Structure of the Microtubule-Binding Domain of Flagellar Dynein Yusuke S. Kato, Toshiki Yagi, Sarah A. Harris, Shin-ya Ohki, Kei Yura, Youské Shimizu, Shinya Honda, Ritsu Kamiya, Stan A. Burgess, Masaru Tanokura  Structure  Volume 22, Issue 11, Pages 1628-1638 (November 2014) DOI: 10.1016/j.str.2014.08.021 Copyright © 2014 Elsevier Ltd Terms and Conditions

Structure 2014 22, 1628-1638DOI: (10.1016/j.str.2014.08.021) Copyright © 2014 Elsevier Ltd Terms and Conditions

Figure 1 Structure of the Microtubule-Binding Domain of Dynein-c (A) Superposition of the 20 best structures of dynein-c MTBD and the nomenclatures of secondary structure elements with rainbow colors from the N- to C-termini (blue to red). This figure is depicted with Pymol (Schrödinger, LLC., New York, NY). (B) Mean structure viewed from the opposite side. Structure 2014 22, 1628-1638DOI: (10.1016/j.str.2014.08.021) Copyright © 2014 Elsevier Ltd Terms and Conditions

Figure 2 The Microtubule-Binding Domains of Dynein-c and Cytoplasmic Dynein (A) Dynein-c MTBD from C. reinhardtii. Conserved prolines in the distal coiled coil are illustrated as spheres (red and blue). (B) Cytoplasmic MTBD from mouse (Carter et al., 2008). (C) Superposition of dynein-c MTBD (pink) and mouse cytoplasmic MTBD (blue). (D) Details of the distal coiled coil of dynein-c MTBD. G2914 and L2807 are the distal end pair of the stalk coiled coil. L2800 and L2807 in CC1 (blue) are at the “d” positions in the heptad repeat. A2806 and L2799 are at the “e” positions. A2921 and G2914 in CC2 (red) are at the “a” positions. Structure 2014 22, 1628-1638DOI: (10.1016/j.str.2014.08.021) Copyright © 2014 Elsevier Ltd Terms and Conditions

Figure 3 Alignment of Microtubule-Binding Domains of various Dyneins Alignment of MTBD sequences from flagellar inner arm dynein-c from C. reinhardtii, flagellar outer arm dynein-β from sea urchin (Anthocidaris crassispina) and cytoplasmic dynein from mouse. Residue numbers of dynein-c are shown. Heptad repeats (“d” positions in CC1 and “a” positions in CC2) are indicated in pink (located in the dynein-c MTBD structure) and blue bands (hypothetical). Blue and red bars define respectively, the CC1 and CC2 numbers that represent the dynein-c MTBD boundaries of each construct incorporated into an SRS-MTBD chimera. Proline residues (green asterisks) are the starting points for the nomenclatures of these numbers. For example, SRS-MTBD19:9 has 19 residues in CC1 and nine in CC2 counted from these prolines. Structure 2014 22, 1628-1638DOI: (10.1016/j.str.2014.08.021) Copyright © 2014 Elsevier Ltd Terms and Conditions

Figure 4 Dynamic Analysis of the Microtubule-Binding Domain of Dynein-c (A) Plot showing the result of 1H-15N heteronuclear NOE experiments. Vertical axis shows 1H-15N heteronuclear NOE values, which approximately correspond to the structural stability of backbone amides in dynein-c MTBD. Together with (B), the horizontal axes show the residue numbers in the MTBD. Residues with high flexibility show low NOE values. Error bars indicate the SD. (B) Plot of rmsd values from all trajectories of MD simulations. We carried out two sets of MD simulations, 45 ns each, using two structures out of the ensemble of 20 NMR structures. Red and blue lines plot rmsd values of these two sets of trajectories. Both of the plots show the similarity of the dynamic behaviors of the two individual simulations. High rmsd regions correspond to flexible portions in the simulation. The region of the flap (P2843–Y2858) shows high rmsd values corresponding to the low NOE region in (A). (C) Mapping the result of 1H-15N heteronuclear NOE experiments shown in (A). Residues shaded orange corresponds to NOE < 0.7 and yellow to 0.7 < NOE < 0.75. (D) Mapping of one of the rmsd plots shown in (B) on the structure of dynein-c MTBD. Structure 2014 22, 1628-1638DOI: (10.1016/j.str.2014.08.021) Copyright © 2014 Elsevier Ltd Terms and Conditions

Figure 5 Microtubule-Binding Assays of SRS-MTBD Chimeras and Full-Length Dyneins (A) Microtubule-binding assays of SRS-MTBD chimeras of dynein-c with imposed registries of the coiled coil. There are four different chimeras with the same CC1 length, but different registries that were centrifuged with and without microtubules (upper and lower panels, respectively). The paired number nomenclature for constructs (e.g., 19:9) is the same as that used in previous studies (Carter et al., 2008; Gibbons et al., 2005) and denotes the number of residues between the SRS splice site and the proline marking the stalk-MTBD boundary for CC1 and CC2, respectively. (B) Summary of apparent microtubule affinity of the SRS-MTBD chimeras with different lengths of CC1 and CC2. Dashed diagonal lines show the “+4” (α-registry), “+8” (+β-registry), and “+11” (α+1-registry) constructs. (C) Axonemal dyneins from the oda1 mutant of C. reinhardtii (i.e., lacking outer arm dyneins) were copelleted in the presence and absence of microtubules and ATP. The bands of inner arm dynein species -b and -c overlap as expected (Kagami and Kamiya, 1992), and both show little copelleting under any condition tested here, whereas most of the dynein-fα copellets under the so-called rigor condition (+ microtubule and − ATP). Structure 2014 22, 1628-1638DOI: (10.1016/j.str.2014.08.021) Copyright © 2014 Elsevier Ltd Terms and Conditions

Figure 6 Prediction of Binding Surface of the Microtubule-Binding Domain of Dynein-c to Microtubule from KYG Analysis Hot colors indicate a high propensity for microtubule-binding. Buried residues are colored deep blue. Structure 2014 22, 1628-1638DOI: (10.1016/j.str.2014.08.021) Copyright © 2014 Elsevier Ltd Terms and Conditions

Figure 7 Surface Charge Distribution Ribbon diagram and surface representation with calculated electrostatic charges of the MTBDs of dynein-c/DHC9 (left) and cytoplasmic dynein1 (right). Blue and red in surface representation correspond to positive and negative charges. This figure is depicted with Swiss PDB Viewer (Guex and Peitsch, 1997). Structure 2014 22, 1628-1638DOI: (10.1016/j.str.2014.08.021) Copyright © 2014 Elsevier Ltd Terms and Conditions