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Manoj KM. Murburn posttranslational modifications of proteins: Cellular redox processes and murzyme-mediated metabolo-proteomics. J Cell Physiol 2024; 239:e30954. [PMID: 36716112 DOI: 10.1002/jcp.30954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 01/31/2023]
Abstract
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.
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Nguyen TM, Jang WB, Lee Y, Kim YH, Lim HJ, Lee EJ, Nguyen TMT, Choi EJ, Kwon SM, Oh JW. Non-intrusive quality appraisal of differentiation-induced cardiovascular stem cells using E-Nose sensor technology. Biosens Bioelectron 2024; 246:115838. [PMID: 38042052 DOI: 10.1016/j.bios.2023.115838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/23/2023] [Accepted: 11/11/2023] [Indexed: 12/04/2023]
Abstract
Stem cell technology holds immense potential for revolutionizing medicine, particularly in regenerative treatment for heart disease. The unique capacity of stem cells to differentiate into diverse cell types offers promise in repairing damaged tissues and implanting organs. Ensuring the quality of differentiated cells, essential for specific functions, demands in-depth analysis. However, this process consumes time and incurs substantial costs while invasive methods may alter stem cell features during differentiation and deplete cell numbers. To address these challenges, we propose a non-invasive strategy, using cellular respiration, to assess the quality of differentiation-induced stem cells, notably cardiovascular stem cells. This evaluation employs an electronic nose (E-Nose) and neural pattern separation (NPS). Our goal is to assess differentiation-induced cardiac stem cells (DICs) quality through E-Nose data analysis and compare it with standard commercial human cells (SCHCs). Sensitivity and specificity were evaluated by interacting SCHCs and DICs with the E-Nose, achieving over 90% classification accuracy. Employing selective combinations optimized by NPS, E-Nose successfully classified all six cell types. Consequently, the relative similarity among DICs like cardiomyocytes, endothelial cells with SCHCs was established relied on comparing response data from the E-Nose sensor without resorting to complex evaluations.
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Affiliation(s)
- Thanh Mien Nguyen
- Bio-IT Fusion Technology Research Institute, Pusan National University, Busan, 46241, Republic of Korea
| | - Woong Bi Jang
- Laboratory for Vascular Medicine and Stem Cell Biology, Department of Physiology, Medical Research Institute, School of Medicine, Pusan National University, Yangsan, 50612, Republic of Korea; Convergence Stem Cell Research Center, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Yujin Lee
- Department of Nano Fusion Technology, Pusan National University, Busan, 46214, Republic of Korea
| | - You Hwan Kim
- Department of Nano Fusion Technology, Pusan National University, Busan, 46214, Republic of Korea
| | - Hye Ji Lim
- Laboratory for Vascular Medicine and Stem Cell Biology, Department of Physiology, Medical Research Institute, School of Medicine, Pusan National University, Yangsan, 50612, Republic of Korea; Convergence Stem Cell Research Center, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Eun Ji Lee
- Laboratory for Vascular Medicine and Stem Cell Biology, Department of Physiology, Medical Research Institute, School of Medicine, Pusan National University, Yangsan, 50612, Republic of Korea; Convergence Stem Cell Research Center, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Thu M T Nguyen
- Department of Nano Fusion Technology, Pusan National University, Busan, 46214, Republic of Korea
| | - Eun-Jung Choi
- Bio-IT Fusion Technology Research Institute, Pusan National University, Busan, 46241, Republic of Korea.
| | - Sang-Mo Kwon
- Laboratory for Vascular Medicine and Stem Cell Biology, Department of Physiology, Medical Research Institute, School of Medicine, Pusan National University, Yangsan, 50612, Republic of Korea; Convergence Stem Cell Research Center, Pusan National University, Yangsan, 50612, Republic of Korea.
| | - Jin-Woo Oh
- Bio-IT Fusion Technology Research Institute, Pusan National University, Busan, 46241, Republic of Korea; Department of Nano Fusion Technology, Pusan National University, Busan, 46214, Republic of Korea.
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Adar O, Hollander A, Ilan Y. The Constrained Disorder Principle Accounts for the Variability That Characterizes Breathing: A Method for Treating Chronic Respiratory Diseases and Improving Mechanical Ventilation. Adv Respir Med 2023; 91:350-367. [PMID: 37736974 PMCID: PMC10514877 DOI: 10.3390/arm91050028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023]
Abstract
Variability characterizes breathing, cellular respiration, and the underlying quantum effects. Variability serves as a mechanism for coping with changing environments; however, this hypothesis does not explain why many of the variable phenomena of respiration manifest randomness. According to the constrained disorder principle (CDP), living organisms are defined by their inherent disorder bounded by variable boundaries. The present paper describes the mechanisms of breathing and cellular respiration, focusing on their inherent variability. It defines how the CDP accounts for the variability and randomness in breathing and respiration. It also provides a scheme for the potential role of respiration variability in the energy balance in biological systems. The paper describes the option of using CDP-based artificial intelligence platforms to augment the respiratory process's efficiency, correct malfunctions, and treat disorders associated with the respiratory system.
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Affiliation(s)
- Ofek Adar
- Faculty of Medicine, Hebrew University, Jerusalem P.O. Box 1200, Israel; (O.A.); (A.H.)
- Department of Medicine, Hadassah Medical Center, Jerusalem P.O. Box 1200, Israel
| | - Adi Hollander
- Faculty of Medicine, Hebrew University, Jerusalem P.O. Box 1200, Israel; (O.A.); (A.H.)
- Department of Medicine, Hadassah Medical Center, Jerusalem P.O. Box 1200, Israel
| | - Yaron Ilan
- Faculty of Medicine, Hebrew University, Jerusalem P.O. Box 1200, Israel; (O.A.); (A.H.)
- Department of Medicine, Hadassah Medical Center, Jerusalem P.O. Box 1200, Israel
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Saleem A, Zulfiqar A, Saleem MZ, Ali B, Saleem MH, Ali S, Tufekci ED, Tufekci AR, Rahimi M, Mostafa RM. Alkaline and acidic soil constraints on iron accumulation by Rice cultivars in relation to several physio-biochemical parameters. BMC PLANT BIOLOGY 2023; 23:397. [PMID: 37596537 PMCID: PMC10439600 DOI: 10.1186/s12870-023-04400-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/03/2023] [Indexed: 08/20/2023]
Abstract
Agricultural production is severely limited by an iron deficiency. Alkaline soils increase iron deficiency in rice crops, consequently leading to nutrient deficiencies in humans. Adding iron to rice enhances both its elemental composition and the nutritional value it offers humans through the food chain. The purpose of the current pot experiment was to investigate the impact of Fe treatment in alkaline (pH 7.5) and acidic (pH 5.5) soils to introduce iron-rich rice. Iron was applied to the plants in the soil in the form of an aqueous solution of FeSO4 with five different concentrations (100, 200, 300, 400, and 500 mM). The results obtained from the current study demonstrated a significant increase in Fe content in Oryza sativa with the application of iron in both alkaline and acidic pH soils. Specifically, Basmati-515, one of the rice cultivars tested, exhibited a notable 13% increase in iron total accumulation per plant and an 11% increase in root-to-shoot ratio in acidic soil. In contrast to Basmati-198, which demonstrated maximum response in alkaline soil, Basmati-515 exhibited notable increases in all parameters, including a 31% increase in dry weight, 16% increase in total chlorophyll content, an 11% increase in CAT (catalase) activity, 7% increase in APX (ascorbate peroxidase) activity, 26% increase in POD (peroxidase) activity, and a remarkable 92% increase in SOD (superoxide dismutase) in acidic soil. In alkaline soil, Basmati-198 exhibited respective decreases of 40% and 39% in MDA and H2O2 content, whereas Basmati-515 demonstrated a more significant decrease of 50% and 67% in MDA and H2O2 in acidic soil. These results emphasize the potential for targeted soil management strategies to improve iron nutrition and address iron deficiency in agricultural systems. By considering soil conditions, it is possible to enhance iron content and promote its availability in alkaline and acidic soils, ultimately contributing to improved crop nutrition and human health.
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Affiliation(s)
- Ammara Saleem
- Institute of Botany, University of the Punjab Lahore, Lahore, 54590, Pakistan
| | - Asma Zulfiqar
- Institute of Botany, University of the Punjab Lahore, Lahore, 54590, Pakistan.
| | - Muhammad Zafar Saleem
- Centre for Applied Molecular Biology, University of the Punjab Lahore, Lahore, 54590, Pakistan
| | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Hamzah Saleem
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shafaqat Ali
- Department of Environmental Sciences and Engineering, Government College University, Faisalabad, 38040, Pakistan
- Department of Biological Sciences and Technology, China Medical University (CMU), Taichung City, 40402, Taiwan
| | - Ebru Derelli Tufekci
- Food and Agriculture Vocational School, Department of Field Crops, Cankiri Karatekin Universitesi, 18100, Cankiri, Turkey
| | - Ali Rıza Tufekci
- Faculty of Science, Department of Chemistry, Cankiri Karatekin Universitesi, Cankiri18100, Turkey
| | - Mehdi Rahimi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
| | - Reham M Mostafa
- Department of Botany and Microbiology, Faculty of Science, Benha University, Benha, 13518, Egypt
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Manoj KM, Jacob VD, Kavdia M, Tamagawa H, Jaeken L, Soman V. Questioning rotary functionality in the bacterial flagellar system and proposing a murburn model for motility. J Biomol Struct Dyn 2023; 41:15691-15714. [PMID: 36970840 DOI: 10.1080/07391102.2023.2191146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/09/2023] [Indexed: 03/29/2023]
Abstract
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.
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Affiliation(s)
- Kelath Murali Manoj
- Satyamjayatu, The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Vivian David Jacob
- Satyamjayatu, The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Mahendra Kavdia
- Department of Biomedical Engineering, Wayne State University, Detroit, Michigan, USA
| | - Hirohisa Tamagawa
- Department of Mechanical Engineering, Gifu University, Gifu City, Japan
| | - Laurent Jaeken
- Department of Industrial Sciences and Technology, Karel de Grote-Hogeschool, Antwerp University Association, Belgium
| | - Vidhu Soman
- Department of Bioscience & Bioengineering, IIT Bombay (& DSS Imagetech Pvt. Ltd), Mumbai, Maharashtra, India
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Manoj KM, Gideon DA, Parashar A, Nirusimhan V, Annadurai P, Jacob VD, Manekkathodi A. Validating the predictions of murburn model for oxygenic photosynthesis: Analyses of ligand-binding to protein complexes and cross-system comparisons. J Biomol Struct Dyn 2022; 40:11024-11056. [PMID: 34328391 DOI: 10.1080/07391102.2021.1953607] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this second half of our treatise on oxygenic photosynthesis, we provide support for the murburn model of the light reaction of photosynthesis and ratify key predictions made in the first part. Molecular docking and visualization of various ligands of quinones/quinols (and their derivatives) with PS II/Cytochrome b6f complexes did not support chartered 2e-transport role of quinols. A broad variety of herbicides did not show any affinity/binding-based rationales for inhibition of photosynthesis. We substantiate the proposal that disubstituted phenolics (perceived as protonophores/uncouplers or affinity-based inhibitors in the classical purview) serve as interfacial modulators of diffusible reactive (oxygen) species or DR(O)S. The DRS-based murburn model is evidenced by the identification of multiple ADP-binding sites on the extra-membraneous projection of protein complexes and structure/distribution of the photo/redox catalysts. With a panoramic comparison of the redox metabolic machinery across diverse organellar/cellular systems, we highlight the ubiquitous one-electron murburn facets (cofactors of porphyrin, flavin, FeS, other metal centers and photo/redox active pigments) that enable a facile harnessing of the utility of DRS. In the summative analyses, it is demonstrated that the murburn model of light reaction explains the structures of membrane supercomplexes recently observed in thylakoids and also accounts for several photodynamic experimental observations and evolutionary considerations. In toto, the work provides a new orientation and impetus to photosynthesis research. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kelath Murali Manoj
- RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Daniel Andrew Gideon
- RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Abhinav Parashar
- RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Vijay Nirusimhan
- RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Pushparaj Annadurai
- RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Vivian David Jacob
- RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Afsal Manekkathodi
- RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India
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Manoj KM, Bazhin NM, Jacob VD, Parashar A, Gideon DA, Manekkathodi A. Structure-function correlations and system dynamics in oxygenic photosynthesis: classical perspectives and murburn precepts. J Biomol Struct Dyn 2022; 40:10997-11023. [PMID: 34323659 DOI: 10.1080/07391102.2021.1953606] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
HIGHLIGHTS Contemporary beliefs on oxygenic photosynthesis are critiqued.Murburn model is suggested as an alternative explanation.In the new model, diffusible reactive species are the main protagonists.All pigments are deemed photo-redox active in the new stochastic mechanism.NADPH synthesis occurs via simple electron transfers, not via elaborate ETC.Oxygenesis is delocalized and not just centered at Mn-Complex.Energetics of murburn proposal for photophosphorylation is provided.The proposal ushers in a paradigm shift in photosynthesis research.
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Affiliation(s)
| | | | - Vivian David Jacob
- Satyamjayatu: The Science & Ethics Foundation, Kulappully, Kerala, India
| | - Abhinav Parashar
- Satyamjayatu: The Science & Ethics Foundation, Kulappully, Kerala, India
| | | | - Afsal Manekkathodi
- Satyamjayatu: The Science & Ethics Foundation, Kulappully, Kerala, India
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Murali Manoj K, Bazhin N, Parashar A, Manekkathodi A, Wu Y. Comprehensive Analyses of the Enhancement of Oxygenesis in Photosynthesis by Bicarbonate and Effects of Diverse Additives: Z-scheme Explanation Versus Murburn Model. Physiology (Bethesda) 2022. [DOI: 10.5772/intechopen.106996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
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.
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Manoj KM, Gideon DA. Structural foundations for explaining the physiological roles of murzymes embedded in diverse phospholipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183981. [PMID: 35690100 DOI: 10.1016/j.bbamem.2022.183981] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
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'.
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Affiliation(s)
- Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation, Snehatheeram, Shoranur-2 (PO), Kerala 679122, India.
| | - Daniel Andrew Gideon
- Satyamjayatu: The Science & Ethics Foundation, Snehatheeram, Shoranur-2 (PO), Kerala 679122, India.
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Manoj KM, Bazhin NM, Tamagawa H, Jaeken L, Parashar A. The physiological role of complex V in ATP synthesis: Murzyme functioning is viable whereas rotary conformation change model is untenable. J Biomol Struct Dyn 2022; 41:3993-4012. [PMID: 35394896 DOI: 10.1080/07391102.2022.2060307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Complex V or FoF1-ATPase is a multimeric protein found in bioenergetic membranes of cells and organelles like mitochondria/chloroplasts. The popular perception on Complex V deems it as a reversible molecular motor, working bi-directionally (breaking or making ATP) via a conformation-change based chemiosmotic rotary ATP synthesis (CRAS) mechanism, driven by proton-gradients or trans-membrane potential (TMP). In continuance of our pursuits against the CRAS model of cellular bioenergetics, herein we demonstrate the validity of the murburn model based in diffusible reactive (oxygen) species (DRS/DROS). Supported by new in silico derived data (that there are ∼12 adenosine nucleotide binding sites on the F1 bulb and not merely 3 sites, as perceived earlier), available structural information, known experimental observations, and thermodynamic/kinetic considerations (that de-solvation of protons from hydronium ions is facile), we deduce that Complex V serves as a physiological chemostat and a murzyme (enzyme working via murburn scheme, employing DRS). That is- Complex V uses ATP (via consumption at ε or proteins of F1 module) as a Michaelis-Menten substrate to serve as a pH-stat by inletting protons via the c-ring of Fo module. Physiologically, Complex V also functions as a murzyme by presenting ADP/Pi (or their reaction intermediates) on the αβ bulb, thereby enabling greater opportunities for DRS/proton-assisted ATP formation. Thus, the murburn paradigm succeeds the CRAS hypothesis for explaining the role of oxygen in mitochondrial physiologies of oxidative phosphorylation, thermogenesis, TMP and homeostasis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kelath Murali Manoj
- Biochemistry Department, Satyamjayatu: The Science & Ethics Foundation, Palakkad, Kerala, India
| | - Nikolai Mikhailovich Bazhin
- Environmental Chemistry Department, Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Laurent Jaeken
- Industrial Sciences and Technology, Karel de Grote University College, Antwerp University Association, Hoboken, Belgium
| | - Abhinav Parashar
- Biochemistry Department, Satyamjayatu: The Science & Ethics Foundation, Palakkad, Kerala, India
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Manoj KM, Gideon DA, Jaeken L. Interaction of membrane-embedded cytochrome b-complexes with quinols: Classical Q-cycle and murburn model. Cell Biochem Funct 2022; 40:118-126. [PMID: 35026863 DOI: 10.1002/cbf.3682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 01/07/2023]
Abstract
We recently proposed a diffusible reactive (oxygen) species (DRS/DROS) based function for cytochrome b complexes (CBC) and quinones (Q)/quinols (QH2 ) in the murburn model of bioenergetics. This proposal is in direct conflict with the classical purview of Q-cycle. Via extensive analyses of the structure-function correlations of membrane-quinones/quinols and proteins, we present qualitative and quantitative arguments to infer that the classical model cannot explain the energetics, kinetics, mechanism and probabilistic considerations. Therefore, it is proposed that Q-cycle is neither necessary nor feasible at CBCs. In contrast, we substantiate that the murburn model explains: (a) crucial structural data of CBCs, (b) why quinones/quinols are utilized in bioenergetic membranes, (c) how trans-membrane potential is generated owing to effective charge separation at CBCs, (d) mobility data of O2 , DRS, Q/QH2 , and (e) utility of other reaction/membrane components. Further, the murburn model also accommodates the absence of quinones in anaerobic Archaea, wherein methanophenazines are prevalent. The work mandates that the textbooks and research agendas are refreshed to reflect the new perception. SIGNIFICANCE: The current article must be seen as a critical and detailed analysis of the role and working mechanism of quinone (Q) /quinols (QH2 ) in bioenergetic membranes. In the classical model, QH2 are perceived as highly mobile electron-transport agents that bind and donate electrons to cytochrome b complexes (CBCs), using sophisticated electronic circuitries, in order to recycle Q and pump protons. The classical perception sees radicals (such as Q*-, O2 *-, etc., also called diffusible reactive species, DRS) as wasteful or toxic (patho) physiological manifestations. It is highlighted herein that QH2 has low mobility and matrix has little protons to pump. New insights from the structural analyses of diverse CBCs and quinols, in conjunction with murburn reaction thermodynamics suggest that the electrons from substrates/quinols are effectively utilized via DRS. This perception fits into a much broader analysis of 1 and 2 electron transfers in overall redox metabolism, as recently brought out by the murburn model, wherein DRS are considered obligatory ingredients of physiology. Thus, the findings mandate a reorientation in the pertinent research field.
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Affiliation(s)
- Kelath Murali Manoj
- Biochemistry, Satyamjayatu: The Science & Ethics Foundation, Palakkad, India
| | | | - Laurent Jaeken
- Karel de Grote University College, Antwerp University Association, Campus Hoboken, Hoboken, Belgium
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Manoj KM, Nirusimhan V, Parashar A, Edward J, Gideon DA. Murburn precepts for lactic-acidosis, Cori cycle, and Warburg effect: Interactive dynamics of dehydrogenases, protons, and oxygen. J Cell Physiol 2021; 237:1902-1922. [PMID: 34927737 DOI: 10.1002/jcp.30661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 12/24/2022]
Abstract
It is unresolved why lactate is transported to the liver for further utilization within the physiological purview of Cori cycle, when muscles have more lactate dehydrogenase (LDH) than liver. We point out that the answer lies in thermodynamics/equilibriums. While the utilization of NADH for the reduction of pyruvate to lactate can be mediated via the classical mechanism, the oxidation of lactate (with/without the uphill reduction of NAD+ ) necessitates alternative physiological approaches. The latter pathway occurs via interactive equilibriums involving the enzyme, protons and oxygen or diffusible reactive oxygen species (DROS). Since liver has high DROS, the murburn activity at LDH would enable the cellular system to tide over the unfavorable energy barriers of the forward reaction (~476 kJ/mol; earlier miscalculated as ~26 kJ/mole). Further, the new mechanism does not necessitate any "smart decision-making" or sophisticated control by/of proteins. The DROS-based murburn theory explains the invariant active-site structure of LDH isozymes and their multimeric nature. The theoretical insights, in silico evidence and analyses of literature herein also enrich our understanding of the underpinnings of "lactic acidosis" (lowering of physiological pH accompanied by lactate production), Warburg effect (increased lactate production at high pO2 by cancer cells) and approach for cancer therapy.
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Affiliation(s)
- Kelath Murali Manoj
- Department of Biochemistry, Satyamjayatu: The Science & Ethics Foundation, Palakkad, Kerala, India
| | - Vijay Nirusimhan
- Department of Biochemistry, Satyamjayatu: The Science & Ethics Foundation, Palakkad, Kerala, India
| | - Abhinav Parashar
- Department of Biochemistry, Satyamjayatu: The Science & Ethics Foundation, Palakkad, Kerala, India
| | - Jesucastin Edward
- Department of Biochemistry, Satyamjayatu: The Science & Ethics Foundation, Palakkad, Kerala, India
| | - Daniel Andrew Gideon
- Department of Biochemistry, Satyamjayatu: The Science & Ethics Foundation, Palakkad, Kerala, India
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Manoj KM, Gideon DA, Jaeken L. Why do cells need oxygen? Insights from mitochondrial composition and function. Cell Biol Int 2021; 46:344-358. [PMID: 34918410 DOI: 10.1002/cbin.11746] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 02/03/2023]
Abstract
Mitochondrial membrane-embedded redox proteins are classically perceived as deterministic "electron transport chain" (ETC) arrays cum proton pumps; and oxygen is seen as an "immobile terminal electron acceptor." This is untenable because: (1) there are little free protons to be pumped out of the matrix; (2) proton pumping would be highly endergonic; (3) ETC-chemiosmosis-rotary ATP synthesis proposal is "irreducibly complex"/"non-evolvable" and does not fit with mitochondrial architecture or structural/distribution data of the concerned proteins/components; (4) a plethora of experimental observations do not conform to the postulates/requisites; for example, there is little evidence for viable proton-pumps/pH-gradient in mitochondria, trans-membrane potential (TMP) is non-fluctuating/non-trappable, oxygen is seen to give copious "diffusible reactive (oxygen) species" (DRS/DROS) in milieu, etc. Quite contrarily, the newly proposed murburn model's tenets agree with known principles of energetics/kinetics, and builds on established structural data and reported observations. In this purview, oxygen is needed to make DRS, the principal component of mitochondrial function. Complex V and porins respectively serve as proton-inlet and turgor-based water-exodus portals, thereby achieving organellar homeostasis. Complexes I to IV possess ADP-binding sites and their redox-centers react/interact with O2 /DRS. At/around these complexes, DRS cross-react or activate/oxidize ADP/Pi via fast thermogenic one-electron reaction(s), condensing to form two-electron stabilized products (H2 O2 /H2 O/ATP). The varied architecture and distribution of components in mitochondria validate DRS as (i) the coupling agent of oxidative reactions and phosphorylations, and (ii) the primary reason for manifestation of TMP in steady-state. Explorations along the new precepts stand to provide greater insights on mitochondrial function and pathophysiology.
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Affiliation(s)
- Kelath Murali Manoj
- Department of Biochemistry, Satyamjayatu: The Science & Ethics Foundation, Kerala, India
| | - Daniel Andrew Gideon
- Department of Biochemistry, Satyamjayatu: The Science & Ethics Foundation, Kerala, India
| | - Laurent Jaeken
- Industrial Sciences and Technology, Karel de Grote-Hogeschool, Association University and High Schools Antwerp, Antwerpen, Belgium
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Khojastehnezhad A, Taghavi F, Yaghoobi E, Ramezani M, Alibolandi M, Abnous K, Taghdisi SM. Recent achievements and advances in optical and electrochemical aptasensing detection of ATP based on quantum dots. Talanta 2021; 235:122753. [PMID: 34517621 DOI: 10.1016/j.talanta.2021.122753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/07/2021] [Accepted: 07/28/2021] [Indexed: 12/23/2022]
Abstract
The design and fabrication of high sensitive and selective biosensing platforms areessential goals to precisely recognize biomaterials in biological assays. In particular, determination of adenosine triphosphate (ATP) as the main energy currency of the cells and one of the most important biomolecules in living organisms is a pressing need in advanced biological detection. Recently, aptamer-based biosensors are introduced as a new direct strategy in which the aptamers (Apts) directly bind to the different targets and detect them on the basis of conformational changes and physical interactions. They can also be conjugated to optical and electronic probes such as quantum dot (QD) nanomaterials and provide unique QD aptasensing platforms. Currently, these Apt-based biosensors with excellent recognition features have attracted extensive attention due to the high specificity, rapid response and facile construction. Therefore, in this review article, recent achievements and advances in aptasensing detection of ATP based on different detection methods and types of QDs are discussed. In this regard, the optical and electrochemical aptasensors have been categorized based on detection methods; fluorescence (FL), electrochemiluminescence (ECL) and photoelectrochemical (PEC) and they have been also divided to two main groups based on QDs; metal-based (M-based) and carbon-based (C-based) materials. Then, their advantages and limitations have been highlighted, compared and discussed in detail.
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Affiliation(s)
- Amir Khojastehnezhad
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Faezeh Taghavi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elnaz Yaghoobi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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Manoj KM, Tamagawa H. Critical analysis of explanations for cellular homeostasis and electrophysiology from murburn perspective. J Cell Physiol 2021; 237:421-435. [PMID: 34515340 DOI: 10.1002/jcp.30578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 01/20/2023]
Abstract
Pursuits in modern cellular electrophysiology are fraught with disagreements at a fundamental level. While the membrane theory of homeostasis deems the cell membrane and proteins embedded therein as the chief players, the association-induction (or sorption/bulk-phase) hypothesis considers the aqueous phase of dissolved proteins (cytoplasm/protoplasm) as the key determinant of cellular composition and ionic fluxes. In the first school of thought, trans-membrane potential (TMP) and selective ion pumps/channels are deemed as key operative principles. In the latter theory, sorption-desorption dynamics and rearrangements of bulk phase determine the outcomes. In both these schools of thought, theorists believe that the macroscopic phase electroneutrality holds, TMP (whether in resting or in activated state) results solely due to ionic concentration differentials across the membrane, and the concerned proteins undergo major conformation changes to affect/effect the noted outcomes. The new entry into the field, murburn concept, builds starting from molecular considerations to macroscopic observations. It moots "effective charge separation" and intricate "molecule-ion-radical" electron transfer equilibriums as a rationale for ionic concentration differentials and TMP variation. After making an unbiased appraisal of the two classical schools of thought, the review makes a point-wise analysis of some hitherto unresolved observations/considerations and suggests the need to rethink the mechanistic perspectives.
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Affiliation(s)
- Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation, Kulappully, Palakkad District, Shoranur-2 (PO), Kerala, India
| | - Hirohisa Tamagawa
- Department of Mechanical Engineering, Gifu University, Yanagido, Gifu City, Japan
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A novel vision for mathematical model between electromagnetic radiation and thermodynamic parameters in biochemistry frame. APPLIED NANOSCIENCE 2021. [DOI: 10.1007/s13204-021-01989-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Manoj KM, Bazhin N. The murburn precepts for aerobic respiration and redox homeostasis. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:104-120. [DOI: 10.1016/j.pbiomolbio.2021.05.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/13/2021] [Accepted: 05/31/2021] [Indexed: 12/13/2022]
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Gideon DA, Nirusimhan V, E JC, Sudarsha K, Manoj KM. Mechanism of electron transfers mediated by cytochromes c and b5 in mitochondria and endoplasmic reticulum: classical and murburn perspectives. J Biomol Struct Dyn 2021; 40:9235-9252. [PMID: 33998974 DOI: 10.1080/07391102.2021.1925154] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We explore the mechanism of electron transfers mediated by cytochrome c, a soluble protein involved in mitochondrial oxidative phosphorylation and cytochrome b5, a microsomal membrane protein acting as a redox aide in xenobiotic metabolism. We found minimal conservation in the sequence and surface amino acid residues of cytochrome c/b5 proteins among divergent species. Therefore, we question the evolutionary logic for electron transfer (ET) occurring through affinity binding via recognition of specific surface residues/topography. Also, analysis of putative protein-protein interactions in the crystal structures of these proteins and their redox partners did not point to any specific interaction logic. A comparison of the kinetic and thermodynamic constants of wildtype vs. mutants did not provide strong evidence to support the binding-based ET paradigm, but indicated support for diffusible reactive species (DRS)-mediated process. Topographically divergent cytochromes from one species have been substituted for reaction with proteins from other species, implying the involvement of non-specific interactions. We provide a viable alternative (murburn concept) to classical protein-protein binding-based long range ET mechanism. To account for the promiscuity of interactions and solvent-accessible hemes, we propose that the two proteins act as non- specific redox capacitors, mediating one-electron redox equilibriums involving DRS and unbound ions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Daniel Andrew Gideon
- Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala State, India.,Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Vijay Nirusimhan
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Jesu Castin E
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Karthik Sudarsha
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala State, India
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Nath S. Coupling mechanisms in ATP synthesis: Rejoinder to "Response to molecular-level understanding of biological energy coupling and transduction". Biophys Chem 2021; 272:106579. [PMID: 33773332 DOI: 10.1016/j.bpc.2021.106579] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 11/29/2022]
Abstract
Recently, an exchange of views on key fundamental aspects of biological energy coupling and ATP synthesis in the vital process of oxidative phosphorylation appeared in the pages of this journal. The very difficult scientific problems are analyzed and clarified. Errors in the mathematical/thermodynamic equations of a previous analysis have been identified that invalidate previous assertions, and the correct equations are derived. The major differences between the two competing models - localized versus delocalized - for biological energy coupling and transduction are discussed from physical, chemical, and mathematical perspectives. The opposing views are summarized, so that the reader can assess for himself or herself the merits of the two coupling mechanisms. A fresh attempt has been made to go to the root of bioenergetics by calculating the desolvation free energy barrier, ∆Gdesolvation for ion transport across biomembranes. Several constructive suggestions are made that have the power to resolve the basic contradictions and the areas of fundamental conflict, and reach a consensus by catalyzing the progress of future research in this interdisciplinary field.
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Affiliation(s)
- Sunil Nath
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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Manoj KM, Manekkathodi A. Light's interaction with pigments in chloroplasts: The murburn perspective. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2021. [DOI: 10.1016/j.jpap.2020.100015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Manoj KM, Gideon DA, Parashar A. What is the Role of Lipid Membrane-embedded Quinones in Mitochondria and Chloroplasts? Chemiosmotic Q-cycle versus Murburn Reaction Perspective. Cell Biochem Biophys 2020; 79:3-10. [PMID: 32989571 DOI: 10.1007/s12013-020-00945-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2020] [Indexed: 01/23/2023]
Abstract
Quinones are found in the lipid membranes of prokaryotes like E. coli and cyanobacteria, and are also abundant in eukaryotic mitochondria and chloroplasts. They are intricately involved in the reaction mechanism of redox phosphorylations. In the Mitchellian chemiosmotic school of thought, membrane-lodged quinones are perceived as highly mobile conveyors of two-electron equivalents from the first leg of Electron Transport Chain (ETC) to the 'second pit-stop' of Cytochrome bc1 or b6f complex (CBC), where they undergo a regenerative 'Q-cycle'. In Manoj's murburn mechanism, the membrane-lodged quinones are perceived as relatively slow-moving one- or two- electron donors/acceptors, enabling charge separation and the CBC resets a one-electron paradigm via 'turbo logic'. Herein, we compare various purviews of the two mechanistic schools with respect to: constraints in mobility, protons' availability, binding of quinones with proteins, structural features of the protein complexes, energetics of reaction, overall reaction logic, etc. From various perspectives, the murburn mechanism appeals as a viable alternative explanation well-rooted in thermodynamics/kinetics and one which lends adequate structure-function correlations for the roles of quinones, lipid membrane and associated proteins.
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Affiliation(s)
- Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation, Kulappully, Shoranur-2 (PO), Palakkad, Kerala, 679122, India.
| | - Daniel Andrew Gideon
- Satyamjayatu: The Science & Ethics Foundation, Kulappully, Shoranur-2 (PO), Palakkad, Kerala, 679122, India
| | - Abhinav Parashar
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, 522213, India.
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Silva PJ. Chemiosmotic misunderstandings. Biophys Chem 2020; 264:106424. [PMID: 32717593 DOI: 10.1016/j.bpc.2020.106424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 02/04/2023]
Abstract
Recent publications have questioned the appropriateness of the chemiosmotic theory, a key tenet of modern bioenergetics originally described by Mitchell and since widely improved upon and applied. In one of them, application of Gauss' law to a model charge distribution in mitochondria was argued to refute the possibility of ATP generation through H+ movement in the absence of a counterion, whereas a different author advocated, for other reasons, the impossibility of chemiosmosis and proposed that a novel energy-generation scheme (referred to as "murburn") relying on superoxide-catalyzed (or superoxide-promoted) ADP phosphorylation would operate instead. In this letter, those proposals are critically examined and found to be inconsistent with established experimental data and new theoretical calculations.
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Affiliation(s)
- Pedro J Silva
- FP-ENAS/Fac. de Ciências da Saúde, Universidade Fernando Pessoa, Porto, Portugal; UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Porto, Portugal.
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Manoj KM. Refutation of the cation-centric torsional ATP synthesis model and advocating murburn scheme for mitochondrial oxidative phosphorylation. Biophys Chem 2019; 257:106278. [PMID: 31767207 DOI: 10.1016/j.bpc.2019.106278] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/08/2019] [Indexed: 12/18/2022]
Abstract
The acclaimed explanation for mitochondrial oxidative phosphorylation (mOxPhos) is a proton or cation centric scheme. Such ideas were recently disclaimed and in lieu, an evidence-based oxygen-centric explanation, murburn concept, was proposed. The new understanding vouches for catalytic roles of diffusible reactive oxygen species (DROS). The involvement of DROS explains the "non-discoverability of an enzyme-linked high-energy phosphorylating intermediate", a historical predicament, which had fueled several trans-membrane potential (TMP) based mechano-electrical explanations like the Nath model. This communication aims to briefly apprise the readers some lacunae and inadmissible aspects of the Nath model and project the appeal of murburn scheme of mOxPhos.
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Affiliation(s)
- Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation, Shoranur-2 PO, Palakkad District, Kerala 679122, India.
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Nath S. Consolidation of Nath's torsional mechanism of ATP synthesis and two-ion theory of energy coupling in oxidative phosphorylation and photophosphorylation. Biophys Chem 2019; 257:106279. [PMID: 31757522 DOI: 10.1016/j.bpc.2019.106279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 11/08/2019] [Indexed: 01/09/2023]
Abstract
In a recent publication, Manoj raises criticisms against consensus views on the ATP synthase. The radical statements and assertions are shown to contradict a vast body of available knowledge that includes i) pioneering single-molecule biochemical and biophysical studies from the respected experimental groups of Kinosita, Yoshida, Noji, Börsch, Dunn, Gräber, Frasch, and Dimroth etc., ii) state-of-the-art X-ray and EM/cryo-EM structural information garnered over the decades by the expert groups of Leslie-Walker, Kühlbrandt, Mueller, Meier, Rubinstein, Sazanov, Duncan, and Pedersen on ATP synthase, iii) the pioneering energy-based computer simulations of Warshel, and iv) the novel theoretical and experimental works of Nath. Valid objections against Mitchell's chemiosmotic theory and Boyer's binding change mechanism put forth by Manoj have been addressed satisfactorily by Nath's torsional mechanism of ATP synthesis and two-ion theory of energy coupling and published 10 to 20 years ago, but these papers are not cited by him. This communication shows conclusively and in great detail that none of his objections apply to Nath's mechanism/theory. Nath's theory is further consolidated based on its previous predictive record, its consistency with biochemical evidence, its unified nature, its application to other related energy transductions and to disease, and finally its ability to guide the design of new experiments. Some constructive suggestions for high-resolution structural experiments that have the power to delve into the heart of the matter and throw unprecedented light on the nature of coupled ion translocation in the membrane-bound FO portion of F1FO-ATP synthase are made.
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Affiliation(s)
- Sunil Nath
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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Manoj KM, Soman V, David Jacob V, Parashar A, Gideon DA, Kumar M, Manekkathodi A, Ramasamy S, Pakshirajan K, Bazhin NM. Chemiosmotic and murburn explanations for aerobic respiration: Predictive capabilities, structure-function correlations and chemico-physical logic. Arch Biochem Biophys 2019; 676:108128. [PMID: 31622585 DOI: 10.1016/j.abb.2019.108128] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 12/18/2022]
Abstract
Since mid-1970s, the proton-centric proposal of 'chemiosmosis' became the acclaimed explanation for aerobic respiration. Recently, significant theoretical and experimental evidence were presented for an oxygen-centric 'murburn' mechanism of mitochondrial ATP-synthesis. Herein, we compare the predictive capabilities of the two models with respect to the available information on mitochondrial reaction chemistry and the membrane proteins' structure-function correlations. Next, fundamental queries are addressed on thermodynamics of mitochondrial oxidative phosphorylation (mOxPhos): (1) Can the energy of oxygen reduction be utilized for proton transport? (2) Is the trans-membrane proton differential harness-able as a potential energy capable of doing useful work? and (3) Whether the movement of miniscule amounts of mitochondrial protons could give rise to a potential of ~200 mV and if such an electrical energy could sponsor ATP-synthesis. Further, we explore critically if rotary ATPsynthase activity of Complex V can account for physiological ATP-turnovers. We also answer the question- "What is the role of protons in the oxygen-centric murburn scheme of aerobic respiration?" Finally, it is demonstrated that the murburn reaction model explains the fast kinetics, non-integral stoichiometry and high yield of mOxPhos. Strategies are charted to further demarcate the two explanations' relevance in the cellular physiology of aerobic respiration.
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Affiliation(s)
- Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation, Snehatheeram, Kulappully, Shoranur-2 (PO), Kerala, 679122, India.
| | - Vidhu Soman
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Vivian David Jacob
- Satyamjayatu: The Science & Ethics Foundation, Snehatheeram, Kulappully, Shoranur-2 (PO), Kerala, 679122, India
| | - Abhinav Parashar
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, 522213, India
| | - Daniel Andrew Gideon
- Department of Biotechnology & Bioinformatics, Bishop Heber College (Autonomous), Tennur, Tiruchirappalli, 620017, India
| | - Manish Kumar
- Satyamjayatu: The Science & Ethics Foundation, Snehatheeram, Kulappully, Shoranur-2 (PO), Kerala, 679122, India
| | - Afsal Manekkathodi
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, Al-Rayyan PO Box 34110, Qatar
| | - Surjith Ramasamy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Kannan Pakshirajan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Nikolai Mikhailovich Bazhin
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, St. Institutskaya 3, 630090, Novosibirsk, Russia.
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Manoj KM, Parashar A, David Jacob V, Ramasamy S. Aerobic respiration: proof of concept for the oxygen-centric murburn perspective. J Biomol Struct Dyn 2019; 37:4542-4556. [PMID: 30488771 DOI: 10.1080/07391102.2018.1552896] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The inner mitochondrial membrane protein complexes (I-V) and prokaryotic respiratory machinery are examined for a deeper understanding of their structure-function correlations and dynamics. In silico analysis of the structure of complexes I-IV, docking studies and erstwhile literature confirm that they carry sites which are in close proximity to DROS (diffusible reactive oxygen species) generating redox centers. These findings provide supportive evidence for the newly proposed oxygen-centric chemical-coupling mechanism (murburn concept), wherein DROS catalyzes the esterification of inorganic phosphate to ADP. Further, in a reductionist system, we demonstrate that a DROS (like superoxide) can effectively esterify inorganic phosphate to ADP. The impact of these findings and the interactive dynamics of classical inhibitors (rotenone and cyanide), uncouplers (dinitrophenol and uncoupling protein) and other toxins (atractyloside and oligomycin) are briefly discussed. Highlights • Earlier perception: Complexes (I-IV) pump protons and Complex V make ATP (aided by protons) • Herein: Respiratory molecular machinery is probed for new structure-function correlations • Analyses: Quantitative arguments discount proton-centric ATP synthesis in mitochondria and bacteria • In silico data: ADP-binding sites and O2/ diffusible reactive oxygen species (DROS)-accessible channels are unveiled in respiratory proteins • In vitro data: Using luminometry, ATP synthesis is demonstrated from ADP, Pi and superoxide • Inference: Findings agree with decentralized ADP-Pi activation via oxygen-centric murburn scheme Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Abhinav Parashar
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research , Vadlamudi , Guntur, Andhra Pradesh, India
| | | | - Surjith Ramasamy
- Department of Biotechnology, Indian Institute of Technology Guwahati , Guwahati , Assam, India
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