Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA

被引：23

作者：

Bardiaux, Benjamin

Bernard, Aymeric

Rieping, Wolfgang ^{[2
]}

Habeck, Michael ^{[3
,4
]}

Malliavin, Therese E. ^{[1
]}

Nilges, Michael

机构：

[1] Inst Pasteur, CNRS, URA 2185, Unite Bioinformat Struct,Dept Biol Struct & Chim, F-75724 Paris, France

[2] Univ Cambridge, Dept Biochem, Cambridge CB2 1GA, England

[3] Max Planck Inst Dev Biol, D-72076 Tubingen, Germany

[4] Max Planck Inst Biol Cybernet, D-72076 Tubingen, Germany

来源：

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | 2009年 / 75卷 / 03期

关键词：

NMR; ARIA; protein structure determination; NMR spectral assignment; network anchoring; symmetric homodimer calculation; spin-diffusion; MACROMOLECULAR STRUCTURE DETERMINATION; AUTOMATED NOE ASSIGNMENT; NMR SOLUTION STRUCTURE; PROTEIN STRUCTURES; DISTANCE CONSTRAINTS; MAGNETIC-RESONANCE; HOMO-OLIGOMERS; DOMAIN; ALGORITHM; RESTRAINTS;

D O I：

10.1002/prot.22268

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 ambiguous restraint for iterative assignment ARIA approach for NMR structure calculation is evaluated for symmetric homodimeric proteins by assessing the effect of several data analysis and assignment methods on the structure quality. In particular, we study the effects of network anchoring and spin-diffusion correction. The spin-diffusion correction improves the protein structure quality systematically, whereas network anchoring enhances the assignment efficiency by speeding up the convergence and coping with highly ambiguous data. For some homodimeric folds, network anchoring has been proved essential for unraveling both chain and proton assignment ambiguities.

引用

页码：569 / 585

页数：17

共 49 条

[1] Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA [J].

Bardiaux, Benjamin ;

Bernard, Aymeric ;

Rieping, Wolfgang ;

Habeck, Michael ;

Malliavin, Therese E. ;

Nilges, Michael .

BMC STRUCTURAL BIOLOGY, 2008, 8

[2] ITERATIVE PROCEDURE FOR STRUCTURE DETERMINATION FROM PROTON PROTON NOES USING A FULL RELAXATION MATRIX APPROACH - APPLICATION TO A DNA OCTAMER [J].

BOELENS, R ;

KONING, TMG ;

VANDERMAREL, GA ;

VANBOOM, JH ;

KAPTEIN, R .

JOURNAL OF MAGNETIC RESONANCE, 1989, 82 (02) :290-308

[3] The structure of docking domains in modular polyketide synthases [J].

Broadhurst, RW ;

Nietlispach, D ;

Wheatcroft, MP ;

Leadlay, PF ;

Weissman, KJ .

CHEMISTRY & BIOLOGY, 2003, 10 (08) :723-731

[4] Crystallography & NMR system:: A new software suite for macromolecular structure determination [J].

Brunger, AT ;

Adams, PD ;

Clore, GM ;

DeLano, WL ;

Gros, P ;

Grosse-Kunstleve, RW ;

Jiang, JS ;

Kuszewski, J ;

Nilges, M ;

Pannu, NS ;

Read, RJ ;

Rice, LM ;

Simonson, T ;

Warren, GL .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998, 54 :905-921

[5] Dual modes of RNA-silencing suppression by flock house virus protein B2 [J].

Chao, JA ;

Lee, JH ;

Chapados, BR ;

Debler, EW ;

Schneemann, A ;

Williamson, JR .

NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2005, 12 (11) :952-957

[6] Gaussian-weighted RMSD superposition of proteins: A structural comparison for flexible proteins and predicted protein structures [J].

Damm, Kelly L. ;

Carlson, Heather A. .

BIOPHYSICAL JOURNAL, 2006, 90 (12) :4558-4573

[7] SANE (Structure assisted NOE evaluation): An automated model-based approach for NOE assignment [J].

Duggan, BM ;

Legge, GB ;

Dyson, HJ ;

Wright, PE .

JOURNAL OF BIOMOLECULAR NMR, 2001, 19 (04) :321-329

[8] A nomenclature and data model to describe NMR experiments [J].

Fogh, Rasmus H. ;

Vranken, Wim F. ;

Boucher, Wayne ;

Stevens, Tim J. ;

Laue, Ernest D. .

JOURNAL OF BIOMOLECULAR NMR, 2006, 36 (03) :147-155

[9] OVERCOMING THE AMBIGUITY PROBLEM ENCOUNTERED IN THE ANALYSIS OF NUCLEAR OVERHAUSER MAGNETIC-RESONANCE SPECTRA OF SYMMETRICAL DIMER PROTEINS [J].

FOLKERS, PJM ;

FOLMER, RHA ;

KONINGS, RNH ;

HILBERS, CW .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993, 115 (09) :3798-3799

[10] Structural symmetry and protein function [J].

Goodsell, DS ;

Olson, AJ .

ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE, 2000, 29 :105-153

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