Beta-Barrel Detection for Medium Resolution Cryo-Electron Microscopy Density Maps Using Genetic Algorithms and Ray Tracing

2018 ◽  
Vol 25 (3) ◽  
pp. 326-336 ◽  
Author(s):  
Albert Ng ◽  
Dong Si
Keyword(s):  
Electron Microscopy ◽  
Genetic Algorithms ◽  
Ray Tracing ◽  
Beta Barrel ◽  
Cryo Electron Microscopy ◽  
Density Maps ◽  
Medium Resolution

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

Cryo-EM structure of the human cohesin-NIPBL-DNA complex

Science ◽  
2020 ◽  
Vol 368 (6498) ◽  
pp. 1454-1459 ◽  
Author(s):  
Zhubing Shi ◽  
Haishan Gao ◽  
Xiao-chen Bai ◽  
Hongtao Yu
Keyword(s):  
Electron Microscopy ◽  
Sister Chromatid ◽  
Base Pair ◽  
Adenosine Triphosphatase ◽  
Cryo Electron Microscopy ◽  
Synergistic Activation ◽  
Medium Resolution ◽  
Chromatid Cohesion ◽  
Dna Complex ◽  
Insight Into

As a ring-shaped adenosine triphosphatase (ATPase) machine, cohesin organizes the eukaryotic genome by extruding DNA loops and mediates sister chromatid cohesion by topologically entrapping DNA. How cohesin executes these fundamental DNA transactions is not understood. Using cryo–electron microscopy (cryo-EM), we determined the structure of human cohesin bound to its loader NIPBL and DNA at medium resolution. Cohesin and NIPBL interact extensively and together form a central tunnel to entrap a 72–base pair DNA. NIPBL and DNA promote the engagement of cohesin’s ATPase head domains and ATP binding. The hinge domains of cohesin adopt an “open washer” conformation and dock onto the STAG1 subunit. Our structure explains the synergistic activation of cohesin by NIPBL and DNA and provides insight into DNA entrapment by cohesin.

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].

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