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

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 (GA95) and an α/β‐fold protein (GB95), which share 95% sequence identity, were targets in the CAS...

Full description

Saved in:
Bibliographic Details
Published in:Protein science 2010-02, Vol.19 (2), p.349-356
Main Authors: Shen, Yang, Bryan, Philip N., He, Yanan, Orban, John, Baker, David, Bax, Ad
Format: Article
Language:English
Subjects:
Amino Acid Sequence
chemical shift
CS‐Rosetta
For the Record
Humans
Models, Molecular
Molecular Sequence Data
NMR
Nuclear magnetic resonance
Protein Folding
Protein Structure, Secondary
Protein Structure, Tertiary
Proteins
Proteins - chemistry
Proteins - genetics
Proteins - metabolism
Sequence Alignment
structure prediction
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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 (GA95) and an α/β‐fold protein (GB95), 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 GA95 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 1HN and 15N or 1HN and 1Hα values.
ISSN:0961-8368
1469-896X
DOI:10.1002/pro.303