De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds.

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TitleDe novo structure generation using chemical shifts for proteins with high-sequence identity but different folds.
Publication TypeJournal Article
Year of Publication2010
AuthorsShen, Y, Bryan, PN, He, Y, Orban, J, Baker, D, Bax, A
JournalProtein Sci
Volume19
Issue2
Pagination349-56
Date Published2010 Feb
ISSN1469-896X
KeywordsAmino Acid Sequence, Humans, Models, Molecular, Molecular Sequence Data, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary, Proteins, Sequence Alignment
Abstract

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 alpha/beta-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(alpha) values.

DOI10.1002/pro.303
Alternate JournalProtein Sci.
PubMed ID19998407
PubMed Central IDPMC2865713
Grant ListGM62154 / GM / NIGMS NIH HHS / United States
/ / Howard Hughes Medical Institute / United States