Protein Folding Absent Selection

Abstract

Biological proteins are known to fold into specific 3D conformations. However, the fundamental question has remained: Do they fold because they are biological, and evolution has selected sequences which fold? Or is folding a common trait, widespread throughout sequence space? To address this question arbitrary, unevolved, random-sequence proteins were examined for structural features found in folded, biological proteins. Libraries of long (71 residue), random-sequence polypeptides, with ensemble amino acid composition near the mean for natural globular proteins, were expressed as cleavable fusions with ubiquitin. The structural properties of both the purified pools and individual isolates were then probed using circular dichroism, fluorescence emission, and fluorescence quenching techniques. Despite this necessarily sparse “sampling” of sequence space, structural properties that define globular biological proteins, namely collapsed conformations, secondary structure, and cooperative unfolding, were found to be prevalent among unevolved sequences. Thus, for polypeptides the size of small proteins, natural selection is not necessary to account for the compact and cooperative folded states observed in nature.

The Coevolutionary Roots of Biochemistry and Cellular Organization Challenge the RNA World Paradigm

“…In other words, coevolution appears to be again responsible for the history of identity elements and specificities responsible for the vocabulary used in the genetic repository. These findings align with remarkable evidence, including the existence of organisms with faulty aaRS enzymes and statistical proteomes [Boniecki and Martinis, 2012], patterns of genetic code complementarity and error tolerance [Rodin and Rodin, 2008], the observation that random protein sequences fold into defined structures and display a multitude of small molecule binding abilities [Cherny et al, 2012;LaBean et al, 2011], the experimental reproduction of a β-barrel fold with only five amino acid components without compromising folding speed and function [Riddle et al, 1997], and evolutionary outcomes in mRNA display experiments [Chao et al, 2013;Seelig, 2011] that point to important tendencies in proteins structure. We will just mention in passing the promise of statistical proteomes for synthetic biology and our understanding of translation.…”

Foldability of a Natural De Novo Evolved Protein

“…Some observations support a molten globule state, but protease resistance suggests a higher level of order, so its placement in common classifications of structural order, such as the Uversky quartet model, remains in some doubt (Uversky, 2002). Bsc4 might be conservatively described as having a “rudimentary fold” (Labean et al, 2011), and it also bears some comparison to a folding or misfolding intermediate. In any case, a nascent structure with such an unusual combination of properties seems reasonable for the “birth” of folding in a de novo evolved protein.…”

“…Soluble proteins with significant secondary structure content have been recovered from unevolved random amino-acid sequence libraries, but they do not have specific, well-defined tertiary structures (Chiarabelli et al, 2006; Davidson et al, 1995; Doi et al, 1998). Even when such libraries are biased toward compositions or patterns found in natural proteins, the structures recovered tend to have “rudimentary” or “molten globule” characteristics lacking clearly specific tertiary structure (Graziano et al, 2008; Labean et al, 2011; Matsuura et al, 2002). Only in a single well-known case, in which random sequence libraries were subjected to extensive in vitro functional evolution, have clearly native-like structures been recovered (Keefe and Szostak, 2001; Lo Surdo et al, 2004; Mansy et al, 2007).…”

Chemical synthetic biology: a mini-review

“…The idea on the NBB moves from the observation that the extant collection of proteins and RNA molecules, currently present in living organisms, are only a minor part of the all theoretical possible sequences (de Duve, 2002; Luisi, 2003; Xia and Levitt, 2004; Chiarabelli et al, 2006a,b, 2011; Dryden et al, 2008; LaBean et al, 2011). For example, the number of possible different peptides of 50 amino acid residues synthesized using the 20 natural amino acids is equal to 20 50 , i.e., 10 65 .…”