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Warman H, Slocombe L, Sacchi M. How proton transfer impacts hachimoji DNA. RSC Adv 2023; 13:13384-13396. [PMID: 37143915 PMCID: PMC10152326 DOI: 10.1039/d3ra00983a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/23/2023] [Indexed: 05/06/2023] Open
Abstract
Hachimoji DNA is a synthetic nucleic acid extension of DNA, formed by an additional four bases, Z, P, S, and B, that can encode information and sustain Darwinian evolution. In this paper, we aim to look into the properties of hachimoji DNA and investigate the probability of proton transfer between the bases, resulting in base mismatch under replication. First, we present a proton transfer mechanism for hachimoji DNA, analogous to the one presented by Löwdin years prior. Then, we use density functional theory to calculate proton transfer rates, tunnelling factors and the kinetic isotope effect in hachimoji DNA. We determined that the reaction barriers are sufficiently low that proton transfer is likely to occur even at biological temperatures. Furthermore, the rates of proton transfer of hachimoji DNA are much faster than in Watson-Crick DNA due to the barrier for Z-P and S-B being 30% lower than in G-C and A-T. Suggesting that proton transfer occurs more frequently in hachimoji DNA than canonical DNA, potentially leading to a higher mutation rate.
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Affiliation(s)
- Harry Warman
- School of Physics and Maths, University of Surrey Guildford GU2 7XH UK
| | - Louie Slocombe
- School of Chemistry and Chemical Engineering, University of Surrey Guildford GU2 7XH UK
| | - Marco Sacchi
- School of Chemistry and Chemical Engineering, University of Surrey Guildford GU2 7XH UK
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Machado TFG, Purg M, Åqvist J, da Silva RG. Transition States for Psychrophilic and Mesophilic ( R)-3-Hydroxybutyrate Dehydrogenase-Catalyzed Hydride Transfer at Sub-zero Temperatures. Biochemistry 2021; 60:2186-2194. [PMID: 34190541 DOI: 10.1021/acs.biochem.1c00322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
(R)-3-Hydroxybutyrate dehydrogenase (HBDH) catalyzes the NADH-dependent reduction of 3-oxocarboxylates to (R)-3-hydroxycarboxylates. The active sites of a pair of cold- and warm-adapted HBDHs are identical except for a single residue, yet kinetics evaluated at -5, 0, and 5 °C show a much higher steady-state rate constant (kcat) for the cold-adapted than for the warm-adapted HBDH. Intriguingly, single-turnover rate constants (kSTO) are strikingly similar between the two orthologues. Psychrophilic HBDH primary deuterium kinetic isotope effects on kcat (Dkcat) and kSTO (DkSTO) decrease at lower temperatures, suggesting more efficient hydride transfer relative to other steps as the temperature decreases. However, mesophilic HBDH Dkcat and DkSTO are generally temperature-independent. The DkSTO data allowed calculation of intrinsic primary deuterium kinetic isotope effects. Intrinsic isotope effects of 4.2 and 3.9 for cold- and warm-adapted HBDH, respectively, at 5 °C, supported by quantum mechanics/molecular mechanics calculations, point to a late transition state for both orthologues. Conversely, intrinsic isotope effects of 5.7 and 3.1 for cold- and warm-adapted HBDH, respectively, at -5 °C indicate the transition state becomes nearly symmetric for the psychrophilic enzyme, but more asymmetric for the mesophilic enzyme. His-to-Asn and Asn-to-His mutations in the psychrophilic and mesophilic HBDH active sites, respectively, swap the single active-site position where these orthologues diverge. At 5 °C, the His-to-Asn mutation in psychrophilic HBDH decreases Dkcat to 3.1, suggesting a decrease in transition-state symmetry, while the His-to-Asn mutation in mesophilic HBDH increases Dkcat to 4.4, indicating an increase in transition-state symmetry. Hence, temperature adaptation and a single divergent active-site residue may influence transition-state geometry in HBDHs.
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Affiliation(s)
- Teresa F G Machado
- School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Miha Purg
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Rafael G da Silva
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
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Liu Y, Yan Y, Xing T, Shi Q. Understanding the Large Kinetic Isotope Effect of Hydrogen Tunneling in Condensed Phases by Using Double-Well Model Systems. J Phys Chem B 2021; 125:5959-5970. [PMID: 34033714 DOI: 10.1021/acs.jpcb.1c02851] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, many experiments have shown large kinetic isotope effects (KIEs) for hydrogen transfer reactions in condensed phases as evidence of strong quantum tunneling effects. Since accurate calculation of the tunneling dynamics in such systems still present significant challenges, previous studies have employed different types of approximations to estimate the tunneling effects and KIEs. In this work, by employing model systems consisting of a double-well coupled to a harmonic bath, we calculate the tunneling effects and KIEs using the numerically exact hierarchical equations of motion (HEOM) method. It is found that hydrogen and deuterium transfer reactions in the same system may show rather different behaviors, where hydrogen transfer is dominated by tunneling between the two lowest vibrational states and deuterium transfer is controlled by excited vibrational states close to the barrier top. The simulation results are also used to test the validity of various approximate methods. It is shown that the Wolynes theory of dissipative tunneling gives a good estimation of rate constants in the over-the-barrier regime, while the nonadiabatic reaction rate theory based on the Landau-Zener formula is more suitable for deep tunneling reactions.
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Affiliation(s)
- Yanying Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
| | - Yaming Yan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
| | - Tao Xing
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
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Das A, Hessin C, Ren Y, Desage-El Murr M. Biological concepts for catalysis and reactivity: empowering bioinspiration. Chem Soc Rev 2020; 49:8840-8867. [PMID: 33107878 DOI: 10.1039/d0cs00914h] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biological systems provide attractive reactivity blueprints for the design of challenging chemical transformations. Emulating the operating mode of natural systems may however not be so easy and direct translation of structural observations does not always afford the anticipated efficiency. Metalloenzymes rely on earth-abundant metals to perform an incredibly wide range of chemical transformations. To do so, enzymes in general have evolved tools and tricks to enable control of such reactivity. The underlying concepts related to these tools are usually well-known to enzymologists and bio(inorganic) chemists but may be a little less familiar to organometallic chemists. So far, the field of bioinspired catalysis has greatly focused on the coordination sphere and electronic effects for the design of functional enzyme models but might benefit from a paradigm shift related to recent findings in biological systems. The goal of this review is to bring these fields closer together as this could likely result in the development of a new generation of highly efficient bioinspired systems. This contribution covers the fields of redox-active ligands, entatic state reactivity, energy conservation through electron bifurcation, and quantum tunneling for C-H activation.
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Affiliation(s)
- Agnideep Das
- Université de Strasbourg, Institut de Chimie, UMR CNRS 7177, 67000 Strasbourg, France.
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Kostenko A, Ray K, Iavarone AT, Offenbacher AR. Kinetic Characterization of the C-H Activation Step for the Lipoxygenase from the Pathogenic Fungus Magnaporthe oryzae: Impact of N-Linked Glycosylation. Biochemistry 2019; 58:3193-3203. [PMID: 31264852 DOI: 10.1021/acs.biochem.9b00467] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lipoxygenases from pathogenic fungi belong to the lipoxygenase family of enzymes, which catalyze C-H activation of polyunsaturated fatty acids to form a diverse set of cell-signaling hydroperoxides. While the lipoxygenase catalytic domains are structurally and functionally similar, these fungal enzymes are decorated with N-linked glycans. The impact of N-linked glycans on the structure and function of these enzymes remains largely unknown. One exemplary system is MoLOX, a lipoxygenase from the fungus Magnaporthe oryzae, that is emerging as an important target for the devastating rice blast disease. Herein, we demonstrate that hydrogen transfer, associated with C-H cleavage of the substrate linoleic acid by MoLOX, is rate-determining and occurs by a hydrogen tunneling mechanism. Using the differential enthalpic barrier for hydrogen and deuterium transfer, ΔEa, as a kinetic reporter of tunneling efficiency, a disproportionate increase in the activation energy for deuterium transfer is observed upon treatment of MoLOX with a peptide:N-glycosidase that cleaves N-linked carbohydrates from the protein. This increased ΔEa is consistent with an impairment of substrate positioning in the enzyme-substrate complex for both the tunneling ready state and the ground state. These results provide new insight into the functional consequences of N-linked glycosylation on lipoxygenase C-H activation and have important implications for MoLOX inhibitor design.
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Affiliation(s)
- Anastasiia Kostenko
- Department of Chemistry , East Carolina University , Greenville , North Carolina 27858 , United States
| | - Katherine Ray
- Department of Biology , East Carolina University , Greenville , North Carolina 27858 , United States
| | - Anthony T Iavarone
- California Institute for Quantitative Biosciences (QB3) , University of California , Berkeley , California 94720 , United States
| | - Adam R Offenbacher
- Department of Chemistry , East Carolina University , Greenville , North Carolina 27858 , United States
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