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A Quantum Mechanical Aspect of Enzyme Action: Enzymes as Information Driven Quantal Measurement Engines

J. David Puett, George A. Perry

Published Jan 1, 2014• 0 citations
OpenAlex

Abstract

In this introductory paper we overview existing approaches to enzyme – catalysed reactions. From the Michaelis – Menten kinetics to quantum scatterings several models are considered. We try to introduce our ”information – d riven measurement engines” (an other model of enzyme action) in relation to existent theories. We conclude that our approach is a special type of quantum mechanical treatment of enzyme catalysed reactions, in its nascent form. It is, we suppose, stands mor e in relation to a hypothetical gas – phase scattering, maybe even resonance scattering, as a one – dimensional vacuum energy – dependent motion along the reaction path. We are aware that at this time, no realistic gas – phase scattering is available in th e area, and our approach is thus similarly hypothetical. Still, it might provide a fresh view on enzyme – catalysed reactions, utilising a somewhat unusual Hamiltonian second – order tensor operator formalism. During arriving at our goal, we give some mor e extensive review devoted to current cataly s ed and uncatal y s ed reaction investigations, of a pure chemical and biochemical nature, exploring both experimental and theoretical procedures.

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A Quantum Mechanical Aspect of Enzyme Action: Enzymes as Information Driven Quantal Measurement Engines

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In this introductory paper we overview existing approaches to enzyme – catalysed reactions. From the Michaelis – Menten kinetics to quantum scatterings several models are considered. We try to introduce our ”information – driven measurement engines” (an other model of enzyme action) in relation to existent theories. We conclude that our approach is a special type of quantum mechanical treatment of enzyme catalysed reactions, in its nascent form. It is, we suppose, stands more in relation to a hypothetical gas – phase scattering, maybe even resonance scattering, as a one – dimensional vacuum energy – dependent motion along the reaction path. We are aware that at this time, no realistic gas – phase scattering is available in the area, and our approach is thus similarly hypothetical. Still, it might provide a fresh view on enzyme – catalysed reactions, utilising a somewhat unusual Hamiltonian second – order tensor operator formalism. During arriving at our goal, we give some more extensive review devoted to current catalyzed and uncatalized reaction investigations, of a pure chemical and biochemical nature, exploring both experimental and theoretical procedures.

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Enzyme Kinetics and Molecular Motors as Action Compatibility: Variational Foundation of Biological Phase Dynamics

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This work presents a variational reformulation of biochemical kinetics, in which molecular interactions are described as discrete action compatibility events, rather than continuous processes based solely on stochastic collisions. The construction is based on minimal hypotheses---cumulative action, independent parameterizations, and interferential dependence---without the introduction of new physical postulates. It is shown that the effective interaction between systems occurs only when the action difference satisfies $$\Delta S = 2\pi n\hbar,$$ which implies a characteristic temporal scale $$\Delta t \sim \frac{\hbar}{|\dot{\Delta S}|}.$$ The analysis establishes a general relationship between action, phase, and frequency, $$\omega = \frac{\dot{S}}{\hbar},$$ valid for massive and massless particles, consistent with special relativity and quantum field theory. Applied to biology, the formalism allows interpreting enzymatic reactions, molecular motors, and pharmacological effects as action coherence phenomena. The work also presents testable experimental predictions in femtochemistry and single-molecule manipulation systems. From an epistemological standpoint, this is not a new theory, but a structural consequence of fundamental variational principles when applied to composite systems.

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Quantum Simulation of Enzyme Catalysis

Nicholas Boekelheide

Separating the dynamics of variables that evolve on different timescales is a common assumption in exploring complex systems, and a great deal of progress has been made in understanding chemical systems by treating independently the fast processes of an activated chemical species from the slower processes that proceed activation. Protein motion underlies all biocatalytic reactions, and understanding the nature of this motion is central to understanding how enzymes catalyze reactions with such specificity and such rate enhancement. This understanding is challenged by evidence of breakdowns in the separability of timescales of dynamics in the active site form motions of the solvating protein. Quantum simulation methods that bridge these timescales by simultaneously evolving quantum and classical degrees of freedom provide an important method on which to explore this breakdown. In the following dissertation, three problems of enzyme catalysis are explored through quantum simulation.

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Proton tunnelling in hydrogen bonds and its implications in an induced-fit model of enzyme catalysis

Onur Pusuluk, Tristan Farrow, Cemsinan Deliduman B +2 more

Abstract 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 induced in the binding site of the enzyme spreads the quantum correlations among all of the four hydrogen-bonded atoms thanks to the directionality of hydrogen bonds. If the enzyme rapidly returns to its initial state after the binding stage, the substrate ends in a new transition state corresponding to a quantum superposition. Open quantum system dynamics can then naturally drive the reaction in the forward direction from the major tautomeric form to the minor tautomeric form without needing any additional catalytic activity. We find that in this scenario the enzyme lowers the activation energy so much that there is no energy barrier left in the tautomerization, even if the quantum correlations quickly decay.

arXiv:1703.00789•Proceedings of the Royal Society A Mathematical Physical and Engineering Sciences•Oct 3, 2018•28 citations
In this introductory paper we overview existing approaches to enzyme – catalysed reactions. From the Michaelis – Menten kinetics to quantum scatterings several models are considered. We try to introduce our ”information – d riven measurement engines” (an other model of enzyme action) in relation to existent theories. We conclude that our approach is a special type of quantum mechanical treatment of enzyme catalysed reactions, in its nascent form. It is, we suppose, stands mor e in relation to a hypothetical gas – phase scattering, maybe even resonance scattering, as a one – dimensional vacuum energy – dependent motion along the reaction path. We are aware that at this time, no realistic gas – phase scattering is available in th e area, and our approach is thus similarly hypothetical. Still, it might provide a fresh view on enzyme – catalysed reactions, utilising a somewhat unusual Hamiltonian second – order tensor operator formalism. During arriving at our goal, we give some mor e extensive review devoted to current cataly s ed and uncatal y s ed reaction investigations, of a pure chemical and biochemical nature, exploring both experimental and theoretical procedures.
In this introductory paper we overview existing approaches to enzyme – catalysed reactions. From the Michaelis – Menten kinetics to quantum scatterings several models are considered. We try to introduce our ”information – driven measurement engines” (an other model of enzyme action) in relation to existent theories. We conclude that our approach is a special type of quantum mechanical treatment of enzyme catalysed reactions, in its nascent form. It is, we suppose, stands more in relation to a hypothetical gas – phase scattering, maybe even resonance scattering, as a one – dimensional vacuum energy – dependent motion along the reaction path. We are aware that at this time, no realistic gas – phase scattering is available in the area, and our approach is thus similarly hypothetical. Still, it might provide a fresh view on enzyme – catalysed reactions, utilising a somewhat unusual Hamiltonian second – order tensor operator formalism. During arriving at our goal, we give some more extensive review devoted to current catalyzed and uncatalized reaction investigations, of a pure chemical and biochemical nature, exploring both experimental and theoretical procedures.
This work presents a variational reformulation of biochemical kinetics, in which molecular interactions are described as discrete action compatibility events, rather than continuous processes based solely on stochastic collisions. The construction is based on minimal hypotheses---cumulative action, independent parameterizations, and interferential dependence---without the introduction of new physical postulates. It is shown that the effective interaction between systems occurs only when the action difference satisfies ΔS=2πnℏ,\Delta S = 2\pi n\hbar,ΔS=2πnℏ, which implies a characteristic temporal scale Δt∼ℏ∣ΔS˙∣.\Delta t \sim \frac{\hbar}{|\dot{\Delta S}|}.Δt∼∣ΔS˙∣ℏ​. The analysis establishes a general relationship between action, phase, and frequency, ω=S˙ℏ,\omega = \frac{\dot{S}}{\hbar},ω=ℏS˙​, valid for massive and massless particles, consistent with special relativity and quantum field theory. Applied to biology, the formalism allows interpreting enzymatic reactions, molecular motors, and pharmacological effects as action coherence phenomena. The work also presents testable experimental predictions in femtochemistry and single-molecule manipulation systems. From an epistemological standpoint, this is not a new theory, but a structural consequence of fundamental variational principles when applied to composite systems.
Separating the dynamics of variables that evolve on different timescales is a common assumption in exploring complex systems, and a great deal of progress has been made in understanding chemical systems by treating independently the fast processes of an activated chemical species from the slower processes that proceed activation. Protein motion underlies all biocatalytic reactions, and understanding the nature of this motion is central to understanding how enzymes catalyze reactions with such specificity and such rate enhancement. This understanding is challenged by evidence of breakdowns in the separability of timescales of dynamics in the active site form motions of the solvating protein. Quantum simulation methods that bridge these timescales by simultaneously evolving quantum and classical degrees of freedom provide an important method on which to explore this breakdown. In the following dissertation, three problems of enzyme catalysis are explored through quantum simulation.
Abstract 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 induced in the binding site of the enzyme spreads the quantum correlations among all of the four hydrogen-bonded atoms thanks to the directionality of hydrogen bonds. If the enzyme rapidly returns to its initial state after the binding stage, the substrate ends in a new transition state corresponding to a quantum superposition. Open quantum system dynamics can then naturally drive the reaction in the forward direction from the major tautomeric form to the minor tautomeric form without needing any additional catalytic activity. We find that in this scenario the enzyme lowers the activation energy so much that there is no energy barrier left in the tautomerization, even if the quantum correlations quickly decay.