scholarly journals 20 YEARS OF LEPTIN: Insights into signaling assemblies of the leptin receptor

2014 ◽  
Vol 223 (1) ◽  
pp. T9-T23 ◽  
Author(s):  
Frank Peelman ◽  
Lennart Zabeau ◽  
Kedar Moharana ◽  
Savvas N Savvides ◽  
Jan Tavernier
Keyword(s):  
Electron Microscopy ◽  
Energy Homeostasis ◽  
Leptin Receptor ◽  
Structural Information ◽  
Cell Types ◽  
Activation Mechanism ◽  
Peripheral Cell ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering

Leptin plays a central role in the control of body weight and energy homeostasis, but is a pleiotropic cytokine with activities on many peripheral cell types. In this review, we discuss the interaction of leptin with its receptor, and focus on the structural and mechanistic aspects of the extracellular aspects of leptin receptor (LR) activation. We provide an extensive overview of all structural information that has been obtained for leptin and its receptor via X-ray crystallography, electron microscopy, small-angle X-ray scattering, homology modeling, and mutagenesis studies. The available knowledge is integrated into putative models toward a recapitulation of the LR activation mechanism.

scholarly journals Structure of the Lassa Virus Nucleoprotein Revealed by X-ray Crystallography, Small-angle X-ray Scattering, and Electron Microscopy

2011 ◽  
Vol 286 (44) ◽  
pp. 38748-38756 ◽  
Author(s):  
Linda Brunotte ◽  
Romy Kerber ◽  
Weifeng Shang ◽  
Florian Hauer ◽  
Meike Hass ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Small Angle ◽  
Lassa Virus ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Ray Scattering

Bridging the resolution gap between x-ray crystallography and electron microscopy

1994 ◽  
Vol 52 ◽  
pp. 92-93
Author(s):  
P. L. Stewart ◽  
S. D. Fuller ◽  
R. M. Burnett
Keyword(s):  
Electron Microscopy ◽  
Transfer Function ◽  
Electron Micrographs ◽  
Structural Information ◽  
Crystallographic Structure ◽  
Contrast Transfer Function ◽  
X Ray ◽  
X Ray Crystallography ◽  
Intact Virus

While x-ray crystallography provides atomic resolution structures of proteins and small viruses, electron microscopy can provide complementary structural information on larger assemblies. A significant computational challenge is faced in bridging the resolution gap between the two techniques. X-ray crystallographic data is collected in the range of 2-10 Å, while image reconstructions from electron micrographs are at a resolution of 25-35 Å. A further problem is that density derived from cryo-electron micrographs is distorted by the contrast transfer function of the microscope, whichaccentuates certain resolution bands.A novel combination of electron microscopy and x-ray crystallography has revealed the various structural components forming the capsid of human type 2 adenovirus. An image reconstruction of the intact virus (Fig. 1), derived from cryo-electron micrographs, was deconvolved with an approximate contrast transfer function to mitigate microscope distortions (Fig. 2). A model capsid was calculated from 240 copies of the crystallographic structure of the major capsid protein and filtered to the correct resolution (Fig. 3).

scholarly journals Validation of electron microscopy initial models via small angle X-ray scattering curves

2018 ◽  
Vol 35 (14) ◽  
pp. 2427-2433
Author(s):  
Amaya Jiménez ◽  
Slavica Jonic ◽  
Tomas Majtner ◽  
Joaquín Otón ◽  
Jose Luis Vilas ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Small Angle ◽  
Structural Information ◽  
3D Models ◽  
Particle Analysis ◽  
Biological Macromolecules ◽  
Low Resolution ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Abstract Motivation Cryo electron microscopy (EM) is currently one of the main tools to reveal the structural information of biological macromolecules. The re-construction of three-dimensional (3D) maps is typically carried out following an iterative process that requires an initial estimation of the 3D map to be refined in subsequent steps. Therefore, its determination is key in the quality of the final results, and there are cases in which it is still an open issue in single particle analysis (SPA). Small angle X-ray scattering (SAXS) is a well-known technique applied to structural biology. It is useful from small nanostructures up to macromolecular ensembles for its ability to obtain low resolution information of the biological sample measuring its X-ray scattering curve. These curves, together with further analysis, are able to yield information on the sizes, shapes and structures of the analyzed particles. Results In this paper, we show how the low resolution structural information revealed by SAXS is very useful for the validation of EM initial 3D models in SPA, helping the following refinement process to obtain more accurate 3D structures. For this purpose, we approximate the initial map by pseudo-atoms and predict the SAXS curve expected for this pseudo-atomic structure. The match between the predicted and experimental SAXS curves is considered as a good sign of the correctness of the EM initial map. Availability and implementation The algorithm is freely available as part of the Scipion 1.2 software at http://scipion.i2pc.es/.

scholarly journals Molecular architecture of the yeast Mediator complex

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Philip J Robinson ◽  
Michael J Trnka ◽  
Riccardo Pellarin ◽  
Charles H Greenberg ◽  
David A Bushnell ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Structural Information ◽  
Internal Controls ◽  
Mediator Complex ◽  
Amino Acid Residues ◽  
Molecular Architecture ◽  
Structural Elements ◽  
X Ray ◽  
X Ray Crystallography ◽  
D Model

The 21-subunit Mediator complex transduces regulatory information from enhancers to promoters, and performs an essential role in the initiation of transcription in all eukaryotes. Structural information on two-thirds of the complex has been limited to coarse subunit mapping onto 2-D images from electron micrographs. We have performed chemical cross-linking and mass spectrometry, and combined the results with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an integrative modeling approach to determine a 3-D model of the entire Mediator complex. The approach is validated by the use of X-ray crystal structures as internal controls and by consistency with previous results from electron microscopy and yeast two-hybrid screens. The model shows the locations and orientations of all Mediator subunits, as well as subunit interfaces and some secondary structural elements. Segments of 20–40 amino acid residues are placed with an average precision of 20 Å. The model reveals roles of individual subunits in the organization of the complex.

scholarly journals Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal

2019 ◽  
Author(s):  
Steve P. Meisburger ◽  
David A. Case ◽  
Nozomi Ando
Keyword(s):  
Diffuse Scattering ◽  
Structural Information ◽  
Bragg Diffraction ◽  
Protein Crystal ◽  
Dynamic Information ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Correlated Motions ◽  
Hinge Bending

AbstractProtein dynamics are integral to biological function, yet few techniques are sensitive to collective atomic motions. A long-standing goal of X-ray crystallography has been to combine structural information from Bragg diffraction with dynamic information contained in the diffuse scattering background. However, the origin of macromolecular diffuse scattering has been poorly understood, limiting its applicability. We present a detailed diffuse scattering map from triclinic lysozyme that resolves both inter- and intramolecular correlations. These correlations are studied theoretically using both all-atom molecular dynamics and simple vibrational models. Although lattice dynamics reproduce most of the diffuse pattern, protein internal dynamics, which include hinge-bending motions, are needed to explain the short-ranged correlations revealed by Patterson analysis. These insights lay the groundwork for animating crystal structures with biochemically relevant motions.

Microtubule nucleation sequence studied by time-resolved x-ray scattering and electron microscopy

1983 ◽  
Vol 41 ◽  
pp. 766-767
Author(s):  
Eva-Maria Mandelkow ◽  
Eckhard Mandelkow ◽  
Joan Bordas
Keyword(s):  
Electron Microscopy ◽  
Dynamic Equilibrium ◽  
Time Resolved ◽  
X Ray ◽  
Additional Information ◽  
X Ray Scattering ◽  
Low Concentrations ◽  
Microtubule Growth ◽  
Ray Patterns ◽  
Ray Scattering

When a solution of microtubule protein is changed from non-polymerising to polymerising conditions (e.g. by temperature jump or mixing with GTP) there is a series of structural transitions preceding microtubule growth. These have been detected by time-resolved X-ray scattering using synchrotron radiation, and they may be classified into pre-nucleation and nucleation events. X-ray patterns are good indicators for the average behavior of the particles in solution, but they are difficult to interpret unless additional information on their structure is available. We therefore studied the assembly process by electron microscopy under conditions approaching those of the X-ray experiment. There are two difficulties in the EM approach: One is that the particles important for assembly are usually small and not very regular and therefore tend to be overlooked. Secondly EM specimens require low concentrations which favor disassembly of the particles one wants to observe since there is a dynamic equilibrium between polymers and subunits.

Electron microscopy of rabbit FC crystals

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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