LRRK2 binds to the Rab32 subfamily in a GTP-dependent manner via its armadillo domain
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McGrath, Emma↗
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Structural underpinnings of Ric8A function as a G-protein α-subunit chaperone and guanine-nucleotide exchange factor
Resistance to inhibitors of cholinesterase 8A (Ric8A) is an essential regulator of G protein α-subunits (Gα), acting as a guanine nucleotide exchange factor and a chaperone. We report two crystal structures of Ric8A, one in the apo form and the other in complex with a tagged C-terminal fragment of Gα. These structures reveal two principal domains of Ric8A: an armadillo-fold core and a flexible C-terminal tail. Additionally, they show that the Gα C-terminus binds to a highly-conserved patch on the concave surface of the Ric8A armadillo-domain, with selectivity determinants residing in the Gα sequence. Biochemical analysis shows that the Ric8A C-terminal tail is critical for its stability and function. A model of the Ric8A/Gα complex derived from crosslinking mass spectrometry and molecular dynamics simulations suggests that the Ric8A C-terminal tail helps organize the GTP-binding site of Gα. This study lays the groundwork for understanding Ric8A function at the molecular level.
59 BASIC BIOLOGICAL SCIENCES↗
Structural basis for the regulation of nuclear import of Epstein-Barr virus nuclear antigen 1 (EBNA1) by phosphorylation of the nuclear localization signal
Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) is expressed in every EBV-positive tumor and is essential for the maintenance, replication, and transcription of the EBV genome in the nucleus of host cells. EBNA1 is a serine phosphoprotein, and it has been shown that phosphorylation of S385 in the nuclear localization signal (NLS) of EBNA1 increases the binding affinity to the nuclear import adaptor importin-α1 as well as importin-α5, and stimulates nuclear import of EBNA1. To gain insights into how phosphorylation of the EBNA1 NLS regulates nuclear import, we have determined the crystal structures of two peptide complexes of importin-α1: one with S385-phosphorylated EBNA1 NLS peptide, determined at 2.0 Å resolution, and one with non-phosphorylated EBNA1 NLS peptide, determined at 2.2 Å resolution. The structures show that EBNA1 NLS binds to the major and minor NLS-binding sites of importin-α1, and indicate that the binding affinity of the EBNA1 NLS to the minor NLS-binding site could be enhanced by phosphorylation of S385 through electrostatic interaction between the phosphate group of phospho-S385 and K392 of importin-α1 (corresponding to R395 of importin-α5) on armadillo repeat 8. - Highlights: • Nuclear import of EBNA1 can be regulated by phosphorylation of NLS. • Crystal structures of importin-α1 bound to the NLS peptides of EBNA1 are solved. • Structures provide insights into how phosphorylation can regulate nuclear import.
60 APPLIED LIFE SCIENCES↗
Crystal structure of importin-α3 bound to the nuclear localization signal of Ran-binding protein 3
Ran-binding protein 3 (RanBP3) is a primarily nuclear Ran-binding protein that functions as an accessory factor in the Ran GTPase system. RanBP3 associates with Ran-specific nucleotide exchange factor RCC1 and enhances its catalytic activity towards Ran. RanBP3 also promotes CRM1-mediated nuclear export as well as CRM1-independent nuclear export of β-catenin, Smad2, and Smad3. Nuclear import of RanBP3 is dependent on the nuclear import adaptor protein importin-α and, RanBP3 is imported more efficiently by importin-α3 than by other members of the importin-α family. Protein kinase signaling pathways control nucleocytoplasmic transport through phosphorylation of RanBP3 at Ser58, immediately C-terminal to the nuclear localization signal (NLS) in the N-terminal region of RanBP3. Here we report the crystal structure of human importin-α3 bound to an N-terminal fragment of human RanBP3 containing the NLS sequence that is necessary and sufficient for nuclear import. The structure reveals that RanBP3 binds to importin-α3 residues that are strictly conserved in all seven isoforms of human importin-α at the major NLS-binding site, indicating that the region of importin-α outside the NLS-binding site, possibly the autoinhibotory importin-β1-binding domain, may be the key determinant for the preferential binding of RanBP3 to importin-α3. Computational docking simulation indicates that phosphorylation of RanBP3 at Ser58 could potentially stabilize the association of RanBP3 with importin-α through interactions between the phosphate moiety of phospho-Ser58 of RanBP3 and a cluster of basic residues (Arg96 and Lys97 in importin-α3) on armadillo repeat 1 of importin-α. - Highlights: • Ran-binding protein 3 (RanBP3) is an accessory factor in the Ran GTPase system. • The N-terminal region of RanBP3 contains a nuclear localization signal (NLS). • Crystal structure of importin-α3 bound to the NLS of RanBP3 is solved. • Phosphorylation of RanBP3 at Ser58 may modulate binding affinity to importin-α.
60 APPLIED LIFE SCIENCES↗
Molecular basis for the lack of auto-inhibition of Plasmodium falciparum importin α
Highlights: • P. falciparum contains a single gene for importin α which lacks auto-inhibition. • Mutation of a single motif in P. falciparum importin α restores auto-inhibition. • Auto-inhibition is not crucial for viability of the parasite, unlike in yeast. • The parasite may employ unique strategies for cargo binding and release. • Lack of auto-inhibition may confer advantages to parasites for faster growth. Importin α is nuclear transport receptor that recognises nuclear localisation sequences (NLS). The protein has two domains: armadillo (ARM) repeats containing NLS-binding sites and the importin β-binding (IBB) domain. The IBB domain mimics an NLS and can bind to the ARM repeats, preventing NLS binding. This phenomenon, called auto-inhibition, is a key regulatory feature for binding and release of NLS-containing cargo by importin α and mutants that lack auto-inhibition show impaired viability in Saccharomyces cerevisiae. The genome of the human malaria parasite, Plasmodium falciparum, contains a single gene for importin α and here we show that the native protein expressed by this gene lacks auto-inhibition, suggesting that P. falciparum parasites possess unconventional mechanisms for regulation of cargo binding and release. Mutation of a single SKR motif (conserved in Plasmodium species) to KRR in P. falciparum importin α restores auto-inhibition. This is the first report of a single-celled eukaryote that has evolved with a single importin α isoform lacking auto-inhibition.
60 APPLIED LIFE SCIENCES↗
Distinct hydrophobic “patches” in the N- and C-tails of beta-catenin contribute to nuclear transport
β-catenin is a key mediator of Wnt signaling and its deregulated nuclear accumulation can drive cancer progression. While the central armadillo (Arm) repeats of β-catenin stimulate nuclear entry, the N- and C-terminal “tail” sequences are thought to regulate turnover and transactivation. We show here that the N- and C-tails are also potent transport sequences. The unstructured tails of β-catenin, when individually fused to a GFP-reporter, could enter and exit the nucleus rapidly in live cells. Proximity ligation assays and pull-down assays identified a weak interaction between the tail sequences and the FG-repeats of nucleoporins, consistent with a possible direct translocation of β-catenin through the nuclear pore complex. Extensive alanine mutagenesis of the tail sequences revealed that nuclear translocation of β-catenin was dependent on specific uniformly distributed patches of hydrophobic residues, whereas the mutagenesis of acidic amino acids had no effect. Moreover, the mutation of hydrophobic patches within the N-tail and C-tail of full length β-catenin reduced nuclear transport rate and diminished its ability to activate transcription. We propose that the tail sequences can contribute to β-catenin transport and suggest a possible similar role for hydrophobic unstructured regions in other proteins. - Highlights: • We show that the N- and C-tails of beta-catenin possess nuclear transport activity. • Nuclear transport of the N- or C-tails requires specific hydrophobic amino acids. • Mutagenesis of the N-terminus diminished nuclear entry of full-length beta-catenin. • We propose the N-tail contributes to beta-catenin nuclear entry and transactivation.
60 APPLIED LIFE SCIENCES↗
Large-scale conformational rearrangement of the α5-helix of Gα subunits in complex with the guanine nucleotide exchange factor Ric8A
Resistance to inhibitors of cholinesterase 8A (Ric8A) protein is an important G protein–coupled receptor (GPCR)-independent regulator of G protein α-subunits (Gα), acting as a guanine nucleotide exchange factor (GEF) and a chaperone. Insights into the complex between Ric8A and Gα hold the key to understanding the mechanisms underlying noncanonical activation of G-protein signaling as well as the folding of nascent Gα proteins. In this work, we examined the structure of the complex of Ric8A with minimized Gαi (miniGα i ) in solution by small-angle X-ray scattering (SAXS) and exploited the scattering profile in modeling of the Ric8A/miniGα i complex by steered molecular dynamics (SMD) simulations. A small set of models of the complex featured minimal clash scores, excellent agreement with the experimental SAXS data, and a large-scale rearrangement of the signal-transducing α5-helix of Gα away from its β-sheet core. The resulting interface involved the Gα α5-helix bound to the concave surface of Ric8A and the Gα β-sheet that wraps around the C-terminal part of the Ric8A armadillo domain, leading to a severe disruption of the GDP-binding site. Further modeling of the flexible C-terminal tail of Ric8A indicated that it interacts with the effector surface of Gα. This smaller interface may enable the Ric8A-bound Gα to interact with GTP. The two-interface interaction with Gα described here distinguishes Ric8A from GPCRs and non-GPCR regulators of G-protein signaling.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Investigation of onshore wind farm wake recovery with in situ aircraft measurements during AWAKEN
The share of wind power for electricity supply is increasing worldwide. This highly variable resource requires the improved prediction of power output for network stability. The interaction between wind farm wakes and the atmospheric boundary layer (ABL) introduces uncertainties in power production that warrant detailed investigation. The flow downwind of wind farms is characterized by a reduction in wind speed and an increase in turbulence, which both vary with atmospheric conditions. During the American WAKE experimeNt (AWAKEN), the Technische Universität Braunschweig conducted measurement flights with a research aircraft upwind and downwind of onshore wind farms in the southern Great Plains in Oklahoma in the USA. This study utilizes data from 20 flights conducted at approximately hub height in September 2023 to investigate the wind field variability downwind of the wind farms and vertical profiles to observe atmospheric stratification. The flights were aligned perpendicular to the main wind direction downwind of the King Plains and Armadillo Flats wind farms. Additionally, lidar data from both upwind and downwind ground-based measurement sites and sonic anemometer data were used for comprehensive analysis. Results indicate that under stable ABL conditions, the wake persists at greater downwind distances with a higher velocity deficit in the wake relative to the undisturbed flow compared to unstable stratification. In homogeneous terrain under stable conditions, wake recovery to 95 % occurs between a distance of 4.5 and 9 km downwind of the wind farm. In the semi-complex terrain characterized by shallow hills, slopes, and valleys, the wake exhibits a higher velocity deficit compared to homogeneous terrain, while in some cases the wake was amplified by the terrain resulting in higher velocity deficit 10 km downwind of the wind farm compared to the measurements closer to the wind farm. The turbulent kinetic energy (TKE) and “TKE difference” was found to be a valuable measure in understanding wakes in a semi-complex terrain, showing a clear wake recovery and formation depending on the stratification of the ABL.
17 WIND ENERGY↗
Centipod WEC, Advanced Controls, MPC Controller MATLAB Code
This archive contains the MATLAB code for the model predictive control (MPC) controller developed in this project. The archive containing the WaveDyn models used for analysis of the Centipod with the MPC controller is linked in this submission.
16 TIDAL AND WAVE POWER↗