Network representation and analysis of energy coupling mechanisms in cellular metabolism by a graph-theoretical approach

Abstract

Mechanisms coupling the chemical reactions of oxidation and ATP synthesis in cellular metabolism by the fundamental biological process of oxidative phosphorylation (OX PHOS) in mitochondria provide > 90% of the energy requirements in living organisms. Mathematical graph theory methods have been extensively used to characterize various metabolic, regulatory, and disease networks in biology. However, networks of energy coupling mechanisms in OX PHOS have not been represented and analyzed previously by these approaches. Here, the problem of biological energy coupling is translated into a graph-theoretical framework, and all possible coupling schemes between oxidation and ATP synthesis are represented as graphs connecting these processes by various intermediates or states. The problem is shown to be transformed into the hard problem of finding a Hamiltonian tour in the networks of possible constituent mechanisms, given the constraints of a cyclical nature of operation of enzymes and biological molecular machines. Accessible mathematical proofs of three theorems that guarantee sufficient conditions for the existence of a Hamiltonian cycle in simple graphs are provided. The results of the general theorems are applied to the set of possible coupling mechanisms in OX PHOS and shown to (1) unequivocally differentiate between the major theories and mechanisms of energy coupling, (2) greatly reduce the possibilities for detailed consideration, and (3) deduce the biologically selected mechanism using additional constraints from the cumulative experimental record. Finally, an algorithm is constructed to implement the graph-theoretical procedure. In summary, the enormous power and generality of mathematical theorems and approaches in graph theory are shown to help solve a fundamental problem in biology.

Keywords: ATP synthesis; Algorithms; Bioenergetics; Bondy–Chvátal theorem; Cell metabolism; Closure; Coupling mechanisms; Dirac’s theorem; Energy coupling; F O F 1-ATP synthase; Graph theory; Graphs; Hamiltonian cycles; Mathematical biology; Metabolic regulation and control; Mitchell’s chemiosmotic theory; Molecular motors; Nath’s torsional mechanism of energy transduction and ATP synthesis; Nath’s two-ion theory of energy coupling and ATP synthesis; Networks; Ore’s theorem; Oxidative phosphorylation (OX PHOS); Sufficient conditions for Hamiltonian circuits; Traveling Salesman Problem.