Figure 1.
(A) Subdomain arrangement. Subdomains 1, 2, 3 and 4 are shown in cyan, red, yellow and green, respectively. The pink sphere represents Mg2+ at the active site. (B) Positions of substituted residues in C. yaquinae actin as compared to rabbit/chicken actin. The residues shown in red and cyan in the licorice model represent the specific substitutions in deep-sea fish actins and those of terrestrial animals and shallow-water fish species, respectively. (C) Chemical formula of ATP. Oxygen atoms in the phosphate tail of ATP are distinguished by α, β, and γ.
Table 1.
Sequence features of the various actins examined in this study [10].
Figure 2.
The root mean-square fluctuation (RMSF) per residue at 60 MPa.
The RMSF was calculated by best-fitting the backbone heavy atoms of each snapshot to the average structure. Secondary structure and subdomain assignments are also shown.
Table 2.
Effect of high pressure on excluded volume (Vex), solvent accessible surface area (SASA) and isothermal compressibility (κT).
Table 3.
Energy differences between 60 and 0.1
Table 4.
Number of salt bridges formed between ATP and surrounding residues.
Figure 3.
Salt bridge and hydrophobic interactions in actin.
The salt bridges (A) between secondary structures and (B) between subdomains in Yaq at 60 MPa. The residues that form salt bridges with a formation rate of more than 0.5 are shown in Yaq at 60 MPa. Red and blue represent acidic and basic amino acids, respectively. (C) Hydrophobic interactions involving specific substituted residues in Ac1 actin. Red broken lines indicate the hydrophobic interaction. Residues 54 and 67 are different in the actins of deep-sea fish and other species.
Table 5.
Number of salt bridges formed between secondary structures and subdomains.
Figure 4.
Arrangement of the water molecule expected to initiate nucleophilic attack on the γ-phosphate of ATP.
The arrangement of non-deep-sea fish actins (A) and deep-sea fish actins (B). Green spheres show water molecules expected to be nucleophilic water for ATP hydrolysis. Red spheres indicate the water molecules coordinated to Mg2+ and those bridging the expected nucleophilic water and H161 with hydrogen bonds. Black dotted lines show typical hydrogen bonds formed during the MD simulation. Angle θ and distance dNu are defined by Oβ-Pγ-Ow and Pγ-Ow, respectively, where Ow represents the oxygen of the expected nucleophilic water (see Figure 1C for the definition of the other atoms).
Figure 5.
Spatial distribution of expected nucleophilic water.
Distribution of expected nucleophilic water as a function of angle θ and distance dNu, as defined in the legend for Figure 4, converted as free energy scale at (A) 0.1 and (B) 60 MPa. A water molecule having the minimum dNu value and a θ greater than 109.3° was assigned as the expected nucleophilic water in each simulation snapshot. The free energy was shown as the relative value against the minimum free energy in kBT.