Computational analysis of sequence selection mechanisms.
Mechanisms leading to gene variations are responsible for the diversity of species and are important components of the theory of evolution. One constraint on gene evolution is that of protein foldability; the three-dimensional shapes of proteins must be thermodynamically stable. We explore the impact of this constraint and calculate properties of foldable sequences using 3660 structures from the Protein Data Bank. We seek a selection function that receives sequences as input, and outputs survival probability based on sequence fitness to structure. We compute the number of sequences that match a particular protein structure with energy lower than the native sequence, the density of the number of sequences, the entropy, and the "selection" temperature. The mechanism of structure selection for sequences longer than 200 amino acids is approximately universal. For shorter sequences, it is not. We speculate on concrete evolutionary mechanisms that show this behavior.
Meyerguz
Leonid
L
Department of Computer Science, 4130 Upson Hall, Cornell University, Ithaca, NY 14853, USA.
Grasso
Catherine
C
Kleinberg
Jon
J
Elber
Ron
R
D003198:Computer Simulation; D030562:Databases, Protein; D019143:Evolution, Molecular; D008958:Models, Molecular; D017510:Protein Folding; D012641:Selection, Genetic; D013696:Temperature; D013816:Thermodynamics