DockAFM: benchmarking protein structures by docking under AFM topographs

被引：16

作者：

Chaves, Rui C. ^{[1
]}

Pellequer, Jean-Luc ^{[1
]}

机构：

[1] CEA, iBEB, Serv Biochim & Toxicol Nucl, F-30207 Bagnols Sur Ceze, France

来源：

BIOINFORMATICS | 2013年 / 29卷 / 24期

关键词：

ATOMIC-FORCE MICROSCOPY; FACTOR VA; MEMBRANE-PROTEINS; RESOLUTION; COMPLEX;

D O I：

10.1093/bioinformatics/btt561

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Proteins can adopt a variety of conformations. We present a simple server for scoring the agreement between 3D atomic structures and experimental envelopes obtained by atomic force microscopy. Three different structures of immunoglobulins (IgG) or blood coagulation factor V activated were tested and their agreement with several topographical surfaces was computed. This approach can be used to test structural variability within a family of proteins.

引用

页码：3230 / 3231

页数：2

共 19 条

[1] The crystal structure of activated protein C-inactivated bovine factor Va: Implications for cofactor function [J].

Adams, TE ;

Hockin, MF ;

Mann, KG ;

Everse, SJ .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (24) :8918-8923

[2] High-speed atomic force microscopy for observing dynamic biomolecular processes [J].

Ando, Toshio ;

Uchihashi, Takayuki ;

Kodera, Noriyuki ;

Yamamoto, Daisuke ;

Taniguchi, Masaaki ;

Miyagi, Atsushi ;

Yamashita, Hayato .

JOURNAL OF MOLECULAR RECOGNITION, 2007, 20 (06) :448-458

[3] ATOMIC FORCE MICROSCOPE [J].

BINNIG, G ;

QUATE, CF ;

GERBER, C .

PHYSICAL REVIEW LETTERS, 1986, 56 (09) :930-933

[4]

Casuso I, 2012, NAT NANOTECHNOL, V7, P525, DOI [10.1038/nnano.2012.109, 10.1038/NNANO.2012.109]

[5] Conformational dynamics of individual antibodies using computational docking and AFM [J].

Chaves, Rui C. ;

Teulon, Jean-Marie ;

Odorico, Michael ;

Parot, Pierre ;

Chen, Shu-wen W. ;

Pellequer, Jean-Luc .

JOURNAL OF MOLECULAR RECOGNITION, 2013, 26 (11) :596-604

[6] Nanoscale structural features determined by AFM for single virus particles [J].

Chen, Shu-Wen W. ;

Odorico, Michael ;

Meillan, Matthieu ;

Vellutini, Luc ;

Teulon, Jean-Marie ;

Parot, Pierre ;

Bennetau, Bernard ;

Pellequer, Jean-Luc .

NANOSCALE, 2013, 5 (22) :10877-10886

[7] High-Speed Atomic Force Microscopy: Cooperative Adhesion and Dynamic Equilibrium of Junctional Microdomain Membrane Proteins [J].

Colom, Adai ;

Casuso, Ignacio ;

Boudier, Thomas ;

Scheuring, Simon .

JOURNAL OF MOLECULAR BIOLOGY, 2012, 423 (02) :249-256

[8] Complex of linker histone H5 with the nucleosome and its implications for chromatin packing [J].

Fan, Li ;

Roberts, Victoria A. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (22) :8384-8389

[9] Structural Information, Resolution, and Noise in High-Resolution Atomic Force Microscopy Topographs [J].

Fechner, Peter ;

Boudier, Thomas ;

Mangenot, Stephanie ;

Jaroslawski, Szymon ;

Sturgis, James N. ;

Scheuring, Simon .

BIOPHYSICAL JOURNAL, 2009, 96 (09) :3822-3831

[10] Characterization of a factor Xa binding site on factor Va near the Arg-506 activated protein C cleavage site [J].

Gale, Andrew J. ;

Yegneswaran, Subramanian ;

Xu, Xiao ;

Pellequer, Jean-Luc ;

Griffin, John H. .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2007, 282 (30) :21848-21855

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