Structure characterisation method for ideal and non-ideal twisted plywoods

Soft Matter ◽  
2014 ◽  
Vol 10 (47) ◽  
pp. 9446-9453 ◽  
Author(s):  
Oscar F. Aguilar Gutierrez ◽  
Alejandro D. Rey
Keyword(s):  
3D Structure ◽  
Intrinsic Curvature

We provide a proposed methodology for characterizing and reconstructing the 3D structure of biological plywoods from 2D experimental observations by considering the periodicity of the observed arcs and its intrinsic curvature, allowing the determination of p0 and h.

scholarly journals 3D structure determination of native mammalian cells using cryo-FIB and cryo-electron tomography

2012 ◽  
Vol 180 (2) ◽  
pp. 318-326 ◽  
Author(s):  
Ke Wang ◽  
Korrinn Strunk ◽  
Gongpu Zhao ◽  
Jennifer L. Gray ◽  
Peijun Zhang
Keyword(s):  
Structure Determination ◽  
Mammalian Cells ◽  
Electron Tomography ◽  
3D Structure ◽  
Cryo Electron Tomography ◽  
3D Structure Determination

scholarly journals 3D structure determination of amyloid fibrils using solid-state NMR spectroscopy

Methods ◽  
2018 ◽  
Vol 138-139 ◽  
pp. 26-38 ◽  
Author(s):  
Antoine Loquet ◽  
Nadia El Mammeri ◽  
Jan Stanek ◽  
Mélanie Berbon ◽  
Benjamin Bardiaux ◽  
...  
Keyword(s):  
Solid State ◽  
Nmr Spectroscopy ◽  
Structure Determination ◽  
Solid State Nmr ◽  
Amyloid Fibrils ◽  
3D Structure ◽  
Solid State Nmr Spectroscopy ◽  
3D Structure Determination

scholarly journals Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 432 ◽  
Author(s):  
Chandran Nithin ◽  
Pritha Ghosh ◽  
Janusz Bujnicki
Keyword(s):  
Rna Splicing ◽  
Structure Prediction ◽  
Protein Complexes ◽  
3D Structure ◽  
Structural Models ◽  
Computational Prediction ◽  
Computational Docking ◽  
3D Structure Prediction ◽  
Rna Protein Complexes

RNA-protein (RNP) interactions play essential roles in many biological processes, such as regulation of co-transcriptional and post-transcriptional gene expression, RNA splicing, transport, storage and stabilization, as well as protein synthesis. An increasing number of RNP structures would aid in a better understanding of these processes. However, due to the technical difficulties associated with experimental determination of macromolecular structures by high-resolution methods, studies on RNP recognition and complex formation present significant challenges. As an alternative, computational prediction of RNP interactions can be carried out. Structural models obtained by theoretical predictive methods are, in general, less reliable compared to models based on experimental measurements but they can be sufficiently accurate to be used as a basis for to formulating functional hypotheses. In this article, we present an overview of computational methods for 3D structure prediction of RNP complexes. We discuss currently available methods for macromolecular docking and for scoring 3D structural models of RNP complexes in particular. Additionally, we also review benchmarks that have been developed to assess the accuracy of these methods.

scholarly journals Individual subunits of a rhinovirus causing common cold exhibit largely different protein-RNA contact site conformations

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Dieter Blaas
Keyword(s):  
Common Cold ◽  
3D Structure ◽  
Conformational Heterogeneity ◽  
Amino Acid Residues ◽  
Assembly Mechanism ◽  
Gradual Loss ◽  
Density Map ◽  
The Common

Abstract Rhinoviruses cause the common cold. They are icosahedral, built from sixty copies each of the capsid proteins VP1 through VP4 arranged in a pseudo T = 3 lattice. This shell encases a ss(+) RNA genome. Three-D classification of single and oligomeric asymmetric units computationally excised from a 2.9 Å cryo-EM density map of rhinovirus A89, showed that VP4 and the N-terminal extension of VP1 adopt different conformations within the otherwise identical 3D-structures. Analysis of up to sixty classes of single subunits and of six classes of subunit dimers, trimers, and pentamers revealed different orientations of the amino acid residues at the interface with the RNA suggesting that local asymmetry is dictated by disparities of the interacting nucleotide sequences. The different conformations escape detection by 3-D structure determination of entire virions with the conformational heterogeneity being only indicated by low density. My results do not exclude that the RNA follows a conserved assembly mechanism, contacting most or all asymmetric units in a specific way. However, as suggested by the gradual loss of asymmetry with increasing oligomerization and the 3D-structure of entire virions reconstructed by using Euler angles selected in the classification of single subunits, RNA path and/or folding likely differ from virion to virion.

Comparison of the structure of Aβ(1-40) amyloid with the one in complex with polyphenol ε-viniferin glucoside (EVG)

2018 ◽  
Vol 14 (2) ◽  
Author(s):  
Dawid Dułak ◽  
Mateusz Banach ◽  
Zdzisław Wiśniowski ◽  
Leszek Konieczny ◽  
Irena Roterman
Keyword(s):  
Nuclear Magnetic Resonance ◽  
3D Structure ◽  
Soluble Form ◽  
Hydrophobic Core ◽  
Nuclear Magnetic Resonance Technique ◽  
Resonance Technique ◽  
Magnetic Resonance Technique ◽  
Gauss Function ◽  
The One

Abstract The analysis of amyloid structures is much easier recently due to the availability of the solid-state nuclear magnetic resonance technique, which allows the determination of the 3D structure of amyloid forms. The amyloidogenic polypeptide Aβ(1-40) (PDB ID 2M9R, 2M9S) in its soluble form is the object of analysis in this paper. The solubility of this polypeptide is reached due to the presence of a complexed ligand: polyphenol ε-viniferin glucoside. Two forms of complexes available in the PDB were taken for analysis with respect to the presence of a hydrophobic core in the 3D structure of these complexes. The idealized hydrophobic core structure assumed to be accordant with the 3D Gauss function distribution was taken as the pattern. The aim of this analysis is the possible further comparison to the structures of the hydrophobic core present in amyloids. It is shown that the discordant (versus the 3D Gauss function) fragments present in amyloids appear accordant in the discussed complexes.

A theory on the determination of 3D motion and 3D structure from features

1987 ◽  
Vol 2 (2) ◽  
pp. 151-168 ◽  
Author(s):  
Shun-Ichi Amari ◽  
Minoru Maruyama
Keyword(s):  
3D Structure ◽  
3D Motion

Structural Analysis of Proteins on Lipid Substrates

2000 ◽  
Vol 6 (S2) ◽  
pp. 1182-1183
Author(s):  
Elizabeth M. Wilson-Kubalek
Keyword(s):  
Structural Information ◽  
Rapid Determination ◽  
3D Structure ◽  
Three Dimensional ◽  
Molecular Complexes ◽  
Structural Data ◽  
X Ray Crystallography ◽  
Helical Protein ◽  
3D Structure Determination

Electron microscopy (EM) has become an increasingly powerful method for the determination of three-dimensional (3D) structures of proteins and macromolecular complexes. EM offers advantages over X-ray crystallography and NMR for obtaining structural information about proteins in physiological conditions, as components of large assemblies, that cannot be obtained in large quantity, or that fail to yield 3D crystals. EM has been used to obtain structural data from images of isolated molecules and molecular complexes, two-dimensional (2D) protein crystals, and helical protein arrays. Helically arranged proteins allow the most rapid determination of 3D maps because they contain a complete range of equally spaced molecular views, therefore no tilting of the sample with respect to the electron beam is required. However, so far 3D structure determination of helical assemblies has been limited to proteins that naturally adopt this organization and to proteins that fortuitously crystallize as helices.

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