Supporting Information
Table S1. Residue alignment of two dynein X-ray structures (PDB codes: 3qmz, 3ay1)
Residue range of 3qmz
PHE 1365 - TRP 1378
GLN 1403 - LYS 1416
CYS 1428 - ILE 1458
ILE 1465 - SER 1474
PHE 1476 - ASP 1494
HIS 1501 - PHE 1526
ALA 1604 - GLY 1633
VAL 1638 - ILE 1644
TYR 1672 - LYS 1689
ASP 1692 - GLY 1713
ALA 1780 - TYR 1790
GLY 1801 - GLN 1811
LEU 1831 - GLY 1842
LEU 1955 - MET 1963
LEU 1970 - SER 1981
GLU 1986 - ILE 2002
GLU 2051 - THR 2066
ALA 2076 - THR 2086
LEU 2129 - ASP 2140
SER 2223 - ASP 2238
SER 2242 - ILE 2253
SER 2254 - ASN 2270
GLU 2285 - GLN 2303
ASP 2307 - LEU 2323
HIS 2735 - GLN 2751
GLY 2760 - ARG 2771
LEU 2792 - CYS 2806
LEU 2828 - LEU 2834
ALA 2901 - ALA 2907
PHE 2909 - CYS 2912
VAL 2928 - MET 2938
PHE 2940 - GLN 2959
PRO 2989 - LEU 2996
ARG 2997 - GLY 3020
LEU 3021 - VAL 3028
LEU 3289 - ILE 3325
SER 3327 - GLU 3331
TYR 3389 - GLN 3401
SER 3411 - TYR 3422
PHE 3436 - ALA 3443
GLU 3456 - PRO 3460
ILE 3462 - PHE 3470
ILE 3507 - ARG 3512
THR 3520 - GLU 3546
LEU 3548 - LEU 3567
ASP 3581 - GLU 3603
SER 3604 - ILE 3620
ILE 3621 - PHE 3638
SER 3645 - LYS 3659
ALA 3666 - VAL 3682
ASN 3773 - GLU 3782
PHE 3798 - LYS 3805
SER 3810 - ILE 3813
ASN 3821 - GLY 3836
LYS 3852 - THR 3862
VAL 3907 - GLY 3918
VAL 3923 - ILE 3939
ASP 3958 - GLU 3969
PRO 3981 - ALA 3990
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Residue range of 3ay1
UNK 1655 - UNK 1668
UNK 1673 - UNK 1686
UNK 1693 - UNK 1723
UNK 1738 - UNK 1747
UNK 1749 - UNK 1767
UNK 1782 - UNK 1807
UNK 1810 - UNK 1840
UNK 1846 - UNK 1852
UNK 1872 - UNK 1889
UNK 1898 - UNK 1919
UNK 1942 - UNK 1952
UNK 1974 - UNK 1984
UNK 2000 - UNK 2011
UNK 2116 - UNK 2124
UNK 2143 - UNK 2154
UNK 2189 - UNK 2205
UNK 2245 - UNK 2260
UNK 2278 - UNK 2288
UNK 2322 - UNK 2333
UNK 2419 - UNK 2434
UNK 2436 - UNK 2447
UNK 2449 - UNK 2465
UNK 2478 - UNK 2496
UNK 2508 - UNK 2524
UNK 2983 - UNK 2999
UNK 3018 - UNK 3029
UNK 3043 - UNK 3057
UNK 3098 - UNK 3104
UNK 3152 - UNK 3158
UNK 3159 - UNK 3162
UNK 3173 - UNK 3183
UNK 3197 - UNK 3216
UNK 3261 - UNK 3268
UNK 3270 - UNK 3293
UNK 3296 - UNK 3303
UNK 3560 - UNK 3596
UNK 3597 - UNK 3601
UNK 3639 - UNK 3651
UNK 3669 - UNK 3680
UNK 3695 - UNK 3702
UNK 3725 - UNK 3729
UNK 3730 - UNK 3738
UNK 3763 - UNK 3768
UNK 3844 - UNK 3867
UNK 3868 - UNK 3887
UNK 3911 - UNK 3933
UNK 3935 - UNK 3951
UNK 3953 - UNK 3970
UNK 3980 - UNK 3994
UNK 4010 - UNK 4026
UNK 4101 - UNK 4110
UNK 4143 - UNK 4150
UNK 4168 - UNK 4171
UNK 4194 - UNK 4209
UNK 4228 - UNK 4238
UNK 4262 - UNK 4273
UNK 4301 - UNK 4317
UNK 4329 - UNK 4340
UNK 4389 - UNK 4398
Table S2. Residue alignment between AAA1-AAA2 and AAA3-AAA4 of a dynein X-ray
structure (PDB code: 3qmz)
Residue range of AAA1-AAA2 <=> Residue range of AAA3-AAA4
ILE 1777 - LYS 1789 <=> PRO 2393 - TYR 2405
TYR 1790 - GLN 1811 <=> ASN 2409 - ASN 2430
ASN 1812 - ILE 1838 <=> LEU 2432 - LEU 2458
ALA 1843 - PHE 1850 <=> ILE 2479 - CYS 2486
SER 1859 - ILE 1868 <=> VAL 2502 - GLU 2511
ILE 1879 - GLU 1884 <=> LYS 2512 - LYS 2517
GLU 1885 - LEU 1888 <=> GLU 2520 - TRP 2523
PRO 1890 - LEU 1898 <=> VAL 2524 - VAL 2532
PRO 1909 - LYS 1913 <=> GLU 2548 - ARG 2552
PHE 1916 - PHE 1919 <=> HIS 2553 - ILE 2556
GLN 1925 - GLN 1935 <=> SER 2563 - ILE 2573
MET 1937 - GLU 1940 <=> TYR 2574 - ALA 2577
ASP 1941 - LYS 1959 <=> LEU 2581 - LEU 2599
MET 1963 - TYR 1966 <=> TYR 2607 - GLY 2610
GLY 1969 - SER 1985 <=> LEU 2616 - ALA 2632
GLU 1986 - GLU 1989 <=> GLN 2639 - ARG 2642
GLY 1990 - LYS 2020 <=> LEU 2644 - LYS 2679
LYS 2032 - GLY 2042 <=> ILE 2716 - GLU 2726
GLU 2051 - THR 2066 <=> GLU 2736 - GLN 2751
GLN 2068 - ALA 2076 <=> VAL 2752 - GLY 2760
CYS 2078 - ALA 2092 <=> ALA 2761 - TRP 2775
HIS 2097 - LYS 2107 <=> LEU 2776 - ILE 2786
VAL 2108 - SER 2117 <=> ARG 2788 - MET 2797
LEU 2129 - ASP 2139 <=> ILE 2798 - LEU 2808
ASN 2147 - ASP 2155 <=> GLU 2810 - ASP 2818
SER 2156 - VAL 2169 <=> SER 2820 - THR 2833
LEU 2170 - GLY 2181 <=> ASN 2837 - GLY 2846
PRO 2185 - ASN 2198 <=> GLU 2880 - ASP 2893
LEU 2199 - PHE 2215 <=> SER 2900 - TRP 2916
SER 2223 - GLU 2235 <=> SER 2926 - MET 2938
LEU 2249 - LEU 2252 <=> GLU 2939 - ASP 2942
ILE 2253 - SER 2256 <=> ILE 2944 - GLU 2947
PHE 2257 - ASN 2270 <=> ASN 2949 - ARG 2962
ASN 2282 - GLN 2289 <=> PRO 2989 - LEU 2996
ALA 2291 - GLN 2303 <=> ARG 2997 - ASP 3009
ASN 2304 - ASP 2307 <=> LYS 3311 - SER 3314
SER 2309 - ASP 2329 <=> LYS 3315 - GLY 3335
SER 2330 - PHE 2346 <=> LEU 3337 - LEU 3353
Figure S1. Other models of pre-powerstroke conformation of dynein motor domain aligned with
corresponding post-powerstroke conformation: (a) obtained by computationally inducing the
change of large domain of AAA1 toward AAA3 conformation of 3qmz; (b) obtained by
computationally inducing the opening of AAA3-AAA4 interface toward AAA1-AAA2
conformation of 3qmz, and then the closing of AAA1-AAA2 interface toward AAA3-AAA4
conformation of 3qmz. In both cases, only a small rotation of linker domain is observed relative
to the post-powerstroke conformation. The same color scheme as Fig 1d is used (the postpowerstroke conformation is colored lighter than the pre-powerstroke conformation).
Figure S2. Results of reaction coordinate (RC) analysis for the transition from pre- to postpowerstroke conformation of dynein motor domain: RC curves for linker domain, AAA1-AAA2,
AAA3-AAA4, AAA4-AAA5, AAA5-AAA6, and stalk are colored red, green, blue, purple,
yellow, and cyan, respectively. By observing how fast each curve ascends from 0 to 1, one can
determine the following motional order: stalk  AAA4-AAA5  AAA3-AAA4 and linker
domain  AAA1-AAA2  AAA5-AAA6.
Movie S1. This movie shows the top view of dynein motor domain undergoing a transition from
pre- to post-powerstroke conformation. The same color scheme as Fig 1d is used.
Movie S2. This movie shows the side view of dynein motor domain undergoing a transition from
pre- to post-powerstroke conformation. The same color scheme as Fig 1d is used. The residues
involved in linker-ring contacts are colored lighter and shown as thick tubes.
prepowerstroke_model.pdb: C coordinate file in PDB format for the predicted prepowerstroke conformation of dynein motor domain
traj_dynein_ienm.pdb: C coordinate file in PDB format for the predicted transition trajectory
from the pre- to the post-powerstroke conformation of dynein motor domain