Effective selection system for experimental evolution of random polypeptides towards DNA-binding protein

Biophysical connection between evolutionary dynamics and thermodynamics in in vitro evolution

We analyzed a mathematical model of in vitro evolution conducted by repetition of mutagenesis and selection processes. The selection process consists of the selective enrichment and subsequent sampling as follows: each mutant with fitness W is amplified by the Boltzmann factor exp(rW/k(B)T(the)), where the fitness W is defined as the negative Gibbs free energy (-ΔG) in a reaction of the phenotypic molecules and r is the round number of the selective enrichment; then, an arbitrary mutant is randomly chosen from the resulting mutant population and it becomes a new parent in the next generation. As a result, we found that the evolutionary dynamics is described in a mathematical framework similar to thermodynamics: the "evolution constant" k(E) and "evolutionary temperature" T(evo) play key roles similar to the Boltzmann constant k(B) and thermodynamic temperature T(the), respectively. In the stationary state of the evolutionary dynamics, the attractor of the fitness is in inverse proportion to k(E)T(evo). Furthermore, beyond the mathematical analogy, we obtained a biophysical connection between evolutionary dynamics and thermodynamics. Particularly, we found that T(evo) and T(the) are connected by k(E)T(evo)≈k(B)T(the)/2r. These results suggest that we can predict the fitness value in the stationary state by the thermodynamic temperature T(the) in the experimental setup.

Emergence of polyproline II-like structure at early stages of experimental evolution from random polypeptides

To examine whether a primordial functional protein at the early stages of evolution has structural features, we carried out experimental evolution consisting of 25 cycles (generations) of mutation and selection toward DNA-binding function using a random-sequence polypeptide of 139 amino acid residues with no secondary structure as the initial sequence. In each generation, 16 clones were sampled arbitrarily for sequence analysis, and a phylogenetic tree was constructed. Polypeptide evolution proceeded from the initial point on branch I in 2 main directions of branches II and III. The initial and 2 evolved polypeptides (one at the 24th generation on branch III and the other at the 25th generation on branch II) were purified to examine their functional and structural properties. Although binding of the initial polypeptide to the target DNA was not detected by surface plasmon resonance measurements, the 2 evolved polypeptides bound to the DNA with dissociation constants of 1.6 and 1.0 microM, respectively, indicating an increase in affinity during the experimental evolution. Circular dichroism spectra of the evolved polypeptides, but not of the initial polypeptide, showed features characteristic of the polyproline II (PPII)-like structure, a left-handed helical structure commonly found in natural proteins, suggesting that the structure emerged through the experimental evolution. The same structural feature was found in another experimental evolution toward catalytic activity. These results demonstrate that the PPII-like structure is one of the common features that could have appeared in the early evolutionary stages of primordial functional protein.