The Structure of the Coiled-Coil Domain of Ndel1 and the Basis of Its Interaction with Lis1, the Causal Protein of Miller-Dieker Lissencephaly

Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.
Structure (Impact Factor: 5.62). 12/2007; 15(11):1467-81. DOI: 10.1016/j.str.2007.09.015
Source: PubMed

ABSTRACT Ndel1 and Nde1 are homologous and evolutionarily conserved proteins, with critical roles in cell division, neuronal migration, and other physiological phenomena. These functions are dependent on their interactions with the retrograde microtubule motor dynein and with its regulator Lis1--a product of the causal gene for isolated lissencephaly sequence (ILS) and Miller-Dieker lissencephaly. The molecular basis of the interactions of Ndel1 and Nde1 with Lis1 is not known. Here, we present a crystallographic study of two fragments of the coiled-coil domain of Ndel1, one of which reveals contiguous high-quality electron density for residues 10-166, the longest such structure reported by X-ray diffraction at high resolution. Together with complementary solution studies, our structures reveal how the Ndel1 coiled coil forms a stable parallel homodimer and suggest mechanisms by which the Lis1-interacting domain can be regulated to maintain a conformation in which two supercoiled alpha helices cooperatively bind to a Lis1 homodimer.

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    • "The elution volume of Ndel11–201 in isolation (Fig. 3C, blue trace) is compatible with either a monomer with elongated shape or an oligomer. To distinguish between the two possibilities, we performed Static Light Scattering analysis of the same construct, which revealed that Ndel11–201 is dimeric in solution (data not included; Derewenda et al., 2007). The elution profile of p6004480–5183 presents two peaks (red trace). "
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    ABSTRACT: Apical neural progenitors (aNPs) drive neurogenesis by means of a program consisting of self-proliferative and neurogenic divisions. The balance between these two manners of division sustains the pool of apical progenitors into late neurogenesis, thereby ensuring their availability to populate the brain with terminal cell types. Using knockout and in utero electroporation mouse models, we report a key role for the microtubule-associated protein 600 (p600) in the regulation of spindle orientation in aNPs, a cellular event that has been associated with cell fate and neurogenesis. We find that p600 interacts directly with the neurogenic protein Ndel1 and that aNPs knockout for p600, depleted of p600 by shRNA or expressing a Ndel1-binding p600 fragment all display randomized spindle orientation. Depletion of p600 by shRNA or expression of the Ndel1-binding p600 fragment also results in a decreased number of Pax6-positive aNPs and an increased number of Tbr2-positive basal progenitors destined to become neurons. These Pax6-positive aNPs display a tilted mitotic spindle. In mice wherein p600 is ablated in progenitors, the production of neurons is significantly impaired and this defect is associated with microcephaly. We propose a working model in which p600 controls spindle orientation in aNPs and discuss its implication for neurogenesis.
    Biology Open 05/2014; 3(6). DOI:10.1242/bio.20147807 · 2.42 Impact Factor
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    • "The deletion of NDE1 could act at another, for example submicroscopic, level; it is also possible that the deletion unmasks a recessive mutation on the remaining allele, but this is unlikely given the normal appearance and cognitive abilities of our two patients and previous examination of this possibility [10]. Alternatively, loss of NDE1 in patients with heterozygous NDE1 deletion may possibly be compensated by other proteins with similar functions such as LIS1 or NDE1-related protein 1 (NDEL1), a homolog of NDE1 [14], [15], [49]. "
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    ABSTRACT: 16p13.11 genomic copy number variants are implicated in several neuropsychiatric disorders, such as schizophrenia, autism, mental retardation, ADHD and epilepsy. The mechanisms leading to the diverse clinical manifestations of deletions and duplications at this locus are unknown. Most studies favour NDE1 as the leading disease-causing candidate gene at 16p13.11. In epilepsy at least, the deletion does not appear to unmask recessive-acting mutations in NDE1, with haploinsufficiency and genetic modifiers being prime candidate disease mechanisms. NDE1 encodes a protein critical to cell positioning during cortical development. As a first step, it is important to determine whether 16p13.11 copy number change translates to detectable brain structural alteration. We undertook detailed neuropathology on surgically resected brain tissue of two patients with intractable mesial temporal lobe epilepsy (MTLE), who had the same heterozygous NDE1-containing 800 kb 16p13.11 deletion, using routine histological stains and immunohistochemical markers against a range of layer-specific, white matter, neural precursor and migratory cell proteins, and NDE1 itself. Surgical temporal lobectomy samples from a MTLE case known not to have a deletion in NDE1 and three non-epilepsy cases were included as disease controls. We found that apart from a 3 mm hamartia in the temporal cortex of one MTLE case with NDE1 deletion and known hippocampal sclerosis in the other case, cortical lamination and cytoarchitecture were normal, with no differences between cases with deletion and disease controls. How 16p13.11 copy changes lead to a variety of brain diseases remains unclear, but at least in epilepsy, it would not seem to be through structural abnormality or dyslamination as judged by microscopy or immunohistochemistry. The need to integrate additional data with genetic findings to determine their significance will become more pressing as genetic technologies generate increasingly rich datasets. Detailed examination of brain tissue, where available, will be an important part of this process in neurogenetic disease specifically.
    PLoS ONE 04/2012; 7(4):e34813. DOI:10.1371/journal.pone.0034813 · 3.23 Impact Factor
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    • "We identified dynein-binding activity in the N-terminal DID domain and the addition of this peptide enhanced retrograde movements but the duration decreased. This activity may require dimerization properties embedded within the domain that were defined in structural and interaction-based studies (Bradshaw et al., 2009; Derewenda et al., 2007). An independent recent study demonstrated that the first eighty amino acids of Ndel1 (included in DID) binds directly to dynein intermediate chain and is essential for spindle pole organization in Xenopus egg extracts (Wang and Zheng, 2010). "
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    ABSTRACT: Bidirectional transport is a key issue in cellular biology. It requires coordination between microtubule-associated molecular motors that work in opposing directions. The major retrograde and anterograde motors involved in bidirectional transport are cytoplasmic dynein and conventional kinesin, respectively. It is clear that failures in molecular motor activity bear severe consequences, especially in the nervous system. Neuronal migration may be impaired during brain development, and impaired molecular motor activity in the adult is one of the hallmarks of neurodegenerative diseases leading to neuronal cell death. The mechanisms that regulate or coordinate kinesin and dynein activity to generate bidirectional transport of the same cargo are of utmost importance. We examined how Ndel1, a cytoplasmic dynein binding protein, may regulate non-vesicular bidirectional transport. Soluble Ndel1 protein, Ndel1-derived peptides or control proteins were mixed with fluorescent beads, injected into the squid giant axon, and the bead movements were recorded using time-lapse microscopy. Automated tracking allowed for extraction and unbiased analysis of a large data set. Beads moved in both directions with a clear bias to the anterograde direction. Velocities were distributed over a broad range and were typically slower than those associated with fast vesicle transport. Ironically, the main effect of Ndel1 and its derived peptides was an enhancement of anterograde motion. We propose that they may function primarily by inhibition of dynein-dependent resistance, which suggests that both dynein and kinesin motors may remain engaged with microtubules during bidirectional transport.
    Biology Open 03/2012; 1(3):220-31. DOI:10.1242/bio.2012307 · 2.42 Impact Factor
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