Cradle-loop barrels and the concept of metafolds in protein classification by natural descent

被引：48

作者：

Alva, Vikram ^{[1
]}

Koretke, Kristin K. ^{[2
]}

Coles, Murray ^{[1
]}

Lupas, Andrei N. ^{[1
]}

机构：

[1] Max Planck Inst Dev Biol, Dept Prot Evolut, D-72076 Tubingen, Germany

[2] GlaxoSmithKline Inc, Computat Chem Grp, Collegeville, PA 19426 USA

来源：

CURRENT OPINION IN STRUCTURAL BIOLOGY | 2008年 / 18卷 / 03期

关键词：

D O I：

10.1016/j.sbi.2008.02.006

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：

Current classification systems for protein structure show many inconsistencies both within and between systems. The metafold concept was introduced to identify fold similarities by consensus and thus provide a more unified view of fold space. Using cradle-loop barrels as an example, we propose to use the metafold as the next hierarchical level above the fold, encompassing a group of topologically related folds for which a homologous relationship has been substantiated. We see this as an important step on the way to a classification of proteins by natural descent.

引用

页码：358 / 365

页数：8

共 22 条

[1] A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels [J].

Ammelburg, Moritz ;

Hartmann, Marcus D. ;

Djuranovic, Sergej ;

Alva, Vikrarn ;

Koretke, Kristin K. ;

Martin, Joerg ;

Sauer, Guido ;

Truffault, Vincent ;

Zeth, Kornelius ;

Lupas, Andrei N. ;

Coles, Murray .

STRUCTURE, 2007, 15 (12) :1577-1590

[2] Data growth and its impact on the SCOP database: new developments [J].

Andreeva, Antonina ;

Howorth, Dave ;

Chandonia, John-Marc ;

Brenner, Steven E. ;

Hubbard, Tim J. P. ;

Chothia, Cyrus ;

Murzin, Alexey G. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D419-D425

[3] SISYPHUS - structural alignments for proteins with non-trivial relationships [J].

Andreeva, Antonina ;

Prlic, Andreas ;

Hubbard, Tim J. P. ;

Murzin, Alexey G. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D253-D259

[4] Evolution of protein fold in the presence of functional constraints [J].

Andreeva, Antonina ;

Murzin, Alexey G. .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 2006, 16 (03) :399-408

[5]

[Anonymous], COMPUTATIONAL STRUCT

[6] Structuring the universe of proteins [J].

Burley, SK ;

Bonanno, JB .

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, 2002, 3 :243-262

[7] A six-stranded double-psi β barrel is shared by several protein superfamilies [J].

Castillo, RM ;

Mizuguchi, K ;

Dhanaraj, V ;

Albert, A ;

Blundell, TL ;

Murzin, AG .

STRUCTURE, 1999, 7 (02) :227-236

[8] AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi β barrels [J].

Coles, M ;

Djuranovic, S ;

Söding, J ;

Frickey, T ;

Koretke, K ;

Truffault, V ;

Martin, J ;

Lupas, AN .

STRUCTURE, 2005, 13 (06) :919-928

[9] The solution structure of VAT-N reveals a 'missing link' in the evolution of complex enzymes from a simple βαββ element [J].

Coles, M ;

Diercks, T ;

Liermann, J ;

Gröger, A ;

Rockel, B ;

Baumeister, W ;

Koretke, KK ;

Lupas, A ;

Peters, J ;

Kessler, H .

CURRENT BIOLOGY, 1999, 9 (20) :1158-1168

[10] Common evolutionary origin of swapped-hairpin and double-psi β barrels [J].

Coles, Murray ;

Hulko, Michael ;

Djuranovic, Sergej ;

Truffault, Vincent ;

Koretke, Kristin ;

Martin, Joerg ;

Lupas, Andrei N. .

STRUCTURE, 2006, 14 (10) :1489-1498

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