Unfolding simulation to verify the concept of limited conformational sub-space for early-stage intermediate

Model introducing the limited conformational sub-space for early-stage intermediate definition for protein folding process presented formerly is verified in respect to the unfolding process treated as reverse process to folding. It was expected to receive the step-wise unfolded structure keeping the structural alphabet. It is shown that as long as the secondary structure is present in the gradually unfolded structures, the codes for structural alphabet are changed for relatively low number of residues. The high temperature molecular dynamics simulations revealed the structures with significantly increased distance versus the limited conformational sub-space and large change of alphabet codes. The test was performed for ubiquitine in 300K, 350K, 400K, 500K, 700K and 1000K. It suggests that the structural codes found for crystal structures can not be treated rigorously to be kept during the folding process simulation. Although some tendencies for structural codes changes are observed suggesting the corrections for the definition of early stage structural forms.