Leopoldini Monica, Russo Nino, Toscano Marirosa
Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MIUR, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy.
J Am Chem Soc. 2007 Jun 27;129(25):7776-84. doi: 10.1021/ja068168t. Epub 2007 May 25.
The catalytic hydrolysis of a methionyl-peptide substrate by a methionine aminopeptidase active site model cluster was investigated at the DF/B3LYP level of theory, in the gas-phase and in the protein environment. Zn(II), Co(II), Mn(II), and Fe(II) transition metals were examined as the potential catalytic metals of this enzyme involved in protein maturation. Two different mechanisms in which Glu204 was present as protonated or deprotonated residue were considered. The energetic profiles show lower barriers as the protonated glutamate is involved. The rate-determining step of the hydrolysis reaction is always the nucleophilic addition of the hydroxide on substrate carbon, followed by less energetically demanding methionine-peptide C-N bond scission. The lowest activation energy is obtained in the case of zinc dication while the other metals show very high energetic barriers, so that methionine aminopeptidase can be in principle recognized as a dizinc enzyme.
在理论的DF/B3LYP水平上，在气相和蛋白质环境中研究了甲硫氨酸氨基肽酶活性位点模型簇对甲硫氨酰肽底物的催化水解作用。研究了锌（II）、钴（II）、锰（II）和铁（II）过渡金属作为参与蛋白质成熟的该酶的潜在催化金属。考虑了两种不同的机制，其中谷氨酸204以质子化或去质子化残基存在。能量分布图显示，当质子化谷氨酸参与时，势垒较低。水解反应的速率决定步骤始终是氢氧根在底物碳上的亲核加成，随后是能量需求较低的甲硫氨酸 - 肽C - N键断裂。在二价锌的情况下获得了最低的活化能，而其他金属显示出非常高的能量势垒，因此原则上可以将甲硫氨酸氨基肽酶识别为双锌酶。
