Fig. 2: Structure of XL5-ligated hRpn13 Pru. | Nature Communications

Fig. 2: Structure of XL5-ligated hRpn13 Pru.

From: Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma

Fig. 2

a, b Chemical structure of XL5 (left panel) including the ligated sulfur atom from hRpn13 C88. Hydrogen atoms are labeled with numbers used in the text and figures. Chiral center C15 or C16 is labeled and indicated with a star in red. Selected regions from a 1H, 13C half-filtered NOESY (100 ms) experiment (a, right panel and b) acquired on a sample containing 0.25 mM 13C-labeled hRpn13 Pru and twofold molar excess unlabeled XL5 dissolved in NMR buffer. c LC-MS analysis of 2 μM purified hRpn13 Pru (MW: 17017.3 g/mol) incubated with 20 μM XL5 for 2 h at 4 °C. The resulting compound adduct and unmodified hRpn13 Pru are labeled along with the detected molecular weight (Da). d LC-MS analysis of 40 μM XL5 incubated with 2 mM reduced L-glutathione (GSH, MW: 307.3 g/mol) for 2 h at 4 °C. Detected GSH adducts are indicated and a table is included that lists relative abundance. e Chemical structure of XL5-13C6-BA (upper panel) illustrating 13C-labeling. Selected region from a 1H, 1H plane of a 3-dimensional 1H, 13C half-filtered NOESY (100 ms) experiment (lower panel) acquired without incrementing the 13C dimension on a sample with 0.4 mM unlabeled hRpn13 Pru and equimolar of XL5-13C6-BA dissolved in NMR buffer containing 70% 2H2O. f Structural ensemble (left panel) or ribbon diagram (right panel) of hRpn13 (purple) ligated to XL5 (orange) with C15 and C16 in the SS stereoconfiguration. hRpn13 secondary structural elements and XL5 chemical groups are labeled with the two chiral centers indicated by an asterisk (*). The C88 sulfur, nitrogen, and oxygen atoms are colored yellow, blue, and red respectively in the ribbon diagram. g Enlarged view highlighting interactions between hRpn13 M31, V85, and V93 with XL5 H13 and H19 as well as hRpn13 V38 and P89 with the XL5 central benzene. A weak hydrogen bond is formed between the hRpn13 S90 hydroxy group and XL5 cyanide group (red line). Key interactions are highlighted (gray lines) including distances (Å) for XL5 hydrogen or cyanide nitrogen atoms with hRpn13 carbon atoms (colored as in f right panel).

Back to article page