SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes

Background: The activity of proteins within the cell is characterized by their motions, flexibility, interactions or even the particularly intriguing case of partially unfolded states. In the last two cases, a part of the protein is affected either by binding or unfolding and the detection of the respective perturbed and unperturbed region(s) is a fundamental part of the structural characterization of these states. This can be achieved by comparing experimental data of the same protein in two different states (bound/unbound, folded/unfolded). For instance, measurements of chemical shift perturbations (CSPs) from NMR 1 H-15 N HSQC experiments gives an excellent opportunity to discriminate both moieties. Results: We describe an innovative, automatic and unbiased method to distinguish perturbed and unperturbed regions in a protein existing in two distinct states (folded/partially unfolded, bound/unbound). The SAMPLEX program takes as input a set of data and the corresponding three-dimens...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Mickaël Krzeminski, Karine Loth, Rolf Boelens, Alexandre M. J. J. Bonvin
• Keywords: BMCBI 2010, Chemical Shift Perturbations, Protein, Unfolded States