Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL

• 来源期刊: 生物物理学报
• 年，卷（期）: 2017,（4）
• 页码范围: 100-108
• 页数: 9页
• 语种: 中文

摘要

Chemical cross-linking coupled with mass spectroscopy (CXMS) is a powerful technique for investigating protein structures.CXMS has been mostly used to characterize the predominant structure for a protein,whereas cross-links incompatible with a unique structure of a protein or a protein complex are often discarded.We have recently shown that the so-called over-length cross-links actually contain protein dynamics information.We have thus established a method called DynaXL,which allow us to extract the information from the over-length cross-links and to visualize protein ensemble structures.In this protocol,we present the detailed procedure for using DynaXL,which comprises five steps.They are identification of highly confident cross-links,delineation of protein domains/subunits,ensemble rigidbody refinement,and final validation/assessment.The DynaXL method is generally applicable for analyzing the ensemble structures of multi-domain proteins and protein-protein complexes,and is freely available at www.tanglab.org/resources.