Bioinformatics Advance Access originally published online on February 18, 2005
Bioinformatics 2005 21(10):2167-2170; doi:10.1093/bioinformatics/bti330
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Recoverable one-dimensional encoding of three-dimensional protein structures
Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics Mishima 411-8540 Japan and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI) Mishima 411-8540, Japan
*To whom correspondence should be addressed.
Summary: One-dimensional (1D) structures of proteins such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it is still not clear whether a given set of 1D structures contains sufficient information for recovering the underlying 3D structure. Here we show that the 3D structure of a protein can be recovered from a set of three types of 1D structures, namely, secondary structure, contact number and residue-wise contact order which is introduced here for the first time. Using simulated annealing molecular dynamics simulations, the structures satisfying the given native 1D structural restraints were sought for 16 proteins of various structural classes and of sizes ranging from 56 to 146 residues. By selecting the structures best satisfying the restraints, all the proteins showed a coordinate RMS deviation of <4 Å from the native structure, and, for most of them, the deviation was even <2 Å. The present result opens a new possibility to protein structure prediction and our understanding of the sequence–structure relationship.
Contact: akinjo{at}genes.nig.ac.jp
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