Comparing protein folding in vitro and in vivo: foldability meets the fitness challenge

Abstract

In this review, we compare and contrast current knowledge about in-vitro and in-vivo protein folding. Major advances in understanding fundamental principles underlying protein folding in optimized in-vitro conditions have yielded detailed physicochemical principles of folding landscapes for small, single domain proteins. In addition, there has been increased research focusing on the key features of protein folding in the cell that differentiate it from in-vitro folding, such as co-translational folding, chaperone-facilitated folding, and folding in crowded conditions with many weak interactions. Yet these two research areas have not been bridged effectively in research carried out to date. This review points to gaps between the two that are ripe for future research. Moreover, we emphasize the biological selection pressures that impact protein folding in-vivo and how fitness drives the evolution of protein sequences in ways that may place foldability in tension with other requirements on a given protein. We suggest that viewing the physicochemical process of protein folding through the lens of evolution will unveil new insights and pose novel challenges about in-cell folding landscapes.

Using Transcriptional Control To Increase Titers of Secreted Heterologous Proteins by the Type III Secretion System

“…Cultures that did not carry the upregulation vector are denoted "ϪhilA." lular space (48)(49)(50). It is worth noting that Bla is natively secreted to the periplasm by the general secretory (Sec) pathway (51), and the mechanism of the Sec pathway also requires the protein to unfold during translocation and subsequently refold in the periplasm (52).…”

Protein folding, binding, and droplet formation in cell-like conditions

“…covered this topic [3]. Complementary coverage of the experimental literature can be found in two recent surveys in this journal [4,9,10]. …”

Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics

“…This balance indeed occurs in the regime of moderate protein folding stability and gives rise to the observation that proteins are “marginally” stable [19,20]. It is important to note the common misconception that selection for stability must result in very stable proteins and that the observed modest stabilities of proteins (in comparison for example with de novo designed ones [21]) therefore implies a “stability-activity tradeoff’’ [22] or provides the evidence against selection for stability altogether [23*]. As discussed here and in [9,11,19,20,24,25*,26*], selection for folding stability should not lead to most stable proteins.…”