Bridging Themes: Short Protein Segments Found in Different Architectures

Abstract

The vast majority of theoretically possible polypeptide chains do not fold, let alone confer function. Hence, protein evolution from preexisting building blocks has clear potential advantages over ab initio emergence from random sequences. In support of this view, sequence similarities between different proteins is generally indicative of common ancestry, and we collectively refer to such homologous sequences as ‘themes’. At the domain level, sequence homology is routinely detected. However, short themes which are segments, or fragments of intact domains, are particularly interesting because they may provide hints about the emergence of domains, as opposed to divergence of preexisting domains, or their mixing-and-matching to form multi-domain proteins. Here we identified 525 representative short themes, comprising 20-to-80 residues, that are unexpectedly shared between domains considered to have emerged independently. Among these ‘bridging themes’ are ones shared between the most ancient domains, e.g., Rossmann, P-loop NTPase, TIM-barrel, Flavodoxin, and Ferredoxin-like. We elaborate on several particularly interesting cases, where the bridging themes mediate ligand binding. Ligand binding may have contributed to the stability and the plasticity of these building blocks, and to their ability to invade preexisting domains or serve as starting points for completely new domains.

Evidence for the preferential reuse of sub‐domain motifs in primordial protein folds

“…AncPept , 23 the bridging themes , 27 Fuzzle 26 and our CA_motifs specify four sets of putatively ancestral protein motifs. AncPept , the bridging themes , and Fuzzle recruit motifs from pairwise alignments of HMMs representing SCOP domains.…”

“…For the determination of AncPept and CA_motifs , the cut‐off values were 0.5 and 0.55, respectively. In the set of the bridging themes , 30% have a TM‐score < 0.3 and only 25% a score > 0.5 27 . For the identification of Fuzzle motifs, a TM‐score threshold of 0.3 in combination with an RMSD threshold of 3 Å and no upper or lower bound for the length of the motifs has been used 26 .…”

“…Due to their superior sensitivity, profile hidden Markov models (HMMs) are the method of choice for the detection of remote sequence homology 22 . Although several studies 23‐27 used HMMs to account for sequence homology, the number of fragments that were found in similar sets of protein folds differ drastically: The database Fuzzle comprises more than 1000 fragments of various length, 26 whereas not more than 40 fragments to be found in 118 folds have been reported by A. Lupas and coworkers 23 …”

Exploiting enzyme evolution for computational protein design

“…This approach is attractive because it effectively allows new proteins to be assembled as if they are made of molecular LEGO® building blocks. Modular design is relevant from an evolutionary perspective, as there is increasing evidence that natural proteins evolve from fragments or motifs, such as short propellor-like motifs that have evolved into modern β-barrels [71], an omnipresent Rossman ribose-binding motif that hints at common ancestry among Rossman-fold enzymes that use ribose-based cofactors [72], and a β-α-β fragment that appears to be the minimal functional motif leading to modern P-loop NTPase and Rossman enzymes [73], among other examples [74][75][76]. Therefore, modular design mimics the repeating themes that lead to the natural evolution of functional protein scaffolds.…”

“…These are most commonly classified in terms of 'domains', typically comprising ~50-250 amino acids that represent an independent folding unit [84]. However, a number of studies have suggested that duplication and recombination of segments shorter than domains could have been the origin of the domains themselves and that these are therefore the ultimate building blocks [71,75,81,85,86].…”