LIFE IN THE CYTOPLASM: PROTEIN-PROTEIN INTERACTIONS, PROTEIN FOLDING, AND METABOLITE DYNAMICS

The cell is a crowded space where macromolecules, metabolites, and ions are present in high concentrations. While decades of research revealed a vast amount of information about dynamics of these molecules in vitro, the investigation of in-cell environments is still in early stages, and many questions about the role of crowding remain to be answered. Here we employed a long (>225 µs) all-atom classical molecular dynamics simulation of a small volume of E. coli cytoplasm, containing a dozen of macromolecules (proteins and tRNA) and physiological concentrations of metabolites and ions, to reveal a dramatic influence of crowding and sticking. We discovered that transient nonfunctional protein-protein interactions have a very short half-life of ~1 µs, comparable to the time scale of the fastest protein folding, which hints at co-evolution to prevent sticking. For protein folding, a small fast-folding triple-stranded WW domain GTT protein was not able to fold completely in silico even at the timescales longer than its experimentally measured folding time. We captured folding of one of the two hairpins as GTT is being kinetically trapped in an intermediate state by non-specific protein-protein interactions. We hypothesize that sticking in crowded conditions, perhaps enhanced by the non-native mutations of GTT, is responsible. Finally, we contrasted the dynamic behavior of adenosine triphosphate, ATP, one of the most abundant metabolites in the cell, between the in-cell, crystallographic, and in-water environments. We observed formation of pitched ATP conformations in-cell in the vicinity of macromolecules and in-crystal, perhaps driven by functional needs. Interestingly, we also observed ATP populations unique to the crystal environment that are absent in-cell and in-water, which we attribute in part to the strained conformations induced by host proteins. Our work shows dramatic influence of cellular environment on dynamics of proteins and metabolites and will guide future theoretical and experimental investigations.

Seminar Host
Matthias Heyden
Seminar Speaker
Taras Pogorelov
Seminar Speaker Affiliation
University of Illinois at Urbana-Champaign
Seminar Date
Seminar Semester
Spring