Background: The rapidly increasing number of known protein sequences calls for
more efficient methods to predict the Three-Dimensional (3D) structures of proteins, thus
providing basic knowledge for rational drug design. Understanding the folding mechanism of
proteins is valuable for predicting their 3D structures and for designing proteins with new
functions and medicinal applications. Levinthal’s paradox is that although the astronomical
number of conformations possible even for proteins as small as 100 residues cannot be fully
sampled, proteins in nature normally fold into the native state within timescales ranging from
microseconds to hours. These conflicting results reveal that there are factors in organisms
that can assist in protein folding.
Methods: In this paper, we selected a crowded cell-like environment and temperature, and
the top three Posttranslational Modifications (PTMs) as examples to show that Levinthal’s
paradox does not reflect the folding mechanism of proteins. We then revealed the effects of
these factors on protein folding.
Results: The results summarized in this review indicate that a crowded cell-like environment,
temperature, and the top three PTMs reshape the Free Energy Landscapes (FELs) of proteins,
thereby regulating the folding process. The balance between entropy and enthalpy is the key
to understanding the effect of the crowded cell-like environment and PTMs on protein folding.
In addition, the stability/flexibility of proteins is regulated by temperature.
Conclusion: This paper concludes that the cellular environment could directly intervene in
protein folding. The long-term interactions of the cellular environment and sequence evolution
may enable proteins to fold efficiently. Therefore, to correctly understand the folding
mechanism of proteins, the effect of the cellular environment on protein folding should be