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Quantification of CH and NH/π-Stacking Interactions in Cells Using Nuclear Magnetic Resonance Spectroscopy
Xiaoxu Chen1,2,3, Xueying Zhang1,2,3,4, Jingfei Chen1,2,3
1Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
Protein stacking interactions, like CH/π and NH/π, are weaker inside Escherichia coli cells than in solution. This weakening affects protein dynamics and conformational flexibility within the cellular environment.
Area of Science:
- Biochemistry
- Structural Biology
- Molecular Biophysics
Background:
- π-Stacking interactions, including CH/π and NH/π, are crucial for protein folding and function.
- Understanding these interactions within a cellular context is vital for comprehending protein behavior in vivo.
Purpose of the Study:
- To quantify CH/π and NH/π stacking interactions in a protein within Escherichia coli cells.
- To investigate the impact of the cellular environment on these noncovalent interactions and protein dynamics.
Main Methods:
- Utilized a combined double-mutant cycle and nuclear magnetic resonance (NMR) spectroscopy approach.
- Measured stacking interactions and amide hydrogen/deuterium exchange rates in both cellular and buffer conditions.
Main Results:
- CH/π and NH/π stacking interactions were found to be generally weaker in E. coli cells compared to buffer solutions.
- Faster amide hydrogen/deuterium exchange rates in cells indicated enhanced local conformational opening for specific residues.
- Transient interactions with the cellular environment likely compete with and weaken intra-protein stacking interactions.
Conclusions:
- The cellular environment significantly influences the strength of π-stacking interactions in proteins.
- Weakened stacking interactions in vivo can lead to increased local conformational flexibility and opening.
- This study provides insights into the interplay between noncovalent interactions, cellular milieu, and protein dynamics.
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