[Paper Review] Unveiling ADP-binding sites and channels in respiratory complexes: Validation of Murburn concept as a holistic explanation for oxidative phosphorylation

Kelath Murali Manoj, Abhinav Parashar|arXiv (Cornell University)|Jun 6, 2018

Mitochondrial Function and Pathology114 references16 citations

TL;DR

This paper proposes the 'murburn concept' as a holistic explanation for mitochondrial oxidative phosphorylation, positing that diffusible reactive oxygen species (DROS) in the mitochondrial matrix act as chemical coupling agents linking NADH oxidation to ATP synthesis, rather than a proton gradient. Using structural and computational analyses, the authors identify multiple ADP-binding sites and solvent-accessible DROS channels in respiratory complexes, validating the murburn mechanism and challenging the classical chemiosmotic theory.

ABSTRACT

Mitochondrial oxidative phosphorylation (mOxPhos) makes ATP, the energy currency of life. Chemiosmosis, a proton centric mechanism, advocates that Complex V harnesses a transmembrane potential (TMP) for ATP synthesis. This perception of cellular respiration requires oxygen to stay tethered at Complex IV (an association inhibited by cyanide) and diffusible reactive oxygen species (DROS) are considered wasteful and toxic products. With new mechanistic insights on heme and flavin enzymes, an oxygen or DROS centric explanation (called murburn concept) was recently proposed for mOxPhos. In the new mechanism, TMP is not directly harnessed, protons are a rate limiting reactant and DROS within matrix serve as the chemical coupling agents that directly link NADH oxidation with ATP synthesis. Herein, we report multiple ADP binding sites and solvent accessible DROS channels in respiratory proteins, which validate the oxygen or DROS centric power generation (ATP synthesis) system in mOxPhos. Since cyanide's heme binding Kd is high (mM), low doses (uM) of cyanide is lethal because cyanide disrupts DROS dynamics in mOxPhos. The critical study also provides comprehensive arguments against Mitchell's and Boyer's explanations and extensive support for murburn concept based holistic perspectives for mOxPhos.

Motivation & Objective

• To challenge the classical chemiosmotic theory of oxidative phosphorylation, which relies on proton gradients for ATP synthesis.
• To investigate whether diffusible reactive oxygen species (DROS) serve as direct chemical coupling agents in ATP production.
• To identify and characterize ADP-binding sites and DROS-accessible channels in respiratory chain complexes.
• To provide structural and mechanistic evidence supporting the murburn concept as a holistic explanation for mOxPhos.
• To explain the high toxicity of low-dose cyanide in terms of disruption of DROS dynamics rather than simple inhibition of Complex IV.

Proposed method

• High-resolution structural analysis of respiratory chain complexes (I–IV) to identify potential ADP-binding sites.
• Molecular dynamics and solvent accessibility simulations to map pathways for DROS diffusion within mitochondrial respiratory complexes.
• Biochemical and thermodynamic analysis of cyanide binding to heme in Complex IV, focusing on dissociation constants (Kd) in the millimolar range.
• Comparative analysis of the murburn concept against Mitchell’s chemiosmotic theory and Boyer’s binding change mechanism.
• Use of computational modeling to assess proton movement and DROS dynamics in the mitochondrial matrix.
• Integration of structural, kinetic, and thermodynamic data to support a non-proton-gradient-dependent ATP synthesis mechanism.

Experimental results

Research questions

• RQ1 Do multiple ADP-binding sites exist within respiratory complexes, and are they functionally relevant for ATP synthesis?
• RQ2 Are there solvent-accessible channels that allow the diffusion of diffusible reactive oxygen species (DROS) within the mitochondrial respiratory chain?
• RQ3 Can the murburn concept—where DROS act as chemical coupling agents—provide a more coherent explanation for oxidative phosphorylation than the chemiosmotic theory?
• RQ4 Why is low-dose cyanide lethal despite its high Kd for heme binding in Complex IV?
• RQ5 How does the disruption of DROS dynamics explain the cytotoxicity of cyanide, independent of direct Complex IV inhibition?

Key findings

• Multiple ADP-binding sites were identified in respiratory complexes I, III, and IV, suggesting direct involvement in ATP synthesis.
• Solvent-accessible channels for DROS were mapped in respiratory complexes, enabling their diffusion through the mitochondrial matrix.
• Cyanide’s high Kd (mM) for heme binding explains why low-dose (μM) cyanide is lethal—due to disruption of DROS dynamics rather than direct inhibition.
• The murburn concept provides a more coherent and holistic explanation for oxidative phosphorylation than the classical chemiosmotic theory.
• Structural and kinetic evidence contradicts the necessity of a transmembrane proton gradient for ATP synthesis, supporting a DROS-mediated coupling mechanism.
• The study presents extensive arguments against Mitchell’s and Boyer’s models, emphasizing the role of reactive oxygen species as functional mediators in energy transduction.