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Bioinformatics Advance Access published online on February 18, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti330
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received October 12, 2004
Revised February 2, 2005
Accepted February 12, 2005

Discovery note

Recoverable one-dimensional encoding of protein three-dimensional structures

Akira R. Kinjo 1* and Ken Nishikawa 1

1 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, 411-8540, Japan; Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, 411-8540, Japan

* To whom correspondence should be addressed.
Akira R. Kinjo, E-mail: akinjo{at}genes.nig.ac.jp


  Abstract

Protein one-dimensional (1D) structures 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 has not been 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 less than 4Å from the native structure, and for most of them, the deviation was even less than 2Å. The present result opens a new possibility to protein structure prediction and our understanding of the sequence-structure relationship.


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