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A global representation of the protein fold space.

ABSTRACT: One of the principal goals of the structural genomics initiative is to identify the total repertoire of protein folds and obtain a global view of the "protein structure universe." Here, we present a 3D map of the protein fold space in which structurally related folds are represented by spatially adjacent points. Such a representation reveals a high-level organization of the fold space that is intuitively interpretable. The shape of the fold space and the overall distribution of the folds are defined by three dominant trends: secondary structure class, chain topology, and protein domain size. Random coil-like structures of small proteins and peptides are mapped to a region where the three trends converge, offering an interesting perspective on both the demography of fold space and the evolution of protein structures.

SUBMITTER: Hou J

PROVIDER: S-EPMC151350 | biostudies-literature | 2003 Mar

REPOSITORIES: biostudies-literature

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A global representation of the protein fold space.

Hou Jingtong J Sims Gregory E GE Zhang Chao C Kim Sung-Hou SH

Proceedings of the National Academy of Sciences of the United States of America 20030226 5

One of the principal goals of the structural genomics initiative is to identify the total repertoire of protein folds and obtain a global view of the "protein structure universe." Here, we present a 3D map of the protein fold space in which structurally related folds are represented by spatially adjacent points. Such a representation reveals a high-level organization of the fold space that is intuitively interpretable. The shape of the fold space and the overall distribution of the folds are def ...[more]

PMID: 12606708

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