Intracellular environment can change protein conformational dynamics in cells through weak interactions

Conformational dynamics is important for protein functions, many of which are performed in cells. How the intracellular environment may affect protein conformational dynamics is largely unknown. Here, loop conformational dynamics is studied for a model protein in Escherichia coli cells by using nuclear magnetic resonance (NMR) spectroscopy. The weak interactions between the protein and surrounding macromolecules in cells hinder the protein rotational diffusion, which extends the dynamic detection timescale up to microseconds by the NMR spin relaxation method. The loop picosecond to microsecond dynamics is confirmed by nanoparticle-assisted spin relaxation and residual dipolar coupling methods. The loop interactions with the intracellular environment are perturbed through point mutation of the loop sequence. For the sequence of the protein that interacts stronger with surrounding macromolecules, the loop becomes more rigid in cells. In contrast, the mutational effect on the loop dynamics in vitro is small. This study provides direct evidence that the intracellular environment can modify protein loop conformational dynamics through weak interactions.

Automated summary

Conformational dynamics of proteins play a crucial role in cellular functions. However, the influence of the intracellular environment on protein conformational dynamics is not well understood. In this study, the loop conformational dynamics of a model protein in Escherichia coli cells was investigated using nuclear magnetic resonance (NMR) spectroscopy. Weak interactions between the protein and surrounding macromolecules in cells hindered the rotational diffusion of the protein, allowing the detection of dynamics in the microsecond timescale using NMR spin relaxation method. The loop dynamics in the picosecond to microsecond range were confirmed using nanoparticle-assisted spin relaxation and residual dipolar coupling methods. Point mutation of the loop sequence perturbed the loop interactions with the intracellular environment. For the protein sequence with stronger interactions with surrounding macromolecules, the loop became more rigid in cells. In contrast, the effect of mutation on the loop dynamics in vitro was small. This study provides direct evidence that the intracellular environment can modify protein loop conformational dynamics through weak interactions.