Supplementary Materials for
The conserved Arg241-Glu439 salt bridge determines flexibility of the
inositol 1,4,5-trisphosphate receptor binding core in the ligand-free state
Yoichi Ida and Akinori Kidera
Contents
Figure S1
Figure S2
Figure S3
Table S1
Table S2
Figure S1
Left: Distances of the direct interactions between the IBC and InsP3 during the
InsP3-bound simulation. The amino acid residues and phosphate atoms involved in
binding are given in the upper left corner of each column. Upper right: Distances of
water-mediated interactions with InsP3. Lower right: Distances of intra-domain polar
interactions involving K249 and R506. Mutation of these residues was reported to
significantly reduce the binding affinity for InsP3. The interactions were defined in the
crystal structures (1n4k) using LIGPLOT.26
e
Figure S2
Results of InsP3-free simulations of the R241Q mutant started from the closed crystal
structure.
(a) Root-mean-square displacement (RMSD) of C atoms in the secondary structure
regions (defined in the legend for Fig. 1b) of the crystal structure (PDBid: 1n4k).
The entire molecule (upper black), -IBC (lower black), and -IBC (lower gray) are
indicated.
(b) Hinge angle (defined in Fig. 1b). The horizontal gray line represents the hinge angle
of the crystal structure of the InsP3-bound form.
(c) Twist angle (defined in Fig. 1c). The horizontal gray line represents the twist angle
of the crystal structure of the InsP3-bound form.
(d) Inter-domain polar contacts defined over a 100-ps interval using LIGPLOT.26
Contacts with more than 20% possibility of occurrence are shown.
(e) Superimposition of the crystal structure (green) and a snapshot at 71.6 ns (red) is
shown. Due to the mutation of R241Q, the distance between Q241 and E439 is more
than 10 A. The inter-domain hydrogen bonds are indicated in stick.
Figure S3
Amino acids at the mutation sites (residues indicated in red) that significantly affect
InsP3-binding affinity,27 together with their hydrogen bonding partners (shown in black).
Hydrogen bonding relations are indicated by arrows. The alignment is based on
Supplementary Figure 7 of Seo et al.10 InsP3R1, InsP3R2, and InsP3R3 are rat InsP3
receptor types 1, 2, and 3, respectively. RyR1, RyR2, and RyR3 are rabbit ryanodine
receptor types 1, 2, and 3, respectively.
Table S1
The hinge angle and the twist angle of the crystal structures
PDB ID
#
3t8s_A
3t8s_B
3uj0_A
3uj0_B
3uj4_A
3uj4_B
Hinge angle (°)#
97.8
94.0
91.0
90.9
99.2
97.7
Twist angle (°)*
5.8
3.7
1.2
1.5
2.9
5.0
Hinge angle of 1n4k is 87.5º.
*Twist angle was defined on the basis of the crystal structure of 1n4k,7 whose twist
angle was defined to be 0.
Table S2
Probability of the interaction between R241 and E439
Probability of the interactions (%)
Number of
interactions*
InsP3-bound form
InsP3-free form
(20-150ns)
InsP3-free form
(170-300ns)
0
01
03
21
1
26
36
27
2
73
61
52
* R241 and E439 can have the interactions between N1 or N2 of R241 and O1 or
O2 of E439. The maximum number of the interactions is two and the minimum is zero.