Abstract
BackgroundThe studies on protein folding/unfolding indicate that the native state topology is an important determinant of protein folding mechanism. The folding/unfolding behaviors of proteins which have similar topologies have been studied under Cartesian space and the results indicate that some proteins share the similar folding/unfolding characters.ResultsWe construct physical property space with twelve different physical properties. By studying the unfolding process of the protein G and protein L under the property space, we find that the two proteins have the similar unfolding pathways that can be divided into three types and the one which with the umbrella-shape represents the preferred pathway. Moreover, the unfolding simulation time of the two proteins is different and protein L unfolding faster than protein G. Additionally, the distributing area of unfolded state ensemble of protein L is larger than that of protein G.ConclusionUnder the physical property space, the protein G and protein L have the similar folding/unfolding behaviors, which agree with the previous results obtained from the studies under Cartesian coordinate space. At the same time, some different unfolding properties can be detected easily, which can not be analyzed under Cartesian coordinate space.
Highlights
The studies on protein folding/unfolding indicate that the native state topology is an important determinant of protein folding mechanism
Studies on some small single-domain proteins suggest that proteins that have similar native structures with low sequence identity have similar transition state ensemble [3,4] and folding rates of two-state proteins have shown to correlate very well with contact order, a quality linked to topology [5,6]
The physical property space was constructed with twelve physical parameters and decreased to threedimensional essential property subspace
Summary
The studies on protein folding/unfolding indicate that the native state topology is an important determinant of protein folding mechanism. The folding/unfolding behaviors of proteins which have similar topologies have been studied under Cartesian space and the results indicate that some proteins share the similar folding/unfolding characters. The most popular theory is that native state topology is an important determinant of protein folding mechanism [1,2]. Studies on some small single-domain proteins suggest that proteins that have similar native structures with low sequence identity have similar transition state ensemble [3,4] and folding rates of two-state proteins have shown to correlate very well with contact order, a quality linked to topology [5,6]. Some studies indicated that proteins with the similar native structures maybe have different folding pathway [7,8,9]
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