Fast, cheap and out of control — Insights into thermodynamic and informatic constraints on natural protein sequences from de novo protein design

Abstract

The accumulated results of thirty years of rational and computational de novo protein design have taught us important lessons about the stability, information content, and evolution of natural proteins. First, de novo protein design has complicated the assertion that biological function is equivalent to biological structure - demonstrating the capacity to abstract active sites from natural contexts and paste them into non-native topologies without loss of function. The structure-function relationship has thus been revealed to be either a generality or strictly true only in a local sense. Second, the simplification to —maquette topologies carried out by rational protein design also has demonstrated that even sophisticated functions such as conformational switching, cooperative ligand binding, and light-activated electron transfer can be achieved with low-information design approaches. This is because for simple topologies the functional footprint in sequence space is enormous and easily exceeds the number of structures which could have possibly existed in the history of life on Earth. Finally, the pervasiveness of extraordinary stability in designed proteins challenges accepted models for the —marginal stability of natural proteins, suggesting that there must be a selection pressure against highly stable proteins. This can be explained using recent theories which relate non-equilibrium thermodynamics and self-replication.

Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers

“…Those studies show that unique folded structures can be encoded simply in the binary patterning of polar and hydrophobic residues, with finer tuning by specific interresidue contacts. This binary encoding of unique folding is confirmed by experiments (74)(75)(76)(77). Subsequently, the HP model has contributed several notable insights and advances, including sequence space superfunnels (64), the nonrandomess of uniquely encoding sequences (65), the determination of all uniquely encoding sequences of chain length 25 (66), recombination (67), homology-like comparative modeling features (68), and evolutionary switches (69).…”

Maquette Strategy for Creation of Light- and Redox-Active Proteins

“…The resistance of this homodimeric two-heme maquette to pH change became routinely recognized; ferrous hemes dissociate from the maquette at pH values below 4 and above 12, while the ferric heme dissociates at below 2.5 and 10. Furthermore, heme maquettes (beyond this first maquette) resist unfolding and heme dissociation not just at elevated temperatures already mentioned [Regan and DeGrado, 1988;Marshall and Mayo, 2001;Huang et al, 2014;Brisendine and Koder, 2016] but at autoclave temperatures above 100°C [Ennist, 2017]. Another demonstration of the controlled maquette stability was seen when assembled on surfaces.…”

“…glutamate or aspartate) amino acids positioned to optimize charge interactions and add thermal stability to the folded bundle (e.g. resisting unfolding in near boiling water) [Regan and DeGrado, 1988;Marshall and Mayo, 2001;Huang et al, 2014;Brisendine and Koder, 2016]. These seven amino acid helical heptads are well known to form two complete turns to extend the length of a helix by close to 10.8 Å.…”

“…Figure 2 is a molecular level representation of Darwin's principle of multiple utility [Darwin, 1872] that presents some of the roles any single amino acid or peptide motif can play in the lifetime of a natural protein in a cell from translation to final breakdown and removal for recycling [Moser et al, 2006a;Brisendine and Koder, 2016]. A particular amino acid may be critical not only in promoting the chemical catalysis for which the protein is named, but also and certainly not only, in folding and unfolding the protein and hence in establishing stability and dynamics.…”

Driving forces in the origins of life

“…Today's protein folding code is dominated by the binary HP patterning in the sequence [53,55]. This is proven in experiments where proteins that have been massively mutated, in ways that preserve only a given HP pattern, still fold to their appropriate native structures [56][57][58][59]. 6 Moreover, HP foldability does not even require that the polymer backbone be a peptide.…”