Ramachandran outliers in ligand‐induced protein structural changes
Korbin H. J. West, Walter R. P. Novak · The FASEB Journal · 2016
Ramachandran outliers are amino acid residues that have unfavorable dihedral angles in proteins. Often found in protein structure analysis, the presence of these outliers may be simply errors in the structure; however, other times these outliers existence is supported by structural data. There has been little investigation into the role that these energetically unfavorable outliers have in protein structure. Of special interest is how ligand binding may affect protein structures with respect to Ramachandran outliers. These structural changes may drastically alter the properties of proteins: ligand affinities, protein‐protein interactions, or activity levels. In this study, we survey the Ramachandran outliers in pairs of proteins in the ligand‐bound and unliganded states available in the Protein Structural Change Database ( http://idp1.force.cs.is.nagoya‐u.ac.jp/pscdb/ ). We also examine whether these outliers are supported by the structural data using PDB_REDO ( http://xtal.nki.nl/PDB_REDO/ ). Support or Funding Information This research is supported by the Wabash College Haines Biochemistry Fund.