Influence of the chain stiffness on the thermodynamics of a Gō-type model for protein folding.
The relative importance of local and long range interactions in the characteristics of the protein folding process has long been a matter of controversy. Computer simulations based on Gō-type models have been widely used to study this topic, but without much agreement on which type of interactions is more relevant for the foldability of a protein. In this work, the authors also employ a topology-based potential and simulation model to analyze the influence of local and long range interactions on the thermodynamics of the folding transition. The former are mainly used to control the degree of flexibility (or stiffness) of the chain, mostly appreciable in the unfolded (noncompact) state. Our results show the different effects that local and nonlocal interactions have on the entropy and the energy of the system. This implies that a balance between both types of interactions is required, so that a free energy barrier exists between the native and the denatured states. The variations in the contribution of both types of interactions have also a direct effect on the stability of the chain conformations, including the possible appearance of thermodynamic folding intermediates.
Prieto
Lidia
L
Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense, E-28040 Madrid, Spain.
Rey
Antonio
A
D000465:Algorithms; D003198:Computer Simulation; D008962:Models, Theoretical; D009010:Monte Carlo Method; D017510:Protein Folding; D013816:Thermodynamics