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A R Faruqi

Publications and source records attributed to A R Faruqi.

17 recordsLinked to original sources
PubMed2006

Electron imaging with Medipix2 hybrid pixel detector.

The electron imaging performance of Medipix2 is described. Medipix2 is a hybrid pixel detector composed of two layers. It has a sensor layer and a layer of readout electronics, in which each 55 microm x 55 microm pixel has upper and lower energy discrimination and MHz rate counting. The sensor layer consists of a 300 microm slab of pixellated monolithic silicon and this is bonded to the readout chip. Experimental measurement of the detective quantum efficiency, DQE(0) at 120 keV shows that it can reach approximately 85% independent of electron exposure, since the detector has zero noise, and the DQE(Nyquist) can reach approximately 35% of that expected for a perfect detector (4/pi(2)). Experimental measurement of the modulation transfer function (MTF) at Nyquist resolution for 120 keV electrons using a 60 keV lower energy threshold, yields a value that is 50% of that expected for a perfect detector (2/pi). Finally, Monte Carlo simulations of electron tracks and energy deposited in adjacent pixels have been performed and used to calculate expected values for the MTF and DQE as a function of the threshold energy. The good agreement between theory and experiment allows suggestions for further improvements to be made with confidence. The present detector is already very useful for experiments that require a high DQE at very low doses.

Computer Simulation↗
PubMed2006

Digitisation of electron microscope films: six useful tests applied to three film scanners.

A series of simple tests have been used to measure the performance of flat-bed film scanners suitable for digitisation of electron micrographs. Two of the film scanners evaluated are commercially available and one has been constructed in the laboratory paying special attention to the needs of the electron microscopist. The tests may be useful for others.

Image Processing, Computer-Assisted↗
PubMed2003

Evaluation of a hybrid pixel detector for electron microscopy.

We describe the application of a silicon hybrid pixel detector, containing 64 by 64 pixels, each 170 microm(2), in electron microscopy. The device offers improved resolution compared to CCDs along with faster and noiseless readout. Evaluation of the detector, carried out on a 120 kV electron microscope, demonstrates the potential of the device.

Electrons↗
PubMed1999

Protein conformational changes in the bacteriorhodopsin photocycle.

We report a comprehensive electron crystallographic analysis of conformational changes in the photocycle of wild-type bacteriorhodopsin and in a variety of mutant proteins with kinetic defects in the photocycle. Specific intermediates that accumulate in the late stages of the photocycle of wild-type bacteriorhodopsin, the single mutants D38R, D96N, D96G, T46V, L93A and F219L, and the triple mutant D96G/F171C/F219L were trapped by freezing two-dimensional crystals in liquid ethane at varying times after illumination with a light flash. Electron diffraction patterns recorded from these crystals were used to construct projection difference Fourier maps at 3.5 A resolution to define light-driven changes in protein conformation. Our experiments demonstrate that in wild-type bacteriorhodopsin, a large protein conformational change occurs within approximately 1 ms after illumination. Analysis of structural changes in wild-type and mutant bacteriorhodopsins under conditions when either the M or the N intermediate is preferentially accumulated reveals that there are only small differences in structure between M and N intermediates trapped in the same protein. However, a considerably larger variation is observed when the same optical intermediate is trapped in different mutants. In some of the mutants, a partial conformational change is present even prior to illumination, with additional changes occurring upon illumination. Selected mutations, such as those in the D96G/F171C/F219L triple mutant, can sufficiently destabilize the wild-type structure to generate almost the full extent of the conformational change in the dark, with minimal additional light-induced changes. We conclude that the differences in structural changes observed in mutants that display long-lived M, N or O intermediates are best described as variations of one fundamental type of conformational change, rather than representing structural changes that are unique to the optical intermediate that is accumulated. Our observations thus support a simplified view of the photocycle of wild-type bacteriorhodopsin in which the structures of the initial state and the early intermediates (K, L and M1) are well approximated by one protein conformation, while the structures of the later intermediates (M2, N and O) are well approximated by the other protein conformation. We propose that in wild-type bacteriorhodopsin and in most mutants, this conformational change between the M1 and M2 states is likely to make an important contribution towards efficiently switching proton accessibility of the Schiff base from the extracellular side to the cytoplasmic side of the membrane.

Bacteriorhodopsins↗
PubMed1998

Design principles and applications of a cooled CCD camera for electron microscopy.

Cooled CCD cameras offer a number of advantages in recording electron microscope images with CCDs rather than film which include: immediate availability of the image in a digital format suitable for further computer processing, high dynamic range, excellent linearity and a high detective quantum efficiency for recording electrons. In one important respect however, film has superior properties: the spatial resolution of CCD detectors tested so far (in terms of point spread function or modulation transfer function) are inferior to film and a great deal of our effort has been spent in designing detectors with improved spatial resolution. Various instrumental contributions to spatial resolution have been analysed and in this paper we discuss the contribution of the phosphor-fibre optics system in this measurement. We have evaluated the performance of a number of detector components and parameters, e.g. different phosphors (and a scintillator), optical coupling with lens or fibre optics with various demagnification factors, to improve the detector performance. The camera described in this paper, which is based on this analysis, uses a tapered fibre optics coupling between the phosphor and the CCD and is installed on a Philips CM12 electron microscope equipped to perform cryo-microscopy. The main use of the camera so far has been in recording electron diffraction patterns from two dimensional crystals of bacteriorhodopsin--from wild type and from different trapped states during the photocycle. As one example of the type of data obtained with the CCD camera a two dimensional Fourier projection map from the trapped O-state is also included. With faster computers, it will soon be possible to undertake this type of work on an on-line basis. Also, with improvements in detector size and resolution, CCD detectors, already ideal for diffraction, will be able to compete with film in the recording of high resolution images.

Fiber Optic Technology↗
PubMed1997

Electron diffraction studies of light-induced conformational changes in the Leu-93 --> Ala bacteriorhodopsin mutant.

We previously have presented evidence for prominent structural changes in helices F and G of bacteriorhodopsin during the photocycle. These changes were determined by carrying out electron diffraction analysis of illuminated two-dimensional crystals of wild-type bacteriorhodopsin or the Asp-96 --> Gly mutant that were trapped at a stage in the photocycle after light-driven proton release, but preceding proton uptake from the aqueous medium. Here, we report structural analysis of the long-lived O intermediate observed in the photocycle of the Leu-93 --> Ala mutant, which accumulates after the release and uptake of protons, but before the reisomerization of retinal to its initial all-trans state. Projection Fourier difference maps show that upon illumination of the Leu-93 --> Ala mutant, significant structural changes occur in the vicinity of helices C, B, and G, and to a lesser extent near helix F. Our results suggest that (i) all four helices that line the proton channel (B, C, F, and G) participate in structural changes during the late stages of the photocycle, and (ii) completion of the photocycle involves significant conformational changes in addition to those that are associated with steps in proton transport.

Bacteriorhodopsins↗
PubMed1993

Structural studies on the conformations of myosin.

Myosin is the major motor protein found in vertebrate striated and smooth muscle and in non-muscle cells where, in association with actin, its main role is to convert chemical energy into mechanical work. Smooth muscle and non-muscle myosin adopts a number of different conformations: for example an unfolded (6S) form which is capable of forming filaments and generating force and a 'folded' (10S) form, which is most probably a storage form incapable of forming filaments. In the 10S form the products of ATP cleavage are trapped by the folded tails and the ATPase activity of myosin is greatly reduced. It is believed that a transition to the unfolded 6S form is necessary prior to filament formation. We report here on two relatively low resolution structural techniques for studying hydrated myosin. We have used a relatively recent development in microscopy, the scanning tunneling microscope, to image a series of biologically interesting specimen, mainly to evaluate the potential of the technique. There are significant potential advantages for imaging biological specimen with the STM as the imaging is done in air and the specimen can be imaged without a metal coating. Our experience with imaging myosin suggests that good images of hydrated myosin can be obtained but with poor reproducibility. We have also carried out small angle solution x-ray scattering studies on the two myosin conformations to explore the possibilities of doing kinetic measurements on the transition between the two states. Small angle scattering from the S1 fragment are re-constituted parts of the rod have also been carried out and the data is compared with expected scattering from model structures.

Animals↗
PubMed1991

Small angle X-ray scattering studies on myosin.

Small angle X-ray scattering (SAXS) is a potentially powerful method for obtaining structural information from biological molecules in solution. The use of this technique in the laboratory has hitherto been limited by the long exposures necessary to obtain patterns on photographic film. Multi-wire area detectors, due to their high efficiency and absence of noise, enable patterns to be collected much more rapidly, typically in 1-2 h for a typical protein using laboratory sources. This opens up the possibility of using the technique on a semi-routine basis for a wide variety of problems. We outline the use of SAXS to characterise a large conformational change of myosin.

Animals↗
PubMed1986

Structural changes during activation of frog muscle studied by time-resolved X-ray diffraction.

The pattern given by contracting frog muscle can be followed with high time resolution using synchrotron radiation as a high-intensity X-ray source. We have studied the behaviour of the second actin layer-line (axial spacing of approximately 179 A) at an off-meridional spacing of approximately 0.023 A-1, a region of the diagram that is sensitive to the position of tropomyosin in the thin filaments. In confirmation of earlier work, we find that there is a substantial increase in the intensity of this part of the pattern during contraction. We find that the reflection reaches half its final intensity about 17 milliseconds after the stimulus at 6 degrees C. The changes in the equatorial reflections, which arise from movement of crossbridges towards the thin filaments, occur with a delay of about 12 to 17 milliseconds relative to this change in the actin pattern. In over-stretched muscle, where thick and thin filaments no longer overlap, the changes in the actin second layer-line still take place upon stimulation with a time course and intensity similar to that observed at full overlap. This indicates that tropomyosin movement, in response to calcium binding to troponin, is the first structural step in muscular contraction, and is the prerequisite for myosin binding. A change in intensity similar to that found in contracting muscle is seen in rigor, where tropomyosin is probably locked in the active position. During relaxation the earlier stages in the decrease in intensity of the second actin layer-line take place significantly sooner after the last stimulus than tension decay. In over-stretched muscles the intensity decay is appreciably faster than in the same muscles at rest length, where attached crossbridges may interfere with the return of tropomyosin to its resting position.

Actins↗
PubMed1983

Changes in the X-ray reflections from contracting muscle during rapid mechanical transients and their structural implications.

During normal contractions of vertebrate striated muscle, it is believed that the cross-bridges which produce the sliding force undergo asynchronous cyclical changes in their structure. Thus, an X-ray diffraction diagram from a muscle under these conditions will give structural information averaged over the whole range of cross-bridge states. Such diagrams show characteristic and informative differences from those given by relaxed muscle, but can give little information about changes in the configuration of the cross-bridges at different stages of their working stroke. However, it is possible to effect a partial synchronization of these changes by applying very rapid changes in length, completed in less than one millisecond to an otherwise isometrically contracting muscle. If the amplitude of these length changes is comparable to the length of the cross-bridge stroke (say 100 A per half-sarcomere), then it should bring about a transient but significant redistribution of cross-bridge states, which would show up in the X-ray diagram. We have made use of synchrotron radiation as a high intensity X-ray source in order to record such patterns with the necessary time resolution (1 ms or less) and have found major changes in the intensity of the 143 A meridional reflection accompanying the rapid length changes of the muscle. These changes appear to arise from specific configurational changes in the cross-bridges during the working stroke. A model is suggested in which the 143 A meridional intensity in a contracting muscle arises mainly from attached cross-bridges and is generated by the part of the myosin head near the S1-S2 junction. During normal contraction, cross-bridges go through their structural cycle asynchronously with each other, since they start at different times, but if the S2 changes in length rather little, then the configurational changes in the myosin heads are synchronized with the actin filament movement in such a way that the S1-S2 junction remains relatively fixed in its axial position. In a quick release, it is suggested that bringing many S1 heads simultaneously to the end of their working strokes on actin disrupts the 143 A axial repeat of their distal ends near S2, and brings about the large decrease of the 143 A meridional reflection. This model therefore involves a large change in the position of part of the myosin head structure relative to actin during the working stroke of the cross-bridge.

Animals↗
PubMed1981

Millisecond time-resolved changes in x-ray reflections from contracting muscle during rapid mechanical transients, recorded using synchrotron radiation.

Low-angle x-ray diffraction diagrams have been recorded from frog sartorius muscles by using synchrotron radiation as a high-intensity x-ray source. This has enabled changes in some of the principal reflections of interest to be followed with a time resolution of 1 ms, during small but very rapid length changes imposed on a contracting muscle. The 143-A meridional reflection, which is believed to arise from a repeating pattern of myosin cross-bridges along the length of the muscle, shows large changes in intensity in these circumstances. During both rapid releases and rapid stretches, by amounts that produce a translation of actin and myosin filaments past each other by about 100 A and that are completed in about a millisecond (i.e., before significant cross-bridge detachment would be expected), an almost synchronous decrease in 143-A intensity occurs, by 50% or more. This is followed, in the case of quick releases, by a rapid partial recovery of intensity lasting 5--6 ms (which may represent cross-bridge release and reattachment) and then by a more gradual return to the normal isometric value. Quick stretches show only the slower return of intensity. Immediately after the length change, the initial drop in 143-A intensity can be reversed if the release (or stretch) is reversed. These changes provide evidence of a more direct kind than has hitherto been available that the active sliding of actin filaments past myosin filaments during contraction is produced by longitudinal movement of attached cross-bridges.

Actins↗
PubMed1980

The use of synchrotron radiation in time-resolved X-ray diffraction studies of myosin layer-line reflections during muscle contraction.

Experiments on striated muscle have been carried out at the EMBL Outstation at DESY, Hamburg, using the electron-positron storage ring DORIS as a high-intensity X-ray source. The low-angle reflections from the myosin cross-bridges could be recorded more than 1,000 times more rapidly than with the best conventional X-ray sources, and could be followed during contraction with a time resolution of 10 ms.

Animals↗