Transition state structure invariance to model system size and calculation levels: a QM/MM study of the carboxylation step catalyzed by Rubisco |
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Authors: | V Moliner J Andrés M Oliva V S Safont O Tapia |
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Institution: | (1) Department of Experimental Sciences, University Jaume I, Box 224, E-12080 Castelló, Spain, ES;(2) Department of Physical Chemistry, Uppsala University, Box 532, S-75121 Uppsala, Sweden, SE |
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Abstract: | The present study elucidates structural features related to the molecular mechanism in the carboxylation step of the reaction
catalyzed by Rubisco. Starting from the initial X-ray Protein Data Bank structure of a Rubisco monomer, the reactive subsystem
in vacuo is subjected to quantum chemical semiempirical and ab initio studies, while the effects of the protein environments
are included by means of a hybrid quantum mechanical/molecular mechanical (QM/MM) approach. The QM/MM is used to characterize
the transition structure for carboxylation inside the protein. The calculations were made with the AM1/CHARMM/GRACE scheme.
Comparisons between the in vacuo and in situ transition structures show remarkable invariance with respect to geometric parameters,
index and transition vector amplitudes. The transition state couples the carbon dioxide attack to the C2 center of the substrate
in its dienol form with a simultaneous intramolecular hydrogen transfer from the C2 atom to the hydroxyl group linked to the
C3 center. This study suggests that carboxylation may be simultaneously coupled to the activation of the C3 center in the
enzyme.
Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998 |
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Keywords: | : Rubisco Carboxylation step QM/MM Hybrid theoretical calculations Transition state structure |
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