Motif sequence logo and surface analysis of LC8.

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Motif sequence logo and surface analysis of LC8. Motif sequence logo and surface analysis of LC8. (A) Crystal structure of a representative LC8 dimer (protomers shown in shades of green) bound to a peptide (shades of red). (B) Electrostatic charge potential for the LC8 pocket structure using PyMOL’s charge-smoothed potential calculator, with positive potentials shown in blue, negative in red, and neutral in white. Peptides from available crystal structures of bound LC8 are shown, and colored based upon amino acid chemical characteristics (right). Amino acid enrichment is shown below each position within the LC8-binding motif, calculated from 79 known binder motifs listed on the LC8 database (http://lc8hub.cgrb.oregonstate.edu). Amino acid letter heights represent relative enrichment of that amino acid. (C) Solvent accessible surface area depiction of the same LC8/peptide pair shown in (A). Color scheme was defined at the atomic level using the GetArea program (Fraczkiewicz & Braun, 1998), with magenta representing more solvent exposed and orange regions more buried atoms. Nathan Jespersen et al. LSA 2019;2:e201900366 © 2019 Jespersen et al.