FILM COMING SOON | 2025

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KEY MOLECULES

Kinesin motors, microtubules


RELEVANCE: BIOPHYSICS, PHYSIOLOGY, PATHOLOGY

Motor Mechanism
Nervous System Development
Degenerative Neurological Diseases

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IN BRIEF

N Molecular Systems, Inc. via comparative structural analysis across species of the kinesin superfamily of microtubule motors, implicates a labile 3(10)-helical element as key structural locus important for sensing association with the microtubule lattice, and coupling to the kinesin motor domain mechanochemical cycle.

In collaboration with Shinsuke Niwa (Tohoku University), Arne Gennerich (Albert Einstein College of Medicine, Biophotonics Center), and Rick McKenney (University of California Davis) – in vivo, biophysical, and single-molecule experiments of mutations in this PYRD 3(10) element, which is highly conserved at the sequence as well as structural level across all kinesins – establish the element as critical for motor function and human health.


MODEL & RELEVANCE

Kinesins are critical cargo transport motors in neurons. The kinesin superfamily of microtubule motors is diverse and large, consisting of 45 genes in humans. Our analysis of human mutation data finds multiple mutations within the PYRD 3(10) element which lead to degenerative neurological disorders, including P305L, Y306C, and R307G/P/Q in the kinesin KIF1A, P278L and R280H/C/L in KIF5A, and R301G in KIF1C – which highlights the critical function of this understudied element in human health.

Structural studies of kinesin motor domain bound to microtubules implicate contact between the PYRD-element and tubulin (see also models in Figures 1-4, below). In vivo and single-molecule experiments uncover family member specific biophysical and microtubule-sensing properties.


MOLECULAR HIGHLIGHTS:





comparative structural analysis, modeling & visualization by: N MOLECULAR SYSTEMS, INC.


REFERENCES & LINKS

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KEY MOLECULES

microtubule-associated proteins (MAPs), kinesin motors, dynein/dynactin

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IN BRIEF

N Molecular Systems, Inc., in collaboration with Kassie Ori-McKenney, Department of Molecular and Cellular Biology at University of California Davis, publishes work proposing a general MAP Code underlying molecular traffic in cells. Most cells are polarized. Depending on particular physiological need, highly polarized cells such as neurons, allocate their molecular components and machinery to distinct cellular compartments (such as dendrites, axons, etc.) using active ATP-driven transport of directional motor proteins that travel on long microtubule (MT) tracks. A combinatorial MAP code reveals molecular insights into specific cellular processes and facilities, involving a finite set of MT-Associated Proteins, which have the capability to strongly bias polarized movement of molecular cargo along microtubule tracks.


MODEL & RELEVANCE

The model helps elucidate rules (at the level of association between proteins) that govern orchestrated bi-directional 'cellular traffic' during physiological responses, which require sorting of distinct proteins and RNAs, as well as molecular machinery and other cellular components / cargo, or more broadly for adaptability and the establishment and maintenance of cell polarity, in neurons and polarized cells generally.


MOLECULAR HIGHLIGHTS


modeling & visualization by: N MOLECULAR SYSTEMS, INC.


REFERENCES & LINKS

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KEY MOLECULES

Doublecortin-like kinase 1 (DCLK1), microtubule-associated proteins (MAPs)


RELEVANCE: PHYSIOLOGY, PATHOLOGY

Brain Development, Cancer

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IN BRIEF

N Molecular Systems, Inc., in collaboration with Kassie Ori-McKenney, Department of Molecular and Cellular Biology at University of California Davis, publishes work discovering molecular insights into unique autoregulatory control of the microtubule-associated protein and oncogene DCLK1 (doublecortin-like kinase 1).

DCLK1 is a multi-faceted molecule prominently implicated in many types of cancers. It is implicated as part of the macro-molecular mitotic spindle machine important for cell division. But it also functions in normal physiology, most notably in neurogenesis (neocortex, cerebellum), and neuronal migration and differentiation processes during brain development. At the molecular level, as a microtubule-associated protein (MAP), DCLK1 can alter polymerization of microtubules. It can also gate access to the microtubule lattice, providing for fine spatial control of, for example, molecular motor function and directional sub-cellular traffic. Its role in these processes provides clues about the collective capabilities of its multiple domains.


MODEL & CANCER RELEVANCE

DCLK1 has been a leading target for the development of therapeutic kinase inhibitors against cancer. However, how its enzymatic (serine/threonine kinase) activity relates to its microtubule-associated properties, in neuronal and non-neuronal cells, is poorly understood.

DCLK1 contains three globular domains connected by linkers and flanked by projection tail regions, which are predicted to be unstructured. Two tandem N-terminal doublecortin (DC) domains are implicated to bind the microtubule lattice with different affinities. DC domains may also provide an interface for dimerization events, via partial protein unfolding and 3D-domain swapping pathways. As revealed in the study, enzymatic activity of the C-terminal kinase domain is regulated by the C-terminal tail region, which then controls phosphorylation of DC1 and DC2 domains within DCLK1 itself.

Functionally, increased phosphorylation of DC2 (as measured by mass-spectrometry) Fig. 3, below, reduces DCLK1 affinity for the microtubule lattice. These data uncover unique insight into autoregulatory control of DCLK1 enzymatic activity with respect to microtubule-associated functions. The integrative model of full-length DCLK1 (Fig. 1, below), provides further useful context for future efforts in designing molecules for therapeutic interventions against cancer.

See also: "MAPs: lattice-view" integrative-model.


MOLECULAR HIGHLIGHTS




modeling & visualization by: N MOLECULAR SYSTEMS, INC.

Fig. 2 and 3. Changes in auto-phosphorylation due to deletion of DCLK1 C-term regulatory tail domain (∆C). Serine (S) and threonine (T) residues are shown as CPK/ball representations. Level of saturation is used to convey fold change in phosphorylation on those residues: increase in WT (blue), increase in ∆C (orange/red colors).


REFERENCES & LINKS

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KEY MOLECULES

tau, microtubules, dynein/dynactin, kinesin motors, severing enzymes


PATHOLOGY RELEVANCE

Neurodegenerative Diseases

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IN BRIEF

N Molecular Systems, Inc., in collaboration with Rick McKenney, Department of Molecular and Cellular Biology at University of California Davis, publishes work on molecular insights into the functional interplay between microtubules (MTs), MT motor proteins, MT severing enzymes, and the disordered protein tau. tau oligomers / condensates form characteristic dynamical barriers that are selectively permissible and spatially regulate the enzyme activity of severing proteins, and the movement of molecular motors on microtubule tracks.


MODEL & RELEVANCE

tau is a major intrinsically disordered protein abundant in neurons, principally implicated in Alzheimer's disease and other dementias. A model is proposed in which reversible self-association of tau molecules is controlled by the microtubule as a key mechanism of tau’s biological functions, and in which oligomerization of tau is a common property shared between the physiological and disease forms of the molecule.


MOLECULAR HIGHLIGHTS


comparative modeling & visualization by: N MOLECULAR SYSTEMS, INC.


REFERENCES & LINKS

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KEY MOLECULES

CRISPR-Cas12a, Cpf1


BIOTECHNOLOGY RELEVANCE

Genome Editing

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IN BRIEF

N Molecular Systems, Inc. In the December 13, 2018 issue of Cell, the Montoya Lab of the Protein Structure and Function Programme at University of Copenhagen reports the structural landscape of CRISPR-Cas12a (Cpf1) in the intermediate state by cryo-EM, revealing the activation mechanism for target DNA cleavage and possible ssDNA degradation, as part of conformational recycling of the endonuclease.


MODEL & RELEVANCE

Cas12a, also known as Cpf1, is a CRISPR-Cas endonuclease commonly used for genome editing via dsDNA break formation; e.g. it has been used for correction of mutations responsible for muscular dystrophy in human and mice cardiomyocytes (Swarts and Jinek, 2018; Zhang et al., 2017).






REFERENCES & LINKS

KEY MOLECULES

Kif26b, kinesin-11 family (unconventional)


PATHOLOGY RELEVANCE

Brain Development & Neurologic Disease

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IN BRIEF

N Molecular Systems, Inc., identifies P-loop motif in KIF26B (unconventional member of the kinesin superfamily of proteins), and in collaboration with Henry Ho, Department of Cell Biology & Human Anatomy at University of California Davis, and Pankaj Agrawal, Boston Children's Hospital and Harvard Medical School, publishes work on de novo human variant in KIF26B.


MODEL & RELEVANCE

The Kif26b (G546S) variant / mutation which is deemed pathogenic (mapping to the P-loop of the motor-like domain of KIF26B, via whole exome sequencing), reduces KIF26B function in promoting cell-cell adhesion in vitro, and implicates KIF26B in the development of brain stem, cerebellum, spinal cord / anterior horn cells and motor nerve.


MOLECULAR HIGHLIGHTS


comparative structural analysis by: N MOLECULAR SYSTEMS, INC.


REFERENCES & LINKS

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KEY MOLECULES

γ-secretase complex, presenilin (PS1), PEN-2, nicastrin (NCT), Aβ amyloids


PATHOLOGY RELEVANCE

Alzheimer's Disease

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IN BRIEF

N Molecular Systems, Inc., in collaboration with Bill Comer, NeuroGenetic Pharmaceuticals, Inc., and Joachim Herz, Department of Molecular Genetics (Center for Translational Neurodegeneration Research) at University of Texas Southwestern Medical Center, publishes work on the γ-Secretase complex proteolytic modulator NGP 555 - a small molecule compound developed for prevention of Alzheimer's disease.

Alzheimer’s disease (AD) is a progressive and fatal brain disease afflicting one in eight people over age 65. One in three seniors die with Alzheimer's or another dementia. AD is characterized by progressive accumulation of amyloid plaques (consisting primarily of amyloid β-peptides) and neurofibrillary tangles (comprised mostly of hyperphosphorylated tau) in the brain, which precedes cognitive decline by years.


MODEL & RELEVANCE

γ-secretase is a multi-subunit membrane protease that cleaves single-pass transmembrane protein targets. γ-secretase processing of targets such as APP (Amyloid Precursor Protein), Notch, cadherins, ephrin, and ErbB proteins, is important for normal physiology. Processing of APP can produce peptides whose abnormally folded fibrillar form is the primary component of amyloid plaques.

Multiple amyloid therapies have failed in clinical studies - in particular due to testing in patients with disease that was too far advanced, and in other cases due to mechanism-based toxicities. For example, inhibitors of γ-secretase (GSIs) showed failure attributable to Notch inhibition or APP C-terminal fragment accumulation. NGP 555 is a γ-secretase modulator, and acts by binding directly to the complex without inhibiting ε-site proteolysis of amyloid precursor protein (APP), Notch, or E-cadherin. NGP 555 is molecule aimed at preventative therapy for AD.


MOLECULAR HIGHLIGHTS



simulation, analysis & visualization by: N MOLECULAR SYSTEMS, INC.


REFERENCES & LINKS

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