Proton tunnelling in hydrogen bonds and its implications in an induced-fit model of enzyme catalysis
@article{Pusuluk2018ProtonTI, title={Proton tunnelling in hydrogen bonds and its implications in an induced-fit model of enzyme catalysis}, author={Onur Pusuluk and Tristan Farrow and Cemsinan Deliduman and Keith Burnett and Vlatko Vedral}, journal={Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences}, year={2018}, volume={474} }
The role of proton tunnelling in biological catalysis is investigated here within the frameworks of quantum information theory and thermodynamics. We consider the quantum correlations generated through two hydrogen bonds between a substrate and a prototypical enzyme that first catalyses the tautomerization of the substrate to move on to a subsequent catalysis, and discuss how the enzyme can derive its catalytic potency from these correlations. In particular, we show that classical changes…
16 Citations
Emergence of correlated proton tunnelling in water ice
- PhysicsProceedings of the Royal Society A
- 2019
A pseudo-spin model for the quantum motion of protons in a hexameric H2O ring is constructed and extended to open system dynamics that takes environmental effects into account in the form of O–H stretch vibrations, concluding that long-range intra-ring interactions do not appear to be a necessary condition for correlated proton tunnelling in water ice.
Fundamental limitations on photoisomerization from thermodynamic resource theories
- PhysicsPhysical Review A
- 2020
Small, out-of-equilibrium, and quantum systems defy simple thermodynamic
expressions. Such systems are exemplified by molecular switches, which exchange
heat with a bath and which can…
Sodium and Magnesium Ion Location at the Backbone and at the Nucleobase of RNA: Ab Initio Molecular Dynamics in Water Solution
- Chemistry, Materials ScienceACS Omega
- 2022
The interactions between Na+ or Mg2+ ions with different parts of single-stranded RNA molecules, namely, the oxygen atoms from the phosphate groups or the guanine base, in water solution have been…
Proton tunneling in a two-dimensional potential energy surface with a non-linear system-bath interaction: Thermal suppression of reaction rate.
- PhysicsThe Journal of chemical physics
- 2020
This study introduces an exponential-linear (EL) system-bath interaction, which is derived from the analysis of a PTR-RPV system in a realistic situation, and exhibits opposite temperature dependence.
Bad vibrations: Quantum tunnelling in the context of SARS-CoV-2 infection
- Biology
- 2021
Evidence that quantum tunnelling might be important in the context of infection with SARS-CoV-2 is investigated, and a simple model relating the vibronic mode of a viral spike protein to the likelihood of charge transfer in an idealised receptor is illustrated.
Why Is Catalase So Fast ? Part 2 : Schemes for Rapid , Exo-enzymatic Disproportionation of Hydrogen Peroxide
- Biology
- 2018
Grotthuss-like proton transfer in and between QED-type water coherent domains, could partially explain how catalase might accomplish ultra-fast exo-enzymatic “unzipping” (disproportionation) of…
Chronobiology Meets Quantum Biology: A New Paradigm Overlooking the Horizon?
- BiologyFrontiers in Physiology
- 2022
The study of quantum phenomena in biological cycles proposes a profitable “entanglement” between the areas of interest of these seemingly distant scientific disciplines to enlighten functional roles for quantum effects in rhythmic biosystems.
Simulating molecules on a cloud-based 5-qubit IBM-Q universal quantum computer
- Physics
- 2021
Simulating the behaviour of complex quantum systems is impossible on classical supercomputers due to the exponential scaling of the number of quantum states with the number of particles in the…
CDR3 binding chemistry controls TCR V-domain rotational probability and germline CDR2 scanning of polymorphic MHC.
- BiologyMolecular immunology
- 2022
References
SHOWING 1-10 OF 67 REFERENCES
Hydrogen tunneling links protein dynamics to enzyme catalysis.
- Chemistry, BiologyAnnual review of biochemistry
- 2013
It is shown how the quantum mechanical hydrogen tunneling associated with enzymatic C-H bond cleavage provides a unique window into the necessity of protein dynamics for achieving optimal catalysis.
Internal Enzyme Motions as a Source of Catalytic Activity: Rate-Promoting Vibrations and Hydrogen Tunneling
- Physics
- 2001
The standard view of the origin of the catalytic properties of enzymes focuses on the binding energy differences between the ground state and the transition state arising from the arrangement of…
The role of quantum effects in proton transfer reactions in enzymes: quantum tunneling in a noisy environment?
- Physics
- 2010
We consider the role of quantum effects in the transfer of hydrogen-like species in enzyme-catalyzed reactions. This review is stimulated by claims that the observed magnitude and temperature…
Hydrogen tunnelling in enzyme-catalysed H-transfer reactions: flavoprotein and quinoprotein systems
- Biology, ChemistryPhilosophical Transactions of the Royal Society B: Biological Sciences
- 2006
Tunnelling mechanisms in enzymes are supported by atomistic computational studies performed within the framework of modern TST, which incorporates quantum nuclear effects.
Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems
- ChemistryPhilosophical Transactions of the Royal Society B: Biological Sciences
- 2006
It seems that TST provides a quantitative tool for studies of enzyme catalysis and that the key open questions are related to the nature of the factors that lead to transition state stabilization.
Quantum Tunnelling in Enzyme-Catalysed Reactions
- Physics
- 2009
Introduction. Preface: Beyond the Historical Perspective on Hydrogen and Electron Transfers. Chapter 1: The Transition State Theory Description of Enzyme Catalysis for Classically Activated…
How Important Are Quantum Mechanical Nuclear Motions in Enzyme Catalysis
- Physics, Chemistry
- 1996
The role of quantum mechanical nuclear motions in enzymatic reactions is examined by realistic simulations that take into account the fluctuations of an entire enzyme−substrate complex. This is done…
Quantum catalysis? A comment on tunnelling contributions for catalysed and uncatalysed reactions
- Chemistry, Physics
- 2010
Appreciation for the contribution of nuclear quantum effects to chemical reactivity predates transition-state theory. Quantum corrections to rate constants for the reactions catalyzed by lactate…
Effect of quantum nuclear motion on hydrogen bonding.
- PhysicsThe Journal of chemical physics
- 2014
This work considers how the properties of hydrogen bonded complexes, X-H⋯Y, are modified by the quantum motion of the shared proton, using a simple two-diabatic state model Hamiltonian to offer key insights into the defining features of H-bonds and semi-quantitatively captures several trends.
Hydride transfer catalysed by Escherichia coli and Bacillus subtilis dihydrofolate reductase: coupled motions and distal mutations
- ChemistryPhilosophical Transactions of the Royal Society B: Biological Sciences
- 2006
Results from hybrid quantum/classical molecular dynamics simulations of the hydride transfer reaction catalysed by wild-type and mutant Escherichia coli and WT Bacillus subtilis dihydrofolate reductase are reviewed, suggesting a balance of conservation and flexibility across species.