1
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Polêto MD, Allen KD, Lemkul JA. Structural Dynamics of the Methyl-Coenzyme M Reductase Active Site Are Influenced by Coenzyme F 430 Modifications. Biochemistry 2024; 63:1783-1794. [PMID: 38914925 DOI: 10.1021/acs.biochem.4c00168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Methyl-coenzyme M reductase (MCR) is a central player in methane biogeochemistry, governing methanogenesis and the anaerobic oxidation of methane (AOM) in methanogens and anaerobic methanotrophs (ANME), respectively. The prosthetic group of MCR is coenzyme F430, a nickel-containing tetrahydrocorphin. Several modified versions of F430 have been discovered, including the 172-methylthio-F430 (mtF430) used by ANME-1 MCR. Here, we employ molecular dynamics (MD) simulations to investigate the active site dynamics of MCR from Methanosarcina acetivorans and ANME-1 when bound to the canonical F430 compared to 172-thioether coenzyme F430 variants and substrates (methyl-coenzyme M and coenzyme B) for methane formation. Our simulations highlight the importance of the Gln to Val substitution in accommodating the 172 methylthio modification in ANME-1 MCR. Modifications at the 172 position disrupt the canonical substrate positioning in M. acetivorans MCR. However, in some replicates, active site reorganization to maintain substrate positioning suggests that the modified F430 variants could be accommodated in a methanogenic MCR. We additionally report the first quantitative estimate of MCR intrinsic electric fields that are pivotal in driving methane formation. Our results suggest that the electric field aligned along the CH3-S-CoM thioether bond facilitates homolytic bond cleavage, coinciding with the proposed catalytic mechanism. Structural perturbations, however, weaken and misalign these electric fields, emphasizing the importance of the active site structure in maintaining their integrity. In conclusion, our results deepen the understanding of MCR active site dynamics, the enzyme's organizational role in intrinsic electric fields for catalysis, and the interplay between active site structure and electrostatics.
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Affiliation(s)
- Marcelo D Polêto
- Department of Biochemistry, Virginia Tech, 111 Engel Hall, 340 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Kylie D Allen
- Department of Biochemistry, Virginia Tech, 111 Engel Hall, 340 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Justin A Lemkul
- Department of Biochemistry, Virginia Tech, 111 Engel Hall, 340 West Campus Drive, Blacksburg, Virginia 24061, United States
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2
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Yu J, Ramirez LM, Lin Q, Burz DS, Shekhtman A. Ribosome External Electric Field Regulates Metabolic Enzyme Activity: The RAMBO Effect. J Phys Chem B 2024. [PMID: 39012038 DOI: 10.1021/acs.jpcb.4c00628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Ribosomes bind to many metabolic enzymes and change their activity. A general mechanism for ribosome-mediated amplification of metabolic enzyme activity, RAMBO, was formulated and elucidated for the glycolytic enzyme triosephosphate isomerase, TPI. The RAMBO effect results from a ribosome-dependent electric field-substrate dipole interaction energy that can increase or decrease the ground state of the reactant and product to regulate catalytic rates. NMR spectroscopy was used to determine the interaction surface of TPI binding to ribosomes and to measure the corresponding kinetic rates in the absence and presence of intact ribosome particles. Chemical cross-linking and mass spectrometry revealed potential ribosomal protein binding partners of TPI. Structural results and related changes in TPI energetics and activity show that the interaction between TPI and ribosomal protein L11 mediate the RAMBO effect.
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Affiliation(s)
- Jianchao Yu
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Lisa M Ramirez
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Qishan Lin
- RNA Epitranscriptomics & Proteomics Resource, University at Albany, State University of New York, Albany, New York 12222, United States
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
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3
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Maitra A, Lake WR, Mohamed A, Edington SC, Das P, Thompson BC, Hammes-Schiffer S, Johnson M, Dawlaty JM. Measuring the Electric Fields of Ions Captured in Crown Ethers. J Phys Chem Lett 2024:7458-7465. [PMID: 39008844 DOI: 10.1021/acs.jpclett.4c01303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Controlling reactivity with electric fields is a persistent challenge in chemistry. One approach is to tether ions at well-defined locations near a reactive center. To quantify fields arising from ions, we report crown ethers that capture metal cations as field sources and a covalently bound vibrational Stark shift probe as a field sensor. We use experiments and computations in both the gas and liquid phases to quantify the vibrational frequencies of the probe and estimate the electric fields from the captured ions. Cations, in general, blue shift the probe frequency, with effective fields estimated to vary in the range of ∼0.2-3 V/nm in the liquid phase. Comparison of the gas and liquid phase data provides insight into the effects of mutual polarization of the molecule and solvent and screening of the ion's field. These findings reveal the roles of charge, local screening, and geometry in the design of tailored electric fields.
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Affiliation(s)
- Anwesha Maitra
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - William R Lake
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Ahmed Mohamed
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Sean C Edington
- Department of Molecular, Cellular, and Biomedical Sciences and Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Pratyusha Das
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Barry C Thompson
- Department of Chemistry and Loker Hydrocarbon Institute, University of Southern California, Los Angeles, California 90089, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mark Johnson
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Jahan M Dawlaty
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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4
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024. [PMID: 38959423 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
- Zachary Birch-Price
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Florence J Hardy
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Thomas M Lister
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Anna R Kohn
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
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5
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Cruz R, Ataka K, Heberle J, Kozuch J. Evaluating aliphatic CF, CF2, and CF3 groups as vibrational Stark effect reporters. J Chem Phys 2024; 160:204308. [PMID: 38814010 DOI: 10.1063/5.0198303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/09/2024] [Indexed: 05/31/2024] Open
Abstract
Given the extensive use of fluorination in molecular design, it is imperative to understand the solvation properties of fluorinated compounds and the impact of the C-F bond on electrostatic interactions. Vibrational spectroscopy can provide direct insights into these interactions by using the C-F bond stretching [v(C-F)] as an electric field probe through the vibrational Stark effect (VSE). In this work, we explore the VSE of the three basic patterns of aliphatic fluorination, i.e., mono-, di-, and trifluorination in CF, CF2, and CF3 groups, respectively, and compare their response to the well-studied aromatic v(C-F). Magnitudes (i.e., Stark tuning rates) and orientations of the difference dipole vectors of the v(C-F)-containing normal modes were determined using density functional theory and a molecular dynamics (MD)-assisted solvatochromic analysis of model compounds in solvents of varying polarity. We obtain Stark tuning rates of 0.2-0.8 cm-1/(MV/cm), with smallest and largest electric field sensitivities for CFaliphatic and CF3,aliphatic, respectively. While average electric fields of solvation were oriented along the main symmetry axis of the CFn, and thus along its static dipole, the Stark tuning rate vectors were tilted by up to 87° potentially enabling to map electrostatics in multiple dimensions. We discuss the influence of conformational heterogeneity on spectral shifts and point out the importance of multipolar and/or polarizable MD force fields to describe the electrostatics of fluorinated molecules. The implications of this work are of direct relevance for studies of fluorinated molecules as found in pharmaceuticals, fluorinated peptides, and proteins.
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Affiliation(s)
- R Cruz
- Fachbereich Physik, Freie Universität Berlin, Berlin 14195, Germany
| | - K Ataka
- Fachbereich Physik, Freie Universität Berlin, Berlin 14195, Germany
| | - J Heberle
- Fachbereich Physik, Freie Universität Berlin, Berlin 14195, Germany
- Forschungsbau SupraFAB, Freie Universität Berlin, Berlin 14195, Germany
| | - J Kozuch
- Fachbereich Physik, Freie Universität Berlin, Berlin 14195, Germany
- Forschungsbau SupraFAB, Freie Universität Berlin, Berlin 14195, Germany
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6
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Shaik S. My Vision of Electric-Field-Aided Chemistry in 2050. ACS PHYSICAL CHEMISTRY AU 2024; 4:191-201. [PMID: 38800723 PMCID: PMC11117677 DOI: 10.1021/acsphyschemau.3c00064] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 05/29/2024]
Abstract
This manuscript outlines my outlook on the development of electric-field (EF)-mediated-chemistry and the vision of its state by 2050. I discuss applications of oriented-external electric-fields (OEEFs) on chemical reactions and proceed with relevant experimental verifications. Subsequently, the Perspective outlines other ways of generating EFs, e.g., by use of pH-switchable charges, ionic additives, water droplets, and so on. A special section summarizes conceptual principles for understanding and predicting OEEF effects, e.g., the "reaction-axis rule", the capability of OEEFs to act as tweezers that orient reactants and accelerate their reaction, etc. Finally, I discuss applications of OEEFs in continuous-flow setups, which may, in principle, scale-up to molar concentrations. The Perspective ends with the vision that by 2050, OEEF usage will change chemical education, if not also the art of making new molecules.
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Affiliation(s)
- Sason Shaik
- Institute of Chemistry, The
Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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7
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Lu J, Yu Y, Li Z, Luo J, Deng L. Practical Synthesis of Chiral α-Aminophosphonates with Weak Bonding Organocatalysis at ppm Loading. J Am Chem Soc 2024. [PMID: 38762889 DOI: 10.1021/jacs.4c04129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
α-Aminophosphonic acids as an important class of bioisosteres of α-amino acids demonstrate various biologically important activities. We report here the development of a highly enantioselective isomerization of α-iminophosphonates enabled by an extraordinarily efficient organocatalyst. This organocatalyst afforded a total turnover number (TON) of 20,000-1,000,000 for a wide range of α-alkyl iminophosphonates. Even at a parts-per-million (ppm) loading, this catalyst achieved a complete reaction in greater than 93% enantiomeric excess (ee). Computational studies revealed that this small-molecule catalyst achieved enzyme-like efficiency via a network of weak bonding interactions that effectively preorganized the substrate and catalyst toward a transition-state-like complex. Considering the substrate tolerance, catalytic efficiency, and mechanism, this organocatalyst could be regarded as a small-molecule isomerase.
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Affiliation(s)
- Jiaxiang Lu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Yang Yu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Zhenghua Li
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Jisheng Luo
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Li Deng
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
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8
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Alvarez-Hernandez JL, Zhang X, Cui K, Deziel AP, Hammes-Schiffer S, Hazari N, Piekut N, Zhong M. Long-range electrostatic effects from intramolecular Lewis acid binding influence the redox properties of cobalt-porphyrin complexes. Chem Sci 2024; 15:6800-6815. [PMID: 38725508 PMCID: PMC11077573 DOI: 10.1039/d3sc06177a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/02/2024] [Indexed: 05/12/2024] Open
Abstract
A CoII-porphyrin complex (1) with an appended aza-crown ether for Lewis acid (LA) binding was synthesized and characterized. NMR spectroscopy and electrochemistry show that cationic group I and II LAs (i.e., Li+, Na+, K+, Ca2+, Sr2+, and Ba2+) bind to the aza-crown ether group of 1. The binding constant for Li+ is comparable to that observed for a free aza-crown ether. LA binding causes an anodic shift in the CoII/CoI couple of between 10 and 40 mV and also impacts the CoIII/CoII couple. The magnitude of the anodic shift of the CoII/CoI couple varies linearly with the strength of the LA as determined by the pKa of the corresponding metal-aqua complex, with dications giving larger shifts than monocations. The extent of the anodic shift of the CoII/CoI couple also increases as the ionic strength of the solution decreases. This is consistent with electric field effects being responsible for the changes in the redox properties of 1 upon LA binding and provides a novel method to tune the reduction potential. Density functional theory calculations indicate that the bound LA is 5.6 to 6.8 Å away from the CoII ion, demonstrating that long-range electrostatic effects, which do not involve changes to the primary coordination sphere, are responsible for the variations in redox chemistry. Compound 1 was investigated as a CO2 reduction electrocatalyst and shows high activity but rapid decomposition.
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Affiliation(s)
| | - Xiaowei Zhang
- Department of Chemical and Environmental Engineering, Yale University New Haven CT 06520 USA
| | - Kai Cui
- Department of Chemistry, Princeton University Princeton NJ 08544 USA
| | | | | | - Nilay Hazari
- Department of Chemistry, Yale University New Haven CT 06520 USA
| | - Nicole Piekut
- Department of Chemistry, Yale University New Haven CT 06520 USA
| | - Mingjiang Zhong
- Department of Chemical and Environmental Engineering, Yale University New Haven CT 06520 USA
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9
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Sakpal S, Chakrabarty S, Reddy KD, Deshmukh SH, Biswas R, Bagchi S, Ghosh A. Perturbation of Fermi Resonance on Hydrogen-Bonded > C═O: 2D IR Studies of Small Ester Probes. J Phys Chem B 2024. [PMID: 38686937 DOI: 10.1021/acs.jpcb.3c06698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
We utilized linear and 2D infrared spectroscopy to analyze the carbonyl stretching modes of small esters in different solvents. Particularly noteworthy were the distinct carbonyl spectral line shapes in aqueous solutions, prompting our investigation of the underlying factors responsible for these differences. Through our experimental and theoretical calculations, we identified the presence of the hydrogen-bond-induced Fermi resonance as the primary contributor to the varied line shapes of small esters in aqueous solutions. Furthermore, our findings revealed that the skeletal deformation mode plays a crucial role in the Fermi resonance for all small esters. Specifically, the first overtone band of the skeletal deformation mode intensifies when hydrogen bonds form with the carbonyl group of esters, whereas such coupling is rare in aprotic organic solvents. These spectral insights carry significant implications for the utilization of esters as infrared probes in both biological and chemical systems.
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Affiliation(s)
- Sushil Sakpal
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suranjana Chakrabarty
- Department of Condensed Matter Physics and Materials Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Kambham Devendra Reddy
- Department of Chemistry, Indian Institute of Technology Tirupati, Tirupati, Andhra Pradesh, India 517619
| | - Samadhan H Deshmukh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rajib Biswas
- Department of Chemistry, Indian Institute of Technology Tirupati, Tirupati, Andhra Pradesh, India 517619
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anup Ghosh
- Department of Condensed Matter Physics and Materials Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
- Department of Chemical Science, Bose Institute, Kolkata 700091, India
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10
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Meyer KAE, Garand E. The impact of solvation on the structure and electric field strength in Li +GlyGly complexes. Phys Chem Chem Phys 2024; 26:12406-12421. [PMID: 38623633 DOI: 10.1039/d3cp06264c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
To scrutinise the impact of electric fields on the structure and vibrations of biomolecules in the presence of water, we study the sequential solvation of lithium diglycine up to three water molecules with cryogenic infrared action spectroscopy. Conformer-specific IR-IR spectroscopy and H2O/D2O isotopic substitution experiments provide most of the information required to decipher the structure of the observed conformers. Additional confirmation is provided by scaled harmonic vibrational frequency calculations using MP2 and DFT. The first water molecule is shown to bind to the Li+ ion, which weakens the electric field experienced by the peptide and as a consequence, also the strength of an internal NH⋯NH2 hydrogen bond in the diglycine backbone. The strength of this hydrogen bond decreases approximately linearly with the number of water molecules as a result of the decreasing electric field strength and coincides with an increase in the number of conformers observed in our spectra. The addition of two water molecules is already sufficient to change the preferred conformation of the peptide backbone, allowing for Li+ coordination to the lone pair of the terminal amine group.
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Affiliation(s)
- Katharina A E Meyer
- University of Wisconsin-Madison, Department of Chemistry, 1101 University Ave, Madison, WI 53706, USA.
| | - Etienne Garand
- University of Wisconsin-Madison, Department of Chemistry, 1101 University Ave, Madison, WI 53706, USA.
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11
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Pan X, Yan M, Liu Q, Zhou X, Liao X, Sun C, Zhu J, McAleese C, Couture P, Sharpe MK, Smith R, Peng N, England J, Tsang SCE, Zhao Y, Mai L. Electric-field-assisted proton coupling enhanced oxygen evolution reaction. Nat Commun 2024; 15:3354. [PMID: 38637529 PMCID: PMC11026508 DOI: 10.1038/s41467-024-47568-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
The discovery of Mn-Ca complex in photosystem II stimulates research of manganese-based catalysts for oxygen evolution reaction (OER). However, conventional chemical strategies face challenges in regulating the four electron-proton processes of OER. Herein, we investigate alpha-manganese dioxide (α-MnO2) with typical MnIV-O-MnIII-HxO motifs as a model for adjusting proton coupling. We reveal that pre-equilibrium proton-coupled redox transition provides an adjustable energy profile for OER, paving the way for in-situ enhancing proton coupling through a new "reagent"- external electric field. Based on the α-MnO2 single-nanowire device, gate voltage induces a 4-fold increase in OER current density at 1.7 V versus reversible hydrogen electrode. Moreover, the proof-of-principle external electric field-assisted flow cell for water splitting demonstrates a 34% increase in current density and a 44.7 mW/cm² increase in net output power. These findings indicate an in-depth understanding of the role of proton-incorporated redox transition and develop practical approach for high-efficiency electrocatalysis.
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Affiliation(s)
- Xuelei Pan
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P.R. China
- Wolfson Catalysis Centre, Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK
| | - Mengyu Yan
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P.R. China.
| | - Qian Liu
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Xunbiao Zhou
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P.R. China
| | - Xiaobin Liao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P.R. China
| | - Congli Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P.R. China
| | - Jiexin Zhu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P.R. China
| | - Callum McAleese
- UK National Ion Beam Centre, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Pierre Couture
- UK National Ion Beam Centre, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Matthew K Sharpe
- UK National Ion Beam Centre, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Richard Smith
- UK National Ion Beam Centre, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Nianhua Peng
- UK National Ion Beam Centre, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Jonathan England
- UK National Ion Beam Centre, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Shik Chi Edman Tsang
- Wolfson Catalysis Centre, Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK.
| | - Yunlong Zhao
- Dyson School of Design Engineering, Imperial College London, London, SW7 2BX, UK.
- National Physical Laboratory, Teddington, Middlesex, TW11 0LW, UK.
| | - Liqiang Mai
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P.R. China.
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12
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Song Z, Zhu C, Gong K, Wang R, Zhang J, Zhao S, Li Z, Zhang X, Xie J. Deciphering the Microdroplet Acceleration Factors of Aza-Michael Addition Reactions. J Am Chem Soc 2024; 146:10963-10972. [PMID: 38567839 DOI: 10.1021/jacs.4c02312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Microdroplet chemistry is emerging as a great tool for accelerating reactions by several orders of magnitude. Several unique properties such as extreme pHs, interfacial electric fields (IEFs), and partial solvation have been reported to be responsible for the acceleration; however, which factor plays the key role remains elusive. Here, we performed quantum chemical calculations to explore the underlying mechanisms of an aza-Michael addition reaction between methylamine and acrylamide. We showed that the acceleration in methanol microdroplets results from the cumulative effects of several factors. The acidic surface of the microdroplet plays a dominating role, leading to a decrease of ∼9 kcal/mol in the activation barrier. We speculated that the dissociation of both methanol and trace water contributes to the surface acidity. An IEF of 0.1 V/Å can further decrease the barrier by ∼2 kcal/mol. Partial solvation has a negligible effect on lowering the activation barrier in microdroplets but can increase the collision frequency between reactants. With acidity revealed to be the major accelerating factor for methanol droplets, reactions on water microdroplets should have even higher rates because water is more acidic. Both theoretically and experimentally, we confirmed that water microdroplets significantly accelerate the aza-Michael reaction, achieving an acceleration factor that exceeds 107. This work elucidates the multifactorial influences on the microdroplet acceleration mechanism, and with such detailed mechanistic investigations, we anticipate that microdroplet chemistry will be an avenue rich in opportunities in the realm of green synthesis.
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Affiliation(s)
- Zhexuan Song
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Chenghui Zhu
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Ke Gong
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Ruijing Wang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Jianze Zhang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Supin Zhao
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Zesheng Li
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Xinxing Zhang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Jing Xie
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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13
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Shenderovich IG. The Scope of the Applicability of Non-relativistic DFT Calculations of NMR Chemical Shifts in Pyridine-Metal Complexes for Applied Applications. Chemphyschem 2024; 25:e202300986. [PMID: 38259119 DOI: 10.1002/cphc.202300986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 01/24/2024]
Abstract
Heavy metals are toxic, but it is impossible to stop using them. Considering the variety of molecular systems in which they can be present, the multicomponent nature and disorder of the structure of such systems, one of the most effective methods for studying them is NMR spectroscopy. This determines the need to calculate NMR chemical shifts for expected model systems. For elements beyond the third row of the periodic table, corrections for relativistic effects are necessary when calculating NMR parameters. Such corrections may be necessary even for light atoms due to the shielding effect of a neighboring heavy atom. This work examines the extent to which non-relativistic DFT calculations are able to reproduce experimental 15N and 113Cd NMR chemical shift tensors in pyridine-metal coordination complexes. It is shown that while for the calculation of 15N NMR chemical shift tensors there is no real need to consider relativistic corrections, for 113Cd, on the contrary, none of the tested calculation methods could reproduce the experimentally obtained tensor to any extent correctly.
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Affiliation(s)
- Ilya G Shenderovich
- NMR Department, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040, Regensburg, Germany
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14
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Gardner A, Neri G, Siritanaratkul B, Jang H, Saeed KH, Donaldson PM, Cowan AJ. Potential Dependent Reorientation Controlling Activity of a Molecular Electrocatalyst. J Am Chem Soc 2024; 146:7130-7134. [PMID: 38441442 PMCID: PMC10958496 DOI: 10.1021/jacs.3c13076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/21/2024]
Abstract
The activity of molecular electrocatalysts depends on the interplay of electrolyte composition near the electrode surface, the composition and morphology of the electrode surface, and the electric field at the electrode-electrolyte interface. This interplay is challenging to study and often overlooked when assessing molecular catalyst activity. Here, we use surface specific vibrational sum frequency generation (VSFG) spectroscopy to study the solvent and potential dependent activation of Mo(bpy)(CO)4, a CO2 reduction catalyst, at a polycrystalline Au electrode. We find that the parent complex undergoes potential dependent reorientation at the electrode surface when a small amount of N-methyl-2-pyrrolidone (NMP) is present. This preactivates the complex, resulting in greater yields at less negative potentials, of the active electrocatalyst for CO2 reduction.
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Affiliation(s)
- Adrian
M. Gardner
- Department
of Chemistry and Stephenson Institute for Renewable Energy, University of Liverpool, Liverpool L69 7ZD, United Kingdom
- Early
Career Laser Laboratory, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Gaia Neri
- Department
of Chemistry and Stephenson Institute for Renewable Energy, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Bhavin Siritanaratkul
- Department
of Chemistry and Stephenson Institute for Renewable Energy, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Hansaem Jang
- Department
of Chemistry and Stephenson Institute for Renewable Energy, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Khezar H. Saeed
- Department
of Chemistry and Stephenson Institute for Renewable Energy, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Paul M. Donaldson
- Central
Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Alexander J. Cowan
- Department
of Chemistry and Stephenson Institute for Renewable Energy, University of Liverpool, Liverpool L69 7ZD, United Kingdom
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15
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Kirsh J, Weaver JB, Boxer SG, Kozuch J. Critical Evaluation of Polarizable and Nonpolarizable Force Fields for Proteins Using Experimentally Derived Nitrile Electric Fields. J Am Chem Soc 2024; 146:6983-6991. [PMID: 38415598 PMCID: PMC10941190 DOI: 10.1021/jacs.3c14775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
Molecular dynamics (MD) simulations are frequently carried out for proteins to investigate the role of electrostatics in their biological function. The choice of force field (FF) can significantly alter the MD results, as the simulated local electrostatic interactions lack benchmarking in the absence of appropriate experimental methods. We recently reported that the transition dipole moment (TDM) of the popular nitrile vibrational probe varies linearly with the environmental electric field, overcoming well-known hydrogen bonding (H-bonding) issues for the nitrile frequency and, thus, enabling the unambiguous measurement of electric fields in proteins (J. Am. Chem. Soc. 2022, 144 (17), 7562-7567). Herein, we utilize this new strategy to enable comparisons of experimental and simulated electric fields in protein environments. Specifically, previously determined TDM electric fields exerted onto nitrile-containing o-cyanophenylalanine residues in photoactive yellow protein are compared with MD electric fields from the fixed-charge AMBER FF and the polarizable AMOEBA FF. We observe that the electric field distributions for H-bonding nitriles are substantially affected by the choice of FF. As such, AMBER underestimates electric fields for nitriles experiencing moderate field strengths; in contrast, AMOEBA robustly recapitulates the TDM electric fields. The FF dependence of the electric fields can be partly explained by the presence of additional negative charge density along the nitrile bond axis in AMOEBA, which is due to the inclusion of higher-order multipole parameters; this, in turn, begets more head-on nitrile H-bonds. We conclude by discussing the implications of the FF dependence for the simulation of nitriles and proteins in general.
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Affiliation(s)
- Jacob
M. Kirsh
- Department
of Chemistry, Stanford University, Stanford, California 94305-5012, United
States
| | - Jared Bryce Weaver
- Department
of Chemistry, Stanford University, Stanford, California 94305-5012, United
States
| | - Steven G. Boxer
- Department
of Chemistry, Stanford University, Stanford, California 94305-5012, United
States
| | - Jacek Kozuch
- Experimental
Molecular Biophysics, Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
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16
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Westendorff KS, Hülsey MJ, Wesley TS, Román-Leshkov Y, Surendranath Y. Electrically driven proton transfer promotes Brønsted acid catalysis by orders of magnitude. Science 2024; 383:757-763. [PMID: 38359117 DOI: 10.1126/science.adk4902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/11/2024] [Indexed: 02/17/2024]
Abstract
Electric fields play a key role in enzymatic catalysis and can enhance reaction rates by 100,000-fold, but the same rate enhancements have yet to be achieved in thermochemical heterogeneous catalysis. In this work, we probe the influence of catalyst potential and interfacial electric fields on heterogeneous Brønsted acid catalysis. We observed that variations in applied potential of ~380 mV led to a 100,000-fold rate enhancement for 1-methylcyclopentanol dehydration, which was catalyzed by carbon-supported phosphotungstic acid. Mechanistic studies support a model in which the interfacial electrostatic potential drop drives quasi-equilibrated proton transfer to the adsorbed substrate prior to rate-limiting C-O bond cleavage. Large increases in rate with potential were also observed for the same reaction catalyzed by Ti/TiOyHx and for the Friedel Crafts acylation of anisole with acetic anhydride by carbon-supported phosphotungstic acid.
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Affiliation(s)
- Karl S Westendorff
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Max J Hülsey
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Thejas S Wesley
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuriy Román-Leshkov
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yogesh Surendranath
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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17
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Juretić D, Bonačić Lošić Ž. Theoretical Improvements in Enzyme Efficiency Associated with Noisy Rate Constants and Increased Dissipation. ENTROPY (BASEL, SWITZERLAND) 2024; 26:151. [PMID: 38392406 PMCID: PMC10888251 DOI: 10.3390/e26020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024]
Abstract
Previous studies have revealed the extraordinarily large catalytic efficiency of some enzymes. High catalytic proficiency is an essential accomplishment of biological evolution. Natural selection led to the increased turnover number, kcat, and enzyme efficiency, kcat/KM, of uni-uni enzymes, which convert a single substrate into a single product. We added or multiplied random noise with chosen rate constants to explore the correlation between dissipation and catalytic efficiency for ten enzymes: beta-galactosidase, glucose isomerase, β-lactamases from three bacterial strains, ketosteroid isomerase, triosephosphate isomerase, and carbonic anhydrase I, II, and T200H. Our results highlight the role of biological evolution in accelerating thermodynamic evolution. The catalytic performance of these enzymes is proportional to overall entropy production-the main parameter from irreversible thermodynamics. That parameter is also proportional to the evolutionary distance of β-lactamases PC1, RTEM, and Lac-1 when natural or artificial evolution produces the optimal or maximal possible catalytic efficiency. De novo enzyme design and attempts to speed up the rate-limiting catalytic steps may profit from the described connection between kinetics and thermodynamics.
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Affiliation(s)
- Davor Juretić
- Mediterranean Institute for Life Sciences, Šetalište Ivana Meštrovića 45, 21000 Split, Croatia
- Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
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18
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Mao J, Jin X, Shi M, Heidenreich D, Brown LJ, Brown RCD, Lelli M, He X, Glaubitz C. Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins. SCIENCE ADVANCES 2024; 10:eadj0384. [PMID: 38266078 PMCID: PMC10807816 DOI: 10.1126/sciadv.adj0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
Proteorhodopsins are widely distributed photoreceptors from marine bacteria. Their discovery revealed a high degree of evolutionary adaptation to ambient light, resulting in blue- and green-absorbing variants that correlate with a conserved glutamine/leucine at position 105. On the basis of an integrated approach combining sensitivity-enhanced solid-state nuclear magnetic resonance (ssNMR) spectroscopy and linear-scaling quantum mechanics/molecular mechanics (QM/MM) methods, this single residue is shown to be responsible for a variety of synergistically coupled structural and electrostatic changes along the retinal polyene chain, ionone ring, and within the binding pocket. They collectively explain the observed color shift. Furthermore, analysis of the differences in chemical shift between nuclei within the same residues in green and blue proteorhodopsins also reveals a correlation with the respective degree of conservation. Our data show that the highly conserved color change mainly affects other highly conserved residues, illustrating a high degree of robustness of the color phenotype to sequence variation.
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Affiliation(s)
- Jiafei Mao
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Man Shi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - David Heidenreich
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Lynda J. Brown
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ UK
| | - Richard C. D. Brown
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ UK
| | - Moreno Lelli
- Department of Chemistry “Ugo Schiff” and Magnetic Resonance Center (CERM), University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Italy
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Italy
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
- New York University–East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, China
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Straße 9, 60438 Frankfurt am Main, Germany
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19
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Sevim S, Sanchis-Gual R, Franco C, Aragonès AC, Darwish N, Kim D, Picca RA, Nelson BJ, Ruiz E, Pané S, Díez-Pérez I, Puigmartí-Luis J. Electrostatic catalysis of a click reaction in a microfluidic cell. Nat Commun 2024; 15:790. [PMID: 38278792 PMCID: PMC10817948 DOI: 10.1038/s41467-024-44716-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/02/2024] [Indexed: 01/28/2024] Open
Abstract
Electric fields have been highlighted as a smart reagent in nature's enzymatic machinery, as they can directly trigger or accelerate chemical processes with stereo- and regio-specificity. In enzymatic catalysis, controlled mass transport of chemical species is also key in facilitating the availability of reactants in the active reaction site. However, recent progress in developing a clean catalysis that profits from oriented electric fields is limited to theoretical and experimental studies at the single molecule level, where both the control over mass transport and scalability cannot be tested. Here, we quantify the electrostatic catalysis of a prototypical Huisgen cycloaddition in a large-area electrode surface and directly compare its performance to the conventional Cu(I) catalysis. Our custom-built microfluidic cell enhances reagent transport towards the electrified reactive interface. This continuous-flow microfluidic electrostatic reactor is an example of an electric-field driven platform where clean large-scale electrostatic catalytic processes can be efficiently implemented and regulated.
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Affiliation(s)
- Semih Sevim
- Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, CH-8092, Zurich, Switzerland
| | - Roger Sanchis-Gual
- Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, CH-8092, Zurich, Switzerland
| | - Carlos Franco
- Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, CH-8092, Zurich, Switzerland
| | - Albert C Aragonès
- Departament de Ciència de Materials i Química Física, Institut de Química Teòrica i Computacional, University of Barcelona (UB), Marti i Franquès 1, 08028, Barcelona, Spain
| | - Nadim Darwish
- School of Molecular and Life Sciences, Curtin University, Bentley, 6102, WA, Australia
| | - Donghoon Kim
- Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, CH-8092, Zurich, Switzerland
| | - Rosaria Anna Picca
- Chemistry Department, University of Bari "Aldo Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Bradley J Nelson
- Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, CH-8092, Zurich, Switzerland
| | - Eliseo Ruiz
- Departament de Química Inorgànica i Orgànica, Institut de Química Teòrica i Computacional, University of Barcelona (UB), Diagonal 645, 08028, Barcelona, Spain
| | - Salvador Pané
- Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, CH-8092, Zurich, Switzerland.
| | - Ismael Díez-Pérez
- Department of Chemistry, Faculty of Natural, Mathematical & Engineering Sciences, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK.
| | - Josep Puigmartí-Luis
- Departament de Ciència de Materials i Química Física, Institut de Química Teòrica i Computacional, University of Barcelona (UB), Marti i Franquès 1, 08028, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
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20
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Schulke S, Nolten M, Schwaab G, Havenith M. Studying Local Electrostatics by Terahertz Spectroscopy Using Amines as a Probe. Chemphyschem 2024; 25:e202300389. [PMID: 37897334 DOI: 10.1002/cphc.202300389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/20/2023] [Accepted: 10/26/2023] [Indexed: 10/30/2023]
Abstract
In a previous study[1] we could show that a large amplitude mode of the zwitterion glycine can serve as a sensitive probe for protonation and allows to deduce local pKa values. Here we show that the underlying concept is more general: We present the results of a pH dependent measurement of Terahertz-FTIR (THz-FTIR) spectra of solvated amines, i. e. Diethylamine (DEA), Triethylamine (TEA), and Diisopropylamine (DiPA). We show that amines serve as a sensitive, label free probe for local protonation. Protonation of the amines yield intensity changes which can be quantified by precise THz spectroscopy (30 cm-1 -450 cm-1 ). A detailed analysis allows us to correlate the titration spectra of solvated amines in the THz range with pKa values. This demonstrates the potential of THz spectroscopy to probe the charge state of biomolecules in water in a label free manner.
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Affiliation(s)
- Simon Schulke
- Physical Chemistry 2, Ruhr-Univeristy Bochum, Universitaetsstraße 150, 44801, Bochum, Germany
| | - Melinda Nolten
- Physical Chemistry 2, Ruhr-Univeristy Bochum, Universitaetsstraße 150, 44801, Bochum, Germany
| | - Gerhard Schwaab
- Physical Chemistry 2, Ruhr-Univeristy Bochum, Universitaetsstraße 150, 44801, Bochum, Germany
| | - Martina Havenith
- Physical Chemistry 2, Ruhr-Univeristy Bochum, Universitaetsstraße 150, 44801, Bochum, Germany
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21
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Costa GJ, Egbemhenghe A, Liang R. Computational Characterization of the Reactivity of Compound I in Unspecific Peroxygenases. J Phys Chem B 2023; 127:10987-10999. [PMID: 38096487 DOI: 10.1021/acs.jpcb.3c06311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Unspecific peroxygenases (UPOs) are emerging as promising biocatalysts for selective oxyfunctionalization of unactivated C-H bonds. However, their potential in large-scale synthesis is currently constrained by suboptimal chemical selectivity. Improving the selectivity of UPOs requires a deep understanding of the molecular basis of their catalysis. Recent molecular simulations have sought to unravel UPO's selectivity and inform their design principles. However, most of these studies focused on substrate-binding poses. Few researchers have investigated how the reactivity of CpdI, the principal oxidizing intermediate in the catalytic cycle, influences selectivity in a realistic protein environment. Moreover, the influence of protein electrostatics on the reaction kinetics of CpdI has also been largely overlooked. To bridge this gap, we used multiscale simulations to interpret the regio- and enantioselective hydroxylation of the n-heptane substrate catalyzed by Agrocybe aegerita UPO (AaeUPO). We comprehensively characterized the energetics and kinetics of the hydrogen atom-transfer (HAT) step, initiated by CpdI, and the subsequent oxygen rebound step forming the product. Notably, our approach involved both free energy and potential energy evaluations in a quantum mechanics/molecular mechanics (QM/MM) setting, mitigating the dependence of results on the choice of initial conditions. These calculations illuminate the thermodynamics and kinetics of the HAT and oxygen rebound steps. Our findings highlight that both the conformational selection and the distinct chemical reactivity of different substrate hydrogen atoms together dictate the regio- and enantio-selectivity. Building on our previous study of CpdI's formation in AaeUPO, our results indicate that the HAT step is the rate-limiting step in the overall catalytic cycle. The subsequent oxygen rebound step is swift and retains the selectivity determined by the HAT step. We also pinpointed several polar and charged amino acid residues whose electrostatic potentials considerably influence the reaction barrier of the HAT step. Notably, the Glu196 residue is pivotal for both the CpdI's formation and participation in the HAT step. Our research offers in-depth insights into the catalytic cycle of AaeUPO, which will be instrumental in the rational design of UPOs with enhanced properties.
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Affiliation(s)
- Gustavo J Costa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Abel Egbemhenghe
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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22
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Siddiqui SA, Stuyver T, Shaik S, Dubey KD. Designed Local Electric Fields-Promising Tools for Enzyme Engineering. JACS AU 2023; 3:3259-3269. [PMID: 38155642 PMCID: PMC10752214 DOI: 10.1021/jacsau.3c00536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 12/30/2023]
Abstract
Designing efficient catalysts is one of the ultimate goals of chemists. In this Perspective, we discuss how local electric fields (LEFs) can be exploited to improve the catalytic performance of supramolecular catalysts, such as enzymes. More specifically, this Perspective starts by laying out the fundamentals of how local electric fields affect chemical reactivity and review the computational tools available to study electric fields in various settings. Subsequently, the advances made so far in optimizing enzymatic electric fields through targeted mutations are discussed critically and concisely. The Perspective ends with an outlook on some anticipated evolutions of the field in the near future. Among others, we offer some pointers on how the recent data science/machine learning revolution, engulfing all science disciplines, could potentially provide robust and principled tools to facilitate rapid inference of electric field effects, as well as the translation between optimal electrostatic environments and corresponding chemical modifications.
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Affiliation(s)
- Shakir Ali Siddiqui
- Molecular Simulation Lab, Department of Chemistry,
School of Natural Sciences, Shiv Nadar Institution of Eminence,
Delhi NCR, India 201314
| | - Thijs Stuyver
- Ecole Nationale Supérieure de
Chimie de Paris, Université PSL, CNRS, Institute of Chemistry for Life and Health
Sciences, 75 005 Paris, France
| | - Sason Shaik
- Institute of Chemistry, Edmond J Safra Campus,
The Hebrew University of Jerusalem, Givat Ram, Jerusalem,
9190400, Israel
| | - Kshatresh Dutta Dubey
- Molecular Simulation Lab, Department of Chemistry,
School of Natural Sciences, Shiv Nadar Institution of Eminence,
Delhi NCR, India 201314
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23
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Zheng C, Ji Z, Mathews II, Boxer SG. Enhanced active-site electric field accelerates enzyme catalysis. Nat Chem 2023; 15:1715-1721. [PMID: 37563323 PMCID: PMC10906027 DOI: 10.1038/s41557-023-01287-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/29/2023] [Indexed: 08/12/2023]
Abstract
The design and improvement of enzymes based on physical principles remain challenging. Here we demonstrate that the principle of electrostatic catalysis can be leveraged to substantially improve a natural enzyme's activity. We enhanced the active-site electric field in horse liver alcohol dehydrogenase by replacing the serine hydrogen-bond donor with threonine and replacing the catalytic Zn2+ with Co2+. Based on the electric field enhancement, we make a quantitative prediction of rate acceleration-50-fold faster than the wild-type enzyme-which was in close agreement with experimental measurements. The effects of the hydrogen bonding and metal coordination, two distinct chemical forces, are described by a unified physical quantity-electric field, which is quantitative, and shown here to be additive and predictive. These results suggest a new design paradigm for both biological and non-biological catalysts.
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Affiliation(s)
- Chu Zheng
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Zhe Ji
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA, USA.
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24
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Pan X, Van R, Pu J, Nam K, Mao Y, Shao Y. Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions. J Chem Theory Comput 2023; 19:8234-8244. [PMID: 37943896 PMCID: PMC10835707 DOI: 10.1021/acs.jctc.3c00973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
In enzyme mechanistic studies and mutant design, it is highly desirable to know the individual residue contributions to the reaction free energy and barrier. In this work, we show that such free energy contributions from each residue can be readily obtained by postprocessing ab initio quantum mechanical molecular mechanical (ai-QM/MM) free energy simulation trajectories. Specifically, through a mean force integration along the minimum free energy pathway, one can obtain the electrostatic, polarization, and van der Waals contributions from each residue to the free energy barrier. Separately, a similar analysis procedure allows us to assess the contribution from different collective variables along the reaction coordinate. The chorismate mutase reaction is used to demonstrate the utilization of these two trajectory analysis tools.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Richard Van
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, United States
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yuezhi Mao
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, United States
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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25
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Vaissier Welborn V. Understanding Cysteine Reactivity in Protein Environments with Electric Fields. J Phys Chem B 2023; 127:9936-9942. [PMID: 37962274 DOI: 10.1021/acs.jpcb.3c05749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The role cysteine residues play in proteins is mediated by their protonation state, whereby the thiolate form of the side chain is highly reactive while the thiol form is more inert. However, the pKa of cysteine residues is hard to predict as it can differ widely from its reference value in solution, an effect that is accentuated by local effects in the heterogeneous protein environment. Here, we present a new approach to the prediction of cysteine reactivity based on electric field calculations at the thiol/thiolate group. We validated our approach by predicting the protonation state of cysteine residues in different protein environments (in the active site, at the protein surface, and buried within the protein interior), including Cys-25 in papaya protease omega, which was proven problematic for the more traditional constant pH molecular dynamics (MD) technique. We predict pKa shifts consistent with experimental observations, and the decomposition of the electric fields into contributions from molecular fragments provides a direct handle to rationalize local pH and pKa effects in proteins without introducing parameters other than those of the force field used for MD simulations.
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Affiliation(s)
- Valerie Vaissier Welborn
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
- Macromolecules Innovation Institute (MII),Virginia Tech, Blacksburg, Virginia 24060, United States
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26
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Polêto MD, Lemkul JA. Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes. J Chem Inf Model 2023; 63:6851-6862. [PMID: 37847037 PMCID: PMC10841373 DOI: 10.1021/acs.jcim.3c01305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The formation of G-quadruplexes (GQs) occurs in guanine-rich sequences of DNA and RNA, producing highly stable and structurally diverse noncanonical nucleic acid structures. GQs play crucial roles in regulating transcription, translation, and replication and maintaining the genome, among others; thus, changes to their structures can lead to diseases such as cancer. Previous studies using polarizable molecular dynamics simulations have shown differences in ion binding properties between telomeric and telomeric repeat-containing RNA GQs despite architectural similarities. Here, we used volume-based metadynamics and repulsive potential simulations in conjunction with polarizable force fields to quantify the impact of ion binding on the GQ dynamics and ion binding free energies. Furthermore, we describe how GQs exert electric fields on their surroundings to link dynamics with variations in the electronic structure. Our findings provide new insights into the energetic, physical, and conformational properties of GQs and expose subtle but important differences between DNA and RNA GQs with the same fold.
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Affiliation(s)
- Marcelo D Polêto
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Justin A Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
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27
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Gopakumar K, Samantaray V, Prusty MK, Swain L, Ramanan R. Internal charge-transfer in a metal-catalyzed oxidative addition reaction turns an inhibitive electric field stimulus to catalytic. Chem Commun (Camb) 2023; 59:13054-13057. [PMID: 37846773 DOI: 10.1039/d3cc04283a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
In a metal-catalyzed oxidative addition, an oriented external electric field (EEF) catalyzes the reaction along one direction and inhibits it when applied in the opposite direction. Beyond a threshold value, the inhibitory direction becomes catalyzing by swapping the metal-to-ligand charge transfer (MLCT) to ligand-to-metal charge-transfer (LMCT) or vice versa. The change in direction of the charge-transfer mechanism triggers the inversion of the dipole moment along the reaction axis, that results in the resurgence of catalysis. The charge-transfer mechanism in metal-catalyzed oxidative addition is tunable by EEF.
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Affiliation(s)
- Karthik Gopakumar
- Department of Chemistry, National Institute of Technology, Rourkela, Rourkela, Odisha, 769008, India.
| | - Vivekananda Samantaray
- Department of Chemistry, National Institute of Technology, Rourkela, Rourkela, Odisha, 769008, India.
| | - Mithun Kumar Prusty
- Department of Chemistry, National Institute of Technology, Rourkela, Rourkela, Odisha, 769008, India.
| | - Lopita Swain
- Department of Chemistry, National Institute of Technology, Rourkela, Rourkela, Odisha, 769008, India.
| | - Rajeev Ramanan
- Department of Chemistry, National Institute of Technology, Rourkela, Rourkela, Odisha, 769008, India.
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28
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Chaturvedi SS, Bím D, Christov CZ, Alexandrova AN. From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics. Chem Sci 2023; 14:10997-11011. [PMID: 37860658 PMCID: PMC10583697 DOI: 10.1039/d3sc02982d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023] Open
Abstract
Enzymes are versatile and efficient biological catalysts that drive numerous cellular processes, motivating the development of enzyme design approaches to tailor catalysts for diverse applications. In this perspective, we investigate the unique properties of natural, evolved, and designed enzymes, recognizing their strengths and shortcomings. We highlight the challenges and limitations of current enzyme design protocols, with a particular focus on their limited consideration of long-range electrostatic and dynamic effects. We then delve deeper into the impact of the protein environment on enzyme catalysis and explore the roles of preorganized electric fields, second coordination sphere interactions, and protein dynamics for enzyme function. Furthermore, we present several case studies illustrating successful enzyme-design efforts incorporating enzyme strategies mentioned above to achieve improved catalytic properties. Finally, we envision the future of enzyme design research, spotlighting the challenges yet to be overcome and the synergy of intrinsic electric fields, second coordination sphere interactions, and conformational dynamics to push the state-of-the-art boundaries.
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Affiliation(s)
- Shobhit S Chaturvedi
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
| | - Daniel Bím
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
| | - Christo Z Christov
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
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29
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Zhu C, Pham LN, Yuan X, Ouyang H, Coote ML, Zhang X. High Electric Fields on Water Microdroplets Catalyze Spontaneous and Fast Reactions in Halogen-Bond Complexes. J Am Chem Soc 2023; 145:21207-21212. [PMID: 37724917 DOI: 10.1021/jacs.3c08818] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
The use of external electric fields as green and efficient catalysts in synthetic chemistry has recently received significant attention for their ability to deliver remarkable control of reaction selectivity and acceleration of reaction rates. Technically, methods of generating high electric fields in the range of 1-10 V/nm are limited, as in-vacuo techniques have obvious scalability issues. The spontaneous high fields at various interfaces promise to solve this problem. In this study, we take advantage of the spontaneous high electric field at the air-water interface of sprayed water microdroplets in the reactions of several halogen bond systems: Nu:--X-X, where Nu: is pyridine or quinuclidine and X is bromine or iodine. The field facilitates ultrafast electron transfer from Nu:, yielding a Nu-X covalent bond and causing the X-X bond to cleave. This reaction occurs in microseconds in microdroplets but takes days to weeks in bulk solution. Density functional theory calculations predict that the reaction becomes barrier-free in the presence of oriented external electric fields, supporting the notion that the electric fields in the water droplets are responsible for the catalysis. We anticipate that microdroplet chemistry will be an avenue rich in opportunities in the reactions facilitated by high electric fields and provides an alternative way to tackle the scalability problem.
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Affiliation(s)
- Chenghui Zhu
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin, 300071, China
- Beijing National Laboratory for Molecular Sciences, Beijing, 100190, China
| | - Le Nhan Pham
- Institute for Nanoscale Science & Technology, Flinders University, Adelaide, South Australia 5042, Australia
| | - Xu Yuan
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin, 300071, China
- Beijing National Laboratory for Molecular Sciences, Beijing, 100190, China
| | - Haoran Ouyang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin, 300071, China
- Beijing National Laboratory for Molecular Sciences, Beijing, 100190, China
| | - Michelle L Coote
- Institute for Nanoscale Science & Technology, Flinders University, Adelaide, South Australia 5042, Australia
| | - Xinxing Zhang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin, 300071, China
- Beijing National Laboratory for Molecular Sciences, Beijing, 100190, China
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30
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Iwahara J, Pettitt BM, Yu B. Direct measurements of biomolecular electrostatics through experiments. Curr Opin Struct Biol 2023; 82:102680. [PMID: 37573815 PMCID: PMC10947535 DOI: 10.1016/j.sbi.2023.102680] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023]
Abstract
Biomolecular electrostatics has been a subject of computational investigations based on 3D structures. This situation is changing because emerging experimental tools allow us to quantitatively investigate biomolecular electrostatics without any use of structure information. Now, electrostatic potentials around biomolecules can directly be measured for many residues simultaneously by nuclear magnetic resonance (NMR) spectroscopy. This NMR method can be used to study electrostatic aspects of various processes, including macromolecular association and liquid-liquid phase separation. Applications to structurally flexible biomolecules such as intrinsically disordered proteins are particularly useful. The new tools also facilitate examination of theoretical models and methods for biomolecular electrostatics.
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Affiliation(s)
- Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - B Montgomery Pettitt
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
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31
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Wang X, Wang Y, Guo M, Wang X, Li Y, Zhang JZH. Assessment of an Electrostatic Energy-Based Charge Model for Modeling the Electrostatic Interactions in Water Solvent. J Chem Theory Comput 2023; 19:6294-6312. [PMID: 37656610 DOI: 10.1021/acs.jctc.3c00467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
The protein force field based on the restrained electrostatic potential (RESP) charges has limitations in accurately describing hydrogen bonding interactions in proteins. To address this issue, we propose an alternative approach called the electrostatic energy-based charges (EEC) model, which shows improved performance in describing electrostatic interactions (EIs) of hydrogen bonds in proteins. In this study, we further investigate the performance of the EEC model in modeling EIs in water solvent. Our findings demonstrate that the fixed EEC model can effectively reproduce the quantum mechanics/molecular mechanics (QM/MM)-calculated EIs between a water molecule and various water solvent environments. However, to achieve the same level of computational accuracy, the electrostatic potential (ESP) charge model needs to fluctuate according to the electrostatic environment. Our analysis indicates that the requirement for charge adjustments depends on the specific mathematical and physical representation of EIs as a function of the environment for deriving charges. By comparing with widely used empirical water models calibrated to reproduce experimental properties, we confirm that the performance of the EEC model in reproducing QM/MM EIs is similar to that of general purpose TIP4P-like water models such as TIP4P-Ew and TIP4P/2005. When comparing the computed 10,000 distinct EI values within the range of -40 to 0 kcal/mol with the QM/MM results calculated at the MP2/aug-cc-pVQZ/TIP3P level, we noticed that the mean unsigned error (MUE) for the EEC model is merely 0.487 kcal/mol, which is remarkably similar to the MUE values of the TIP4P-Ew (0.63 kcal/mol) and TIP4P/2005 (0.579 kcal/mol) models. However, both the RESP method and the TIP3P model exhibit a tendency to overestimate the EIs, as evidenced by their higher MUE values of 1.761 and 1.293 kcal/mol, respectively. EEC-based molecular dynamics simulations have demonstrated that, when combined with appropriate van der Waals parameters, the EEC model can closely reproduce oxygen-oxygen radial distribution function and density of water, showing a remarkable similarity to the well-established TIP4P-like empirical water models. Our results demonstrate that the EEC model has the potential to build force fields with comparable accuracy to more sophisticated empirical TIP4P-like water models.
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Affiliation(s)
- Xianwei Wang
- College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China
| | - Yiying Wang
- College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China
| | - Man Guo
- College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China
| | - Xuechao Wang
- College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China
| | - Yang Li
- College of Information Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - John Z H Zhang
- Shenzhen Institute of Synthetic Biology, Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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32
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Bofill JM, Severi M, Quapp W, Ribas-Ariño J, Moreira IDPR, Albareda G. An algorithm to find the optimal oriented external electrostatic field for annihilating a reaction barrier in a polarizable molecular system. J Chem Phys 2023; 159:114112. [PMID: 37724726 DOI: 10.1063/5.0167749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023] Open
Abstract
The use of oriented external electric fields (OEEFs) to promote and control chemical reactivity has motivated many theoretical and computational studies in the last decade to model the action of OEEFs on a molecular system and its effects on chemical processes. Given a reaction, a central goal in this research area is to predict the optimal OEEF (oOEEF) required to annihilate the reaction energy barrier with the smallest possible field strength. Here, we present a model rooted in catastrophe and optimum control theories that allows us to find the oOEEF for a given reaction valley in the potential energy surface (PES). In this model, the effective (or perturbed) PES of a polarizable molecular system is constructed by adding to the original, non-perturbed, PES a term accounting for the interaction of the OEEF with the intrinsic electric dipole and polarizability of the molecular system, so called the polarizable molecular electric dipole (PMED) model. We demonstrate that the oOEEF can be established by locating a point in the original PES with unique topological properties: the optimal barrier breakdown or bond-breaking point (oBBP). The essential feature of the oBBP structure is the fact that this point maintains its topological properties for all the applied OEEFs, also for the unperturbed PES, thus becoming much more relevant than the commonly used minima and transition state structures. The PMED model proposed here has been implemented in an open access package and is shown to successfully predict the oOEEF for two processes: an isomerization reaction of a cumulene derivative and the Huisgen cycloaddition reaction.
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Affiliation(s)
- Josep Maria Bofill
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional, (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Marco Severi
- Department of Chemistry G. Ciamician, University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Wolfgang Quapp
- Mathematisches Institut, Universität Leipzig, PF 100920, D-04009 Leipzig, Germany
| | - Jordi Ribas-Ariño
- Institut de Química Teòrica i Computacional, (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Departament de Ciència de Materials i Química Física, Secció de Química Física, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Ibério de P R Moreira
- Institut de Química Teòrica i Computacional, (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Departament de Ciència de Materials i Química Física, Secció de Química Física, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Guillermo Albareda
- Ideaded, Carrer de la Tecnologia, 35, 08840 Viladecans, Barcelona, Spain
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33
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Gopakumar K, Shaik S, Ramanan R. Two-Way Catalysis in a Diels-Alder Reaction Limits Inhibition Induced by an External Electric Field. Angew Chem Int Ed Engl 2023; 62:e202307579. [PMID: 37530131 DOI: 10.1002/anie.202307579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/18/2023] [Accepted: 08/01/2023] [Indexed: 08/03/2023]
Abstract
Oriented external electric fields (EEFs) act as catalysts that can induce selectivity in chemical reactions. The responses of the Diels-Alder (DA) reaction between butadiene and ethylene (BDE-DA) as well as cyclopentadiene and ethylene (CPDE-DA) towards EEF stimuli are investigated here using density functional theory (B3LYP) calculations. EEF is a vector that catalyzes the reaction in one direction while inhibiting it in the opposite direction. Here we report that the inhibitive direction becomes rate-enhancing after some increase in the EEF. The EEF value that brings about the maximum possible inhibition for the reaction is defined as the electrostatic resistance point (ERP). The possibility of both normal and inverse electron-demand DA reactions causes catalytic activity in both directions of the EEF starting at a unique ERP value. The C5 substituents of cyclopentadiene control the ERP values depending upon the resistance power that the functional group provides against the EEF. The endo and exo diastereomeric transition states of the DA reaction have distinct ERP values and the difference (ΔERP) provides the through-space electrostatic contribution to the stereoselectivity on a relative scale. Thus, the ERP values can be used as a gauge for the electrostatic interactions between substituent groups and external stimuli.
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Affiliation(s)
- Karthik Gopakumar
- Department of Chemistry, National Institute of Technology, Rourkela, Rourkela, Odisha, 769008, India
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407, Jerusalem, Israel
| | - Rajeev Ramanan
- Department of Chemistry, National Institute of Technology, Rourkela, Rourkela, Odisha, 769008, India
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34
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Malekshah R, Moharramnejad M, Gharanli S, Shahi M, Ehsani A, Haribabu J, Ouachtak H, Mirtamizdoust B, Kamwilaisak K, Sillanpää M, Erfani H. MOFs as Versatile Catalysts: Synthesis Strategies and Applications in Value-Added Compound Production. ACS OMEGA 2023; 8:31600-31619. [PMID: 37692216 PMCID: PMC10483527 DOI: 10.1021/acsomega.3c02552] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/01/2023] [Indexed: 09/12/2023]
Abstract
Catalysts played a crucial role in advancing modern human civilization, from ancient times to the industrial revolution. Due to high cost and limited availability of traditional catalysts, there is a need to develop cost-effective, high-activity, and nonprecious metal-based electrocatalysts. Metal-organic frameworks (MOFs) have emerged as an ideal candidate for heterogeneous catalysis due to their physicochemical properties, hybrid inorganic/organic structures, uncoordinated metal sites, and accessible organic sections. MOFs are high nanoporous crystalline materials that can be used as catalysts to facilitate polymerization reactions. Their chemical and structural diversity make them effective for various reactions compared to traditional catalysts. MOFs have been applied in gas storage and separation, ion-exchange, drug delivery, luminescence, sensing, nanofilters, water purification, and catalysis. The review focuses on MOF-enabled heterogeneous catalysis for value-added compound production, including alcohol oxidation, olefin oligomerization, and polymerization reactions. MOFs offer tunable porosity, high spatial density, and single-crystal XRD control over catalyst properties. In this review, MOFs were focused on reactions of CO2 fixation, CO2 reduction, and photoelectrochemical water splitting. Overall, MOFs have great potential as versatile catalysts for diverse applications in the future.
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Affiliation(s)
- Rahime
Eshaghi Malekshah
- Medical
Biomaterial Research Centre (MBRC), Tehran
University of Medical Sciences, Tehran 14166-34793, Iran
- Department
of Chemistry, Semnan University, Semnan 35131-19111, Iran
| | - Mojtaba Moharramnejad
- Young
Researcher and Elite Group, Qom University, Qom 37161-46611, Iran
- Department
of Chemistry, Faculty of Science, University
of Qom, Qom 37161-46611, Iran
| | - Sajjad Gharanli
- Department
of Chemical Engineering, Faculty of Engineering, University of Qom, Qom 37161-46611, Iran
| | - Mehrnaz Shahi
- Department
of Chemistry, Semnan University, Semnan 35131-19111, Iran
| | - Ali Ehsani
- Department
of Chemistry, Faculty of Science, University
of Qom, Qom 37161-46611, Iran
| | - Jebiti Haribabu
- Facultad
de Medicina, Universidad de Atacama, Los Carreras 1579, Copiapo 1532502, Chile
- Chennai Institute of Technology (CIT), Chennai 600069, India
| | - Hassan Ouachtak
- Laboratory
of Organic and Physical Chemistry, Faculty of Science, Ibn Zohr University, Agadir 80060, Morocco
- Faculty
of Applied Science, Ait Melloul, Ibn Zohr
University, Agadir 80060, Morocco
| | - Babak Mirtamizdoust
- Department
of Chemistry, Faculty of Science, University
of Qom, Qom 37161-46611, Iran
| | - Khanita Kamwilaisak
- Chemical
Engineering Department, Faculty of Engineering, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Mika Sillanpää
- Department
of Chemical Engineering, School of Mining, Metallurgy and Chemical
Engineering, University of Johannesburg, P.O. Box 17011, Doornfontein 2028, South Africa
- International
Research Centre of Nanotechnology for Himalayan Sustainability (IRCNHS), Shoolini University, Solan, Himachal Pradesh 173212, India
- Department
of Biological and Chemical Engineering, Aarhus University, Nørrebrogade
44, Aarhus C 8000, Denmark
- Department
of Civil Engineering, University Centre for Research & Development, Chandigarh University, Gharuan, Mohali, Punjab 140413, India
| | - Hadi Erfani
- Department
of Chemical Engineering, Central Tehran Branch, Islamic Azad University, Tehran 14778-93855, Iran
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35
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Polêto MD, Lemkul JA. Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552810. [PMID: 37645825 PMCID: PMC10461924 DOI: 10.1101/2023.08.10.552810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The formation of G-quadruplexes (GQs) occurs in guanine-rich sequences of DNA and RNA, producing highly stable and structurally diverse noncanonical nucleic acid structures. GQs play crucial roles in regulating transcription, translation, and replication; and maintaining the genome, among others, thus changes to their structures can lead to diseases such as cancer. Previous studies using polarizable molecular dynamics simulations have shown differences in ion binding properties between telomeric and TERRA GQs despite architectural similarities. Here, we used volume-based metadynamics and repulsive potential simulations in conjunction with polarizable force fields to quantify the impact of ion binding on GQ dynamics and ion binding free energies. Furthermore, we describe how GQs exert electric fields on their surroundings to link dynamics with variations in electronic structure. Our findings provide new insights into the energetic, physical, and conformational properties of GQs and expose subtle, but important, differences between DNA and RNA GQs with the same fold.
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Affiliation(s)
- Marcelo D Polêto
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
| | - Justin A Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
- Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
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36
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Joiret M, Kerff F, Rapino F, Close P, Geris L. A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome and its significance for the elongation cycle kinetics. Comput Struct Biotechnol J 2023; 21:3768-3795. [PMID: 37560126 PMCID: PMC10407619 DOI: 10.1016/j.csbj.2023.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023] Open
Abstract
The central function of the large subunit of the ribosome is to catalyze peptide bond formation. This biochemical reaction is conducted at the peptidyl transferase center (PTC). Experimental evidence shows that the catalytic activity is affected by the electrostatic environment around the peptidyl transferase center. Here, we set up a minimal geometrical model fitting the available x-ray solved structures of the ribonucleic cavity around the catalytic center of the large subunit of the ribosome. The purpose of this phenomenological model is to estimate quantitatively the electrostatic potential and electric field that are experienced during the peptidyl transfer reaction. At least two reasons motivate the need for developing this quantification. First, we inquire whether the electric field in this particular catalytic environment, made only of nucleic acids, is of the same order of magnitude as the one prevailing in catalytic centers of the proteic enzymes counterparts. Second, the protein synthesis rate is dependent on the nature of the amino acid sequentially incorporated in the nascent chain. The activation energy of the catalytic reaction and its detailed kinetics are shown to be dependent on the mechanical work exerted on the amino acids by the electric field, especially when one of the four charged amino acid residues (R, K, E, D) has previously been incorporated at the carboxy-terminal end of the peptidyl-tRNA. Physical values of the electric field provide quantitative knowledge of mechanical work, activation energy and rate of the peptide bond formation catalyzed by the ribosome. We show that our theoretical calculations are consistent with two independent sets of previously published experimental results. Experimental results for E.coli in the minimal case of the dipeptide bond formation when puromycin is used as the final amino acid acceptor strongly support our theoretically derived reaction time courses. Experimental Ribo-Seq results on E. coli and S. cerevisiae comparing the residence time distribution of ribosomes upon specific codons are also well accounted for by our theoretical calculations. The statistical queueing time theory was used to model the ribosome residence time per codon during nascent protein elongation and applied for the interpretation of the Ribo-Seq data. The hypo-exponential distribution fits the residence time observed distribution of the ribosome on a codon. An educated deconvolution of this distribution is used to estimate the rates of each elongation step in a codon specific manner. Our interpretation of all these results sheds light on the functional role of the electrostatic profile around the PTC and its impact on the ribosome elongation cycle.
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Affiliation(s)
- Marc Joiret
- Biomechanics Research Unit, GIGA in silico medicine, Liège University, CHU-B34(+5) 1 Avenue de l'Hôpital, 4000 Liège, Belgium
| | - Frederic Kerff
- UR InBios Centre d'Ingénierie des Protéines, Liège University, Bât B6a, Allèe du 6 Août, 19, B-4000 Liège, Belgium
| | - Francesca Rapino
- Cancer Signaling, GIGA Stem Cells, Liège University, CHU-B34(+2) 1 Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Pierre Close
- Cancer Signaling, GIGA Stem Cells, Liège University, CHU-B34(+2) 1 Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Liesbet Geris
- Biomechanics Research Unit, GIGA in silico medicine, Liège University, CHU-B34(+5) 1 Avenue de l'Hôpital, 4000 Liège, Belgium
- Skeletal Biology & Engineering Research Center, KU Leuven, ON I Herestraat 49 - box 813, 3000 Leuven, Belgium
- Biomechanics Section, KU Leuven, Celestijnenlaan 300C box 2419, B-3001 Heverlee, Belgium
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37
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Lv J, Sun R, Yang Q, Gan P, Yu S, Tan Z. Research on Electric Field-Induced Catalysis Using Single-Molecule Electrical Measurement. Molecules 2023; 28:4968. [PMID: 37446629 DOI: 10.3390/molecules28134968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
The role of catalysis in controlling chemical reactions is crucial. As an important external stimulus regulatory tool, electric field (EF) catalysis enables further possibilities for chemical reaction regulation. To date, the regulation mechanism of electric fields and electrons on chemical reactions has been modeled. The electric field at the single-molecule electronic scale provides a powerful theoretical weapon to explore the dynamics of individual chemical reactions. The combination of electric fields and single-molecule electronic techniques not only uncovers new principles but also results in the regulation of chemical reactions at the single-molecule scale. This perspective focuses on the recent electric field-catalyzed, single-molecule chemical reactions and assembly, and highlights promising outlooks for future work in single-molecule catalysis.
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Affiliation(s)
- Jieyao Lv
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot 010021, China
| | - Ruiqin Sun
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot 010021, China
| | - Qifan Yang
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot 010021, China
| | - Pengfei Gan
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot 010021, China
| | - Shiyong Yu
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot 010021, China
| | - Zhibing Tan
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot 010021, China
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38
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Tang C, Stuyver T, Lu T, Liu J, Ye Y, Gao T, Lin L, Zheng J, Liu W, Shi J, Shaik S, Xia H, Hong W. Voltage-driven control of single-molecule keto-enol equilibrium in a two-terminal junction system. Nat Commun 2023; 14:3657. [PMID: 37339947 DOI: 10.1038/s41467-023-39198-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/30/2023] [Indexed: 06/22/2023] Open
Abstract
Keto-enol tautomerism, describing an equilibrium involving two tautomers with distinctive structures, provides a promising platform for modulating nanoscale charge transport. However, such equilibria are generally dominated by the keto form, while a high isomerization barrier limits the transformation to the enol form, suggesting a considerable challenge to control the tautomerism. Here, we achieve single-molecule control of a keto-enol equilibrium at room temperature by using a strategy that combines redox control and electric field modulation. Based on the control of charge injection in the single-molecule junction, we could access charged potential energy surfaces with opposite thermodynamic driving forces, i.e., exhibiting a preference for the conducting enol form, while the isomerization barrier is also significantly reduced. Thus, we could selectively obtain desired and stable tautomers, which leads to significant modulation of the single-molecule conductance. This work highlights the concept of single-molecule control of chemical reactions on more than one potential energy surface.
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Affiliation(s)
- Chun Tang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
- Shenzhen Grubbs Institute, Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, P. R. China
| | - Thijs Stuyver
- Institute of Chemistry, Edmond J. Safra Campus at Givat Ram, The Hebrew University, Jerusalem, 91904, Israel
- Ecole Nationale Supérieure de Chimie de Paris, Université PSL, CNRS, Institute of Chemistry for Life and Health Sciences, 75 005, Paris, France
| | - Taige Lu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Junyang Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Yiling Ye
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Tengyang Gao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Luchun Lin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Jueting Zheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Wenqing Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Jia Shi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Sason Shaik
- Institute of Chemistry, Edmond J. Safra Campus at Givat Ram, The Hebrew University, Jerusalem, 91904, Israel.
| | - Haiping Xia
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China.
- Shenzhen Grubbs Institute, Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, P. R. China.
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China.
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39
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Yan S, Ji X, Peng W, Wang B. Evaluating the Transition State Stabilization/Destabilization Effects of the Electric Fields from Scaffold Residues by a QM/MM Approach. J Phys Chem B 2023; 127:4245-4253. [PMID: 37155960 DOI: 10.1021/acs.jpcb.3c01054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The protein scaffolds of enzymes not only provide structural support for the catalytic center but also exert preorganized electric fields for electrostatic catalysis. In recent years, uniform oriented external electric fields (OEEFs) have been widely applied to enzymatic reactions to mimic the electrostatic effects of the environment. However, the electric fields exerted by individual residues in proteins may be quite heterogeneous across the active site, with varying directions and strengths at different positions of the active site. Here, we propose a QM/MM-based approach to evaluate the effects of the electric fields exerted by individual residues in the protein scaffold. In particular, the heterogeneity of the residue electric fields and the effect of the native protein environment can be properly accounted for by this QM/MM approach. A case study of the O-O heterolysis reaction in the catalytic cycle of TyrH shows that (1) for scaffold residues that are relatively far from the active site, the heterogeneity of the residue electric field in the active site is not very significant and the electrostatic stabilization/destabilization due to each residue can be well approximated with the interaction energy between a uniform electric field and the QM region dipole; (2) for scaffold residues near the active site, the residue electric fields can be highly heterogeneous along the breaking O-O bond. In such a case, approximating the residue electric fields as uniform fields may misrepresent the overall electrostatic effect of the residue. The present QM/MM approach can be applied to evaluate the residues' electrostatic impact on enzymatic reactions, which also can be useful in computational optimization of electric fields to boost the enzyme catalysis.
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Affiliation(s)
- Shengheng Yan
- 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 and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Xinwei Ji
- 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 and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Wei Peng
- 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 and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. 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 and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
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40
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Abstract
This Perspective presents a review of our work and that of others in the highly controversial topic of the coupling of protein dynamics to reaction in enzymes. We have been involved in studying this topic for many years. Thus, this perspective will naturally present our own views, but it also is designed to present an overview of the variety of viewpoints of this topic, both experimental and theoretical. This is obviously a large and contentious topic.
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Affiliation(s)
- Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
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41
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Eom H, Cao Y, Kim H, de Visser SP, Song WJ. Underlying Role of Hydrophobic Environments in Tuning Metal Elements for Efficient Enzyme Catalysis. J Am Chem Soc 2023; 145:5880-5887. [PMID: 36853654 DOI: 10.1021/jacs.2c13337] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The catalytic functions of metalloenzymes are often strongly correlated with metal elements in the active sites. However, dioxygen-activating nonheme quercetin dioxygenases (QueD) are found with various first-row transition-metal ions when metal swapping inactivates their innate catalytic activity. To unveil the molecular basis of this seemingly promiscuous yet metal-specific enzyme, we transformed manganese-dependent QueD into a nickel-dependent enzyme by sequence- and structure-based directed evolution. Although the net effect of acquired mutations was primarily to rearrange hydrophobic residues in the active site pocket, biochemical, kinetic, X-ray crystallographic, spectroscopic, and computational studies suggest that these modifications in the secondary coordination spheres can adjust the electronic structure of the enzyme-substrate complex to counteract the effects induced by the metal substitution. These results explicitly demonstrate that such noncovalent interactions encrypt metal specificity in a finely modulated manner, revealing the underestimated chemical power of the hydrophobic sequence network in enzyme catalysis.
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Affiliation(s)
- Hyunuk Eom
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Yuanxin Cao
- Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, U.K.,Department of Chemical Engineering, The University of Manchester, Manchester M13 9PL, U.K
| | - Hyunsoo Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, U.K.,Department of Chemical Engineering, The University of Manchester, Manchester M13 9PL, U.K
| | - Woon Ju Song
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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42
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Yang N, Ryan MJ, Son M, Mavrič A, Zanni MT. Voltage-Dependent FTIR and 2D Infrared Spectroscopies within the Electric Double Layer Using a Plasmonic and Conductive Electrode. J Phys Chem B 2023; 127:2083-2091. [PMID: 36821845 DOI: 10.1021/acs.jpcb.2c08431] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Strong electric fields exist between the electric double layer and charged surfaces. These fields impact molecular structures and chemistry at interfaces. We have developed a transparent electrode with infrared plasmonic enhancement sufficient to measure FTIR and two-dimensional infrared spectra at submonolayer coverages on the surface to which a voltage can be applied. Our device consists of an infrared transparent substrate, a 10-20 nm layer of conductive indium tin oxide (ITO), an electrically resistive layer of 3-5 nm Al2O3, and a 3 nm layer of nonconductive plasmonic gold. The materials and thicknesses are set to maximize the surface number density of the monolayer molecules, electrical conductivity, and plasmonic enhancement while minimizing background signals and avoiding Fano line shape distortions. The design was optimized by iteratively characterizing the material roughness and thickness with atomic force microscopy and electron microscopy and by monitoring the plasmon resonance enhancement with spectroscopy. The design is robust to repeated fabrication. This new electrode is tested on nitrile functional groups using a monolayer of 4-mercaptobenzonitrile as well as on CO and CC stretching modes using 4-mercaptobenzoic acid methyl ester. A voltage-dependent Stark shift is observed on both monolayers. We also observe that the transition dipole strength of the CN mode scales linearly with the applied voltage, providing a second way of measuring the surface electric field strength. We anticipate that this cell will enable many new voltage-dependent infrared experiments under applied voltages.
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Affiliation(s)
- Nan Yang
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Matthew J Ryan
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Minjung Son
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Andraž Mavrič
- University of Nova Gorica, Materials Research Laboratory, Vipavska 13, SI-5000 Nova Gorica, Slovenia
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
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43
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Demchenko AP. Proton transfer reactions: from photochemistry to biochemistry and bioenergetics. BBA ADVANCES 2023. [DOI: 10.1016/j.bbadva.2023.100085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
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44
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Datar A, Wright C, Matthews DA. Theoretical Investigation of the X-ray Stark Effect in Small Molecules. J Phys Chem A 2023; 127:1576-1587. [PMID: 36787229 DOI: 10.1021/acs.jpca.2c08311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
We have studied the Stark effect in the soft x-ray region for various small molecules by calculating the field-dependent x-ray absorption spectra. This effect is explained in terms of the response of molecular orbitals (core and valence), the molecular dipole moment, and the molecular geometry to the applied electric field. A number of consistent trends are observed linking the computed shifts in absorption energies and intensities with specific features of the molecular electronic structure. We find that both the virtual molecular orbitals (valence and/or Rydberg) as well as the core orbitals contribute to observed trends in a complementary fashion. This initial study highlights the potential impact of x-ray Stark spectroscopy as a tool to study electronic structure and environmental perturbations at a submolecular scale.
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Affiliation(s)
- Avdhoot Datar
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Catherine Wright
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Devin A Matthews
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
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45
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Zhang B, Schaack C, Prindle CR, Vo EA, Aziz M, Steigerwald ML, Berkelbach TC, Nuckolls C, Venkataraman L. Electric fields drive bond homolysis. Chem Sci 2023; 14:1769-1774. [PMID: 36819847 PMCID: PMC9931054 DOI: 10.1039/d2sc06411a] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/15/2023] [Indexed: 01/17/2023] Open
Abstract
Electric fields have been used to control and direct chemical reactions in biochemistry and enzymatic catalysis, yet directly applying external electric fields to activate reactions in bulk solution and to characterize them ex situ remains a challenge. Here we utilize the scanning tunneling microscope-based break-junction technique to investigate the electric field driven homolytic cleavage of the radical initiator 4-(methylthio)benzoic peroxyanhydride at ambient temperatures in bulk solution, without the use of co-initiators or photochemical activators. Through time-dependent ex situ quantification by high performance liquid chromatography using a UV-vis detector, we find that the electric field catalyzes the reaction. Importantly, we demonstrate that the reaction rate in a field increases linearly with the solvent dielectric constant. Using density functional theory calculations, we show that the applied electric field decreases the dissociation energy of the O-O bond and stabilizes the product relative to the reactant due to their different dipole moments.
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Affiliation(s)
- Boyuan Zhang
- Department of Applied Physics and Applied Mathematics, Columbia University New York 10027 New York US
| | - Cedric Schaack
- Department of Chemistry, Columbia University New York 10027 New York USA
| | | | - Ethan A. Vo
- Department of Chemistry, Columbia UniversityNew York 10027New YorkUSA
| | - Miriam Aziz
- Department of Chemistry, Columbia University New York 10027 New York USA
| | | | - Timothy C. Berkelbach
- Department of Chemistry, Columbia UniversityNew York 10027New YorkUSA,Center for Computational Quantum Physics, Flatiron InstituteNew YorkNew York10010USA
| | - Colin Nuckolls
- Department of Chemistry, Columbia University New York 10027 New York USA
| | - Latha Venkataraman
- Department of Applied Physics and Applied Mathematics, Columbia University New York 10027 New York US .,Department of Chemistry, Columbia University New York 10027 New York USA
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46
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Eberhart ME, Wilson TR, Johnston NW, Alexandrova AN. Geometry of Charge Density as a Reporter on the Role of the Protein Scaffold in Enzymatic Catalysis: Electrostatic Preorganization and Beyond. J Chem Theory Comput 2023; 19:694-704. [PMID: 36562645 DOI: 10.1021/acs.jctc.2c01060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Enzymes host active sites inside protein macromolecules, which have diverse, often incredibly complex, and atom-expensive structures. It is an outstanding question what the role of these expensive scaffolds might be in enzymatic catalysis. Answering this question is essential to both enzymology and the design of artificial enzymes with proficiencies that will match those of the best natural enzymes. Protein rigidifying the active site, contrasted with the dynamics and vibrational motion promoting the reaction, as well as long-range electrostatics (also known as electrostatic preorganization) were all proposed as central contributions of the scaffold to the catalysis. Here, we show that all these effects inevitably produce changes in the quantum mechanical electron density in the active site, which in turn defines the reactivity. The phenomena are therefore fundamentally inseparable. The geometry of the electron density-a scalar field characterized by a number of mathematical features such as critical points-is a rigorous and convenient descriptor of enzymatic catalysis and a reporter on the role of the protein. We show how this geometry can be analyzed, linked to the reaction barriers, and report in particular on intramolecular electric fields in enzymes. We illustrate these tools on the studies of electrostatic preorganization in several representative enzyme classes, both natural and artificial. We highlight the forward-looking aspects of the approach.
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Affiliation(s)
- Mark E Eberhart
- Department of Chemistry, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Timothy R Wilson
- Department of Chemistry, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Nathaniel W Johnston
- Department of Chemistry, and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Anastassia N Alexandrova
- Department of Chemistry, and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
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47
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Ma Z, Yan Z, Li X, Chung LW. Quantum Tunneling in Reactions Modulated by External Electric Fields: Reactivity and Selectivity. J Phys Chem Lett 2023; 14:1124-1132. [PMID: 36705472 DOI: 10.1021/acs.jpclett.2c03461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Quantum tunneling and external electric fields (EEFs) can promote some reactions. However, the synergetic effect of an EEF on a tunneling-involving reaction and its temperature-dependence is not very clear. In this study, we extensively investigated how EEFs affect three reactions that involve hydrogen- or (ground- and excited-state) carbon-tunneling using reliable DFT, DLPNO-CCSD(T1), and variational transition-state theory methods. Our study revealed that oriented EEFs can significantly reduce the barrier and corresponding barrier width (and vice versa) through more electrostatic stabilization in transition states. These EEF effects enhance the nontunneling and tunneling-involving rates. Such EEF effects also decrease the crossover temperatures and quantum tunneling contribution, albeit with lower and thinner barriers. Moreover, EEFs can modulate and switch on/off the tunneling-driven 1,2-H migration of hydroxycarbenes under cryogenic conditions. Furthermore, our study predicts for the first time that EEF/tunneling synergy can control the chemo- or site-selectivity of one molecule bearing two similar/same reactive sites.
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Affiliation(s)
- Zhifeng Ma
- Shenzhen Grubbs Institute, Department of Chemistry, and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, P. R. China
| | - Zeyin Yan
- Shenzhen Grubbs Institute, Department of Chemistry, and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, P. R. China
| | - Xin Li
- Shenzhen Grubbs Institute, Department of Chemistry, and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, P. R. China
| | - Lung Wa Chung
- Shenzhen Grubbs Institute, Department of Chemistry, and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, P. R. China
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48
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A catastrophe theory-based model for optimal control of chemical reactions by means of oriented electric fields. Theor Chem Acc 2023. [DOI: 10.1007/s00214-023-02959-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
AbstractThe effect of oriented external electric fields (OEEF) on chemical reactivity has been studied theoretically and computationally in the last decades. A central goal in this research area is to predict the orientation and the smallest amplitude electric field that renders a barrierless chemical process with the smallest possible strength. Recently, a model to find the optimal electric field has been proposed and described (Bofill JM et al., J. Chem. Theory Comput. 18:935, 2022). We here proof that this model is based on catastrophe and optimum control theories. Based on both theories a technical treatment of the model is given and applied to a two-dimensional generic example that provides insight into its nature and capability. Finally, the model is applied to determine the optimal OEEF for the trans-to-cis isomerization of a [3]cumulene derivative.
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49
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Geerlings P, De Proft F. External fields in conceptual density functional theory. J Comput Chem 2023; 44:442-455. [PMID: 36054623 DOI: 10.1002/jcc.26978] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/30/2022] [Accepted: 07/13/2022] [Indexed: 12/31/2022]
Abstract
The necessity of the recent incorporation of new external variables in the context of conceptual DFT (CDFT) is discussed based on the ever-increasing portfolio of experimental reaction conditions in the endeavor of experimentalists to synthesize new molecules with unprecedented properties. Electric and magnetic fields (ε and B), mechanical forces (F), and confinement are proposed as valuable new variables, extending conventional CDFT and its associated response functions. A finite field approach is used to calculate the evolution of both global and local descriptors in a selected series of atomic and molecular applications, and from it derive new response function involving, with one exception, the first derivative to the field considered. The electric field results, displaying, for example, a case of a field-induced enantioselectivity in the Fukui function, may be instrumental in the recent upsurge of chemistry in oriented external electric fields. The study of atomic electronegativity and hardness in magnetic fields displays a piecewise behavior, associated to configurational jumps upon increasing field strength and reveals an overall compression of their ranges for stronger fields, which may be guiding upon investigating chemistry in extremely high fields like in white dwarfs. The evolution of the electronegativity and hardness of diatomics under mechanical force can elegantly be traced back to differences in their equilibrium distance in the neutral, cationic, and anionic state. The well-known reduction of the polarizability under confinement can be seen as a fore-runner of the increasing hardness of atoms under pressure, presently under investigation. Periodicity showing up in a spontaneous way in the variety of properties is a leitmotiv in this study, as well as the interconnections/analogies between the different response functions.
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Affiliation(s)
- Paul Geerlings
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel, Brussels, Belgium
| | - Frank De Proft
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel, Brussels, Belgium
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50
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Průša J, Cifra M. Electro-detachment of kinesin motor domain from microtubule in silico. Comput Struct Biotechnol J 2023; 21:1349-1361. [PMID: 36814722 PMCID: PMC9939557 DOI: 10.1016/j.csbj.2023.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/15/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023] Open
Abstract
Kinesin is a motor protein essential in cellular functions, such as intracellular transport and cell-division, as well as for enabling nanoscopic transport in bio-nanotechnology. Therefore, for effective control of function for nanotechnological applications, it is important to be able to modify the function of kinesin. To circumvent the limitations of chemical modifications, here we identify another potential approach for kinesin control: the use of electric forces. Using full-atom molecular dynamics simulations (247,358 atoms, total time ∼ 4.4 μs), we demonstrate, for the first time, that the kinesin-1 motor domain can be detached from a microtubule by an intense electric field within the nanosecond timescale. We show that this effect is field-direction dependent and field-strength dependent. A detailed analysis of the electric forces and the work carried out by electric field acting on the microtubule-kinesin system shows that it is the combined action of the electric field pulling on the β-tubulin C-terminus and the electric-field-induced torque on the kinesin dipole moment that causes kinesin detachment from the microtubule. It is shown, for the first time in a mechanistic manner, that an electric field can dramatically affect molecular interactions in a heterologous functional protein assembly. Our results contribute to understanding of electromagnetic field-biomatter interactions on a molecular level, with potential biomedical and bio-nanotechnological applications for harnessing control of protein nanomotors.
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