GeNMR: a web server for rapid NMR-based protein structure determination

Abstract

GeNMR (GEnerate NMR structures) is a web server for rapidly generating accurate 3D protein structures using sequence data, NOE-based distance restraints and/or NMR chemical shifts as input. GeNMR accepts distance restraints in XPLOR or CYANA format as well as chemical shift files in either SHIFTY or BMRB formats. The web server produces an ensemble of PDB coordinates for the protein within 15-25 min, depending on model complexity and completeness of experimental restraints. GeNMR uses a pipeline of several pre-existing programs and servers to calculate the actual protein structure. In particular, GeNMR combines genetic algorithms for structure optimization along with homology modeling, chemical shift threading, torsion angle and distance predictions from chemical shifts/NOEs as well as ROSETTA-based structure generation and simulated annealing with XPLOR-NIH to generate and/or refine protein coordinates. GeNMR greatly simplifies the task of protein structure determination as users do not have to install or become familiar with complex stand-alone programs or obscure format conversion utilities. Tests conducted on a sample of 90 proteins from the BioMagResBank indicate that GeNMR produces high-quality models for all protein queries, regardless of the type of NMR input data. GeNMR was developed to facilitate rapid, user-friendly structure determination of protein structures via NMR spectroscopy. GeNMR is accessible at http://www.genmr.ca.

Figure 1.

A flow chart outlining the general structure of the GeNMR web server and the programs that it calls to generate protein structures from chemical shift and/or NOE data. The specific function of each of the named programs is explained in the text.

Figure 2.

Illustration of how GeNMR is able to generate the structure of ubiquitin using only experimental NOE constraints [scenario (d) in the article]. The initial structure (purple) is a largely random coil polypeptide (∼18 Å RMSD), an intermediate structure (cyan) contains most of the secondary structure elements (∼ 3.9 Å RMSD), while the lowest energy structure (yellow), refined via simulated annealing, is within 1.2 Å of the known X-ray structure. The last panel shows the final ensemble (or bundle) of structures generated by GeNMR.