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

[41] ARIA2: Automated NOE assignment and data integration in NMR structure calculation [J].

Rieping, Wolfgang ;

Habeck, Michael ;

Bardiaux, Benjamin ;

Bernard, Aymeric ;

Malliavin, Therese E. ;

Nilges, Michael .

BIOINFORMATICS, 2007, 23 (03) :381-382

[42] Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem [J].

Theobald, Douglas L. ;

Wuttke, Deborah S. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (49) :18521-18527

[43] BioMagResBank [J].

Ulrich, Eldon L. ;

Akutsu, Hideo ;

Doreleijers, Jurgen F. ;

Harano, Yoko ;

Ioannidis, Yannis E. ;

Lin, Jundong ;

Livny, Miron ;

Mading, Steve ;

Maziuk, Dimitri ;

Miller, Zachary ;

Nakatani, Eiichi ;

Schulte, Christopher F. ;

Tolmie, David E. ;

Wenger, R. Kent ;

Yao, Hongyang ;

Markley, John L. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D402-D408

[44]

Wang CSE, 1998, PROTEINS, V32, P26, DOI 10.1002/(SICI)1097-0134(19980701)32:1<26::AID-PROT5>3.0.CO

[45]

2-C

[46] THE CHEMICAL-SHIFT INDEX - A FAST AND SIMPLE METHOD FOR THE ASSIGNMENT OF PROTEIN SECONDARY STRUCTURE THROUGH NMR-SPECTROSCOPY [J].

WISHART, DS ;

SYKES, BD ;

RICHARDS, FM .

BIOCHEMISTRY, 1992, 31 (06) :1647-1651

[47] PSEUDO-STRUCTURES FOR THE 20 COMMON AMINO-ACIDS FOR USE IN STUDIES OF PROTEIN CONFORMATIONS BY MEASUREMENTS OF INTRAMOLECULAR PROTON PROTON DISTANCE CONSTRAINTS WITH NUCLEAR MAGNETIC-RESONANCE [J].

WUTHRICH, K ;

BILLETER, M ;

BRAUN, W .

JOURNAL OF MOLECULAR BIOLOGY, 1983, 169 (04) :949-961

[48] An NMR approach to structural proteomics [J].

Yee, A ;

Chang, XQ ;

Pineda-Lucena, A ;

Wu, B ;

Semesi, A ;

Le, B ;

Ramelot, T ;

Lee, GM ;

Bhattacharyya, S ;

Gutierrez, P ;

Denisov, A ;

Lee, CH ;

Cort, JR ;

Kozlov, G ;

Liao, J ;

Finak, G ;

Chen, L ;

Wishart, D ;

Lee, W ;

McIntosh, LP ;

Gehring, K ;

Kennedy, MA ;

Edwards, AM ;

Arrowsmith, CH .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (04) :1825-1830

[49] Methods for measurement of intermolecular NOEs by multinuclear NMR spectroscopy: Application to a bacteriophage lambda N-peptide/boxB RNA complex [J].

Zwahlen, C ;

Legault, P ;

Vincent, SJF ;

Greenblatt, J ;

Konrat, R ;

Kay, LE .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1997, 119 (29) :6711-6721

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