, and QM/MM methods. Spectrochim Acta A Mol Biomol Spectrosc 2023; 292:122400. [PMID: 36739665 DOI: 10.1016/j.saa.2023.122400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/31/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Here, we studied the interaction between the food colorant tartrazine (TZ) and double stranded DNA (dsDNA), using spectroscopic, electrochemical, and computational methods such as QM/MM combined with TD-DFT. Despite the UV-vis spectroscopy is widely used to study the interaction between molecules, for the case of TZ there are discrepancies in the analyses presented in the literature available, presenting both hyperchromic and hypochromic effects and consequently different rationalizations for their results. Herein we propose the combination of UV-vis experiments with the design of high-level computational models capable of reproducing the experimental behavior to finally define the proper binding mode at the molecular scale together with the rationalization of the experimental optical response due to the complex formation. To complement the UV-vis experiments, we propose the use of electrochemical measurements, to support the results obtained through UV-vis spectroscopy, as it has been successfully used for the determination of interaction modes between small molecules and biomolecules in any condition. Our UV-vis spectroscopy experiments showed only a hypochromic effect of the absorption spectra of TZ after interaction with DNA, indicative of TZ being deeply buried in the DNA structure. The effect of ionic strength in the experimental procedures led to the dissociation of TZ, thus indicating that the interaction mode was groove binding. On the other hand, the electrochemical studies showed an irreversible reduction peak of TZ, which after the interaction with DNA exhibited a positive shift in potential that can be attributed to groove binding. The binding constant for TZ-DNA was calculated as 4.45x104M-1 (UV-vis) and 5.75x104M-1 (electrochemistry), in line with other groove binder azo dyes. Finally, through the QM/MM calculations we found that the minor-groove binding mode interacting in zones rich in adenine and thymine was the model best suited to reproduce the experimental UV-vis response.
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Affiliation(s)
- S Arsenault-Escobar
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O Box 8940577, San Joaquín, Santiago, Chile
| | - J F Fuentes-Galvez
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O Box 8940577, San Joaquín, Santiago, Chile
| | - C Orellana
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, P.O. Box 653, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - S Bollo
- Centro de Investigación de Procesos Redox (CiPRex), Universidad de Chile. Sergio Livingstone Polhammer 1007, Independencia, Santiago, Chile; Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile. Sergio Livingstone Polhammer 1007, Independencia, Santiago, Chile
| | - P Sierra-Rosales
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O Box 8940577, San Joaquín, Santiago, Chile.
| | - S Miranda-Rojas
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 275, Santiago, Chile.
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González-Viegas M, Kar RK, Miller AF, Mroginski MA. Non-covalent interactions that tune the reactivities of the flavins in bifurcating electron transferring flavoprotein. J Biol Chem 2023:104762. [PMID: 37119850 DOI: 10.1016/j.jbc.2023.104762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/01/2023] Open
Abstract
Bifurcating electron transferring flavoproteins (Bf-ETFs) tune chemically identical flavins to two contrasting roles. To understand how, we used hybrid quantum mechanical molecular mechanical calculations to characterize non-covalent interactions applied to each flavin by the protein. Our computations replicated the differences between the reactivities of the flavins: the electron transferring flavin (ETflavin) was calculated to stabilize anionic semiquinone (ASQ) as needed to execute its single-electron transfers, whereas the Bf flavin (Bfflavin) was found to disfavor the ASQ state more than does free flavin and to be less susceptible to reduction. The stability of ETflavin ASQ was attributed in part to H-bond donation to the flavin O2 from a nearby His side chain, via comparison of models employing different tautomers of His. This H-bond between O2 and the ET site was uniquely strong in the ASQ state, whereas reduction of ETflavin to the anionic hydroquinone (AHQ) was associated with side chain reorientation, backbone displacement and reorganization of its H-bond network including a Tyr from the other domain and subunit of the ETF. The Bf site was less responsive overall, but formation of the Bfflavin AHQ allowed a nearby Arg side chain to adopt an alternative rotamer that can H-bond to the Bfflavin O4. This would stabilize the anionic Bfflavin and rationalize effects of mutation at this position. Thus, our computations provide insights on states and conformations that have not been possible to characterize experimentally, offering explanations for observed residue conservation and raising possibilities that can now be tested.
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Affiliation(s)
- María González-Viegas
- Department of Chemistry, Technische Universität - Berlin, Berlin, Germany; Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Rajiv K Kar
- Department of Chemistry, Technische Universität - Berlin, Berlin, Germany
| | - Anne-Frances Miller
- Department of Chemistry, Technische Universität - Berlin, Berlin, Germany; Department of Chemistry, University of Kentucky, Lexington KY, U.S.A..
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Torbjörnsson M, Hagemann MM, Ryde U, Hedegård ED. Histidine oxidation in lytic polysaccharide monooxygenase. J Biol Inorg Chem 2023; 28:317-328. [PMID: 36828975 PMCID: PMC10036459 DOI: 10.1007/s00775-023-01993-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/10/2023] [Indexed: 02/26/2023]
Abstract
The lytic polysaccharide monooxygenases (LPMOs) comprise a super-family of copper enzymes that boost the depolymerisation of polysaccharides by oxidatively disrupting the glycosidic bonds connecting the sugar units. Industrial use of LPMOs for cellulose depolymerisation has already begun but is still far from reaching its full potential. One issue is that the LPMOs self-oxidise and thereby deactivate. The mechanism of this self-oxidation is unknown, but histidine residues coordinating to the copper atom are the most susceptible. An unusual methyl modification of the NE2 atom in one of the coordinating histidine residues has been proposed to have a protective role. Furthermore, substrate binding is also known to reduce oxidative damage. We here for the first time investigate the mechanism of histidine oxidation with combined quantum and molecular mechanical (QM/MM) calculations, with outset in intermediates previously shown to form from a reaction with peroxide and a reduced LPMO. We show that an intermediate with a [Cu-O]+ moiety is sufficiently potent to oxidise the nearest C-H bond on both histidine residues, but methylation of the NE2 atom of His-1 increases the reaction barrier of this reaction. The substrate further increases the activation barrier. We also investigate a [Cu-OH]2+ intermediate with a deprotonated tyrosine radical. This intermediate was previously proposed to have a protective role, and we also find it to have higher barriers than the corresponding a [Cu-O]+ intermediate.
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Affiliation(s)
- Magne Torbjörnsson
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden
| | - Marlisa M Hagemann
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden.
| | - Erik Donovan Hedegård
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden.
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
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43
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Cupellini L, Qian P, Nguyen-Phan TC, Gardiner AT, Cogdell RJ. Quantum chemical elucidation of a sevenfold symmetric bacterial antenna complex. Photosynth Res 2023; 156:75-87. [PMID: 35672557 PMCID: PMC10070313 DOI: 10.1007/s11120-022-00925-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The light-harvesting complex 2 (LH2) of purple bacteria is one of the most studied photosynthetic antenna complexes. Its symmetric structure and ring-like bacteriochlorophyll arrangement make it an ideal system for theoreticians and spectroscopists. LH2 complexes from most bacterial species are thought to have eightfold or ninefold symmetry, but recently a sevenfold symmetric LH2 structure from the bacterium Mch. purpuratum was solved by Cryo-Electron microscopy. This LH2 also possesses unique near-infrared absorption and circular dichroism (CD) spectral properties. Here we use an atomistic strategy to elucidate the spectral properties of Mch. purpuratum LH2 and understand the differences with the most commonly studied LH2 from Rbl. acidophilus. Our strategy exploits a combination of molecular dynamics simulations, multiscale polarizable quantum mechanics/molecular mechanics calculations, and lineshape simulations. Our calculations reveal that the spectral properties of LH2 complexes are tuned by site energies and exciton couplings, which in turn depend on the structural fluctuations of the bacteriochlorophylls. Our strategy proves effective in reproducing the absorption and CD spectra of the two LH2 complexes, and in uncovering the origin of their differences. This work proves that it is possible to obtain insight into the spectral tuning strategies of purple bacteria by quantitatively simulating the spectral properties of their antenna complexes.
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Affiliation(s)
- Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124, Pisa, Italy.
| | - Pu Qian
- Materials and Structure Analysis, Thermofisher Scientific, Achtseweg Nordic 5, 5651 GTC, Eindhoven, The Netherlands
| | - Tu C Nguyen-Phan
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Alastair T Gardiner
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Novohradská 237 - Opatovický mlýn, 379 01, Třeboň, Czech Republic
| | - Richard J Cogdell
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
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Wojtkowiak K, Jezierska A. Role of Non-Covalent Interactions in Carbonic Anhydrase I-Topiramate Complex Based on QM/MM Approach. Pharmaceuticals (Basel) 2023; 16:ph16040479. [PMID: 37111236 PMCID: PMC10146004 DOI: 10.3390/ph16040479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 04/29/2023] Open
Abstract
Carbonic anhydrase (CA) I with a Topiramate (TPM) complex was investigated on the basis of a Quantum Mechanics/Molecular Mechanics (QM/MM) approach. The QM part was treated using Density Functional Theory (DFT) while the MM was simulated using Amberff14SB and GAFF force fields. In addition, the TIP3P model was applied to reproduce the polar environment influence on the studied complex. Next, three snapshots (after 5 ps, 10 ps, and 15 ps of the simulation time) were taken from the obtained trajectory to provide an insight into the non-covalent interactions present between the ligand and binding pocket of the protein. Our special attention was devoted to the binding site rearrangement, which is known in the literature concerning the complex. This part of the computations was performed using ωB97X functional with Grimme D3 dispersion corrections as well as a Becke-Johnson damping function (D3-BJ). Two basis sets were applied: def2-SVP (for larger models) and def2-TZVPD (for smaller models), respectively. In order to detect and describe non-covalent interactions between amino acids of the binding pocket and the ligand, Independent Gradient Model based on Hirshfeld partitioning (IGMH), Interaction Region Indicator (IRI), Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbitals (NBO) methods were employed. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was applied for energy decomposition between the ligand and protein. It was found that during the simulation time, the ligand position in the binding site was preserved. Nonetheless, amino acids interacting with TPM were exchanging during the simulation, thus showing the binding site reorganization. The energy partitioning revealed that dispersion and electrostatics are decisive factors that are responsible for the complex stability.
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Affiliation(s)
- Kamil Wojtkowiak
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
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Church JR, Olsen JMH, Schapiro I. Induction effects on the absorption maxima of photoreceptor proteins. Biophys Physicobiol 2023; 20:e201007. [PMID: 38362325 PMCID: PMC10865876 DOI: 10.2142/biophysico.bppb-v20.s007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Multiscale simulations have been established as a powerful tool to calculate and predict excitation energies in complex systems such as photoreceptor proteins. In these simulations the chromophore is typically treated using quantum mechanical (QM) methods while the protein and surrounding environment are described by a classical molecular mechanics (MM) force field. The electrostatic interactions between these regions are often treated using electrostatic embedding where the point charges in the MM region polarize the QM region. A more sophisticated treatment accounts also for the polarization of the MM region. In this work, the effect of such a polarizable embedding on excitation energies was benchmarked and compared to electrostatic embedding. This was done for two different proteins, the lipid membrane-embedded jumping spider rhodopsin and the soluble cyanobacteriochrome Slr1393g3. It was found that the polarizable embedding scheme produces absorption maxima closer to experimental values. The polarizable embedding scheme was also benchmarked against expanded QM regions and found to be in qualitative agreement. Treating individual residues as polarizable recovered between 50% and 71% of the QM improvement in the excitation energies, depending on the system. A detailed analysis of each amino acid residue in the chromophore binding pocket revealed that aromatic residues result in the largest change in excitation energy compared to the electrostatic embedding. Furthermore, the computational efficiency of polarizable embedding allowed it to go beyond the binding pocket and describe a larger portion of the environment, further improving the results.
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Affiliation(s)
- Jonathan R. Church
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | | | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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46
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Grigorenko B, Domratcheva T, Nemukhin A. QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase. Molecules 2023; 28:molecules28052405. [PMID: 36903648 PMCID: PMC10005588 DOI: 10.3390/molecules28052405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/21/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Oxygenase activity of the flavin-dependent enzyme RutA is commonly associated with the formation of flavin-oxygen adducts in the enzyme active site. We report the results of quantum mechanics/molecular mechanics (QM/MM) modeling of possible reaction pathways initiated by various triplet state complexes of the molecular oxygen with the reduced flavin mononucleotide (FMN) formed in the protein cavities. According to the calculation results, these triplet-state flavin-oxygen complexes can be located at both re-side and si-side of the isoalloxazine ring of flavin. In both cases, the dioxygen moiety is activated by electron transfer from FMN, stimulating the attack of the arising reactive oxygen species at the C4a, N5, C6, and C8 positions in the isoalloxazine ring after the switch to the singlet state potential energy surface. The reaction pathways lead to the C(4a)-peroxide, N(5)-oxide, or C(6)-hydroperoxide covalent adducts or directly to the oxidized flavin, depending on the initial position of the oxygen molecule in the protein cavities.
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Affiliation(s)
- Bella Grigorenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Tatiana Domratcheva
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Nemukhin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
- Correspondence:
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47
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Abhishek S, Deeksha W, Rajakumara E. Mechanistic insights into allosteric regulation of methylated DNA and histone H3 recognition by SRA and SET domains of SUVH5 and the basis for di-methylation of lysine residue. FEBS J 2023; 290:1060-1077. [PMID: 36128736 DOI: 10.1111/febs.16633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/22/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022]
Abstract
Su-(var)3-9 homologue 5 (SUVH5), a member of SUVH family of histone lysine methyltransferase (HKMT) in Arabidopsis, is involved in epigenetic regulation of chromatin by recognizing 5-methyl-cytosine (5mC), in both CpG and non-CpG DNA context, through SRA domain and simultaneously performing the di-methylation of lysine 9 of histone H3 (H3K9) through SET domain. Here, we establish that the SET domain of SUVH5 allosterically restricts the SRA domain to the 5mC containing strand(s) of fully methylated CpG, hemi-methylated CpG and methylated CpHpH DNA. In addition, SET domain enhances the binding affinity of the SRA-SET dual domains to fully-mCpG but not to hemi-mCpG. Also, the recognition of methylated DNA by the SRA positively influences the recognition of H3K9 by the SET domain. Our further studies revealed that the SET domain recognizes the "A(R/K)KST" motif present in H3K9 and in other histone H2A variants. Further, computational analyses and quantum mechanics/molecular mechanics calculations explain the bases for robust mono-MTase but weak di-MTase activities of SUVH5. Given that the majority of eukaryotic proteins, including those involved in epigenetic gene regulation, contain more than one domain, our study suggests that understanding the allosteric regulation among multiple domains of proteins is relevant for unravelling biological outcomes.
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Affiliation(s)
- Suman Abhishek
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, India
| | - Waghela Deeksha
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, India
| | - Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, India
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48
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Liu Y, Sulaiman HF, Johnson BR, Ma R, Gao Y, Fernando H, Amarasekara A, Ashley-Oyewole A, Fan H, Ingram HN, Briggs JM. QM/MM study of N501 involved intermolecular interaction between SARS-CoV-2 receptor binding domain and antibody of human origin. Comput Biol Chem 2023; 102:107810. [PMID: 36610304 PMCID: PMC9811887 DOI: 10.1016/j.compbiolchem.2023.107810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
Intermolecular interaction between key residue N501 of the epitope on SARS-CoV-2 RBD and screening antibody B38 was studied using the QM/MM and QM approach. The QM/MM optimized geometry shows that angle X-H---Y is 165° for O-H---O between mAb light chain S30 and RBD N501. High level MP2 calculations indicated the interaction between RBD N501 and S30 of B38 Fab light chain provide a relatively strong attractive force of - 3.32 kcal/mol, whereas the hydrogen bond between RBD Q498 and S30 was quantified as 0.10 kcal/mol. The decrease in ESP partial charge on hydrogen atom of hydroxyl group on S30 drops from 0.38 a.u. to 0.31 a.u., exhibiting the sharing of 0.07 a.u. from the lone pair electron oxygen of N501 due to hydrogen bond formation. The NBO occupancy of hydrogen atom also decreases from 25.79 % to 22.93 % in the hydroxyl H-O NBO bond of S30. However, the minor change of NBO hybridization of hydroxyl oxygen of S30 from sp3.00 to sp3.05 implies the rigidity of hydrogen bond tetrahedral geometry in the relative dynamic protein complex. The O-H---O angle is 165° which is close but not exactly linear. The structural requirement for sp3 hybridization of oxygen for hydroxyl group on S30 and dimension of protein likely prevent O-H---O from adopting linear geometry. The hydrogen bond strengths were also calculated using a variety of DFT methods, and the result of - 3.33 kcal/mol from the M06L method is the closest to that of the MP2 calculation. Results of this work may aid in the COVID-19 vaccine and drug screening.
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Affiliation(s)
- Yuemin Liu
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America,Department of Chemistry, Rice University, Houston, TX 77005, the United States of America,Corresponding author at: Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America
| | - Hana F. Sulaiman
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America
| | - Bruce R. Johnson
- Department of Chemistry, Rice University, Houston, TX 77005, the United States of America
| | - Rulong Ma
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, the United States of America
| | - Yunxiang Gao
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America
| | - Harshica Fernando
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America
| | - Ananda Amarasekara
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America
| | - Andrea Ashley-Oyewole
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America
| | - Huajun Fan
- College of Chemical Engineering, Sichuan University Science and Engineering, Zigong, Sichuan 643000, PR China
| | - Heaven N. Ingram
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America
| | - James M. Briggs
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, the United States of America
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49
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Borg AJE, Esquivias O, Coines J, Rovira C, Nidetzky B. Enzymatic C4-Epimerization of UDP-Glucuronic Acid: Precisely Steered Rotation of a Transient 4-Keto Intermediate for an Inverted Reaction without Decarboxylation. Angew Chem Int Ed Engl 2023; 62:e202211937. [PMID: 36308301 PMCID: PMC10107529 DOI: 10.1002/anie.202211937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
UDP-glucuronic acid (UDP-GlcA) 4-epimerase illustrates an important problem regarding enzyme catalysis: balancing conformational flexibility with precise positioning. The enzyme coordinates the C4-oxidation of the substrate by NAD+ and rotation of a decarboxylation-prone β-keto acid intermediate in the active site, enabling stereoinverting reduction of the keto group by NADH. We reveal the elusive rotational landscape of the 4-keto intermediate. Distortion of the sugar ring into boat conformations induces torsional mobility in the enzyme's binding pocket. The rotational endpoints show that the 4-keto sugar has an undistorted 4 C1 chair conformation. The equatorially placed carboxylate group disfavors decarboxylation of the 4-keto sugar. Epimerase variants lead to decarboxylation upon removal of the binding interactions with the carboxylate group in the opposite rotational isomer of the substrate. Substitutions R185A/D convert the epimerase into UDP-xylose synthases that decarboxylate UDP-GlcA in stereospecific, configuration-retaining reactions.
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Affiliation(s)
- Annika J E Borg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010, Graz, Austria
| | - Oriol Esquivias
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain
| | - Joan Coines
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain.,Present address: Nostrum Biodiscovery, Av. De Josep Tarradellas, 8-10, 08029, Barcelona, Spain
| | - Carme Rovira
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08010, Barcelona, Spain
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010, Graz, Austria.,Austrian Center of Industrial Biotechnology (acib), Krenngasse 37, 8010, Graz, Austria
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50
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Taddei M, Garavelli M, Amirjalayer S, Conti I, Nenov A. Modus Operandi of a Pedalo-Type Molecular Switch: Insight from Dynamics and Theoretical Spectroscopy. Molecules 2023; 28:molecules28020816. [PMID: 36677872 PMCID: PMC9863296 DOI: 10.3390/molecules28020816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
Molecular switches which can be triggered by light to interconvert between two or more well-defined conformation differing in their chemical or physical properties are fundamental for the development of materials with on-demand functionalities. Recently, a novel molecular switch based on a the azodicarboxamide core has been reported. It exhibits a volume-conserving conformational change upon excitation, making it a promising candidate for embedding in confined environments. In order to rationally implement and efficiently utilize the azodicarboxamide molecular switch, detailed insight into the coordinates governing the excited-state dynamics is needed. Here, we report a detailed comparative picture of the molecular motion at the atomic level in the presence and absence of explicit solvent. Our hybrid quantum mechanics/molecular mechanics (QM/MM) excited state simulations reveal that, although the energy landscape is slightly modulated by the solvation, the light-induced motion is dominated by a bending-assisted pedalo-type motion independent of the solvation. To support the predicted mechanism, we simulate time-resolved IR spectroscopy from first principles, thereby resolving fingerprints of the light-induced switching process. Our calculated time-resolved data are in good agreement with previously reported measured spectra.
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Affiliation(s)
- Mario Taddei
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, 40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, 40136 Bologna, Italy
- Correspondence: (M.G.); (I.C.); (A.N.)
| | - Saeed Amirjalayer
- Center for Nanotechnology, Center for Multiscale Theory and Computation, Physikalisches Institut, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Irene Conti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, 40136 Bologna, Italy
- Correspondence: (M.G.); (I.C.); (A.N.)
| | - Artur Nenov
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, 40136 Bologna, Italy
- Correspondence: (M.G.); (I.C.); (A.N.)
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