Frameshifting preserves key physicochemical properties of proteins.

Frameshifts in protein coding sequences are widely perceived as resulting in either nonfunctional or even deleterious protein products. Indeed, frameshifts typically lead to markedly altered protein sequences and premature stop codons. By analyzing complete proteomes from all three domains of life, we demonstrate that, in contrast, several key physicochemical properties of protein sequences exhibit significant robustness against +1 and -1 frameshifts.

VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences.

The structure, dynamics and, ultimately, biological function of proteins and nucleic acids are determined by the physicochemical properties of their primary sequences. Such properties are frequently captured via one-dimensional profile plots depicting a given physicochemical variable as a function of sequence position. Hydrophobicity, charge or structural disorder in proteins or nucleobase-density in nucleic acids are routinely visualized in this manner to analyze sequences at a glance.

RNA-protein interactions in an unstructured context.

Despite their importance, our understanding of noncovalent RNA-protein interactions is incomplete. This especially concerns the binding between RNA and unstructured protein regions, a widespread class of such interactions. Here, we review the recent experimental and computational work on RNA-protein interactions in an unstructured context with a particular focus on how such interactions may be shaped by the intrinsic interaction affinities between individual nucleobases and protein side chains.

mRNA/protein sequence complementarity and its determinants: The impact of affinity scales.

It has recently been demonstrated that the nucleobase-density profiles of mRNA coding sequences are related in a complementary manner to the nucleobase-affinity profiles of their cognate protein sequences. Based on this, it has been proposed that cognate mRNA/protein pairs may bind in a co-aligned manner, especially if unstructured. Here, we study the dependence of mRNA/protein sequence complementarity on the properties of the nucleobase/amino-acid affinity scales used.