scholarly journals Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Dong Si ◽  
Jing He
Keyword(s):  
Electron Microscopy ◽  
Amino Acids ◽  
New Approach ◽  
Close Spacing ◽  
Cryo Electron Microscopy ◽  
Density Maps ◽  
Beta Barrels

Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Althoughα-helices can be detected from density maps at 5–8 Å resolutions,β-strands are challenging to detect at such density maps due to close-spacing ofβ-strands. The variety of shapes ofβ-sheets adds the complexity ofβ-strands detection from density maps. We propose a new approach to model traces ofβ-strands forβ-barrel density regions that are extracted from cryo-EM density maps. In the test containing eightβ-barrels extracted from experimental cryo-EM density maps at 5.5 Å–8.25 Å resolution,StrandRollerdetected about 74.26% of the amino acids in theβ-strands with an overall 2.05 Å 2-way distance between the detectedβ-traces and the observed ones, if the best of the fifteen detection cases is considered.

scholarly journals PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps

2016 ◽  
Vol 72 (10) ◽  
pp. 1137-1148 ◽  
Author(s):  
Guray Kuzu ◽  
Ozlem Keskin ◽  
Ruth Nussinov ◽  
Attila Gursoy
Keyword(s):  
Electron Microscopy ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Protein Assemblies ◽  
New Approach ◽  
Cellular Processes ◽  
Cryo Electron Microscopy ◽  
Density Maps ◽  
Crystallographic Structures ◽  
Hiv 1

The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.

scholarly journals Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps

2020 ◽  
Vol 60 (5) ◽  
pp. 2644-2650 ◽  
Author(s):  
Salim Sazzed ◽  
Peter Scheible ◽  
Maytha Alshammari ◽  
Willy Wriggers ◽  
Jing He
Keyword(s):  
Electron Microscopy ◽  
Similarity Measurement ◽  
Cryo Electron Microscopy ◽  
Density Maps ◽  
Medium Resolution

scholarly journals Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Christopher J. Gisriel ◽  
Jimin Wang ◽  
Gary W. Brudvig ◽  
Donald A. Bryant
Keyword(s):  
Electron Microscopy ◽  
Electrostatic Potential ◽  
Protein Function ◽  
Protein Complexes ◽  
Chemical Environment ◽  
Cryo Electron Microscopy ◽  
Functional Differences ◽  
Density Maps ◽  
Structural Differences

AbstractThe accurate assignment of cofactors in cryo-electron microscopy maps is crucial in determining protein function. This is particularly true for chlorophylls (Chls), for which small structural differences lead to important functional differences. Recent cryo-electron microscopy structures of Chl-containing protein complexes exemplify the difficulties in distinguishing Chl b and Chl f from Chl a. We use these structures as examples to discuss general issues arising from local resolution differences, properties of electrostatic potential maps, and the chemical environment which must be considered to make accurate assignments. We offer suggestions for how to improve the reliability of such assignments.

scholarly journals Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps

Molecules ◽  
2019 ◽  
Vol 25 (1) ◽  
pp. 82 ◽  
Author(s):  
Eman Alnabati ◽  
Daisuke Kihara
Keyword(s):  
Electron Microscopy ◽  
De Novo ◽  
Molecular Structures ◽  
Structure Modeling ◽  
Rapid Progress ◽  
Macromolecular Complexes ◽  
Modeling Methods ◽  
Cryo Electron Microscopy ◽  
Density Maps

Cryo-electron microscopy (cryo-EM) has now become a widely used technique for structure determination of macromolecular complexes. For modeling molecular structures from density maps of different resolutions, many algorithms have been developed. These algorithms can be categorized into rigid fitting, flexible fitting, and de novo modeling methods. It is also observed that machine learning (ML) techniques have been increasingly applied following the rapid progress of the ML field. Here, we review these different categories of macromolecule structure modeling methods and discuss their advances over time.

scholarly journals PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. Corrigendum

2018 ◽  
Vol 74 (1) ◽  
pp. 65-66
Author(s):  
Guray Kuzu ◽  
Ozlem Keskin ◽  
Ruth Nussinov ◽  
Attila Gursoy
Keyword(s):  
Electron Microscopy ◽  
Protein Complexes ◽  
Acta Cryst ◽  
Cryo Electron Microscopy ◽  
Density Maps

A revised Table 6 and Supporting Information are provided for the article by Kuzuet al.[(2016),Acta Cryst.D72, 1137–1148].

scholarly journals Cryo-EM structure of the calcium release-activated calcium channel Orai in an open conformation

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Xiaowei Hou ◽  
Ian R Outhwaite ◽  
Leanne Pedi ◽  
Stephen Barstow Long
Keyword(s):  
Electron Microscopy ◽  
Amino Acids ◽  
Calcium Channel ◽  
Calcium Release ◽  
Structural Information ◽  
Excitable Cells ◽  
X Ray ◽  
Cryo Electron Microscopy ◽  
Open Conformation ◽  
Hydrophobic Amino Acids

The calcium release-activated calcium channel Orai regulates Ca2+ entry into non-excitable cells and is required for proper immune function. While the channel typically opens following Ca2+ release from the endoplasmic reticulum, certain pathologic mutations render the channel constitutively open. Previously, using one such mutation (H206A), we obtained low (6.7 Å) resolution X-ray structural information on Drosophila melanogaster Orai in an open conformation (Hou et al., 2018). Here we present a structure of this open conformation at 3.3 Å resolution using fiducial-assisted cryo-electron microscopy. The improved structure reveals the conformations of amino acids in the open pore, which dilates by outward movements of subunits. A ring of phenylalanine residues repositions to expose previously shielded glycine residues to the pore without significant rotational movement of the associated helices. Together with other hydrophobic amino acids, the phenylalanines act as the channel’s gate. Structured M1–M2 turrets, not evident previously, form the channel’s extracellular entrance.

Visualization and analysis of capsid dimorphism in hepatitis B virus to 17 Å resolution by cryo-electron microscopy

1996 ◽  
Vol 54 ◽  
pp. 916-917
Author(s):  
A. Zlotnick ◽  
N. Cheng ◽  
J.F. Conway ◽  
F.P. Booy ◽  
A.C. Steven ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Amino Acids ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Capsid Protein ◽  
Icosahedral Symmetry ◽  
Cryo Electron Microscopy ◽  
B Virus ◽  
Gradient Fractionation ◽  
Protein Constructs

Hepatitis B virus (HBV) is an enveloped virus with an icosahedral capsid. Its homodimeric capsid protein assembles into particles of two sizes - one with T=3 icosahedral symmetry (90 dimers), the other with T=4 symmetry (120 dimers). Both sizes of particle are found in vivo as well as in expression systems. We have developed an in vitro assembly system using purified, bacterially expressed, capsid proteins. Capsids assembled from different protein constructs were studied by cryo-electron microscopy using a Philips CM20 microscope equipped with a field emission gun operating at 120 keV.Capsids assembled from the different protein constructs were assayed by cryo-electron microscopy and sucrose gradient fractionation. Cryo-electron microscopy was required to identify the two different sizes of capsids and the small population of misshapen particles, and also to ascertain the quality of the gradient fractionation (Figure 1, 2). The protein constructs lacked the predominantly basic C-terminal 34 amino acids of the full-length capsid protein (183 amino acids), and were further truncated between residues 138 and 149. Constructs terminating between residue 140 and 149 assembled into mixtures of T=3 and T=4 particles; the smallest construct (138 residues) did not form capsids.

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