Structural glycobiology in the age of electron cryo-microscopy

被引:25
作者
Atanasova, Mihaela [1 ]
Bagdonas, Haroldas [1 ]
Agirre, Jon [1 ]
机构
[1] Univ York, Dept Chem, York Struct Biol Lab, York, N Yorkshire, England
基金
英国工程与自然科学研究理事会;
关键词
BUILDING MEANINGFUL MODELS; SYMBOL NOMENCLATURE; CARBOHYDRATE STRUCTURE; REFINEMENT; VISUALIZATION; REPRESENTATIONS; GLYCOPROTEINS; CONFORMATION; SOFTWARE; GLYCANS;
D O I
10.1016/j.sbi.2019.12.003
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The methodology underpinning the construction, refinement, validation and analysis of atomic models of glycoproteins and protein-carbohydrate complexes has received a long-overdue boost in the last five years. This is a very timely development, as the resolution revolution in electron cryo-microscopy is now routinely delivering structures of key glycomedical importance, with a three-dimensional precision where X-ray crystallographic methods have traditionally floundered. This review will focus on the new software developments that have been introduced in the past two years, and their impact on the field of structural glycobiology in terms of published structures.
引用
收藏
页码:70 / 78
页数:9
相关论文
共 64 条
[1]   The structure of the AliC GH13-amylase from Alicyclobacillus sp. reveals the accommodation of starch branching points in the -amylase family [J].
Agirre, Jon ;
Moroz, Olga ;
Meier, Sebastian ;
Brask, Jesper ;
Munch, Astrid ;
Hoff, Tine ;
Andersen, Carsten ;
Wilson, Keith S. ;
Davies, Gideon J. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2019, 75 :1-7
[2]   Carbohydrate structure: the rocky road to automation [J].
Agirre, Jon ;
Davies, Gideon J. ;
Wilson, Keith S. ;
Cowtan, Kevin D. .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 2017, 44 :39-47
[3]   Strategies for carbohydrate model building, refinement and validation [J].
Agirre, Jon .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2017, 73 :171-186
[4]   Three-dimensional structures of two heavily N-glycosylated Aspergillus sp family GH3 β-D-glucosidases [J].
Agirre, Jon ;
Ariza, Antonio ;
Offen, Wendy A. ;
Turkenburg, Johan P. ;
Roberts, Shirley M. ;
McNicholas, Stuart ;
Harris, Paul V. ;
McBrayer, Brett ;
Dohnalek, Jan ;
Cowtan, Kevin D. ;
Davies, Gideon J. ;
Wilson, Keith S. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2016, 72 :254-265
[5]   Privateer: software for the conformational validation of carbohydrate structures [J].
Agirre, Jon ;
Iglesias-Fernandez, Javier ;
Rovira, Carme ;
Davies, Gideon J. ;
Wilson, Keith S. ;
Cowtan, Kevin D. .
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2015, 22 (11) :833-834
[6]   Carbohydrate anomalies in the PDB [J].
Agirre, Jon ;
Davies, Gideon ;
Wilson, Keith ;
Cowtan, Kevin .
NATURE CHEMICAL BIOLOGY, 2015, 11 (05) :303-303
[7]   The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design [J].
Alford, Rebecca F. ;
Leaver-Fay, Andrew ;
Jeliazkov, Jeliazko R. ;
O'Meara, Matthew J. ;
DiMaio, Frank P. ;
Park, Hahnbeom ;
Shapovalov, Maxim V. ;
Renfrew, P. Douglas ;
Mulligan, Vikram K. ;
Kappel, Kalli ;
Labonte, Jason W. ;
Pacella, Michael S. ;
Bonneau, Richard ;
Bradley, Philip ;
Dunbrack, Roland L., Jr. ;
Das, Rhiju ;
Baker, David ;
Kuhlman, Brian ;
Kortemme, Tanja ;
Gray, Jeffrey J. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2017, 13 (06) :3031-3048
[8]   Azahar: a PyMOL plugin for construction, visualization and analysis of glycan molecules [J].
Arroyuelo, Agustina ;
Vila, Jorge A. ;
Martin, Osvaldo A. .
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2016, 30 (08) :619-624
[9]   Building meaningful models of glycoproteins - Response [J].
Berman, Helen M. ;
Henrick, Kim ;
Nakamura, Haruki ;
Markley, John .
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2007, 14 (05) :354-355
[10]   LINUCS:: LInear Notation for Unique Description of Carbohydrate Sequences [J].
Bohne-Lang, A ;
Lang, E ;
Förster, T ;
von der Lieth, CW .
CARBOHYDRATE RESEARCH, 2001, 336 (01) :1-11