Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data.

ABSTRACT: This protocol describes a workflow for creating structural models of proteins or protein complexes using distance restraints derived from cross-linking mass spectrometry experiments. The distance restraints are used (i) to adjust preliminary models that are calculated on the basis of a homologous template and primary sequence, and (ii) to select the model that is in best agreement with the experimental data. In the case of protein complexes, the cross-linking data are further used to dock the subunits to one another to generate models of the interacting proteins. Predicting models in such a manner has the potential to indicate multiple conformations and dynamic changes that occur in solution. This modeling protocol is compatible with many cross-linking workflows and uses open-source progra

SUBMITTER: Orban-Nemeth Z 

PROVIDER: S-EPMC5999019 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature