Protein structure determination using chemical shifts
Author and article information
Abstract
In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure is determined using only chemical shifts recorded and assigned through automated processes. The CA-RMSD to the experimental X-ray for this structure is 1.1 Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100 residues. For Rhodopsin (225 residues) a structure is found at 2.5 Å CA-RMSD from the experimental X-ray structure, and a structure is determined for the Savinase protein (269 residues) with 2.9 Å CA-RMSD from the experimental X-ray structure.
Cite this as
2014. Protein structure determination using chemical shifts. PeerJ PrePrints 2:e374v1 https://doi.org/10.7287/peerj.preprints.374v1Sections
Additional Information
Competing Interests
The authors declare there are no competing interests.
Author Contributions
Anders S Christensen conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Data Deposition
The following information was supplied regarding the deposition of related data:
https://github.com/andersx/cs-proteins/
Funding
This work was supported by the Novo Nordisk STAR PhD program The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
