Modeling Protein Complexes Using Restraints from Crosslinking Mass Spectrometry.

ABSTRACT: Modeling macromolecular assemblies with restraints from crosslinking mass spectrometry (XL-MS) tends to focus solely on distance violation. Recently, we identified three different modeling features inherent in crosslink data: (1) expected distance between crosslinked residues; (2) violation of the crosslinker's maximum bound; and (3) solvent accessibility of crosslinked residues. Here, we implement these features in a scoring function. cMNXL, and demonstrate that it outperforms the commonlyused crosslink distance violation. We compare the different methods of calculating the distance between crosslinked residues, which shows no significant change in performance when using Euclidean distance compared with the solvent-accessible surface distance. Finally, we create a combined score that inco

SUBMITTER: Bullock JMA 

PROVIDER: S-EPMC6039719 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature