title: Relevance of structural segregation and chain compaction for the thermodynamics of folding of a hydrophobic protein model.
abstract: The relevance of inside-outside segregation and chain compaction for the thermodynamics of folding of a hydrophobic protein model is probed by complete enumeration of two-dimensional chains of up to 18 monomers in the square lattice. The exact computation of Z scores for uniquely designed sequences confirms that Z tends to decrease linearly with sigma square root of N, as previously suggested by theoretical analysis and Monte Carlo simulations, where sigma, the standard deviation of the number of contacts made by different monomers in the target structure, is a measure of structural segregation and N is the chain length. The probability that the target conformation is indeed the unique global energy minimum of the designed sequence is found to increase dramatically with sigma, approaching unity at maximal segregation. However, due to the huge number of conformations with sub-maximal values of sigma, which correspond to intermediate, only mildly discriminative, values of Z, in addition to significant oscillations of Z around its estimated value, the probability that a correctly designed sequence corresponds to a maximally segregated conformation is small. This behavior of Z also explains the observed relation between sigma and different measures of folding cooperativity of correctly designed sequences.
authors.affiliation: Instituto de Física, Universidade de Brasília, Brasília-DF 70910-900, Brazil.
authors.forename: Marco Aurélio A
authors.initials: MA
authors.lastname: Barbosa
authors.forename: Antônio F Pereira
authors.initials: AF
authors.lastname: de Araújo
mesh_terms: D015233:Models, Statistical; D009010:Monte Carlo Method; D011487:Protein Conformation; D017510:Protein Folding; D013696:Temperature; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D014867:Water