Abstract
Domain swapping mechanism is a specialised mode of oligomerization of proteins in which part of a protein is exchanged in a non-covalent manner between constituent subunits. This mechanism is highly affected by several physiological conditions. Here, we present a detailed analysis ofthe effect of pH on different regions of the domain swapped oligomer by considering examples which are known to be sensitive to pH in transiting from monomeric to domain-swapped dimeric form. The energetic calculations were performed using a specialized method which considers changes in pH and subsequent changes in the interactions between subunits. This analysis provides definitive hints about the pH-dependence switch from monomer to domain-swapped oligomer and the steps that may be involved in the swapping mechanism.
Highlights
3D-domain swapping is an oligomerization mechanism in which two or more chains exchange their identical or similar structural elements. 3D-domain swapping term was coined by David Eisenberg [1]
We have examined the local energetics of domain-swapped dimer and non-domain swapped monomer at different interface regions for protein examples that are observed to exhibit pH-dependent domain swapping. pH-dependent energy calculation program [20,21] was employed for this purpose
Analysis of amino acid propensities showed that domainswapped interface (DSI) is rich in charged amino acids compared to general 3D-domain swapped proteins within pH-dependent domain swapped proteins (Table 1)
Summary
3D-domain swapping is an oligomerization mechanism in which two or more chains exchange their identical or similar structural elements. 3D-domain swapping term was coined by David Eisenberg [1]. This method was successfully applied on various systems, for instance comparison of proteins of thermophilic and mesophilic organisms [24], binding of potassium ion in ion channels [25], and to study proteins according to their location in cellular compartments [26] This pH-dependence program, which calculates pH-dependent energy profiles based on FD/DH hybrid scheme and helpful in analyzing misfolded proteins, is highly useful to study pH-dependent domain swapping. As domain swapping process includes partial unfolding step prior to oligomerization, this method is highly relevant to this study This program was applied on domain-swapped proteins and therespective non-domain-swapped forms available in PDB [27]. The change in energy during formation of NSI and disruption of DSI appears to determine the rate of oligomerization through domain-swapping process
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