Multiple crystal forms of human MacroD2

Abstract

MacroD2 is one of the three human macrodomain proteins characterized by their protein-linked mono-ADP-ribosyl-hydrolyzing activity. MacroD2 is a single-domain protein that contains a deep ADP-ribose-binding groove. In this study, new crystallization conditions for MacroD2 were found and three crystal structures of human MacroD2 in the apo state were solved in space groups P41212, P43212 and P43, and refined at 1.75, 1.90 and 1.70 Å resolution, respectively. Structural comparison of the apo crystal structures with the previously reported crystal structure of MacroD2 in complex with ADP-ribose revealed conformational changes in the side chains of Val101, Ile189 and Phe224 induced by the binding of ADP-ribose in the active site. These conformational variations may potentially facilitate design efforts of a MacroD2 inhibitor.

Enhanced Sampling Approach to the Induced-Fit Docking Problem in Protein–Ligand Binding: The Case of Mono-ADP-Ribosylation Hydrolase Inhibitors

“…Such movements of the loops cannot be appreciated in the X-ray structure where the loop conformations in apo and holo states are very similar, with centroid distances of 12.9 and 11.6 Å, respectively (Table S2). Therefore, our simulations reveal key ligand-dependent events involving loop1 and loop2 impacting on the binding pathway, and, in turn, on the binding affinity (see follow-up paragraphs).…”

“…The calculations on the MacroD2 were based on the holo structure of MacroD2 in complex with ADPr . The free energy shows the presence of four basins (Figures and S4a).…”

“…The calculations on the MacroD2 were based on the holo structure of MacroD2 in complex with ADPr. 50 The free energy shows the presence of four basins (Figures 2 and S4a). The lowest free-energy minima (basins 1 and 2) differ by around 0.5 kcal/mol (i.e., the order of thermal fluctuations, thus they are both populated at room temperature) and represent the bound state.…”

An Enhanced Sampling Approach to the Induced Fit Docking Problem in Protein-Ligand Binding: the case of mono-ADP-ribosylation hydrolases inhibitors

“…The transition from the bound to the unbound state, however, triggers a closure and an opening of the loop1-loop2 interface (Figure S4c and S4d), with their centroid distances ranging from a minimum value of ~10.0 Å to a maximum of ~14.5 Å (Table S2 and Figure S4c), indicating the presence of ADPr dependent induced-fit mechanisms. Such movements of the loops cannot be appreciated in the X-ray structure where the loop conformations in apo and holo states are very similar, with centroid distances of 12.9 Å and 11.6 Å, respectively (Table S2) [52]. Therefore, our simulations reveal key ligand-dependent events involving loop1 and loop2 impacting on the binding pathway, and in turn on the binding affinity (see follow-up paragraphs).…”

“…The calculations on the MacroD2 were based on the holo structure of MacroD2 in complex with ADPr [52]. The free energy shows the presence of four basins (Figure 2).…”