MD simulation of SUMO-1-Alt:S2B3 identifies residues critical for isoform specificity. MD simulation of SUMO-1-Alt:S2B3 identifies residues critical for.

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MD simulation of SUMO-1-Alt:S2B3 identifies residues critical for isoform specificity. MD simulation of SUMO-1-Alt:S2B3 identifies residues critical for isoform specificity. (A) Distances from Asp69 to Arg72 (blue line) and to Thr71 (orange line) in the simulation are plotted against simulation time in nanoseconds. Distances of 3 Å or less indicate hydrogen bonding between the side chains of Asp69 and Thr71. Distances of around 4 Å indicate direct hydrogen bond contacts between Asp69 and Arg72. (B) Snapshots of the SUMO-1-Alt:S2B3 simulation at 0 ns, which shows the starting structure around loop 1, and at 48 ns, which shows that Asp69 rotated to interact with neighboring Gln67. The left snapshot at 72 ns shows Arg72 (SUMO-1-Alt) and its proximity to Asp69 (S2B3). The right snapshot at 72 ns is a rotation of the structure to illustrate that Arg54 (SUMO-1-Alt) lost contact with Tyr69 and Glu66 and that Tyr103 (S2B3) lost hydrogen bond with Gln53 (SUMO-1-Alt). SUMO-1-Alt is green, and S2B3 is orange. (C) ELISA of S-Affs with the indicated amino acid substitutions introduced into the loop region based on predictions from the molecular dynamics simulations. S2B3 V-I Y-A is a double substitution of Val68 to Ile in loop 1 and Tyr103 to Ala in loop 2 of S2B3. Data are represented as mean absorbance at 260 nm ± SE from five experiments. Student’s t tests were used to determine statistical significance. P values below 0.05 were deemed statistically significant. n.s., not statistically significant. David J. Hughes et al., Sci. Signal. 2017;10:eaaj2005 Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works