Modeling repetitive, non-globular proteins

Protein modeling

Proteins are essential and versatile polymers consisting of sequenced amino acids that often possess an organized three-dimensional arrangement, (a result of their monomeric composition), which determines their biological role in cellular function. Proteins are involved in enzymatic catalysis; they participate in genetic information decoding and transmission processes, in cell recognition, in signaling, and transport of substances, in regulation of intra and extracellular conditions, and other functions.

Hexapeptide Tandem Repeats Dictate the Formation of Silkmoth Chorion, a Natural Protective Amyloid

Silkmoth chorion is a fibrous structure composed mainly of two major protein classes, families A and B. Both families of silkmoth chorion proteins present a highly conserved, in sequence and in length, central domain, consisting of Gly-rich tandem hexapeptide repetitive segments, flanked by two more variable N-terminal and C-terminal arms. Primary studies identified silkmoth chorion as a functional protective amyloid by unveiling the amyloidogenic properties of the central domain of both protein families. In this work, we attempt to detect the principal source of amyloidogenicity of the central domain by focusing on the role of the tandem hexapeptide sequence repeats. Concurrently, we discuss a possible mechanism for the self-assembly of class A protofilaments, suggesting that the aggregation-prone hexapeptide building blocks may fold into a triangle-shaped β-helical structure.

Protein lipograms

Linguistic analysis of protein sequences is an underexploited technique. Here, we capitalize on the concept of the lipogram to characterize sequences at the proteome levels. A lipogram is a literary composition which omits one or more letters. A protein lipogram likewise omits one or more types of amino acid. In this article, we establish a usable terminology for the decomposition of a sequence collection in terms of the lipogram. Next, we characterize Uniref50 using a lipogram decomposition. At the global level, protein lipograms exhibit power-law properties. A clear correlation with metabolic cost is seen. Finally, we use the lipogram construction to assign proteomes to the four branches of the tree-of-life: archaea, bacteria, eukaryotes and viruses. We conclude from this pilot study that the lipogram demonstrates considerable potential as an additional tool for sequence analysis and proteome classification.