MD simulation of high-resolution X-ray structures reveals post-translational modification dependent conformational changes in HSF-DNA interaction

AbstractMulti-domain proteins (MDPs) show a variety of domain conformations under physiological conditions, regulating their functions through such conformational changes. One of the typical MDPs, ER-60 which is a protein folding enzyme, has a U-shape with four domains and is thought to have different domain conformations in solution depending on the redox state at the active centres of the edge domains. In this work, an aggregation-free small-angle X-ray scattering revealed that the structures of oxidized and reduced ER-60 in solution are different from each other and are also different from those in the crystal. Furthermore, structural modelling with coarse-grained molecular dynamics simulation indicated that the distance between the two edge domains of oxidized ER-60 is longer than that of reduced ER-60. In addition, one of the edge domains has a more flexible conformation than the other.

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Using X-ray Footprinting and Mass Spectrometry to Study the Structure and Function of Membrane Proteins

Protein and Peptide Letters ◽

10.2174/0929866526666181128142401 ◽

2019 ◽

Vol 26 (1) ◽

pp. 44-54

Author(s):

Sayan Gupta

Keyword(s):

Mass Spectrometry ◽

High Resolution ◽

Membrane Proteins ◽

Conformational Changes ◽

Solvent Accessibility ◽

Structural Data ◽

Specific Information ◽

High Concentration ◽

X Ray ◽

And Function

Background: Membrane proteins are crucial for cellular sensory cascades and metabolite transport, and hence are key pharmacological targets. Structural studies by traditional highresolution techniques are limited by the requirements for high purity and stability when handled in high concentration and nonnative buffers. Hence, there is a growing requirement for the use of alternate methods in a complementary but orthogonal approach to study the dynamic and functional aspects of membrane proteins in physiologically relevant conditions. In recent years, significant progress has been made in the field of X-ray radiolytic labeling in combination with mass spectroscopy, commonly known as X-ray Footprinting and Mass Spectrometry (XFMS), which provide residue-specific information on the solvent accessibility of proteins. In combination with both lowresolution biophysical methods and high-resolution structural data, XFMS is capable of providing valuable insights into structure and dynamics of membrane proteins, which have been difficult to obtain by standalone high-resolution structural techniques. The XFMS method has also demonstrated a unique capability for identification of structural waters and their dynamics in protein cavities at both a high degree of spatial and temporal resolution, and thus capable of identifying conformational hot-spots in transmembrane proteins. Conclusion: We provide a perspective on the place of XFMS amongst other structural biology methods and showcase some of the latest developments in its usage for studying conformational changes in membrane proteins.

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Genuine open form of the pentameric ligand-gated ion channel GLIC

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s1399004714026698 ◽

2015 ◽

Vol 71 (3) ◽

pp. 454-460 ◽

Cited By ~ 19

Author(s):

Zaineb Fourati ◽

Ludovic Sauguet ◽

Marc Delarue

Keyword(s):

Crystal Structure ◽

High Resolution ◽

Conformational Changes ◽

Computational Studies ◽

Potential Influence ◽

X Ray ◽

Correct Assignment ◽

High Resolution Structure ◽

Fast Chemical ◽

Resolution Structure

Pentameric ligand-gated ion channels (pLGICs) mediate fast chemical neurotransmission of nerve signalling in the central and peripheral nervous systems. GLIC is a bacterial homologue of eukaryotic pLGIC, the X-ray structure of which has been determined in three different conformations. GLIC is thus widely used as a model to study the activation and the allosteric transition of this family of receptors. The recently solved high-resolution structure of GLIC (2.4 Å resolution) in the active state revealed two bound acetate molecules in the extracellular domain (ECD). Here, it is shown that these two acetates exactly overlap with known sites of pharmacological importance in pLGICs, and their potential influence on the structure of the open state is studied in detail. Firstly, experimental evidence is presented for the correct assignment of these acetate molecules by using the anomalous dispersion signal of bromoacetate. Secondly, the crystal structure of GLIC in the absence of acetate was solved and it is shown that acetate binding induces local conformational changes that occur in strategic sites of the ECD. It is expected that this acetate-free structure will be useful in future computational studies of the gating transition in GLIC and other pLGICs.

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Electron microscopy of rabbit FC crystals

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100077220 ◽

1983 ◽

Vol 41 ◽

pp. 730-731

Author(s):

Robert A. Grant ◽

Laura L. Degn ◽

Wah Chiu ◽

John Robinson

Keyword(s):

Electron Microscopy ◽

High Resolution ◽

High Resolution Electron Microscopy ◽

Molecular Replacement ◽

X Ray ◽

X Ray Crystallography ◽

Resolution Electron ◽

Replacement Technique ◽

Hydrated Crystal ◽

Molecular Structure Analysis

Proteolytic digestion of the immunoglobulin IgG with papain cleaves the molecule into an antigen binding fragment, Fab, and a compliment binding fragment, Fc. Structures of intact immunoglobulin, Fab and Fc from various sources have been solved by X-ray crystallography. Rabbit Fc can be crystallized as thin platelets suitable for high resolution electron microscopy. The structure of rabbit Fc can be expected to be similar to the known structure of human Fc, making it an ideal specimen for comparing the X-ray and electron crystallographic techniques and for the application of the molecular replacement technique to electron crystallography. Thin protein crystals embedded in ice diffract to high resolution. A low resolution image of a frozen, hydrated crystal can be expected to have a better contrast than a glucose embedded crystal due to the larger density difference between protein and ice compared to protein and glucose. For these reasons we are using an ice embedding technique to prepare the rabbit Fc crystals for molecular structure analysis by electron microscopy.

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High Resolution Study of Polytypism: Application to SiC and Au3 Mn

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100055540 ◽

1982 ◽

Vol 40 ◽

pp. 540-541

Author(s):

G. Van Tendeloo ◽

J. Van Landuyt ◽

S. Amelinckx

Keyword(s):

Electron Microscopy ◽

High Resolution ◽

Stacking Sequence ◽

X Ray ◽

Powerful Technique ◽

Resolution Study ◽

The Ideal

Polytypism has been studied for a number of years and a wide variety of stacking sequences has been detected and analysed. SiC is the prototype material in this respect; see e.g. Electron microscopy under high resolution conditions when combined with x-ray measurements is a very powerful technique to elucidate the correct stacking sequence or to study polytype transformations and deviations from the ideal stacking sequence.

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A High Resolution Study of G.P. Zones in Aluminum - 4.2 at % Silver

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100055904 ◽

1982 ◽

Vol 40 ◽

pp. 722-723 ◽

Cited By ~ 1

Author(s):

R. Gronsky

Keyword(s):

Electron Microscopy ◽

Transmission Electron Microscopy ◽

High Resolution ◽

Computer Simulations ◽

Structural Characteristics ◽

X Ray Diffraction ◽

X Ray ◽

Transmission Electron ◽

Resolution Study

The phenomenon of clustering in Al-Ag alloys has been extensively studied since the early work of Guinierl, wherein the pre-precipitation state was characterized as an assembly of spherical, ordered, silver-rich G.P. zones. Subsequent x-ray and TEM investigations yielded results in general agreement with this model. However, serious discrepancies were later revealed by the detailed x-ray diffraction - based computer simulations of Gragg and Cohen, i.e., the silver-rich clusters were instead octahedral in shape and fully disordered, atleast below 170°C. The object of the present investigation is to examine directly the structural characteristics of G.P. zones in Al-Ag by high resolution transmission electron microscopy.

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Scanning Electron Microscopy and x-ray analysis of microparticles and early hydration effects

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100139834 ◽

1995 ◽

Vol 53 ◽

pp. 692-693

Author(s):

Yun Lu ◽

David C. Joy

Keyword(s):

Electron Microscopy ◽

Scanning Electron Microscopy ◽

High Resolution ◽

Morphological Development ◽

Early Hydration ◽

X Ray ◽

Blended Cements ◽

Powder Particles ◽

Chemical Wastes ◽

Scanning Electron

High resolution scanning electron microscopy (SEM) and energy dispersive x-ray analysis (EDXA) were performed to investigate microparticles in blended cements and their hydration products containing sodium-rich chemical wastes. The physical appearance of powder particles and the morphological development at different hydration stages were characterized by using high resolution SEM Hitachi S-900 and by SEM S-800 with a EDX spectrometer. Microparticles were dispersed on the sample holder and glued by 1% palomino solution. Hydrated bulk samples were dehydrated by acetone and mounted on the holder by silver paste. Both fracture surfaces and flat cutting sections of hydrating samples were prepared and examined. Some specimens were coated with an 3 nm thick Au-Pd or Cr layer to provide good conducting surfaces. For high resolution SEM S-900 observations the accelerating voltage of electrons was 1-2 KeV to protect the electron charging. Microchemical analyses were carried out by S800/EDS equipped with a LINK detector of take-off angle =40°.

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Tubulin structure at intermediate resolution

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100140634 ◽

1995 ◽

Vol 53 ◽

pp. 852-853

Author(s):

K. H. Downing ◽

S. G. Wolf ◽

E. Nogales

Keyword(s):

High Resolution ◽

Structural Data ◽

Therapeutic Drug ◽

Zinc Ions ◽

Two Dimensional ◽

X Ray Diffraction ◽

X Ray ◽

Negative Stain ◽

Functional Mechanisms ◽

Tubulin Structure

Microtubules are involved in a host of critical cell activities, many of which involve transport of organelles through the cell. Different sets of microtubules appear to form during the cell cycle for different functions. Knowledge of the structure of tubulin will be necessary in order to understand the various functional mechanisms of microtubule assemble, disassembly, and interaction with other molecules, but tubulin has so far resisted crystallization for x-ray diffraction studies. Fortuitously, in the presence of zinc ions, tubulin also forms two-dimensional, crystalline sheets that are ideally suited for study by electron microscopy. We have refined procedures for forming the sheets and preparing them for EM, and have been able to obtain high-resolution structural data that sheds light on the formation and stabilization of microtubules, and even the interaction with a therapeutic drug.Tubulin sheets had been extensively studied in negative stain, demonstrating that the same protofilament structure was formed in the sheets and microtubules. For high resolution studies, we have found that the sheets embedded in either glucose or tannin diffract to around 3 Å.

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Nano-probe x-ray analysis and high-resolution imaging on planar defects in high-pressure synthesized infinite-layer superconductor

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100171377 ◽

1994 ◽

Vol 52 ◽

pp. 728-729

Author(s):

Y. Y. Wang ◽

H. Zhang ◽

V. P. Dravid ◽

H. Zhang ◽

L. D. Marks ◽

...

Keyword(s):

High Pressure ◽

High Resolution ◽

Atomic Structure ◽

Emission Spectra ◽

High Resolution Electron Microscopy ◽

Planar Defects ◽

X Ray ◽

Infinite Layer ◽

Resolution Electron ◽

Resolution Imaging

Azuma et al. observed planar defects in a high pressure synthesized infinitelayer compound (i.e. ACuO2 (A=cation)), which exhibits superconductivity at ~110 K. It was proposed that the defects are cation deficient and that the superconductivity in this material is related to the planar defects. In this report, we present quantitative analysis of the planar defects utilizing nanometer probe xray microanalysis, high resolution electron microscopy, and image simulation to determine the chemical composition and atomic structure of the planar defects. We propose an atomic structure model for the planar defects.Infinite-layer samples with the nominal chemical formula, (Sr1-xCax)yCuO2 (x=0.3; y=0.9,1.0,1.1), were prepared using solid state synthesized low pressure forms of (Sr1-xCax)CuO2 with additions of CuO or (Sr1-xCax)2CuO3, followed by a high pressure treatment.Quantitative x-ray microanalysis, with a 1 nm probe, was performed using a cold field emission gun TEM (Hitachi HF-2000) equipped with an Oxford Pentafet thin-window x-ray detector. The probe was positioned on the planar defects, which has a 0.74 nm width, and x-ray emission spectra from the defects were compared with those obtained from vicinity regions.

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Characterisation of planar crystal defects in Y2Fe17Cx (0.6 ≤ x ≤ 1.6) magnetic material by High Resolution Electron Microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100177003 ◽

1990 ◽

Vol 48 (4) ◽

pp. 774-775

Author(s):

W. Coene ◽

F. Hakkens ◽

T.H. Jacobs ◽

K.H.J. Buschow

Keyword(s):

Electron Microscopy ◽

High Resolution ◽

Permanent Magnets ◽

Annealing Treatment ◽

High Resolution Electron Microscopy ◽

Crystal Defects ◽

Ordered Structure ◽

X Ray ◽

Planar Crystal ◽

Resolution Electron

Intermetallic compounds of the type RE2Fe17Cx (RE= rare earth element) are promising candidates for permanent magnets. In case of Y2Fe17Cx, the Curie temperature increases from 325 K for x =0 to 550 K for x = 1.6 . X ray and electron diffraction reveal a carbon - induced structural transformation in Y2Fe17Cx from the hexagonal Th2Ni17 - type (x < 0.6 ) to the rhombohedral Th2Zn17 - type ( x ≥ 0.6). Planar crystal defects introduce local sheets of different magnetic anisotropy as compared with the ordered structure, and therefore may have an important impact on the coercivivity mechanism .High resolution electron microscopy ( HREM ) on a Philips CM30 / Super Twin has been used to characterize planar crystal defects in rhombohedral Y2Fe17Cx ( x ≥ 0.6 ). The basal plane stacking sequences are imaged in the [100] - orientation, showing an ABC or ACB sequence of Y - atoms and Fe2 - dumbbells, for both coaxial twin variants, respectively . Compounds resulting from a 3 - week annealing treatment at high temperature ( Ta = 1000 - 1100°C ) contain a high density of planar defects.

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