The high mobility group B1 protein (HMGB1) is a protein that typically acts as a DNA chaperone in the nucleus. It can also be released from the nucleus, where it acts as an inflammatory cytokine and is thought play a role in the development of diseases such as rheumatoid arthritis and cancer. Surface plasmon resonance studies conducted within our laboratory have shown that HMGB1 can form a moderately tightly associated dimer. It is thought that the formation of this dimer may facilitate disulfide exchange between the two domains of HMGB1, one of which features a disulfide (Box A) and the other of which features a free cysteine (Box B). This dimer can then dimerize with lower affinity, forming a tetramer. While the biological relevance of multimerization of HMGB1 is currently unknown, it may contribute to its ability to act as an inflammatory cytokine. Therefore, understanding the structural basis of HMGB1 multimerization may be valuable in the design of molecules to regulate the cytokine activity of HMGB1.

In this study, computational molecular docking and molecular dynamics (MD) simulations were used to propose potential dimers and tetramers of HMGB1. The results of docking the two HMGB1 domains to one another suggest a number of architectures potentially able to facilitate disulfide exchange, which cover parallel, perpendicular and opposite arranged domains. MD simulations of selected poses further suggest that parallel and opposite arrangements are better able to facilitate the generation of the thiolate species required to facilitate disulfide exchange. The complete HMGB1 dimers were then generated from the selected domain complexes and mechanisms for tetramerization were proposed. HMGB1 dimers featuring a parallel arrangement of the domains are proposed as more likely to provide the tetramer species of interest, since the opposite arrangement can be built infinitely and is more likely to represent an aggregating species, rather than a stable multimer.