Structures of human dynein in complex with the lissencephaly 1 protein, LIS1

Abstract

The lissencephaly 1 protein, LIS1, is mutated in type-1 lissencephaly and is a key regulator of cytoplasmic dynein-1. At a molecular level, current models propose that LIS1 activates dynein by relieving its autoinhibited form. Previously we reported a 3.1Å structure of yeast dynein bound to Pac1, the yeast homologue of LIS1, which revealed the details of their interactions (Gillies et al., 2022). Based on this structure, we made mutations that disrupted these interactions and showed that they were required for dynein’s function in vivo in yeast. We also used our yeast dynein-Pac1 structure to design mutations in human dynein to probe the role of LIS1 in promoting the assembly of active dynein complexes. These mutations had relatively mild effects on dynein activation, suggesting that there may be differences in how dynein and Pac1/LIS1 interact between yeast and humans. Here, we report cryo-EM structures of human dynein-LIS1 complexes. Our new structures reveal the differences between the yeast and human systems, provide a blueprint to disrupt the human dynein-LIS1 interaction more accurately, and map type-1 lissencephaly disease mutations, as well as mutations in dynein linked to malformations of cortical development/ intellectual disability, in the context of the dynein-LIS1 complex.

Molecular mechanism of dynein-dynactin complex assembly by LIS1

“…5B). These are consistent with structures of LIS1 bound to isolated motor domains (50)(51)(52)(53). In addition, in the context of our full dynein dimer, LIS1 sits in the cleft between the A1 and A2 motor domains, with the Site ring WD40 domain on dynein-A1 contacting the AAA3 domain of dynein-A2 (Fig.…”

“…It is important for dynein function in many eukaryotes (9,40,(42)(43)(44), and recent evidence suggests it stimulates DDA complex formation (45)(46)(47)(48)(49). The current model is that LIS1 binds dynein's motor domains (50)(51)(52)(53) and opens up an autoinhibited form of dynein called the "phi-particle" (46,48,49,54). However, LIS1 can still stimulate DDA formation in a dynein mutant where the phi-particle is constitutively open (45,46).…”

Nde1 Promotes Lis1-Mediated Activation of Dynein

“…To address this question, we assayed the competitive binding of α2 and Nde1 to Lis1 and determined how α2 affects the regulation of DDR motility by Lis1/Nde1. Previously reported structures of DHC-Lis1 62 and α2-Lis1 14 and our AlphaFold2 model of Nde1-Lis1 show that dynein, α2, and Nde1 share the same binding site on Lis1 (Fig. 6a).…”

“… a. Structures of Lis1-DHC (PDB ID: 8DYV 62 ), Lis1-α2 (PDB ID: 1VYH 14 ), and Lis1-Nde1 1–190 (predicted by AlphaFold2). Insets show that Lis1 residues (R316 and W340) that facilitate binding to dynein are also critical for Lis1 binding to Nde1 and α2.…”

Lis1 binding regulates force-induced detachment of cytoplasmic dynein from microtubules

“…We previously showed that Lis1 stably interacts with a second binding site at the base of dynein’s stalk 17, 45 . To test whether this Lis1-stalk interaction might be responsible for Lis1’s ability to reduce the asymmetry in force-induced detachment of dynein from microtubules, we performed F-V measurements using a dynein mutant, in which three Lis1-interacting residues on its stalk were replaced with alanine (dynein EQN , purified from yeast endogenously expressing dynein subunits) 17 .…”