Stress tensor analysis of the protein quake of photoactive yellow protein.
Immediately after photon absorption, the photoenergy is converted to local stress energy via the ultrafast photoisomerization reaction of the p-coumaric acid (pCA) chromophore in a small water-soluble blue light receptor, photoactive yellow protein (PYP), derived from the halophilic bacterium, Halorhodospira halophila. A series of conformational changes are then induced, which are intimately related with the relaxation process on the energy landscape of PYP. In order to understand the signaling function of PYP in atomic detail, the characterization of the physical mechanism of the protein quake of PYP is important, as is the atomic description of the series of conformational changes associated with the photocycle. Here, we report a theoretical/computational study for the analysis of the intramolecular stress tensor for the dark state and three intermediate states, pR, pB1 and pB2, of PYP. As a result, we found that the magnitude of the stress released during the change from the pR to the pB1 state is significantly large at the hydroxyl oxygen atom of Tyr42, suggesting that this atom is the focus of the protein quake of PYP. This is consistent with previous experimental observations.
Koike
Kana
K
Graduate School of Science, Nagoya University, Furo-chos, Chikusa-ku, Nagoya, Japan.
Kawaguchi
Kazutomo
K
Yamato
Takahisa
T
D000596:Amino Acids / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry* / Q000528:radiation effects; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D003373:Coumaric Acids / Q000737:chemistry / Q000528:radiation effects; D020607:Halorhodospira halophila / Q000737:chemistry; D008027:Light; D008958:Models, Molecular; D010777:Photochemistry; D020283:Photoreceptors, Microbial / Q000737:chemistry* / Q000528:radiation effects; D011487:Protein Conformation; D014732:Vibration
D000596:Amino Acids; D001426:Bacterial Proteins; D003373:Coumaric Acids; D020283:Photoreceptors, Microbial; C050162:photoactive yellow protein, Bacteria