scholarly journals Multiscale simulations reveal key features of the proton pumping mechanism in cytochrome c oxidase

2016 ◽  
Author(s):  
Ruibin Liang ◽  
Jessica M. J. Swanson ◽  
Yuxing Peng ◽  
Mårten Wikström ◽  
Gregory A. Voth
Keyword(s):  
Electron Transfer ◽  
Free Energy ◽  
Proton Transport ◽  
Atp Synthesis ◽  
Quantitative Agreement ◽  
Proton Pumping ◽  
Back Flow ◽  
Transport Dynamics ◽  
Hydrophobic Cavity ◽  
Dynamics Simulations

AbstractCytochrome c oxidase (CcO) reduces oxygen to water and uses the released free energy to pump protons across the membrane, contributing to the transmembrane proton electrochemical gradient that drives ATP synthesis. We have used multiscale reactive molecular dynamics simulations to explicitly characterize (with free energy profiles and calculated rates) the internal proton transport events that enable pumping and chemistry during the A→PR→F transition in the aa3-type CcO. Our results show that proton transport from amino acid residue E286 to both the pump loading site (PLS) and to the binuclear center (BNC) are thermodynamically driven by electron transfer from heme a to the BNC, but that the former (i.e., pumping) is kinetically favored while the latter (i.e., transfer of the chemical proton) is rate-limiting. The calculated rates are in quantitative agreement with experimental measurements. The back flow of the pumped proton from the PLS to E286 and from E286 to the inner side of membrane are prevented by the fast reprotonation of E286 through the D-channel and large free energy barriers for the back flow reactions. Proton transport from E286 to the PLS through the hydrophobic cavity (HC) and from D132 to E286 through the D-channel are found to be strongly coupled to dynamical hydration changes in the corresponding pathways. This work presents a comprehensive description of the key steps in the proton pumping mechanism in CcO.SignificanceThe long studied proton pumping mechanism in cytochrome c oxidase (CcO) continues to be a source of debate. This work provides a comprehensive computational characterization of the internal proton transport dynamics, while explicitly including the role of Grotthuss proton shuttling, that lead to both pumping and catalysis. Focusing on the A to F transition, our results show that the transfer of both the pumped and chemical protons are thermodynamically driven by electron transfer, and explain how proton back leakage is avoided by kinetic gating. This work also explicitly characterizes the coupling of proton transport with hydration changes in the hydrophobic cavity and D-channel, thus advancing our understanding of proton transport in biomolecules in general.

scholarly journals Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase

2016 ◽  
Vol 113 (27) ◽  
pp. 7420-7425 ◽  
Author(s):  
Ruibin Liang ◽  
Jessica M. J. Swanson ◽  
Yuxing Peng ◽  
Mårten Wikström ◽  
Gregory A. Voth
Keyword(s):  
Free Energy ◽  
Proton Transport ◽  
Proton Pumping ◽  
Strongly Coupled ◽  
Reactive Molecular Dynamics ◽  
Hydrophobic Cavity ◽  
Energy Profiles ◽  
Binuclear Center ◽  
Dynamics Simulations ◽  
Rate Limiting

Cytochrome c oxidase (CcO) reduces oxygen to water and uses the released free energy to pump protons across the membrane. We have used multiscale reactive molecular dynamics simulations to explicitly characterize (with free-energy profiles and calculated rates) the internal proton transport events that enable proton pumping during first steps of oxidation of the fully reduced enzyme. Our results show that proton transport from amino acid residue E286 to both the pump loading site (PLS) and to the binuclear center (BNC) are thermodynamically driven by electron transfer from heme a to the BNC, but that the former (i.e., pumping) is kinetically favored whereas the latter (i.e., transfer of the chemical proton) is rate-limiting. The calculated rates agree with experimental measurements. The backflow of the pumped proton from the PLS to E286 and from E286 to the inside of the membrane is prevented by large free-energy barriers for the backflow reactions. Proton transport from E286 to the PLS through the hydrophobic cavity and from D132 to E286 through the D-channel are found to be strongly coupled to dynamical hydration changes in the corresponding pathways and, importantly, vice versa.

scholarly journals Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase

2015 ◽  
Vol 112 (7) ◽  
pp. 2040-2045 ◽  
Author(s):  
Vivek Sharma ◽  
Giray Enkavi ◽  
Ilpo Vattulainen ◽  
Tomasz Róg ◽  
Mårten Wikström
Keyword(s):  
Electron Transfer ◽  
Free Energy ◽  
Proton Transfer ◽  
Short Circuit ◽  
Proton Pumping ◽  
Free Energy Calculations ◽  
Water Molecules ◽  
Transfer Event ◽  
Proton Coupled Electron Transfer ◽  
Dynamics Simulations

Molecular oxygen acts as the terminal electron sink in the respiratory chains of aerobic organisms. Cytochrome c oxidase in the inner membrane of mitochondria and the plasma membrane of bacteria catalyzes the reduction of oxygen to water, and couples the free energy of the reaction to proton pumping across the membrane. The proton-pumping activity contributes to the proton electrochemical gradient, which drives the synthesis of ATP. Based on kinetic experiments on the O–O bond splitting transition of the catalytic cycle (A → PR), it has been proposed that the electron transfer to the binuclear iron–copper center of O2 reduction initiates the proton pump mechanism. This key electron transfer event is coupled to an internal proton transfer from a conserved glutamic acid to the proton-loading site of the pump. However, the proton may instead be transferred to the binuclear center to complete the oxygen reduction chemistry, which would constitute a short-circuit. Based on atomistic molecular dynamics simulations of cytochrome c oxidase in an explicit membrane–solvent environment, complemented by related free-energy calculations, we propose that this short-circuit is effectively prevented by a redox-state–dependent organization of water molecules within the protein structure that gates the proton transfer pathway.

scholarly journals Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale

2020 ◽  
Author(s):  
Chenghan Li ◽  
Zhi Yue ◽  
L. Michel Espinoza-Fonseca ◽  
Gregory A. Voth
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Sarcoplasmic Reticulum ◽  
Binding Site ◽  
Proton Transport ◽  
Computational Study ◽  
Multiscale Simulation ◽  
Proton Pumping ◽  
Reactive Molecular Dynamics ◽  
Free Energy Sampling

ABSTRACTThe sarcoplasmic reticulum Ca2+-ATPase (SERCA) transports two Ca2+ ions from the cytoplasm to the reticulum lumen at the expense of ATP hydrolysis. In addition to transporting Ca2+, SERCA facilitates bidirectional proton transport across the sarcoplasmic reticulum to maintain the charge balance of the transport sites and to balance the charge deficit generated by the exchange of Ca2+. Previous studies have shown the existence of a transient water-filled pore in SERCA that connects the Ca2+-binding sites with the lumen, but the capacity of this pathway to sustain passive proton transport has remained unknown. In this study, we used the multiscale reactive molecular dynamics (MS-RMD) method and free energy sampling to quantify the free energy profile and timescale of the proton transport across this pathway while also explicitly accounting for the dynamically coupled hydration changes of the pore. We find that proton transport from the central binding site to the lumen has a microsecond timescale, revealing a novel passive cytoplasm-to-lumen proton flow beside the well-known inverse proton countertransport occurring in active Ca2+ transport. We propose that this proton transport mechanism is operational and serves as a functional conduit for passive proton transport across the sarcoplasmic reticulum.SIGNIFICANCEMultiscale reactive molecular dynamics combined with free energy sampling was applied to study proton transport through a transient water pore connecting the Ca2+-binding site to the lumen in SERCA. This is the first computational study of this large biomolecular system that treats the hydrated excess proton and its transport through water structures and amino acids explicitly. When also correctly accounting for the hydration fluctuations of the pore, it is found that a transiently hydrated channel can transport protons on a microsecond timescale. These results quantitatively support the hypothesis of the proton intake into the sarcoplasm via SERCA, in addition to the well-known proton pumping by SERCA to the cytoplasm along with Ca2+ transport.

scholarly journals Five decades of research on mitochondrial NADH-quinone oxidoreductase (complex I)

2018 ◽  
Vol 399 (11) ◽  
pp. 1249-1264 ◽  
Author(s):  
Tomoko Ohnishi ◽  
S. Tsuyoshi Ohnishi ◽  
John C. Salerno
Keyword(s):  
Electron Transfer ◽  
Respiratory Chain ◽  
Complex I ◽  
Proton Translocation ◽  
Atp Synthesis ◽  
Mitochondrial Respiratory Chain ◽  
Proton Pumping ◽  
Entry Site ◽  
Quinone Oxidoreductase ◽  
Terminal Electron Acceptor

AbstractNADH-quinone oxidoreductase (complex I) is the largest and most complicated enzyme complex of the mitochondrial respiratory chain. It is the entry site into the respiratory chain for most of the reducing equivalents generated during metabolism, coupling electron transfer from NADH to quinone to proton translocation, which in turn drives ATP synthesis. Dysfunction of complex I is associated with neurodegenerative diseases such as Parkinson’s and Alzheimer’s, and it is proposed to be involved in aging. Complex I has one non-covalently bound FMN, eight to 10 iron-sulfur clusters, and protein-associated quinone molecules as electron transport components. Electron paramagnetic resonance (EPR) has previously been the most informative technique, especially in membranein situanalysis. The structure of complex 1 has now been resolved from a number of species, but the mechanisms by which electron transfer is coupled to transmembrane proton pumping remains unresolved. Ubiquinone-10, the terminal electron acceptor of complex I, is detectable by EPR in its one electron reduced, semiquinone (SQ) state. In the aerobic steady state of respiration the semi-ubiquinone anion has been observed and studied in detail. Two distinct protein-associated fast and slow relaxing, SQ signals have been resolved which were designated SQNfand SQNs. This review covers a five decade personal journey through the field leading to a focus on the unresolved questions of the role of the SQ radicals and their possible part in proton pumping.

scholarly journals Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase

2017 ◽  
Vol 114 (23) ◽  
pp. 5924-5929 ◽  
Author(s):  
Ruibin Liang ◽  
Jessica M. J. Swanson ◽  
Mårten Wikström ◽  
Gregory A. Voth
Keyword(s):  
Free Energy ◽  
Molecular Mechanisms ◽  
Proton Pumping ◽  
Amino Acid Residues ◽  
Reactive Molecular Dynamics ◽  
Chemical Catalysis ◽  
Energy Profiles ◽  
High Proton ◽  
Pumping Efficiency ◽  
Dynamics Simulations

Cytochrome c oxidase (CcO) catalyzes the reduction of oxygen to water and uses the released free energy to pump protons against the transmembrane proton gradient. To better understand the proton-pumping mechanism of the wild-type (WT) CcO, much attention has been given to the mutation of amino acid residues along the proton translocating D-channel that impair, and sometimes decouple, proton pumping from the chemical catalysis. Although their influence has been clearly demonstrated experimentally, the underlying molecular mechanisms of these mutants remain unknown. In this work, we report multiscale reactive molecular dynamics simulations that characterize the free-energy profiles of explicit proton transport through several important D-channel mutants. Our results elucidate the mechanisms by which proton pumping is impaired, thus revealing key kinetic gating features in CcO. In the N139T and N139C mutants, proton back leakage through the D-channel is kinetically favored over proton pumping due to the loss of a kinetic gate in the N139 region. In the N139L mutant, the bulky L139 side chain inhibits timely reprotonation of E286 through the D-channel, which impairs both proton pumping and the chemical reaction. In the S200V/S201V double mutant, the proton affinity of E286 is increased, which slows down both proton pumping and the chemical catalysis. This work thus not only provides insight into the decoupling mechanisms of CcO mutants, but also explains how kinetic gating in the D-channel is imperative to achieving high proton-pumping efficiency in the WT CcO.

scholarly journals Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of Vo complex

2020 ◽  
Vol 6 (41) ◽  
pp. eabb9605 ◽  
Author(s):  
Soung-Hun Roh ◽  
Mrinal Shekhar ◽  
Grigore Pintilie ◽  
Christophe Chipot ◽  
Stephan Wilkens ◽  
...  
Keyword(s):  
Proton Transport ◽  
Specific Protein ◽  
Proton Pumping ◽  
Proton Channel ◽  
Ring Rotation ◽  
Adenosine Triphosphatases ◽  
Dynamics Simulations ◽  
Ordered Water ◽  
Membrane Scaffold

Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a Vo proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive. Here, we determined a 2.7-Å cryo–electron microscopy (cryo-EM) structure of yeast Vo proton channel in nanodisc that reveals the location of ordered water molecules along the proton path, details of specific protein-lipid interactions, and the architecture of the membrane scaffold protein. Moreover, we uncover a state of Vo that shows the c-ring rotated by ~14°. Molecular dynamics simulations demonstrate that the two rotary states are in thermal equilibrium and depict how the protonation state of essential glutamic acid residues couples water-mediated proton transfer with c-ring rotation. Our cryo-EM models and simulations also rationalize a mechanism for inhibition of passive proton transport as observed for free Vo that is generated as a result of V-ATPase regulation by reversible disassembly in vivo.

scholarly journals Stochastic rotational catalysis of proton pumping F-ATPase

2008 ◽  
Vol 363 (1500) ◽  
pp. 2135-2142 ◽  
Author(s):  
Mayumi Nakanishi-Matsui ◽  
Masamitsu Futai
Keyword(s):  
Proton Transport ◽  
Atp Synthesis ◽  
Energy Coupling ◽  
Proton Pumping ◽  
Proton Channel ◽  
Phosphate Binding ◽  
Stochastic Fluctuation ◽  
Rotational Catalysis ◽  
Α Helix

F-ATPases synthesize ATP from ADP and phosphate coupled with an electrochemical proton gradient in bacterial or mitochondrial membranes and can hydrolyse ATP to form the gradient. F-ATPases consist of a catalytic F 1 and proton channel F 0 formed from the α 3 β 3 γδϵ and ab 2 c 10 subunit complexes, respectively. The rotation of γϵ c 10 couples catalyses and proton transport. Consistent with the threefold symmetry of the α 3 β 3 catalytic hexamer, 120° stepped revolution has been observed, each step being divided into two substeps. The ATP-dependent revolution exhibited stochastic fluctuation and was driven by conformation transmission of the β subunit (phosphate-binding P-loop/α-helix B/loop/β-sheet4). Recent results regarding mechanically driven ATP synthesis finally proved the role of rotation in energy coupling.

scholarly journals Ultrafast proton transport in water-methanol mixtures

2019 ◽  
Vol 205 ◽  
pp. 09004
Author(s):  
Maria Ekimova ◽  
Felix Hoffmann ◽  
Gul Bekcioglu-Neff ◽  
Aidan Rafferty ◽  
Erik T. J. Nibbering ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Proton Transport ◽  
Ab Initio Molecular Dynamics ◽  
Transport Pathway ◽  
Pump Probe ◽  
Dynamics Simulations

Femtosecond UV/IR pump-probe experiments and ab initio molecular dynamics simulations of 7-hydroxyquinoline in water-methanol mixtures demonstrate an unexpectedly dominant OH-/CH3O- transport pathway but consistent with a solvent-dependent photoacidity free energy-reactivity correlation behaviour.

ELECTRON TRANSFER INDUCED DISSOCIATION OF CHLORO-CYANO-BENZENE RADICAL ANION: DRIVING CHEMICAL REACTIONS VIA CHARGE RESTRAINTS

2005 ◽  
Vol 04 (04) ◽  
pp. 985-999 ◽  
Author(s):  
MARIALORE SULPIZI ◽  
URSULA ROTHLISBERGER ◽  
ALESSANDRO LAIO
Keyword(s):  
Electron Transfer ◽  
Free Energy ◽  
Energy Barrier ◽  
Radical Anion ◽  
Quantitative Agreement ◽  
Free Energy Barrier ◽  
Nuclear Reorganization ◽  
Structure Changes ◽  
Water Shell ◽  
Saturated Carbon Atom

We introduce a new quantum mechanics/molecular mechanics based method to drive electron transfer reactions. Our approach uses the dynamically restrained electrostatic potential derived charges of the quantum atoms1 as a reaction coordinate, and allows an estimation of the free energy barrier of the electron transfer process. Moreover, it provides an accurate description of the electronic structure changes and of the nuclear reorganization associated with the reaction. We use the method to describe the electron-transfer induced dissociation of the m-chloro-cyano-benzene radical anion in aqueous solution. The reaction is triggered by solvent reorganization by a change in the coordination water shell around the cyano nitrogen atom. At the onset of the reaction, charge-spin segregation is observed. The negative charge is transferred to the leaving Cl , while the spin density localizes on the non-saturated carbon atom of the benzene ring. The calculated free energy barrier of dissociation is in good quantitative agreement with the experimental data.

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