Murburn Bioenergetics and "Origins-Sustenance-Termination-Evolution of Life": Emergence of Intelligence from a Network of Molecules, Unbound Ions, Radicals and Radiations
The paradigm-shift idea of murburn concept is no hypothesis but developed directly from fundamental facts of cellular/ecological existence. Murburn involves spontaneous and stochastic interactions (mediated by murzymes) amongst the molecules and unbound ions of cells. It leads to effective charge separation (ECS) and formation/recruitment of diffusible reactive species (DRS, like radicals whose reactions enable ATP-synthesis and thermogenesis) and emission of radiations (UV/Vis to ELF). These processes also lead to a chemo-electromagnetic matrix (CEM), ascertaining that living cell/organism react/function as a coherent unit. Murburn concept propounds the true utility of oxygen: generating DRS (with catalytic and electrical properties) on the way to becoming water, the life solvent, and ultimately also leading to phase-based macroscopic homeostatic outcomes. Such a layout enables cells to become simple chemical engines (SCEs) with powering, coherence, homeostasis, electro-mechanical and sensing–response (PCHEMS; life’s short-term “intelligence”) abilities. In the current review, we discuss the coacervate nature of cells and dwell upon the ways and contexts in which various radiations (either incident or endogenously generated) could interact in the new scheme of cellular function. Presenting comparative evidence/arguments and listing of systems with murburn models, we argue that the new perceptions explain life processes better and urge the community to urgently adopt murburn bioenergetics and adapt to its views. Further, we touch upon some distinct scientific and sociological contexts with respect to the outreach of murburn concept. It is envisaged that greater awareness of murburn could enhance the longevity and quality of life and afford better approaches to therapies.
Keywords: mitochondria, murburn concept, coacervation, diffusible reactive (oxygen) species (DRS/DROS/ROS), coherence, origin of life, aging, cancer, bioenergetics
Do we have a fair grasp of the principles behind origins, sustenance, termination and evolution of life (OSTEoL) and how aging or degenerative diseases are based on them? Although we have come a significant way to understand life processes, there are many lacunae and misperceptions, particularly in bioenergetics, owing to which we cannot address causes, prophylaxis and therapy in a clear/holistic manner. This review presents a novel “murburn” bioenergetics framework that resolves prevailing confusions.
Research leading to murburn (“mured burning” or closed oxidative process) concept [1] disclosed the previously ignored, yet unavoidable, central physiological function of diffusible reactive (oxygen) species or DRS/DROS (which could be nitrogen or sulfur or hydrogen centered too in anaerobic systems; so DRS is a globally applicable acronym, with suitable derivations thereof!) at low concentrations, namely that of coupling factors in numerous redox processes, like oxidative-/photo-phosphorylation, leading to direct in fluid ATP-synthesis by exergonic radical reactions. (We emphasize the term “diffusible” and do not use ROS alone, to differentiate it from enzyme-bound ROS or BROS, such as Compound I of hemeproteins.) The formation of oxygen-centric DRS (anions/radicals) near proteins/membrane surfaces also leads to effective charge separation (ECS), serving as the origin of “cellular electrical activity”. The stochastic interactive chemical equilibriums of DRS with components in milieu (ADP, Pi and others) are characterized by an observable new type of stochastic, hormetic and idiosyncratic “outside the active site” mechanism/kinetics. In conjunction with coacervate organization, murburn could maintain discrete ion and solute differentials across “islets” of different phases without ion-pumping or deterministic electron transport chains (ETCs). Murburn-type reactions within pre-biotic coacervates afforded powering, coherence, homeostasis, electro-mechanical features and sensing/responding abilities (PCHEMS: the “instant” functions of life [1]), later supplemented and propagated by genetic means in cellular systems.
As murburn (with DRS-ECS as core physiology) and coacervation rooted cellular PCHEMS since life’s origin and continued to sustain it thereafter, normal aging, disease, evolution and termination must be understood within this framework (although these functions became later associated with complex membranes and central dogma’s “deterministic” exertion). Also, radiative emissions associated with DRS reactions and ECS currents are the primary actors in the build-up of the chemo-electromagnetic matrix (CEM, “cement-like binder of life”) that makes a living structure and its activities act as a single unit.
This write-up highlights diverse aspects of the murburn concept above [1], a fundamental revolution unraveled over the last decade, and discusses novel approaches for addressing various (patho)physiological scenarios, giving a new perspective on holistic organellar (e.g., mitochondrial) or cellular function.
The organelle/cellular membranes are seen as “sentient sentinels”, selectively pumping and transporting diverse molecules/ions in and out via high-throughput stoichiometric mechanisms [1]. Although the classical views recognize coacervation to be an important step in life’s origin, it is surprisingly neglected in theoretical models explaining various physiological processes. Since the early 20th century, the laws of dilute solutions, active-site (affinity-based selectivity/specificity) enzyme catalysis and protein-conformational changes have been used to explain key aspects of cellular functioning [1]. Central dogma describes the core information flow with genetic expression regulating proteins and their concentrations, which in turn deterministically control metabolic rates and cellular composition. Most importantly, cellular powering (which supports other crucial functions!) is thought to rely on the generation/maintenance of ion-gradients across the so-called “bioenergetic membranes”. Under the acclaimed schema, ATP is seen as the global bioenergetic currency whose hydrolysis enables cells to carry out otherwise unfavorable and vitally deterministic processes. Mitochondria and chloroplasts in eukaryotes (where ATP synthesis occurs) are accepted to have originated from prokaryote precursors by means of endosymbiosis [1].
Several aspects of this model remain puzzling. For instance: How could the primordial “pre-life” entity have the ability to control its inside as well as outside for maintaining trans-membrane potential (TMP; including proton-motive force or pmf) before such a complex membrane could have ever developed? How can contemporary cells continue to do so, even with a membrane? Why do we acutely need oxygen for life activities, if it only serves as a “terminal electron acceptor” (TEA)? If ROS are toxic, wasteful products of metabolism, why did the redox proteins not acquire structural features to minimize their production and how can a radical like nitric oxide serve as a systemic messenger? How could cells function as a single, whole, self-regulating unit at instant timescales (wherein genetic control cannot be exercised)? We attempt to answer such queries on OSTEoL (the basic skeletal scaffold of “perpetual life intelligence”) with the umbrella of ideas espoused under murburn concept.
Some salient aspects of life’s origins are discussed here for addressing its causality and continuum in time, from “pre-membrane-bound soups of yore” to “membrane-bound life systems of today”. In the anaerobic environment of the young Earth, CH4, NH3, HCN, H2O and H2S were probably the prominent molecular species to start the organic soup. Without DRS, there would have been no hydroxy, keto, carboxylic and amino acids, even under anaerobic conditions. The oxygen atoms in these acids were most probably incorporated via the generation of DRS from the solvent of life, water. This process was likely catalyzed by Fe3+/Fe2+ cycles (as testified by banded iron formations containing both ionic forms) and powered by UV-Vis light (the first photosynthesis). Unlike now, within a reducing environment, Fe2+ would have been the more stable form. During the day, photo-oxidation to Fe3+ would make conditions oxidative, whereas, during the night, they would be reducing [1]. Fe3+ can photoreact with water generating DROS and O2 [2], which continues because the downstream reactions are exothermic (resulting in thermodynamic pull; a feature of murburn!). This circadian iron cycle with alternating oxidative and reductive abilities might be the earliest precursor of catabolic–anabolic cycling, a fundamental hallmark of life [1]. These fundamental reactions (Box 1) via DRS enabled both of the components of the solvent (hydrogen and oxygen atoms) to participate in equilibriums (life’s processes!), forming the first type of auto-regulative logic with respect to chemico–physical transformations. The benefit of having oxygen (via DROS) as the oxidizer was the facilitated delivery of gaseous reactant and voiding of the gaseous product, CO2.
Further, it enabled the full redox window of ~1.2 V (approximately −400 to +800 mV) for conducting cellular redox processes, enabling the synthesis and functionalizing of diverse biomolecules and transition to an aerobic environment.
Thioesters were spontaneously formed in the initial phases, owing to the facile nature of the reaction from H2S; in which case, the intermediary is DRSS, sulfur-centered DRS [3]. In present-day metabolism thioesters (like acetyl-CoA) are still important intermediates, remnants of the early origin. DRSS could have played essential roles in early oligomerization processes [3]. In early nitrogen metabolism DRNS might have been involved (the molecular messenger of nitric oxide, NO, still is). At later times, when nucleobases, ribose and phosphate became available, ADP/ATP could have formed in situ from AMP via simple bimolecular reactions by sequential phosphorylations, like: AMP/ADP + Pi + DRS → ADP/ATP + H2O/H2O2 + heat [1]. They can be executed in vitro in a dense phase without enzymes or membranes, and in vivo indications ensure that this simple, versatile, highly advantageous mechanism has persisted [1,4]. The reactions given above are the primordial murburn-type processes leading to life and sustained to date!
From the “free-burning” activities in the early times, the reactions became milder and “mured”. Murburn activity generates/utilizes ECS and non-deterministic (probabilistic/stochastic) reaction chemistry through formation/utilization of DRS [1,4]. It is a tangible and viable purview for explaining real-time PCHEMS of cells, replacing the classical ETC and Mitchell’s proton-pump proposal.
The Mitchellian bioenergetic explanation requires the establishment of pmf using serial arrays of ETCs that are presumed to serve as proton pumps. Not just that, the classical model also requires Complex V to carry out “chemiosmotic rotational ATP-synthesis” (CRAS) through the sophisticated orchestration of both pmf generation and its harvest by “intelligent system coordinating multiple components spanning three phases” (Figure 1)! (This requires concerted working of dispersed proteins, leading to temporally staggered outcomes of building and dissipation of pmf. However, such coordinated outcomes and voltage fluctuations are not empirically observed!) Clearly, such explanations present “irreducibly-complex, speculative and gambit-logic” [1] that preclude step-wise evolutionary developments and have little basis in thermodynamics or reality. Quite simply, there was/is little scope for a cell to control its internal and external environments (both!) and manipulate it temporally/perpetually for generating/harvesting TMP/pmf by “electrogenic cation pumping” or avail some cyclic ion exchange logic [1,4]; all allegedly by a “highly intelligent” membrane!
When it is easily discernible that the cellular milieu is a complex colloid (evident by breaking open a bird’s egg!) and should be described by the laws of colloid physico-chemistry, cell physiologists have traditionally used Nernst’s laws for calculating ion gradients using the laws of “ideal” dilute solutions. This is when modern microscopy and spectroscopy provide ample support for the colloidal/complex nature of the cellular milieu [5,6,7].
The root cause of the longstanding mischaracterization of taking the cellular milieu as a solution goes back to the unrealistic extrapolations from a limited experiment by the influential Nobel Laureate Archibald Hill in 1930 [8]. He had found that the cell versus environment partition coefficient for urea was close to 1, implying that the cellular interior was just like the exterior! However, other substances such as D-mannitol (0.227) or sucrose (0.132) and over 25 others tested gave lower values, corroborating the coacervate nature of cells [5,6,7,9]. Schrödinger [10] had falsified Hill’s arbitration in an insurmountable way, stating that it would imply that the finest control life could have over its working then has a lower limit dictated by kT. Further, while cyanobacteria are aprotic, the mitochondrial matrix contains finger-countable protons [1,4,5] (Box 2)! How could such a system ever serve tens of thousands of redox complexes (proton pumps) in the cells/organelles? How could so few protons ever build a pmf able to energize ATP synthesis, when water hydrolysis requires >79 kJ/mol (for generating protons)? And how could Complex V synthesize ATP with a non-existent pmf via an esterification mechanism (fusing two negatively charged ionic species), overcoming a ΔG of +36 kJ/mol (Keq ~5 × 10−7), at high physiological ATP/ADP ratios on Walker sites (which have higher affinity for ATP and favor ATP hydrolysis over ATP synthesis by a factor of 108) [4,11]?
Small cyanobacterium → 10−16 L (non-adjusted for internal components) volume × 10−8 moles/L concentration of protons × 6.023 × 1023 protons/mole = ≤1
Average mitochondrion → 2 × 10−16 L (non-adjusted for internal components) volume × 5 × 10−8 moles/L concentration of protons × 6.023 × 1023 protons/mole = 6
Average bacterium → 4 × 10−16 L (non-adjusted for internal components) volume × 4 × 10−8 moles/L concentration of protons × 6.023 × 1023 protons/mole = 10
Average stroma of chloroplast → 3 × 10−17 L (adjusted volume, https://doi.org/10.1016/j.febslet.2013.05.046) × 5 × 10−7 moles/L concentration of protons × 6.023 × 1023 protons/mole = 9
Another error was an aesthetic/deterministic assumption by David Keilin [12], who had pioneered the characterization of cytochromes. The reasoning proposed that electron transport must be organized as a serial system (a chain) with oxygen serving as a terminal electron acceptor at cytochrome oxidase to prevent DROS formation. But the fact that DROS are formed at each of the redox complexes is testament to the reason that one-electron reduction of oxygen is very spontaneous (ΔG = −250 kJ/mol) and oxygen is highly mobile (capable of facile diffusion at the approximate value of ~102 Å/μs). Thus, intra/intermolecular deterministic e-transfers across several Angstroms would be unfeasible in micro- to milli- second timescales (as necessary for ETCs)! Simply put, the serial ETC lacks kinetic and probabilistic feasibility.
By 2018–2019, the untenable and redundant aspects of the classical “ETC–proton pump–pmf–CRAS” paradigm were conclusively pointed out via multiple analytical angles, with more than 30 incisive comparative arguments [4,13,14]. Further, after the in vitro in-fluid demonstration of ATP synthesis from its precursors using DRS [4], with dozens of predictive/comparative queries on available evidence [4], the murburn model was established as the well-substantiated model for oxidative phosphorylation [11,13,14,15,16]. Murburn energy metabolism allows for facile transitions from earlier anaerobic/prokaryotic systems to later aerobic/eukaryotic systems [1]. It obviates the cell/organelle to possess the ability to detect/control components inside/outside (for homeostasis and TMP/pmf) (Figure 2). Modern experimental research has conclusively shown that DRS are effectively formed at each of the respiratory redox complexes, their production rate is correlated with respiratory rate, an adequate O2 supply keeps DRS concentrations low, and DRS have beneficial effects at low concentrations [1,4,17]. In-fluid or interfacial synthesis of ATP (according to murburn bioenergetics) is facile, via exergonic bimolecular reactions. It makes redox complexes the essential ATP-synthases, for which there is detailed structural evidence. These proteins possess intra-protein small cavities, where redox centers can donate single electrons to O2 initially producing O2*− (and secondarily other diffusible reactive species). In conjunction with ADP-presenting sites pointed out on the various respiratory membrane protein complexes, these realities enable effective activation of phosphate groups on ADP/Pi [1,4,10,11]. All reactions going on there are exergonic (Box 3).
Even though we have brought out the fallibility of the ETC-CRAS model and highlighted the viability–tangibility of the murburn explanation via multiple modalities through many publications over the last 8 years, the researchers in the field remain glued to the acclaimed proton-centric idea, disregarding the crucial importance of oxygen. Therefore, to take things beyond reasonable doubt, we present irrefutable evidence/arguments via the three perspectives of: experimental findings (Table 1; which also includes the last six points as the observations misinterpreted to support ETC-CRAS!), structural features (Table 2) and theoretical considerations (Table 3).
Via the three tables above (comparing dozens of agendas), it can be seen that not in a single criterion of comparison (other than aesthetic disposition and the community’s inertia!) does the murburn model fare worse than ETC-CRAS, which should be considered a refuted hypothesis now.
By being a stochastic mechanism [11,13,14,18], non-integral and variable kinetics is a hallmark of murburn reactions, as observed in physiology.
ECS-coupled anionic DRS formation occurs at the redox centers such as d or pi-electron-containing cofactor systems like metals or flavins/retinoids (or both, like hemes) [1,4,18]. Thus, murburn concept is the primary rationale for electrical activity in cells. Even the activity of Na,K-ATPase is explained with DRS [19].
In the murburn model, metabolic reactions work in parallel (deterministic series/chains are not mandated!) [4,16].
They essentially abide by simple thermodynamic principles and pose minimal affinity-based requirements, offering a significant evolutionary advantage [1].
As the presence of substrate exerts a thermodynamic pull, constitutional wastage of redox equivalents and collateral damage are minimized.
The micro-dimensioned life forms were primordial owing to the necessity to curtail the free availability of protons for oxygenic systems to evolve subsequently.
The evolution of Complex V is seen primarily as a pH-chemostat regulating murburn reactions at redox centers through proton supply, and an enhancer of ATP yields by serving as auxiliary murzyme (consuming H+; not recycling it!) at high respiratory rates [11].