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PMID: 19998407 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't

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

Protein science : a publication of the Protein Society ·Vol. 19 ·No. 2 ·2010-02-00 ·Pages 349-56

Shen Y, Bryan PN, He Y, Orban J, Baker D, Bax A

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.

MeSH Terms
Amino Acid Sequence Humans Models, Molecular Molecular Sequence Data Protein Folding Protein Structure, Secondary Protein Structure, Tertiary Proteins/chemistry,genetics,metabolism Sequence Alignment
Chemicals
Proteins
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Shen Yang
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
Bryan Philip N
He Yanan
Orban John
Baker David
Bax Ad
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Article Info
Journal
Protein science : a publication of the Protein Society
Abbr.
Protein Sci
ISSN
1469-896X
DOI
10.1002/pro.303
Published
2010-02-00
Pages
349-56
Language
English
Region
United States
NLM ID
9211750
PMCID
PMC2865713
Subset
IM
Grants
NIGMS NIH HHS · GM62154 · United States
Howard Hughes Medical Institute · United States
Intramural NIH HHS · United States
External Links
PubMed source DOI: 10.1002/pro.303 PMC Full Text View journal details
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