Abstract
To compare folding behavior among lattice proteins which have similar corresponding structures in nature, Crambin homologues are tested in the semi-flexible H0P lattice model using replica-exchange Wang-Landau sampling. Our simulation shows that, at low temperature, these lattice homologues have two common signals in their specific heat curves, implying similarity in the thermodynamic behaviors; while the structural behaviors are more diverse, showing the different stability of their ground state structures at very low temperature. The ground state structures of different homologues can also vary dramatically.
Highlights
The problem of protein folding has been studies for over 80 years
To compare folding behavior among lattice proteins which have similar corresponding structures in nature, Crambin homologues are tested in the semi-flexible H0P lattice model using replica-exchange Wang-Landau sampling
Traditional Monte Carlo methods such as Metropolis sampling are sometimes inefficient at low temperature; for systems with complex free energy landscapes like lattice proteins, these sampling methods are likely to be trapped at some local minima
Summary
The problem of protein folding has been studies for over 80 years. Progress in simulations, as well as experimental and theoretical works, have deepened our understanding of the folding pathway[1], structural prediction[2] and molecular biological function[3]. The further simplification of the HP model is that it places monomers on lattice sites, and only accounts for interactions between nearest neighbor nonbonded HH contacts This model turns out to be very helpful to our understanding of the protein folding problem, giving descriptions about collapse transition[11], structural stability[12, 13], cooperativity[14], etc. The model classifies 20 amino acids into three different types of “beads”, based on their hydrophobicity levels, and all “beads”, or monomers, in a chain are put on different sites of a simple cubic lattice In this H0P polymer system, only contacts between two non-bonded nearest neighbors are taken into consideration. Comparing to their differences in real sequences, which are around 50%, they are more “alike” in the H0P model
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