scholarly journals Structural insight on the mechanism of an electron-bifurcating [FeFe] hydrogenase

2021 ◽  
Author(s):  
Chris Furlan ◽  
Nipa Chongdar ◽  
Pooja Gupta ◽  
Wolfgang Lubitz ◽  
Hideaki Ogata ◽  
...  
Keyword(s):  
Energy Conservation ◽  
Structural Information ◽  
Thermotoga Maritima ◽  
Strongly Interacting ◽  
Domain Movement ◽  
Structural Insight

Electron-bifurcation is a fundamental energy conservation mechanism in nature. The electron-bifurcating [FeFe] hydrogenase from Thermotoga maritima (HydABC) requires both NADH and ferredoxin to reduce protons generating hydrogen. The mechanism of electron-bifurcation in HydABC remains enigmatic primarily due to the lack of structural information. Here, we present a 2.3 Å electron cryo-microscopy structure of HydABC. The structure is a heterododecamer composed of two independent ‘halves’ each made of two strongly interacting HydABC trimers electrically connected via a [4Fe-4S] cluster, forming a bus-bar system. Symmetry expansion identified two conformations: a “closed bridge” and an “open bridge” conformation, where a Zn2+ site may act as a “hinge” allowing domain movement. Based on these structural revelations, we propose two new mechanisms of electron-bifurcation in HydABC.

Structural insight on the mechanism of an electron-bifurcating [FeFe] hydrogenase

2021 ◽  
Author(s):  
James Birrell ◽  
Chris Furlan ◽  
Nipa Chongdar ◽  
Pooja Gupta ◽  
Wolfgang Lubitz ◽  
...  
Keyword(s):  
Active Sites ◽  
Structural Information ◽  
Thermotoga Maritima ◽  
Proton Reduction ◽  
Iron Sulfur Cluster ◽  
Electron Transfer Pathway ◽  
Iron Sulfur ◽  
Domain Movement ◽  
Cluster A ◽  
Structural Insight

Abstract Electron-bifurcation is a fundamental energy conservation mechanism in nature. The electron-bifurcating [FeFe] hydrogenase from Thermotoga maritima (HydABC) requires both NADH and ferredoxin to reduce protons generating hydrogen. The mechanism of electron-bifurcation in HydABC remains enigmatic primarily due to the lack of structural information. Here, we present a 2.3 Å electron cryo-microscopy structure of HydABC. The structure is a heterododecamer composed of two independent ‘halves’ each made of two strongly interacting HydABC heterotrimers electrically connected via a [4Fe-4S] cluster. A central electron transfer pathway connects the active sites for NADH oxidation and proton reduction. Symmetry expansion identified two conformations of a flexible iron-sulfur cluster domain: a “closed bridge” and an “open bridge” conformation, where a Zn2+ site may act as a “hinge” allowing domain movement. Based on these structural revelations, we propose two new mechanisms of electron-bifurcation in HydABC.

scholarly journals Bioenergetics of the Archaea

1999 ◽  
Vol 63 (3) ◽  
pp. 570-620 ◽  
Author(s):  
Günter Schäfer ◽  
Martin Engelhard ◽  
Volker Müller
Keyword(s):  
Energy Conservation ◽  
Structural Information ◽  
Protein Complexes ◽  
Extreme Environments ◽  
Primary Energy ◽  
Atomic Scale ◽  
Archaeal Species ◽  
Electron Transport Chains ◽  
Cumulative Knowledge ◽  
Distinct Features

SUMMARY In the late 1970s, on the basis of rRNA phylogeny, Archaea (archaebacteria) was identified as a distinct domain of life besides Bacteria (eubacteria) and Eucarya. Though forming a separate domain, archaea display an enormous diversity of lifestyles and metabolic capabilities. Many archaeal species are adapted to extreme environments with respect to salinity, temperatures around the boiling point of water, and/or extremely alkaline or acidic pH. This has posed the challenge of studying the molecular and mechanistic bases on which these organisms can cope with such adverse conditions. This review considers our cumulative knowledge on archaeal mechanisms of primary energy conservation, in relationship to those of bacteria and eucarya. Although the universal principle of chemiosmotic energy conservation also holds for Archaea, distinct features have been discovered with respect to novel ion-transducing, membrane-residing protein complexes and the use of novel cofactors in bioenergetics of methanogenesis. From aerobically respiring archaea, unusual electron-transporting supercomplexes could be isolated and functionally resolved, and a proposal on the organization of archaeal electron transport chains has been presented. The unique functions of archaeal rhodopsins as sensory systems and as proton or chloride pumps have been elucidated on the basis of recent structural information on the atomic scale. Whereas components of methanogenesis and of phototrophic energy transduction in halobacteria appear to be unique to archaea, respiratory complexes and the ATP synthase exhibit some chimeric features with respect to their evolutionary origin. Nevertheless, archaeal ATP synthases are to be considered distinct members of this family of secondary energy transducers. A major challenge to future investigations is the development of archaeal genetic transformation systems, in order to gain access to the regulation of bioenergetic systems and to overproducers of archaeal membrane proteins as a prerequisite for their crystallization.

Measurement and Reduction of Radiation Damage in Frozen Hydrated Crystalline Specimens

1978 ◽  
Vol 36 (3) ◽  
pp. 70-77 ◽  
Author(s):  
R.M. Glaeser ◽  
S.B. Hayward
Keyword(s):  
Diffraction Pattern ◽  
Structural Information ◽  
Structural Disorder ◽  
Structural Features ◽  
Biological Macromolecules ◽  
Diffraction Intensity ◽  
Object Structure ◽  
Specimen Material ◽  
Unit Cells ◽  
Identical Unit

Highly ordered or crystalline biological macromolecules become severely damaged and structurally disordered after a brief electron exposure. Evidence that damage and structural disorder are occurring is clearly given by the fading and eventual disappearance of the specimen's electron diffraction pattern. The fading and disappearance of sharp diffraction spots implies a corresponding disappearance of periodic structural features in the specimen. By the same token, there is a oneto- one correspondence between the disappearance of the crystalline diffraction pattern and the disappearance of reproducible structural information that can be observed in the images of identical unit cells of the object structure. The electron exposures that result in a significant decrease in the diffraction intensity will depend somewhat upon the resolution (Bragg spacing) involved, and can vary considerably with the chemical makeup and composition of the specimen material.

Direct visualization of phase-separated domains in lipid membranes

1978 ◽  
Vol 36 (2) ◽  
pp. 290-291
Author(s):  
S. W. Hui ◽  
T. P. Stewart
Keyword(s):  
Lipid Membranes ◽  
Structural Information ◽  
Freeze Fracture ◽  
Biological Molecules ◽  
Vacuum Drying ◽  
Direct Visualization ◽  
X Ray Diffraction ◽  
Electron Microscopic ◽  
X Ray ◽  
Hydrocarbon Chains

Direct electron microscopic study of biological molecules has been hampered by such factors as radiation damage, lack of contrast and vacuum drying. In certain cases, however, the difficulties may be overcome by using redundent structural information from repeating units and by various specimen preservation methods. With bilayers of phospholipids in which both the solid and fluid phases co-exist, the ordering of the hydrocarbon chains may be utilized to form diffraction contrast images. Domains of different molecular packings may be recgnizable by placing properly chosen filters in the diffraction plane. These domains would correspond to those observed by freeze fracture, if certain distinctive undulating patterns are associated with certain molecular packing, as suggested by X-ray diffraction studies. By using an environmental stage, we were able to directly observe these domains in bilayers of mixed phospholipids at various temperatures at which their phases change from misible to inmissible states.

High-Resolution Scanning Electron Microscopy of Biological Specimens

1988 ◽  
Vol 46 ◽  
pp. 186-187
Author(s):  
M. Müller ◽  
R. Hermann
Keyword(s):  
High Resolution ◽  
Freeze Drying ◽  
Room Temperature ◽  
Structural Information ◽  
Freeze Substitution ◽  
Critical Point Drying ◽  
Sem Study ◽  
Major Factors ◽  
Structural Preservation ◽  
Preparation Techniques

Three major factors must be concomitantly assessed in order to extract relevant structural information from the surface of biological material at high resolution (2-3nm).Procedures based on chemical fixation and dehydration in graded solvent series seem inappropriate when aiming for TEM-like resolution. Cells inevitably shrink up to 30-70% of their initial volume during gehydration; important surface components e.g. glycoproteins may be lost. These problems may be circumvented by preparation techniques based on cryofixation. Freezedrying and freeze-substitution followed by critical point drying yields improved structural preservation in TEM. An appropriate preservation of dimensional integrity may be achieved by freeze-drying at - 85° C. The sample shrinks and may partially collapse as it is warmed to room temperature for subsequent SEM study. Observations at low temperatures are therefore a necessary prerequisite for high fidelity SEM. Compromises however have been unavoidable up until now. Aldehyde prefixation is frequently needed prior to freeze drying, rendering the sample resistant to treatment with distilled water.

Ultimate resolution and information in electron microscopy

1991 ◽  
Vol 49 ◽  
pp. 496-497
Author(s):  
D. Van Dyck
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Transfer Function ◽  
Information Transfer ◽  
Communication Channel ◽  
Structural Information ◽  
Information Rate ◽  
Noise Power ◽  
Signal Power ◽  
Imaging Device

An (electron) microscope can be considered as a communication channel that transfers structural information between an object and an observer. In electron microscopy this information is carried by electrons. According to the theory of Shannon the maximal information rate (or capacity) of a communication channel is given by C = B log2 (1 + S/N) bits/sec., where B is the band width, and S and N the average signal power, respectively noise power at the output. We will now apply to study the information transfer in an electron microscope. For simplicity we will assume the object and the image to be onedimensional (the results can straightforwardly be generalized). An imaging device can be characterized by its transfer function, which describes the magnitude with which a spatial frequency g is transferred through the device, n is the noise. Usually, the resolution of the instrument ᑭ is defined from the cut-off 1/ᑭ beyond which no spadal information is transferred.

Automated electron tomography: from data collection to image processing

1995 ◽  
Vol 53 ◽  
pp. 26-27
Author(s):  
Weiping Liu ◽  
Jennifer Fung ◽  
W.J. de Ruijter ◽  
Hans Chen ◽  
John W. Sedat ◽  
...  
Keyword(s):  
Image Processing ◽  
Data Collection ◽  
Structural Information ◽  
Imaging Technique ◽  
Electron Tomography ◽  
Ccd Camera ◽  
Automated Data Collection ◽  
Full Control ◽  
Transmission Electron ◽  
Amorphous Structures

Electron tomography is a technique where many projections of an object are collected from the transmission electron microscope (TEM), and are then used to reconstruct the object in its entirety, allowing internal structure to be viewed. As vital as is the 3-D structural information and with no other 3-D imaging technique to compete in its resolution range, electron tomography of amorphous structures has been exercised only sporadically over the last ten years. Its general lack of popularity can be attributed to the tediousness of the entire process starting from the data collection, image processing for reconstruction, and extending to the 3-D image analysis. We have been investing effort to automate all aspects of electron tomography. Our systems of data collection and tomographic image processing will be briefly described.To date, we have developed a second generation automated data collection system based on an SGI workstation (Fig. 1) (The previous version used a micro VAX). The computer takes full control of the microscope operations with its graphical menu driven environment. This is made possible by the direct digital recording of images using the CCD camera.

Applications of Time-OF-Flight Secondary Ion Mass Spectrometry (TOF-SIMS)

1990 ◽  
Vol 48 (2) ◽  
pp. 308-309
Author(s):  
Bruno Schueler ◽  
Robert W. Odom
Keyword(s):  
Mass Spectrometry ◽  
Secondary Ion Mass Spectrometry ◽  
Structural Information ◽  
Time Of Flight ◽  
Biological Tissues ◽  
Polymer Surfaces ◽  
Tof Sims ◽  
Secondary Ions ◽  
Ion Mass Spectrometry ◽  
Secondary Ion

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) provides unique capabilities for elemental and molecular compositional analysis of a wide variety of surfaces. This relatively new technique is finding increasing applications in analyses concerned with determining the chemical composition of various polymer surfaces, identifying the composition of organic and inorganic residues on surfaces and the localization of molecular or structurally significant secondary ions signals from biological tissues. TOF-SIMS analyses are typically performed under low primary ion dose (static SIMS) conditions and hence the secondary ions formed often contain significant structural information.This paper will present an overview of current TOF-SIMS instrumentation with particular emphasis on the stigmatic imaging ion microscope developed in the authors’ laboratory. This discussion will be followed by a presentation of several useful applications of the technique for the characterization of polymer surfaces and biological tissues specimens. Particular attention in these applications will focus on how the analytical problem impacts the performance requirements of the mass spectrometer and vice-versa.

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