dorsal/arxiv
View SchemaRecoverable One-dimensional Encoding of Three-dimensional Protein Structures
| Authors | Akira R. Kinjo, Ken Nishikawa |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0501005 |
| URL | https://arxiv.org/abs/q-bio/0501005 |
| DOI | 10.1093/bioinformatics/bti330 |
| Journal | Bioinformatics, 21:2167-2170 (2005) |
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 4\AA{} from the native structure, and for most of them, the deviation was even less than 2\AA{}. The present result opens a new possibility to protein structure prediction and our understanding of the sequence-structure relationship.
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"abstract": "Protein one-dimensional (1D) structures such as secondary structure and\ncontact number provide intuitive pictures to understand how the native\nthree-dimensional (3D) structure of a protein is encoded in the amino acid\nsequence. However, it has not been clear whether a given set of 1D structures\ncontains sufficient information for recovering the underlying 3D structure.\nHere we show that the 3D structure of a protein can be recovered from a set of\nthree types of 1D structures, namely, secondary structure, contact number and\nresidue-wise contact order which is introduced here for the first time. Using\nsimulated annealing molecular dynamics simulations, the structures satisfying\nthe given native 1D structural restraints were sought for 16 proteins of\nvarious structural classes and of sizes ranging from 56 to 146 residues. By\nselecting the structures best satisfying the restraints, all the proteins\nshowed a coordinate RMS deviation of less than 4\\AA{} from the native\nstructure, and for most of them, the deviation was even less than 2\\AA{}. The\npresent result opens a new possibility to protein structure prediction and our\nunderstanding of the sequence-structure relationship.",
"arxiv_id": "q-bio/0501005",
"authors": [
"Akira R. Kinjo",
"Ken Nishikawa"
],
"categories": [
"q-bio.BM"
],
"doi": "10.1093/bioinformatics/bti330",
"journal_ref": "Bioinformatics, 21:2167-2170 (2005)",
"title": "Recoverable One-dimensional Encoding of Three-dimensional Protein Structures",
"url": "https://arxiv.org/abs/q-bio/0501005"
},
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