Abstract
The cyanobacterial photosystem II (PSII) crystal structure includes more than 1300 water molecules in each monomer unit; however, their precise roles in water oxidation are unclear. To understand the origins of water molecules in the PSII crystal structure, the accessibility of bulk water molecules to channel inner spaces in PSII was investigated using the water-removed PSII structure and molecular dynamics (MD) simulations. The inner space of the channel that proceeds toward the D1-Glu65/D2-Glu312 pair (E65/E312 channel) was entirely filled with water molecules from the bulk region. In the same channel, a diamond-shaped cluster of water molecules formed near redox-active TyrZ in MD simulations. Reorientation of the D2-Leu352 side chain resulted in formation of a hexagonal water network at the Cl-2 binding site. Water molecules could not enter the main region of the O4-water chain, which proceeds from the O4 site of the Mn4CaO5 cluster. However, in the O4-water chain, the two water binding sites that are most distant from the protein bulk surface were occupied by water molecules that approached along the E65/E312 channel, one of which formed an H-bond with the O4 site. These findings provide key insights into the significance of the channel ends, which may utilize water molecules during the PSII photocycle.
| Original language | English |
|---|---|
| Pages (from-to) | 3049-3057 |
| Number of pages | 9 |
| Journal | Biochemistry |
| Volume | 56 |
| Issue number | 24 |
| DOIs | |
| Publication status | Published - 2017 Jun 20 |
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ASJC Scopus subject areas
- Biochemistry
Cite this
Origins of Water Molecules in the Photosystem II Crystal Structure. / Sakashita, Naoki; Watanabe, Hiroshi; Ikeda, Takuya; Saito, Keisuke; Ishikita, Hiroshi.
In: Biochemistry, Vol. 56, No. 24, 20.06.2017, p. 3049-3057.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Origins of Water Molecules in the Photosystem II Crystal Structure
AU - Sakashita, Naoki
AU - Watanabe, Hiroshi
AU - Ikeda, Takuya
AU - Saito, Keisuke
AU - Ishikita, Hiroshi
PY - 2017/6/20
Y1 - 2017/6/20
N2 - The cyanobacterial photosystem II (PSII) crystal structure includes more than 1300 water molecules in each monomer unit; however, their precise roles in water oxidation are unclear. To understand the origins of water molecules in the PSII crystal structure, the accessibility of bulk water molecules to channel inner spaces in PSII was investigated using the water-removed PSII structure and molecular dynamics (MD) simulations. The inner space of the channel that proceeds toward the D1-Glu65/D2-Glu312 pair (E65/E312 channel) was entirely filled with water molecules from the bulk region. In the same channel, a diamond-shaped cluster of water molecules formed near redox-active TyrZ in MD simulations. Reorientation of the D2-Leu352 side chain resulted in formation of a hexagonal water network at the Cl-2 binding site. Water molecules could not enter the main region of the O4-water chain, which proceeds from the O4 site of the Mn4CaO5 cluster. However, in the O4-water chain, the two water binding sites that are most distant from the protein bulk surface were occupied by water molecules that approached along the E65/E312 channel, one of which formed an H-bond with the O4 site. These findings provide key insights into the significance of the channel ends, which may utilize water molecules during the PSII photocycle.
AB - The cyanobacterial photosystem II (PSII) crystal structure includes more than 1300 water molecules in each monomer unit; however, their precise roles in water oxidation are unclear. To understand the origins of water molecules in the PSII crystal structure, the accessibility of bulk water molecules to channel inner spaces in PSII was investigated using the water-removed PSII structure and molecular dynamics (MD) simulations. The inner space of the channel that proceeds toward the D1-Glu65/D2-Glu312 pair (E65/E312 channel) was entirely filled with water molecules from the bulk region. In the same channel, a diamond-shaped cluster of water molecules formed near redox-active TyrZ in MD simulations. Reorientation of the D2-Leu352 side chain resulted in formation of a hexagonal water network at the Cl-2 binding site. Water molecules could not enter the main region of the O4-water chain, which proceeds from the O4 site of the Mn4CaO5 cluster. However, in the O4-water chain, the two water binding sites that are most distant from the protein bulk surface were occupied by water molecules that approached along the E65/E312 channel, one of which formed an H-bond with the O4 site. These findings provide key insights into the significance of the channel ends, which may utilize water molecules during the PSII photocycle.
UR - http://www.scopus.com/inward/record.url?scp=85021142146&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85021142146&partnerID=8YFLogxK
U2 - 10.1021/acs.biochem.7b00220
DO - 10.1021/acs.biochem.7b00220
M3 - Article
C2 - 28534615
AN - SCOPUS:85021142146
VL - 56
SP - 3049
EP - 3057
JO - Biochemistry
JF - Biochemistry
SN - 0006-2960
IS - 24
ER -