On the modeling of arginine-bound carboxylates: a case study with Pyruvate Formate-Lyase.
High level ab initio and density functional calculations have been employed to determine the most appropriate manner in which to truncate an arginine-bound carboxylate motif, using the substrate mechanism of Pyruvate Formate-Lyase as a case study. The results show that, both qualitatively and quantitatively, a neutral carboxylic acid provides a more realistic approximation to the salt bridge arrangement than does a bare anionic carboxylate substituent.
Condić-Jurkić
Karmen
K
Centre for Computational Solutions in the Life Sciences, Ruder Bosković Institute, Bijenicka 54 HR-10002 Zagreb, Croatia.
Perchyonok
V Tamara
VT
Zipse
Hendrik
H
Smith
David M
DM
D000123:Acetyltransferases / Q000737:chemistry*; D001120:Arginine / Q000737:chemistry*; D002264:Carboxylic Acids / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D011789:Quantum Theory
D002264:Carboxylic Acids; D001120:Arginine; D000123:Acetyltransferases; C022560:formate C-acetyltransferase