Decoding Protein Dynamics in Cells Using Chemical Cross‐Linking and Hierarchical Analysis

• Published in: Angewandte Chemie International Edition 2023-08, Vol.62 (35), p.e202301345-n/a
• Main Authors: Zhang, Beirong, Gong, Zhou, Zhao, Lili, An, Yuxin, Gao, Hang, Chen, Jing, Liang, Zhen, Liu, Maili, Zhang, Yukui, Zhao, Qun, Zhang, Lihua
• Format: Article
• Language: English
• Subjects: Alphafold2; Constraints; Dynamic structural analysis; Dynamics; In Vivo Cross-Linking; In vivo methods and tests; Mass Spectrometry; Mass spectroscopy; Molecular modelling; Protein Dynamics; Protein Structures; Proteins; Sampling
• ISSN: 1433-7851; 1521-3773
• DOI: 10.1002/anie.202301345

Protein dynamics play a crucial role in their diverse functions. The intracellular environment significantly influences protein dynamics, particularly for intrinsically disordered proteins (IDPs). To comprehensively capture structural information from various proteins within cells and characterize protein dynamics, chemical cross‐linking mass spectrometry was employed. In this study, we introduce a hierarchical decoding strategy that enables the investigation of protein dynamics in vivo. Computational analysis based on distance restraints derived from cross‐links is used to infer protein dynamics in cells. To facilitate this analysis, we leverage the prior structure obtained from AlphaFold2. By employing this strategy, we can characterize the full‐length structure of multi‐domain proteins taking into account their distinct dynamic features. Furthermore, by combining restraint sampling with an unbiased sampling and evaluation approach, we can provide a comprehensive description of the intrinsic motion of IDPs. Consequently, the hierarchical strategy we propose holds significant potential in advancing our understanding of the molecular mechanisms that undelie protein functions in cells. Our study presents a hierarchical strategy using in vivo cross‐linking mass spectrometry to decode dynamic protein conformations within cells. By integrating prior structural information and utilizing diverse structure calculation algorithms, we accurately characterize dynamic conformations of multi‐domain proteins and intrinsically disordered proteins. This comprehensive approach enhances our understanding of molecular mechanisms that drive protein functions within cellular environments.