The importance of sequence diversity in the aggregation and evolution of proteins

Abstract

Incorrect folding of proteins, leading to aggregation and amyloid formation, is associated with a group of highly debilitating medical conditions including Alzheimer's disease and late-onset diabetes. The issue of how unwanted protein association is normally avoided in a living system is particularly significant in the context of the evolution of multidomain proteins, which account for over 70% of all eukaryotic proteins, where the effective local protein concentration in the vicinity of each domain is very high. Here we describe the aggregation kinetics of multidomain protein constructs of immunoglobulin domains and the ability of different homologous domains to aggregate together. We show that aggregation of these proteins is a specific process and that the efficiency of coaggregation between different domains decreases markedly with decreasing sequence identity. Thus, whereas immunoglobulin domains with more than about 70% identity are highly prone to coaggregation, those with less than 30-40% sequence identity do not detectably interact. A bioinformatics analysis of consecutive homologous domains in large multidomain proteins shows that such domains almost exclusively have sequence identities of less than 40%, in other words below the level at which coaggregation is likely to be efficient. We propose that such low sequence identities could have a crucial and general role in safeguarding proteins against misfolding and aggregation.

Kinetic modelling indicates that fast-translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates

“…Understanding the process by which proteins fold during their biosynthesis is one of the most fundamental problems in molecular biology, as it is crucial to enable their biological function 3,40 , and its failure can result in their misfolding [40][41][42] , malfunction 7 and aggregation 3,4,43 , events that are associated with a wide range of severe health conditions including neurodegenerative disease 44 . A key challenge in this context is to interpret and predict the influence of individual codon translation rates on cotranslational protein folding and misfolding.…”

Staphylococcal biofilm-forming protein has a contiguous rod-like structure

“…The immediate juxtaposition of domains with identical sequence can promote misfolding events (18). This might explain the apparent evolutionary pressure to maintain sequence identity at less than 40% between adjacent domains that was revealed by an analysis of proteins containing strings of Ig and fibronectin-type III domains (19). The formation of two domains by each sequence repeat, as in SasG, could provide an elegantly simple solution to this problem.…”

“…It has been shown recently that tandemly arrayed domains with high sequence identity are prone to misfolding events (18). This is likely to be a particular problem for long-lived proteins, or those which un-dergo shear stresses, and might explain the apparent evolutionary pressure for sequences of adjacent domains to have less than 40% sequence identity (19). Thus, the SasG and Aap biofilm-forming region also raises the question of how misfolding is avoided when sequence identity between repeats is otherwise advantageous.…”

Experimental support for the foldability–function tradeoff hypothesis: Segregation of the folding nucleus and functional regions in fibroblast growth factor‐1

“…The resulting protein would exhibit exact primary sequence symmetry and contain a foldable structural element at each of the symmetry-related positions. It has been postulated that such a protein might exhibit inefficient folding (due to folding frustration involving regions of identical primary structure), 54,55 or conversely, might possess highly redundant, overlapping folding nuclei, thereby promoting folding co-operativity. 56 We note that a protein with folding pathway redundancy might, in principle, retain efficient folding despite a localized deleterious mutation due to compensation by the folding-competent symmetry-related positions.…”