논문 상세정보
Modeling Protein Excited-state Structures from “Over-length” Chemical Cross-links
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초록
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 mass spectrometry with high confidence. Representing the cross-linkers and cross-linking reactions explicitly, we show that the protein excited-state structure can be modeled with as few as two over-length cross-links. We demonstrate the generality of our method with three systems: calmodulin, enzyme I, and glutamine-binding protein, and we show that these proteins alternate between different conformations for interacting with other proteins and ligands. Taken together, the over-length chemical cross-links contain valuable information about protein dynamics, and our findings here illustrate the relationship between dynamic domain movement and protein function.
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주제어
calmodulin (CaM) . mass spectrometry (MS) . molecular dynamics . protein cross-linking . protein domain . structural model . protein dynamics . protein excited state.
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- DOI : http://dx.doi.org/10.1074/jbc.M116.761841
- PubMed Central : 저널
- American Society for Biochemistry & Molecular Biology : 저널> 권호
- EBSCO Industries, Inc. : 저널
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