Interaction of membrane-embedded cytochrome b-complexes with quinols: Classical Q-cycle and murburn model

Murburn posttranslational modifications of proteins: Cellular redox processes and murzyme-mediated metabolo-proteomics

Murburn concept constitutes the thesis that diffusible reactive species or DRS are obligatorily involved in routine metabolic and physiological activities. Murzymes are defined as biomolecules/proteins that generate/modulate/sustain/utilize DRS. Murburn posttranslational modifications (PTMs) result because murburn/murzyme functionalism is integral to cellular existence. Cells must incorporate the inherently stochastic nature of operations mediated by DRS. Due to the earlier/inertial stigmatic perception that DRS are mere agents of chaos, several such outcomes were either understood as deterministic modulations sponsored by house-keeping enzymes or deemed as unregulated nonenzymatic events resulting out of "oxidative stress". In the current review, I dispel the myths around DRS-functions, and undertake systematic parsing and analyses of murburn modifications of proteins. Although it is impossible to demarcate all PTMs into the classical or murburn modalities, telltale signs of the latter are evident from the relative inaccessibility of the locus, non-specificities and mechanistic details. It is pointed out that while many murburn PTMs may be harmless, some others could have deleterious or beneficial physiological implications. Some details of reversible/irreversible modifications of amino acid residues and cofactors that may be subjected to phosphorylation, halogenation, glycosylation, alkylation/acetylation, hydroxylation/oxidation, etc. are listed, along with citations of select proteins where such modifications have been reported. The contexts of these modifications and their significance in (patho)physiology/aging and therapy are also presented. With more balanced explorations and statistically verified data, a definitive understanding of normal versus pathological contexts of murburn modifications would be obtainable in the future.

Questioning rotary functionality in the bacterial flagellar system and proposing a murburn model for motility

Bacterial flagellar system (BFS) was the primary example of a purported 'rotary-motor' functionality in a natural assembly. This mandates the translation of a circular motion of components inside into a linear displacement of the cell body outside, which is supposedly orchestrated with the following features of the BFS: (i) A chemical/electrical differential generates proton motive force (pmf, including a trans-membrane potential, TMP), which is electro-mechanically transduced by inward movement of protons via BFS. (ii) Membrane-bound proteins of BFS serve as stators and the slender filament acts as an external propeller, culminating into a hook-rod that pierces the membrane to connect to a 'broader assembly of deterministically movable rotor'. We had disclaimed the purported pmf/TMP-based respiratory/photosynthetic physiology involving Complex V, which was also perceived as a 'rotary machine' earlier. We pointed out that the murburn redox logic was operative therein. We pursue the following similar perspectives in BFS-context: (i) Low probability for the evolutionary attainment of an ordered/synchronized teaming of about two dozen types of proteins (assembled across five-seven distinct phases) towards the singular agendum of rotary motility. (ii) Vital redox activity (not the gambit of pmf/TMP!) powers the molecular and macroscopic activities of cells, including flagella. (iii) Flagellar movement is noted even in ambiances lacking/countering the directionality mandates sought by pmf/TMP. (iv) Structural features of BFS lack component(s) capable of harnessing/achieving pmf/TMP and functional rotation. A viable murburn model for conversion of molecular/biochemical activity into macroscopic/mechanical outcomes is proposed herein for understanding BFS-assisted motility. HIGHLIGHTSThe motor-like functionalism of bacterial flagellar system (BFS) is analyzedProton/Ion-differential based powering of BFS is unviable in bacteriaUncouplers-sponsored effects were misinterpreted, resulting in a detour in BFS researchThese findings mandate new explanation for nano-bio-mechanical movements in BFSA minimalist murburn model for the bacterial flagella-aided movement is proposedCommunicated by Ramaswamy H. Sarma.

Comprehensive Analyses of the Enhancement of Oxygenesis in Photosynthesis by Bicarbonate and Effects of Diverse Additives: Z-scheme Explanation Versus Murburn Model

The Z-scheme electron transport chain (ETC) explanation for photosynthesis starts with the serial/sequential transfer of electrons sourced from water molecules bound at Photosystem II via a deterministic array of redox centers (of various stationary/mobile proteins), before \"sinking\" via the reduction of NADP+ bound at flavin-enzyme reductase. Several research groups’ finding that additives (like bicarbonate) enhance the light reaction had divided the research community because it violated the Z-scheme. The untenable aspects of the Z-scheme perception were demonstrated earlier and a murburn bioenergetics (a stochastic/parallel paradigm of ion-radical equilibriums) model was proposed to explain photophosphorylation and Emerson effect. Herein, we further support the murburn model with accurate thermodynamic calculations, which show that the cost of one-electron abstraction from bicarbonate [491 kJ/mol] is lower than water [527 kJ/mol]. Further, copious thioredoxin enables the capture of photoactivated electrons in milieu, which aid in the reduction of nicotinamide nucleotides. The diffusible reactive species (DRS) generated in milieu sponsor phosphorylations and oxygenic reactions. With structural analysis of Photosystems and interacting molecules, we chart out the equations of reactions that explain the loss of labeled O-atom traces in delocalized oxygenesis. Thus, this essay discredits the Z-scheme and explains key outstanding observations in the field.

Structural foundations for explaining the physiological roles of murzymes embedded in diverse phospholipid membranes

The advent of improved structural biology protocols and bioinformatics methodologies have provided paradigm-shifting insights on metabolic or physiological processes catalyzed by homo-/hetero- proteins (super)complexes embedded in phospholipid membranes of cells/organelles. In this panoramic review, we succinctly elucidate the structural features of select redox proteins from four systems: hepatocyte/adrenal cortex endoplasmic reticulum (microsomes), inner mitochondrial membrane (cristae), thylakoid membrane (grana), and in the flattened disks of rod/cone cells (in retina). Besides catalyzing fast/crucial (photo)chemical reactions, these proteins utilize the redox-active diatomic gaseous molecule of oxygen, the elixir of aerobic life. Quite contrary to extant perceptions that invoke primarily deterministic affinity-binding or conformation-change based "proton-pump"/"serial electron-relay" type roles, we advocate murzyme functions for the membrane-embedded proteins in these systems. Murzymes are proteins that generate/stabilize/utilize diffusible reactive (oxygen) species (DRS/DROS) based activities. Herein, we present a brief compendium of the recently revealed wealth of structural information and mechanistic concepts on how the membrane proteins use DRS/DROS to aid 'effective charge separation' and facilitate trans-membrane dynamics of diverse species in milieu, thereby enabling the cells to function as 'simple chemical engines'.

Murburn model of vision: Precepts and proof of concept

The classical paradigm of visual physiology comprises of the following features: (i) rod/cone cells located at the rear end of the retina serve as the primary transducers of incoming photo-information, (ii) cis-trans retinal (C₂₀ H₂₈ O) transformations on rhodopsin act as the transduction switch to generate a transmittable signal, (iii) signal amplification occurs via GDP-GTP exchange at transducin, and (iv) the amplified signal is relayed (as an action potential) as a flux-based ripple of Na-K ions along the axons of neurons. Fundamental physical principles, chemical kinetics, and awareness of architecture of eye/retina prompt a questioning of these classical assumptions. In lieu, based on experimental and in silico findings, a simple space-time resolved murburn model for the physiology of phototransduction in the retina is presented wherein molecular oxygen plays key roles. It is advocated that: (a) photo-induced oxygen to superoxide conversion serves as the key step in signal transduction in the visual cycle, (b) all photoactive cells of the retina serve as photoreceptors and rods/cones serve as the ultimate electron source in the retina (deriving oxygen and nutrients from retinal pigmented epithelium), (c) signal amplification is through superoxide mediated phosphorylation of GDP bound to inactive transducin, thereby activating a GDP-based cascade (a new mechanism for trimeric G-proteins), and (d) signal relay is primarily an electron movement along the neuron, from dendritic source to synaptic sink. In particular, we specify the roles for the various modules of transducin and GDP-based activation of phosphodiesterase-6 in the physiology of visual transduction.