A hierarchical strategy to decipher protein dynamics in vivo with chemical cross-linking mass spectrometry
Zhang, B.; Gong, Z.; Zhao, L.; An, Y.; Gao, H.; Chen, J.; Liang, Z.; Liu, M.; Zhang, Y.; Zhao, Q.; Zhang, L.
Show abstract
Protein dynamics are essential for their various functions. Meanwhile, the intracellular environment would affect protein structural dynamics, especially for the intrinsically disordered proteins (IDPs). Chemical cross-linking mass spectrometry (CXMS) can unbiasedly capture the protein conformation information in cells and can also represent the protein dynamics. Here, we proposed a hierarchy deciphering strategy for protein dynamics in vivo. With the prior structure from AlphaFold2, the steady local conformation can be extensively evaluated. On this basis, the full-length structure of multi-domain proteins with various dynamic features can be characterized using CXMS. Furthermore, the complementary strategy with unbiased sampling and distance-constrained sampling enables an objective description of the intrinsic motion of the IDPs. Therefore, the hierarchy strategy we presented herein could help us better understand the molecular mechanisms of protein functions in cells.
Matching journals
The top 7 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- A conditional protein diffusion model generates artificial programmable endonuclease sequences with enhanced activity 94%
- The molecular mechanism of cytoadherence to placenta or tumor cells through VAR2CSA from Plasmodium falciparum 94%
- Structural and molecular basis of the epistasis effect in enhanced affinity between SARS-CoV-2 KP.3 and ACE2 92%
Similar papers in this journal
- Pathfinder: protein folding pathway prediction based on conformational sampling 97%
- Elucidation of Genome-wide Understudied Proteins targeted by PROTAC-induced degradation using Interpretable Machine Learning 95%
- Membrane contact probability: an essential and predictive character for the structural and functional studies of membrane proteins 95%