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Structure based native-like features of intein insertion sites.

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posted on 23.05.2012, 01:09 authored by James Apgar, Mary Ross, Xiao Zuo, Sarah Dohle, Derek Sturtevant, Binzhang Shen, Humberto de la Vega, Philip Lessard, Gabor Lazar, R. Michael Raab

(a) Local secondary structure of intein insertion sites binned into 6 different groups relative to its location to loop/alpha-helix and loop/beta-sheet junctions. These groups are AH/L-J (within 2 amino acids of an alpha-helix/Loop junction), BS/L-J (within 2 amino acids of an beta-sheet/Loop Junction), mid-AH (middle of an alpha helix and more than two amino acids to a loop junction), mid-BS (middle a beta-sheet and more than two amino acids to a loop junction) mid-L (middle of a loop and more than 2 amino acids to a loop or beta-sheet junction, and other (all remaining sites). (b–c) Proximity of intein insertion sites to the closest (b) active site residue or (c) dimer interface residue. (d) Degree of burial of intein insertion sites divided by C/S/T residue type. The degree of burial was calculated using the Cβ density. (e) Flexibility of the insertion site residue as determined by RMSD of molecular dynamics simulation. This plot shows the flexibility rank of the native versus non-native insertion sites.