Conformational Barrier-Driven Flux Redistribution across Competing Catalytic Pathways Unifies Diverse Enzyme Kinetic Regimes
- 1Indian Association for the Cultivation of Science
Abstract
Enzymes are central to biological function, catalyzing the chemical transformations that sustain metabolism, signalling, molecular transport, and cellular regulation. Understanding their catalytic activity requires connecting molecular structure and conformational dynamics to measurable reaction kinetics. Classical Michaelis--Menten kinetics describes turnover through a dominant catalytic pathway approaching a single saturation limit, whereas conformational-selection, induced-fit, allosteric, and dynamic-disorder models account for additional complexity arising from conformational exchange and heterogeneous catalytic states. Experimental studies further reveal concentration-dependent changes in pathway usage, cooperative or sigmoidal responses, transitions between distinct turnover regimes, and intermittent single-molecule activity. These behaviours are typically treated within separate kinetic descriptions, leaving their mechanistic relationship within a common physical picture incompletely resolved. Here, we formulate a minimal conformational free-energy landscape with interconverting enzyme states and competing catalytic routes to examine whether these apparently distinct kinetic signatures can arise from a shared physical mechanism. In this framework, substrate availability and conformational barriers redistribute catalytic flux between slower and faster pathways, thereby altering both pathway occupancy and turnover times. Stochastic Gillespie simulations together with deterministic mean-first-passage-time analysis show that different parameter regimes generate low- and high-turnover states, concentration-dependent kinetic crossovers, burst--halt intermittency consistent with single-molecule observations, and effectively Michaelis--Menten-like or sigmoidal allosteric-like responses. The same underlying landscape can therefore produce qualitatively different kinetic behaviours depending on how conformational exchange and substrate capture partition catalytic flux. It also explains how finite substrate windows can mask underlying bimodal behaviour. These results provide a physically interpretable framework linking conformational dynamics, pathway selection, and experimentally observed enzyme kinetics.
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BibTeX
@misc{mitra2026conformational,
title = {{Conformational Barrier-Driven Flux Redistribution across Competing Catalytic Pathways Unifies Diverse Enzyme Kinetic Regimes}},
author = {R. Mitra and B. Jana},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.21.753117},
url = {https://www.biorxiv.org/content/10.64898/2026.09.21.753117v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - Conformational Barrier-Driven Flux Redistribution across Competing Catalytic Pathways Unifies Diverse Enzyme Kinetic Regimes
AU - R. Mitra
AU - B. Jana
PY - 2026
DA - 2026/09/21
PB - bioRxiv
DO - 10.64898/2026.09.21.753117
UR - https://www.biorxiv.org/content/10.64898/2026.09.21.753117v1
AB - Enzymes are central to biological function, catalyzing the chemical transformations that sustain metabolism, signalling, molecular transport, and cellular regulation. Understanding their catalytic activity requires connecting molecular structure and conformational dynamics to measurable reaction kinetics. Classical Michaelis--Menten kinetics describes turnover through a dominant catalytic pathway approaching a single saturation limit, whereas conformational-selection, induced-fit, allosteric, and dynamic-disorder models account for additional complexity arising from conformational exchange and heterogeneous catalytic states. Experimental studies further reveal concentration-dependent changes in pathway usage, cooperative or sigmoidal responses, transitions between distinct turnover regimes, and intermittent single-molecule activity. These behaviours are typically treated within separate kinetic descriptions, leaving their mechanistic relationship within a common physical picture incompletely resolved. Here, we formulate a minimal conformational free-energy landscape with interconverting enzyme states and competing catalytic routes to examine whether these apparently distinct kinetic signatures can arise from a shared physical mechanism. In this framework, substrate availability and conformational barriers redistribute catalytic flux between slower and faster pathways, thereby altering both pathway occupancy and turnover times. Stochastic Gillespie simulations together with deterministic mean-first-passage-time analysis show that different parameter regimes generate low- and high-turnover states, concentration-dependent kinetic crossovers, burst--halt intermittency consistent with single-molecule observations, and effectively Michaelis--Menten-like or sigmoidal allosteric-like responses. The same underlying landscape can therefore produce qualitatively different kinetic behaviours depending on how conformational exchange and substrate capture partition catalytic flux. It also explains how finite substrate windows can mask underlying bimodal behaviour. These results provide a physically interpretable framework linking conformational dynamics, pathway selection, and experimentally observed enzyme kinetics.
ER -