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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data
David S Wishart1, David Arndt, Mark Berjanskii
1Department of Computing Science, Department of Biological Sciences, University of Alberta and National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8.
Nucleic Acids Research
|June 3, 2008
Summary
CS23D is a web server that generates accurate 3D protein structures using only chemical shifts and sequence data. This method bypasses the need for traditional NOE/J-coupling data, offering a faster alternative for protein structure determination.
Area of Science:
- Biophysics
- Structural Biology
- Computational Biology
Background:
- Nuclear Magnetic Resonance (NMR) spectroscopy is crucial for determining protein structures.
- Conventional NMR methods often rely on Nuclear Overhauser Effect (NOE) and J-coupling data, which can be challenging to obtain.
- Accurate 3D protein structures are essential for understanding biological function and drug discovery.
Purpose of the Study:
- To introduce CS23D, a novel web server for rapid 3D protein structure generation.
- To demonstrate that CS23D can accurately predict protein structures using only chemical shifts and sequence data.
- To provide an alternative to conventional NMR methods that require NOE and J-coupling data.
Main Methods:
- CS23D utilizes assigned NMR chemical shifts and protein sequence data as input.
- The server employs a pipeline of existing programs, including homology modeling, chemical shift threading, and de novo prediction with Rosetta.
- It refines protein coordinates using chemical shift data.
Main Results:
- CS23D successfully generated 3D protein structures for over 95% of tested proteins from the BioMagResBank.
- The generated structures exhibited Root Mean Square Deviation (RMSD) values of 0.2-2.8 Å compared to experimentally determined structures.
- The accuracy of CS23D is influenced by the completeness of chemical shift assignments and the query protein's similarity to known folds.
Conclusions:
- CS23D provides a rapid and accurate method for 3D protein structure determination using NMR chemical shifts.
- The web server significantly reduces the data requirements compared to traditional NMR techniques.
- CS23D is a valuable tool for structural biologists, accelerating the process of protein structure elucidation.
