Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links.

ABSTRACT: Chemical cross-linking coupled with mass spectroscopy (CXMS) provides proximity information for the cross-linked residues and is used increasingly for modeling protein structures. However, experimentally identified cross-links are sometimes incompatible with the known structure of a protein, as the distance calculated between the cross-linked residues far exceeds the maximum length of the cross-linker. The discrepancies may persist even after eliminating potentially false cross-links and excluding intermolecular ones. Thus the "over-length" cross-links may arise from alternative excited-state conformation of the protein. Here we present a method and associated software DynaXL for visualizing the ensemble structures of multidomain proteins based on intramolecular cross-links identified by m

SUBMITTER: Ding YH 

PROVIDER: S-EPMC5270465 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature