Effect of hydrogen bonds on the folding cooperativity of a minimalist hydrophobic protein model
Barbosa, M. A. A.1; Pereira de Araujo, A. F.2
1Inst. de Física, USP, SP; 2Depto. de Biol. Celular, IB, UnB, DF
We investigate the thermodynamic cooperativity of folding for a
minimalist hydrophobic protein model with an effective reduction in
lattice coordination upon chain compaction. This scheme is intended to
mimic the requirement that polar backbone groups of real proteins must
form hydrogen bonds concomitantly to their burial inside the apolar
protein core. In addition to the square lattice, with z=3 conformations
per monomer, we use extensions in which diagonal step vectors are
allowed, resulting in z=5 and z=7. Thermodynamics are governed by the
hydrophobic energy function, according to which hydrophobic monomers
tend to make contacts unspecifically while the reverse is true for
hydrophilic monomers, with the additional restriction that only
contacts between monomers adopting one of zh < z local conformations contribute to the energy, where zh is the number
of local conformations assumed to be compatible with hydrogen bond
formation. Simulations with different native structures were performed
and resulted in large increases on the folding transition abruptness
and van't Hoff-to-calorimetric-enthalpy ratio. The observed increase in
folding cooperativity is correlated to an increase in the convexity of
the underlying microcanonical conformational entropy as a function of
energy. Simulations in three dimensions, even though using a smaller
relative reduction in effective lattice coordination zh/z=4/5,
display a slight increase in cooperativity for a hydrophobic model of
40 monomers and a more pronounced increase in cooperativity for a
native-centric Go-model with the same native structure, suggesting that
hydrogen bonds are of fundamental importance in the theoretical
description of folding cooperativity.
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