Quantum Chemical Study of the pKa Control Mechanism for the Active Center in Bacteriorhodopsin and Its M Intermediate
| Autor: | and Yoshio Inoue, Sawako Nakajima, Kazuki Ohno, Minoru Sakurai |
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| Rok vydání: | 2003 |
| Předmět: |
Quantum chemical
Schiff base biology Hydrogen bond Bacteriorhodopsin Surfaces Coatings and Films Active center chemistry.chemical_compound Crystallography Matrix (mathematics) chemistry Computational chemistry Materials Chemistry biology.protein Molecular orbital Physical and Theoretical Chemistry Ground state |
| Zdroj: | The Journal of Physical Chemistry B. 107:2867-2874 |
| ISSN: | 1520-5207 1520-6106 |
| Popis: | In this study, integrated (MOZYME + DFT) method (Ohno et al. Chem. Phys. Lett. 2001, 341, 387.) is applied to elucidate how the pKa's of retinal Schiff base (RSB) and Asp85 in bacteriorhodopisn (bR) are controlled by the surrounding protein matrix, especially a hydrogen bonding network involving RSB. The whole protein is divided into two layers. Layer 1 contains only the hydrogen bonding network and is treated at the DFT level of theory. The rest of the protein is calculated using a linear-scaling molecular orbital method called MOZYME that can explicitly take into account the protein three-dimensional structure. Here we focus our attention on the pKa changes of RSB and Asp85 on going from the ground state to the M intermediate, because they are key factors of the proton translocation mechanism in bR. The three-dimensional structures of both states are taken from corresponding X-ray data. The calculation successfully reproduces the experimental fact that RSB and Asp85 form the zwitterions in the ground st... |
| Databáze: | OpenAIRE |
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