scholarly journals Insights into the origin of the high energy-conversion efficiency of F1-ATPase

2019 ◽  
Vol 116 (32) ◽  
pp. 15924-15929 ◽  
Author(s):  
Kwangho Nam ◽  
Martin Karplus
Keyword(s):  
Single Molecule ◽  
Atp Hydrolysis ◽  
Theoretical Models ◽  
Adenosine Diphosphate ◽  
Energy Conversion Efficiency ◽  
High Energy ◽  
Structural Deformation ◽  
Coupling Mechanism ◽  
Surprising Result ◽  
X Ray Crystallography

Our understanding of the rotary-coupling mechanism of F1-ATPase has been greatly enhanced in the last decade by advances in X-ray crystallography, single-molecular imaging, and theoretical models. Recently, Volkán-Kacsó and Marcus [S. Volkán-Kacsó, R. A. Marcus, Proc. Natl. Acad. Sci. U.S.A. 112, 14230 (2015)] presented an insightful thermodynamic model based on the Marcus reaction theory coupled with an elastic structural deformation term to explain the observed γ-rotation angle dependence of the adenosine triphosphate (ATP)/adenosine diphosphate (ADP) exchange rates of F1-ATPase. Although the model is successful in correlating single-molecule data, it is not in agreement with the available theoretical results. We describe a revision of the model, which leads to consistency with the simulation results and other experimental data on the F1-ATPase rotor compliance. Although the free energy liberated on ATP hydrolysis by F1-ATPase is rapidly dissipated as heat and so cannot contribute directly to the rotation, we show how, nevertheless, F1-ATPase functions near the maximum possible efficiency. This surprising result is a consequence of the differential binding of ATP and its hydrolysis products ADP and Pi along a well-defined pathway.

scholarly journals Single-molecular and Ensemble-level Oscillations of Cyanobacterial Circadian Clock

2018 ◽  
Author(s):  
Sumita Das ◽  
Tomoki P. Terada ◽  
Masaki Sasai
Keyword(s):  
Atpase Activity ◽  
Circadian Clock ◽  
Single Molecule ◽  
Structural Changes ◽  
Atp Hydrolysis ◽  
Theoretical Models ◽  
Oscillation Period ◽  
Coarse Grained ◽  
Simulation Results

AbstractWhen three cyanobacterial proteins, KaiA, KaiB, and KaiC, are incubated with ATP in vitro, the phosphorylation level of KaiC hexamers shows stable oscillation with approximately 24 h period. In order to understand this KaiABC clockwork, we need to analyze both the macroscopic synchronization of a large number of KaiC hexamers and the microscopic reactions and structural changes in individual KaiC molecules. In the present paper, we explain two coarse-grained theoretical models, the many-molecule (MM) model and the single-molecule (SM) model, to bridge the gap between macroscopic and microscopic understandings. In the simulation results with these models, ATP hydrolysis drives oscillation of individual KaiC hexamers and ATP hydrolysis is necessary for synchronizing oscillations of a large number of KaiC hexamers. Sensitive temperature dependence of the lifetime of the ADP bound state in the CI domain of KaiC hexamers makes the oscillation period temperature insensitive. ATPase activity is correlated to the frequency of phosphorylation oscillation in the single molecule of KaiC hexamer, which should be the origin of the observed ensemble-level correlation between the ATPase activity and the frequency of phosphorylation oscillation. Thus, the simulation results with the MM and SM models suggest that ATP hydrolysis randomly occurring in each CI domain of individual KaiC hexamers is a key process for oscillatory behaviors of the ensemble of many KaiC hexamers.Significance StatementCyanobacterial proteins, KaiA, KaiB, and KaiC, can reconstitute a circadian clock when they are incubated with ATP in vitro. In order to understand this prototypical oscillator, we need to analyze both synchronization of a macroscopically large number of oscillating molecules and microscopic reactions in individual molecules. We introduced two theoretical models to unify macroscopic and microscopic viewpoints. Simulation results suggest that ATP hydrolysis is necessary for synchronization and temperature compensation and that ATPase activity is correlated to the oscillation frequency in individual molecules. Thus, ATP hydrolysis randomly occurring in individual molecules should determine important features of the ensemble-level oscillation.

Structural dynamics of P-type ATPase ion pumps

2019 ◽  
Vol 47 (5) ◽  
pp. 1247-1257 ◽  
Author(s):  
Mateusz Dyla ◽  
Sara Basse Hansen ◽  
Poul Nissen ◽  
Magnus Kjaergaard
Keyword(s):  
Structural Dynamics ◽  
Single Molecule ◽  
New Technologies ◽  
Atp Hydrolysis ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Time Resolved ◽  
Dynamics Simulations ◽  
Types Of Information ◽  
P Type

Abstract P-type ATPases transport ions across biological membranes against concentration gradients and are essential for all cells. They use the energy from ATP hydrolysis to propel large intramolecular movements, which drive vectorial transport of ions. Tight coordination of the motions of the pump is required to couple the two spatially distant processes of ion binding and ATP hydrolysis. Here, we review our current understanding of the structural dynamics of P-type ATPases, focusing primarily on Ca2+ pumps. We integrate different types of information that report on structural dynamics, primarily time-resolved fluorescence experiments including single-molecule Förster resonance energy transfer and molecular dynamics simulations, and interpret them in the framework provided by the numerous crystal structures of sarco/endoplasmic reticulum Ca2+-ATPase. We discuss the challenges in characterizing the dynamics of membrane pumps, and the likely impact of new technologies on the field.

Current progress and performance improvement of Pt/C catalysts for fuel cells

2020 ◽  
Vol 8 (46) ◽  
pp. 24284-24306
Author(s):  
Xuefeng Ren ◽  
Yiran Wang ◽  
Anmin Liu ◽  
Zhihong Zhang ◽  
Qianyuan Lv ◽  
...  
Keyword(s):  
Fuel Cells ◽  
Fuel Cell ◽  
Energy Conversion ◽  
Performance Improvement ◽  
Electric Energy ◽  
Energy Conversion Efficiency ◽  
High Energy ◽  
Carnot Cycle ◽  
High Energy Conversion Efficiency ◽  
And Performance

Fuel cell is an electrochemical device, which can directly convert the chemical energy of fuel into electric energy, without heat process, not limited by Carnot cycle, high energy conversion efficiency, no noise and pollution.

scholarly journals Lasing at the nanoscale: coherent emission of surface plasmons by an electrically driven nanolaser

Nanophotonics ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 3965-3975 ◽  
Author(s):  
Dmitry Yu. Fedyanin ◽  
Alexey V. Krasavin ◽  
Aleksey V. Arsenin ◽  
Anatoly V. Zayats
Keyword(s):  
Data Storage ◽  
Surface Plasmon ◽  
Single Molecule ◽  
Optical Communication ◽  
Surface Plasmon Polariton ◽  
High Energy ◽  
Photonic Devices ◽  
Sensing Applications ◽  
Diverse Application ◽  
Plasmon Polariton

AbstractPlasmonics offers a unique opportunity to break the diffraction limit of light and bring photonic devices to the nanoscale. As the most prominent example, an integrated nanolaser is a key to truly nanoscale photonic circuits required for optical communication, sensing applications and high-density data storage. Here, we develop a concept of an electrically driven subwavelength surface-plasmon-polariton nanolaser, which is based on a novel amplification scheme, with all linear dimensions smaller than the operational free-space wavelength λ and a mode volume of under λ3/30. The proposed pumping approach is based on a double-heterostructure tunneling Schottky barrier diode and gives the possibility to reduce the physical size of the device and ensure in-plane emission so that the nanolaser output can be naturally coupled to a plasmonic or nanophotonic waveguide circuitry. With the high energy efficiency (8% at 300 K and 37% at 150 K), the output power of up to 100 μW and the ability to operate at room temperature, the proposed surface plasmon polariton nanolaser opens up new avenues in diverse application areas, ranging from ultrawideband optical communication on a chip to low-power nonlinear photonics, coherent nanospectroscopy, and single-molecule biosensing.

Slow magnetic relaxation in dinuclear dysprosium and holmium phenoxide bridged complexes: a Dy2 single molecule magnet with a high energy barrier

2021 ◽  
Author(s):  
Matilde Fondo ◽  
Julio Corredoira-Vázquez ◽  
Ana M. Garcia-Deibe ◽  
Jesus Sanmartin Matalobos ◽  
Silvia Gómez-Coca ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Single Molecule ◽  
Energy Barrier ◽  
Magnetic Relaxation ◽  
High Energy ◽  
Single Molecule Magnet ◽  
High Energy Barrier ◽  
Slow Magnetic Relaxation

Dinuclear [M(H3L1,2,4)]2 (M = Dy, Dy2; M = Ho, Ho2) complexes were isolated from an heptadentate aminophenol ligand. The crystal structures of Dy2·2THF, and the pyridine adducts Dy2·2Py and Ho2·2Py,...

scholarly journals Roles of the C-Terminal Amino Acids of Non-Hexameric Helicases: Insights from Escherichia coli UvrD

2021 ◽  
Vol 22 (3) ◽  
pp. 1018
Author(s):  
Hiroaki Yokota
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Single Molecule ◽  
Underlying Mechanism ◽  
Amino Acid Sequences ◽  
E Coli ◽  
X Ray Crystallography ◽  
Terminal Amino

Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed “helicase motifs”. Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.

scholarly journals A structural framework for unidirectional transport by a bacterial ABC exporter

2020 ◽  
Vol 117 (32) ◽  
pp. 19228-19236
Author(s):  
Chengcheng Fan ◽  
Jens T. Kaiser ◽  
Douglas C. Rees
Keyword(s):  
Conformational Changes ◽  
Iron Homeostasis ◽  
Atp Hydrolysis ◽  
Transmembrane Helix ◽  
Reverse Direction ◽  
Conformational States ◽  
X Ray Crystallography ◽  
Binding Domains ◽  
Structural Framework ◽  
Glutathione Derivatives

The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog fromNovosphingobium aromaticivorans(NaAtm1) can export glutathione derivatives and confer protection against heavy-metal toxicity. To establish the structural framework underlying theNaAtm1 transport mechanism, we determined eight structures by X-ray crystallography and single-particle cryo-electron microscopy in distinct conformational states, stabilized by individual disulfide crosslinks and nucleotides. AsNaAtm1 progresses through the transport cycle, conformational changes in transmembrane helix 6 (TM6) alter the glutathione-binding site and the associated substrate-binding cavity. Significantly, kinking of TM6 in the post-ATP hydrolysis state stabilized by MgADPVO4eliminates this cavity, precluding uptake of glutathione derivatives. The presence of this cavity during the transition from the inward-facing to outward-facing conformational states, and its absence in the reverse direction, thereby provide an elegant and conceptually simple mechanism for enforcing the export directionality of transport byNaAtm1. One of the disulfide crosslinkedNaAtm1 variants characterized in this work retains significant glutathione transport activity, suggesting that ATP hydrolysis and substrate transport by Atm1 may involve a limited set of conformational states with minimal separation of the nucleotide-binding domains in the inward-facing conformation.

scholarly journals The challenging SED of AP Librae

2011 ◽  
Vol 7 (S284) ◽  
pp. 411-413 ◽  
Author(s):  
David Sanchez ◽  
Berrie Giebels ◽  
Pascal Fortin ◽  
Keyword(s):  
Spectral Energy Distribution ◽  
Broad Band ◽  
Low Frequency ◽  
Theoretical Models ◽  
Intermediate Frequency ◽  
High Energy ◽  
Spectral Energy ◽  
Broad Band Emission ◽  
Band Emission ◽  
Bl Lac

AbstractMatching the broad-band emission of active galaxies with the predictions of theoretical models can be used to derive constraints on the properties of the emitting region and to probe the physical processes involved. AP Librae is the third low frequency peaked BL Lac (LBL) detected at very high energy (VHE, E>100GeV) by an Atmospheric Cherenkov Telescope; most VHE BL Lacs (34 out of 39) belong to the high-frequency and intermediate-frequency BL Lac classes (HBL and IBL). LBL objects tend to have a higher luminosity with lower peak frequencies than HBLs or IBLs. The characterization of their time-averaged spectral energy distribution is challenging for emission models such as synchrotron self-Compton (SSC) models.

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