Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor

Abstract

Proteins, like other biomolecules, have a modular and hierarchical structure. Various building blocks are used to construct proteins of high structural complexity and diverse functionality. In multidomain proteins, for example, domains are fused to each other in different combinations to achieve different functions. Although the LEGO brick metaphor is justified as a means of simplifying the complexity of three-dimensional protein structures, several fundamental properties (such as allostery or the induced-fit mechanism) make deviation from it necessary to respect the plasticity, softness, and cross-talk that are essential to protein function. In this work, we illustrate recently reported protein behavior in multidomain proteins that deviates from the LEGO brick analogy. While earlier studies showed that a protein domain is often unaffected by being fused to another domain or becomes more stable following the formation of a new interface between the tethered domains, destabilization due to tethering has been reported for several systems. We illustrate that tethering may sometimes result in a multidomain protein behaving as "less than the sum of its parts". We survey these cases for which structure additivity does not guarantee thermodynamic additivity. Protein destabilization due to fusion to other domains may be linked in some cases to biological function and should be taken into account when designing large assemblies.

Functional and Early Folding Residues are separated in proteins to increase evolvability and robustness

“…53 The data obtained by HDX experiments is still difficult to interpret [41] and results 54 of other experiments or techniques are tedious to compare [29,39]. The Start2Fold 55 database [39] provides an invaluable annotation of EFR which became protected early 56 in a standardized manner [29]. In a previous study [38], EFR have been shown to 57 exhibit lower disorder scores and higher backbone rigidity.…”

“…87 Graph representations of proteins also allow to assess whether proteins feature a 88 3/18 modular design [54,55]. Reinvention is rarely observed in nature and whenever possible 89 existing, established, and safe strategies are reused [56]. This can explain why the 90 conceivable sequence and structure space is explored so little: by evolving established 91 sequences, misfolding sequences or those prone to aggregation are avoided [56,57].…”

“…Reinvention is rarely observed in nature and whenever possible 89 existing, established, and safe strategies are reused [56]. This can explain why the 90 conceivable sequence and structure space is explored so little: by evolving established 91 sequences, misfolding sequences or those prone to aggregation are avoided [56,57]. This 92 behavior is likely the result of a separation of residues relevant for folding and those 93 relevant for protein function [40] such as ligand binding sites or active sites.…”

“…Early Folding Residues are non-functional residues 219 Division of labor is one of the most successful strategies of evolution [40,54,55,[66][67][68][69]. 220 The separation of residues crucial for folding and those furnishing function may allow 221 reuse of established protein folds [32,40,[54][55][56]58]. The sequence and structure space 222 ascertained over the course of evolutions seems small for a truly random exploration.…”

“…Reusing established folds could also avoid slow-folding sequences or those prone to 224 aggregation [31,56,70,71]. There seem to be a delicate balance in proteins between 225 robustness and evolvability [55,58].…”