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De novo structure generation using chemical shifts for proteins with high‐sequence identity but different folds
Author(s) -
Shen Yang,
Bryan Philip N.,
He Yanan,
Orban John,
Baker David,
Bax Ad
Publication year - 2010
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.303
Subject(s) - chemical shift , sequence (biology) , protein structure prediction , fold (higher order function) , protein structure , protein sequencing , computational biology , identity (music) , chemistry , peptide sequence , crystallography , bioinformatics , biology , computer science , biochemistry , physics , gene , acoustics , programming language
Proteins with high‐sequence identity but very different folds present a special challenge to sequence‐based protein structure prediction methods. In particular, a 56‐residue three‐helical bundle protein (GA 95 ) and an α/β‐fold protein (GB 95 ), which share 95% sequence identity, were targets in the CASP‐8 structure prediction contest. With only 12 out of 300 submitted server‐CASP8 models for GA 95 exhibiting the correct fold, this protein proved particularly challenging despite its small size. Here, we demonstrate that the information contained in NMR chemical shifts can readily be exploited by the CS‐Rosetta structure prediction program and yields adequate convergence, even when input chemical shifts are limited to just amide 1 H N and 15 N or 1 H N and 1 H α values.