human lis1 δ298-308  (GenScript corporation)

Journal: bioRxiv

Article Title: Cryo-EM captures early intermediate steps in dynein activation by LIS1

doi: 10.1101/2025.01.10.632485

Figure Lengend Snippet: a . Subunit and domain organization of full-length human dynein. Individual domains and accessory chains (heavy chain (HC), intermediate chain (IC), light intermediate chain (LIC), and three light chains (LC)) are color-coded, and these colors are used throughout the paper. b . Schematic representation of a hypothetical pathway for dynein activation and assembly by LIS1. The numbers identify species—Phi (1), Chi (2), assembly of transport complex (3), and an active transport complex (4)—that are discussed in the text. The asterisk in (3) indicates a LIS1-p150 dynactin interaction , which is also discussed in the text. c . Known LIS1 binding sites on dynein are shown on the Chi motor domain from panel (b). d . Schematic representation of the cryo-EM sample preparation pipeline. e . Distribution of particles corresponding to the three main species identified in the cryo-EM dataset: Phi, Pre-Chi, and Open. Representative 2D class averages are shown. In the case of Phi and Pre-Chi, representative 2D class averages of the dynein tails, which were processed separately, are shown above those for the motor domains. LIS1 is indicated whenever present in the averages. f . Further processing identified six subclasses in the Open species. The particle distribution is indicated with the corresponding cryo-EM maps next to the section in the pie chart.

Article Snippet: Human LIS1 Δ298-308 was generated through Genescript Express Mutagenesis & Site-Directed DNA Mutagenesis service.

Techniques: Activation Assay, Binding Assay, Cryo-EM Sample Prep, Sample Prep

Journal: bioRxiv

Article Title: Cryo-EM captures early intermediate steps in dynein activation by LIS1

doi: 10.1101/2025.01.10.632485

Figure Lengend Snippet: a Heterogeneous processing of Open species class with the linker in the bent conformation. The “Partial Open Bent/LIS1” class is the same one shown in . This class was unbinned and refined to obtain a map for cryoDRGN training. Particles were downsampled and subjected to a round of low-resolution cryoDRGN training. From the training, we pulled the best and most unique clusters from the training and returned the individual subclass particles into cryoSPARC. Each subclass is defined by their linker conformation and the presence or absence of LIS1. These subclasses were further refined to their final map. The Fourier Shell Correlation (FSC) plots are shown next to the respective final maps. b .Heterogeneous processing of the Open species class with the linker in the straight conformation. The “Open Straight/LIS1” class is the same one shown in . This class was unbinned and refined to get a refined map for RELION 3D classification without alignment. The best subclasses were taken back into cryoSPARC to further refine their final map. The Fourier Shell Correlation (FSC) plots are shown next to the respective final maps.

Article Snippet: Human LIS1 Δ298-308 was generated through Genescript Express Mutagenesis & Site-Directed DNA Mutagenesis service.

Techniques:

Journal: bioRxiv

Article Title: Cryo-EM captures early intermediate steps in dynein activation by LIS1

doi: 10.1101/2025.01.10.632485

Figure Lengend Snippet: a-c . Cryo-EM maps and models of the motor and tail domains of the Pre-Chi dynein-LIS1 complex are shown in three orientations: ( a ) LIS1-free face, ( b ) LIS1-bound face, and ( c ) a “top view” where the Pre-Chi motors are shown enlarged and from the perspective of the tail. LIS1 is highlighted in the LIS1-bound ( b ) and top ( c ) views. d . Local resolution map of Pre-Chi. e and f . Nucleotide states of AAA1-AAA4 in Motor 2 (Heavy Chain 2, HC-2) (e) and Motor 1 (Heavy Chain 1, HC-1) (f).

Article Snippet: Human LIS1 Δ298-308 was generated through Genescript Express Mutagenesis & Site-Directed DNA Mutagenesis service.

Techniques: Cryo-EM Sample Prep

Journal: bioRxiv

Article Title: Cryo-EM captures early intermediate steps in dynein activation by LIS1

doi: 10.1101/2025.01.10.632485

Figure Lengend Snippet: The table summarizes the conformations and nucleotide states of the Phi (yellow background) and Open (blue background) motor domains presented in this work. “LIS1” indicates how many LIS1 β-propellers are bound to the dynein motor. “Linker” refers to the overall conformation (bent, intermediate, straight) of that domain. “Stalk” refers to the register between the two helices in the coiled-coil . The nucleotide states of AAA1-AAA4 are based on our interpretation of the densities in our maps.

Article Snippet: Human LIS1 Δ298-308 was generated through Genescript Express Mutagenesis & Site-Directed DNA Mutagenesis service.

Techniques:

Journal: bioRxiv

Article Title: Cryo-EM captures early intermediate steps in dynein activation by LIS1

doi: 10.1101/2025.01.10.632485

Figure Lengend Snippet: a . Superposition of Pre-Chi (rainbow) and Phi (grey) models. HC-1 was used as the reference to align the models. Although the Pre-Chi model is shown from the LIS1-bound face, LIS1 was omitted for clarity. b . Map of interatomic vectors connecting equivalent α carbons in Phi and Pre-Chi. The length of each vector is proportional to the distance between the atoms in Phi and Pre-Chi. c . The four main interfaces between the motors in Phi are highlighted in the context of the boxed model in panel ( a ): Linker:Linker, Linker:AAA4, AAA5:AAA5, and Stalk:Stalk. d-g . Close-ups of the three interfaces highlighted in ( c ) that are disrupted by the formation of Pre-Chi: Linker:Linker ( d ), AAA5:AAA5 ( e ), and Linker:AAA4 ( f-g ). The top panel corresponds to the Phi model and the bottom panel corresponds to the Pre-Chi model. Key residues, motor chains, LIS1 ring, and the domain(s) of the motor being displayed are highlighted on each panel. Interactions are shown with dotted lines, with their distances (in Å) indicated. There was no significant change in the Stalk:Stalk interface. There are differences in the Linker:AAA4 interface between the LIS1-bound face ( f ), and the LIS1-free face ( g ).

Article Snippet: Human LIS1 Δ298-308 was generated through Genescript Express Mutagenesis & Site-Directed DNA Mutagenesis service.

Techniques: Plasmid Preparation

Journal: bioRxiv

Article Title: Cryo-EM captures early intermediate steps in dynein activation by LIS1

doi: 10.1101/2025.01.10.632485

Figure Lengend Snippet: a .cryoDRGN UMAP representation. This analysis focuses on the Pre-Chi k means clusters 2-5 (highlighted by the box) from . b-e . Volumes from clusters 2-5 shown in two views: front view of the LIS1-bound face (top row) and side view (bottom row). The IC-LC Tower (labeled) is used as a reference to determine which side of Phi LIS1 is bound to.

Article Snippet: Human LIS1 Δ298-308 was generated through Genescript Express Mutagenesis & Site-Directed DNA Mutagenesis service.

Techniques: Labeling

Journal: bioRxiv

Article Title: Cryo-EM captures early intermediate steps in dynein activation by LIS1

doi: 10.1101/2025.01.10.632485

Figure Lengend Snippet: a . Superposition between Chi and Pre-Chi. The model of human Chi from our previous work (dark gray) and human Pre-Chi motor (rainbow) were superimposed and aligned using HC-1. b . Interatomic vectors connecting equivalent alpha carbons in Pre-Chi and Chi for the superposition shown in a. c . Pre-Chi model viewed from the LIS1-bound face with interfaces present in both Chi and Pre-Chi (#1-2 in black circles) and Pre-Chi-specific interfaces (#3-4 in red circles) highlighted. d . Close ups of the interfaces high-lighted in (c). Residues involved in the interfaces and the names of the domains interacting with LIS1 ring are highlighted in each panel. Interactions are shown with dotted lines, with their distances (in Å) indicated.

Article Snippet: Human LIS1 Δ298-308 was generated through Genescript Express Mutagenesis & Site-Directed DNA Mutagenesis service.

Techniques:

Journal: bioRxiv

Article Title: Cryo-EM captures early intermediate steps in dynein activation by LIS1

doi: 10.1101/2025.01.10.632485

Figure Lengend Snippet: a . Representative kymographs from single-molecule motility assays with purified TMR–dynein–dynactin–BICD2 in the absence (white circle) or presence (black circle) of human LIS1 wild type or LIS1 Δ298-308 . Scale bars, 10 μm ( x ) and 100 s ( y ). b . Single-molecule velocity (mean ± standard deviation of the means of each replicate) of TMR–dynein–dynactin–BICD2 complexes in the absence (white circles) or presence (black circles) of human LIS1 or LIS1 Δ298-308 . Superplots show all individual data points for each of the four technical replicates. n values for each replicate are: no LIS1, n = 70, 70, 50, 91; LIS1, n = 90, 85, 58, 117; LIS1 Δ298-308 , n = 116, 125, 89, 124. Larger shapes denote the mean of each of the four technical replicates. No LIS1 and LIS1 ** P = 0.0018, No LIS1 and LIS1 Δ298-306 ns P = 0.9955, LIS1 and LIS1 Δ298-308 ** P = 0.0012. Statistics were generated on the means of the four replicates using a One-Way ANOVA with Tukey’s multiple comparison test. c . Superplots show processive events /μm of microtubule length (mean ± standard deviation of the means of each replicate) of TMR–dynein–dynactin–BICD2 complexes in the absence (white circle) or presence (black circle) of unlabeled wild type human LIS1 or LIS1 Δ298-308 . Data points are represented as triangles, circles, squares, and diamonds corresponding to single measurements within each technical replicate (no LIS1, n = 14, 12, 11, 8; LIS1, n = 12, 7, 7, 7; LIS1 Δ298-306 , n = 11, 5, 8, 9). No LIS1 and LIS1 * P = 0.012. Statistical analysis was done using a One-Way ANOVA with Tukey’s multiple comparison test. d . Role of LIS1 in the activation of dynein. This schematic is an updated version of the pathway introduced in that incorporates the Pre-Chi intermediate identified in this study.

Article Snippet: Human LIS1 Δ298-308 was generated through Genescript Express Mutagenesis & Site-Directed DNA Mutagenesis service.

Techniques: Purification, Standard Deviation, Generated, Comparison, Activation Assay