Activation of respiratory Complex I from Escherichia coli studied by fluorescent probes

Belevich, Nikolai P.; Belevich, Galina; Chen, Zhiyong; Sinha, Subhash C.; Verkhovskaya, Marina

doi:10.1016/j.heliyon.2016.e00224

Cited by 8 publications

(7 citation statements)

References 60 publications

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“…Although it is possible that similar conformational transitions could also regulate the activity of the cyanobacterial enzyme (cf. also [ 37 ]), recent structural studies suggest that the yeast complex I is rather rigid [ 38 ], and the motions coupled to the A/D transition might not be universally conserved amongst the complex I superfamily. The functional importance of the global motions observed in the MD simulations of the cyanobacterial NDH-1 complex therefore remains unclear.…”

Section: Resultsmentioning

confidence: 99%

Molecular dynamics and structural models of the cyanobacterial NDH-1 complex

Saura

Kaila

2019

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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NDH-1 is a gigantic redox-driven proton pump linked with respiration and cyclic electron flow in cyanobacterial cells. Based on experimentally resolved X-ray and cryo-EM structures of the respiratory complex I, we derive here molecular models of two isoforms of the cyanobacterial NDH-1 complex involved in redox-driven proton pumping (NDH-1L) and CO 2 -fixation (NDH-1MS). Our models show distinct structural and dynamic similarities to the core architecture of the bacterial and mammalian respiratory complex I. We identify putative plastoquinone-binding sites that are coupled by an electrostatic wire to the proton pumping elements in the membrane domain of the enzyme. Molecular simulations suggest that the NDH-1L isoform undergoes large-scale hydration changes that support proton-pumping within antiporter-like subunits, whereas the terminal subunit of the NDH-1MS isoform lacks such structural motifs. Our work provides a putative molecular blueprint for the complex I-analogue in the photosynthetic energy transduction machinery and demonstrates that general mechanistic features of the long-range proton-pumping machinery are evolutionary conserved in the complex I-superfamily.

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Section: Resultsmentioning

confidence: 99%

Molecular dynamics and structural models of the cyanobacterial NDH-1 complex

Saura

Kaila

2019

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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“…The bacterial complex I lacks a prevalent A/D transition (12,13,55); although the functional residues providing wiring between ND1 (Nqo8/NuoH in Thermus thermophilus/E. coli; SI Appendix, Table S8) and ND2 (Nqo14/NuoN in Thermus thermophilus/ E. coli) are highly conserved (SI Appendix, Table S5), Met63 ND6 , which is involved in blocking the proton wire at the ND4L/ND6 interface, is replaced by bulky nonpolar residues in the bacterial Fig.…”

Section: Discussionmentioning

confidence: 99%

Deactivation blocks proton pathways in the mitochondrial complex I

Röpke

Riepl

Saura

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Cellular respiration is powered by membrane-bound redox enzymes that convert chemical energy into an electrochemical proton gradient and drive the energy metabolism. By combining large-scale classical and quantum mechanical simulations with cryo-electron microscopy data, we resolve here molecular details of conformational changes linked to proton pumping in the mammalian complex I. Our data suggest that complex I deactivation blocks water-mediated proton transfer between a membrane-bound quinone site and proton-pumping modules, decoupling the energy-transduction machinery. We identify a putative gating region at the interface between membrane domain subunits ND1 and ND3/ND4L/ND6 that modulates the proton transfer by conformational changes in transmembrane helices and bulky residues. The region is perturbed by mutations linked to human mitochondrial disorders and is suggested to also undergo conformational changes during catalysis of simpler complex I variants that lack the “active”-to-“deactive” transition. Our findings suggest that conformational changes in transmembrane helices modulate the proton transfer dynamics by wetting/dewetting transitions and provide important functional insight into the mammalian respiratory complex I.

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“…The catalytic A/D transition occurs in vertebrates and in fungi containing complex I ( Neurospora crassa and Yarrowia lipolytica ) ( Agip et al, 2018 ; Blaza et al, 2018 ; Fiedorczuk et al, 2016 ; Gorenkova et al, 2013 ; Grba and Hirst, 2020 ; Grivennikova et al, 2003 ; Kalashnikov et al, 2011 ; Maklashina et al, 2002 , 2003 , 2004 ; Siebels and Dröse, 2016 ; Zhu et al, 2016 ). In contrast, complex I of invertebrate metazoans as well as bacteria ( Paracoccus denitrificans, Thermus thermophilus ) does not undergo a catalytic A/D transition ( Jarman et al, 2021 ; Kotlyar et al, 1998 ; Maklashina et al, 2003 ), although it has been claimed to occur for the Escherichia coli enzyme ( Belevich and Verkhovskaya, 2016 ; Belevich et al, 2017a , 2017b ). The physiological role for the catalytic A/D transition has been proposed as a mechanism to fine-tune catalytic activity in response to oxygen concentration ( Babot et al, 2014 ; Galkin and Moncada, 2017 ).…”

Section: Introductionmentioning

confidence: 99%