On the modeling of arginine-bound carboxylates: a case study with Pyruvate Formate-Lyase |
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| Authors: | Condi?-Jurki? Karmen Perchyonok V Tamara Zipse Hendrik Smith David M |
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| Institution: | 1. Centre for Computational Solutions in the Life Sciences, Ru?er Bo?kovi? Institute, Bijeni?ka 54 HR-10002 Zagreb, Croatia;2. School of Chemistry, Monash University, Clayton Rd, Clayton, 3080, Melbourne, Australia;3. Department Chemie und Biochemie, Ludwig-Maximilians-Universität, Butenandtstrasse 13, 82131 München, Germany |
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| Abstract: | 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. |
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| Keywords: | ab initio DFT enzyme mechanism pyruvate formate-lyase arginine-bound carboxylate |
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