bims-nucpor 2023-04-02 papers

Issue of 2023‒04‒02
four papers selected by
Sara Mingu
Johannes Gutenberg University

NAR Genom Bioinform. 2023 Mar;5(1): lqad025

A library of sensitive position-specific scoring matrices for high-throughput identification of nuclear pore complex subunits.

Andreas N Ioannides, Katerina R Katsani, Christos A Ouzounis, Vasilis J Promponas.

The nuclear pore complex exhibits different manifestations across eukaryotes, with certain components being restricted to specific clades. Several studies have been conducted to delineate the nuclear pore complex composition in various model organisms. Due to its pivotal role in cell viability, traditional lab experiments, such as gene knockdowns, can prove inconclusive and need to be complemented by a high-quality computational process. Here, using an extensive data collection, we create a robust library of nucleoporin protein sequences and their respective family-specific position-specific scoring matrices. By extensively validating each profile in different settings, we propose that the created profiles can be used to detect nucleoporins in proteomes with high sensitivity and specificity compared to existing methods. This library of profiles and the underlying sequence data can be used for the detection of nucleoporins in target proteomes.

DOI: https://doi.org/10.1093/nargab/lqad025

J Phys Chem B. 2023 Mar 31.

Binding of Venezuelan Equine Encephalitis Virus Inhibitors to Importin-α Receptors Explored with All-Atom Replica Exchange Molecular Dynamics.

Bryan M Delfing, Audrey Olson, Xavier E Laracuente, Kenneth W Foreman, Mikell Paige, Kylene Kehn-Hall, Christopher Lockhart, Dmitri K Klimov.

Although Venezuelan equine encephalitis virus (VEEV) is a life-threatening pathogen with a capacity for epidemic outbreaks, there are no FDA-approved VEEV antivirals for humans. VEEV cytotoxicity is partially attributed to the formation of a tetrameric complex between the VEEV capsid protein, the nuclear import proteins importin-α and importin-β, and the nuclear export protein CRM1, which together block trafficking through the nuclear pore complex. Experimental studies have identified small molecules from the CL6662 scaffold as potential inhibitors of the viral nuclear localization signal (NLS) sequence binding to importin-α. However, little is known about the molecular mechanism of CL6662 inhibition. To address this issue, we employed all-atom replica exchange molecular dynamics simulations to probe, in atomistic detail, the binding mechanism of CL6662 ligands to importin-α. Three ligands, including G281-1485 and two congeners with varying hydrophobicities, were considered. We investigated the distribution of ligand binding poses, their locations, and ligand specificities measured by the strength of binding interactions. We found that G281-1485 binds nonspecifically without forming well-defined binding poses throughout the NLS binding site. Binding of the less hydrophobic congener becomes strongly on-target with respect to the NLS binding site but remains nonspecific. However, a more hydrophobic congener is a strongly specific binder and the only ligand out of three to form a well-defined binding pose, while partially overlapping with the NLS binding site. On the basis of free energy estimates, we argue that all three ligands weakly compete with the viral NLS sequence for binding to importin-α in an apparent compromise to preserve host NLS binding. We further show that all-atom replica exchange binding simulations are a viable tool for studying ligands binding nonspecifically without forming well-defined binding poses.

DOI: https://doi.org/10.1021/acs.jpcb.3c00429

Antiviral Res. 2023 Mar 27. pii: S0166-3542(23)00066-9. [Epub ahead of print] 105588

Importin α/β-dependent nuclear transport of human parvovirus B19 nonstructural protein 1 is essential for viral replication.

Gualtiero Alvisi, Elisabetta Manaresi, Emily M Cross, Mikayla Hoad, Nasim Akbari, Silvia Pavan, Daryl Ariawan, Gloria Bua, Gayle F Petersen, Jade Forwood, Giorgio Gallinella.

Human parvovirus B19 (B19V) is a major human pathogen causing a variety of diseases, characterized by a selective tropism to human progenitor cells in bone marrow. In similar fashion to all Parvoviridae members, the B19V ssDNA genome is replicated within the nucleus of infected cells through a process which involves both cellular and viral proteins. Among the latter, a crucial role is played by non-structural protein (NS)1, a multifunctional protein involved in genome replication and transcription, as well as modulation of host gene expression and function. Despite the localization of NS1 within the host cell nucleus during infection, little is known regarding the mechanism of its nuclear transport pathway. In this study we undertake structural, biophysical, and cellular approaches to characterize this process. Quantitative confocal laser scanning microscopy (CLSM), gel mobility shift, fluorescence polarization and crystallographic analysis identified a short sequence of amino acids (GACHAKKPRIT-182) as the classical nuclear localization signal (cNLS) responsible for nuclear import, mediated in an energy and importin (IMP) α/β-dependent fashion. Structure-guided mutagenesis of key residue K177 strongly impaired IMPα binding, nuclear import, and viral gene expression in a minigenome system. Further, treatment with ivermectin, an antiparasitic drug interfering with the IMPα/β dependent nuclear import pathway, inhibited NS1 nuclear accumulation and viral replication in infected UT7/Epo-S1 cells. Thus, NS1 nuclear transport is a potential target of therapeutic intervention against B19V induced disease.

Keywords: Antiviral; B19V; Importins; Ivermectin; Nuclear transport; cNLS

DOI: https://doi.org/10.1016/j.antiviral.2023.105588

J Biol Eng. 2023 Mar 28. 17(1): 22

Unravelling the mechanotransduction pathways in Alzheimer's disease.

Francesca Donnaloja, Emma Limonta, Christian Mancosu, Francesco Morandi, Lucia Boeri, Diego Albani, Manuela Teresa Raimondi.

Alzheimer's disease (AD) represents one of the most common and debilitating neurodegenerative disorders. By the end of 2040, AD patients might reach 11.2 million in the USA, around 70% higher than 2022, with severe consequences on the society. As now, we still need research to find effective methods to treat AD. Most studies focused on the tau and amyloid hypothesis, but many other factors are likely involved in the pathophysiology of AD. In this review, we summarize scientific evidence dealing with the mechanotransduction players in AD to highlight the most relevant mechano-responsive elements that play a role in AD pathophysiology. We focused on the AD-related role of extracellular matrix (ECM), nuclear lamina, nuclear transport and synaptic activity. The literature supports that ECM alteration causes the lamin A increment in the AD patients, leading to the formation of nuclear blebs and invaginations. Nuclear blebs have consequences on the nuclear pore complexes, impairing nucleo-cytoplasmic transport. This may result in tau hyperphosphorylation and its consequent self-aggregation in tangles, which impairs the neurotransmitters transport. It all exacerbates in synaptic transmission impairment, leading to the characteristic AD patient's memory loss. Here we related for the first time all the evidence associating the mechanotransduction pathway with neurons. In addition, we highlighted the entire pathway influencing neurodegenerative diseases, paving the way for new research perspectives in the context of AD and related pathologies.

Keywords: Alzheimer’s disease; Extracellular matrix; Nuclear lamina; Nuclear-cytoplasmic transport; Synaptic loss; Tau

DOI: https://doi.org/10.1186/s13036-023-00336-w