Biology subjects

Nguyen, P. T.

Publications and source records attributed to Nguyen, P. T..

27 records · Page 2Linked to original sources

bioRxiv2023

α-synuclein preformed fibrils bind to β-neurexins and impair β-neurexin-mediated presynaptic organization

Synucleinopathies form a group of neurodegenerative diseases defined by misfolding and aggregation of alpha-synuclein (-syn). Abnormal accumulation and spreading of -syn aggregates lead to synapse dysfunction and neuronal cell death. Yet, little is known about synaptic mechanisms underlying -syn pathology. Here we identified {beta}-isoforms of neurexins ({beta}-NRXs) as presynaptic organizing proteins that interact with -syn preformed fibrils (-syn PFFs), toxic -syn aggregates, but not -syn monomers. Our cell surface protein binding assays and surface plasmon resonance assays reveal that -syn PFFs bind directly to {beta}-NRX through their N-terminal histidine-rich domain (HRD) at nanomolar range (Kd: ~500 nM monomer equivalent). Furthermore, our artificial synapse formation assays show that -syn PFFs diminish excitatory and inhibitory presynaptic organization induced by a specific isoform of neuroligin 1 that binds only {beta}-NRXs, but not -isoforms of neurexins. Thus, our data suggest that -syn PFFs interact with {beta}-NRXs to inhibit {beta}-NRX-mediated presynaptic organization, providing novel molecular insight into how -syn PFFs induce synaptic pathology in synucleinopathies such as Parkinsons disease and dementia with Lewy bodies.

neuroscience↗

bioRxiv2023

TRPV1 Opening is Stabilized Equally by Its Four Subunits

Capsaicin receptor TRPV1 is a nociceptor for vanilloid molecules such as capsaicin and resiniferatoxin (RTX). Even though cryo-EM structures of TRPV1 in complex with these molecules are available, how their binding energetically favors the open conformation is not known. Here we report an approach to control the number of bound RTX molecules (0-to-4) in functional mouse TRPV1. The approach allowed direct measurements of each of the intermediate open states under equilibrium conditions at both macroscopic and single-molecule levels. We found that RTX binding to each of the four subunits contributes virtually the same activation energy, which we estimated to be 1.86 kcal/mol and found to arise predominately from destabilizing the closed conformation. We further showed that sequential bindings of RTX increase open probability without altering single-channel conductance, confirming that there is likely a single open-pore conformation for TRPV1 activated by RTX.

biophysics↗

bioRxiv2022

Computational design of peptides to target Nav1.7 channel with high potency and selectivity for the treatment of pain

The voltage-gated sodium NaV1.7 channel plays a key role as a mediator of action potential propagation in C-fiber nociceptors and is an established molecular target for pain therapy. ProTx-II is a potent and moderately selective peptide toxin from tarantula venom that inhibits human NaV1.7 activation. Here we used available structural and experimental data to guide Rosetta design of potent and selective ProTx-II-based peptide inhibitors of human NaV1.7 channels. Functional testing of designed peptides using electrophysiology identified the PTx2-3127 and PTx2-3258 peptides with IC50s of 7 nM and 4 nM for hNaV1.7 and more than 1,000-fold selectivity over human NaV1.1, NaV1.3, NaV1.4, NaV1.5, NaV1.8, and NaV1.9 channels. PTx2-3127 inhibits NaV1.7 currents in mouse and human sensory neurons and shows efficacy in rat models of chronic and thermal pain when administered intrathecally. Rationally-designed peptide inhibitors of human NaV1.7 channels have transformative potential to define a new class of biologics to treat pain.

biophysics↗

bioRxiv2022

The Influences of Stomatal Size and Density on Rice Drought, Salinity and VPD Resilience

O_LIA warming climate coupled with reductions in water availability and rising salinity are increasingly affecting rice yields (Oryza sativa L.). Elevated temperatures are causing vapour pressure deficit (VPD) rises, leading to stomata closure, further reducing plant productivity and cooling. It is unclear which conformation of stomatal size (SS) and stomatal density (SD) will best suit these future environmental extremes. C_LIO_LITo understand the influence of stomatal characteristics on rice abiotic stress tolerance, we screened the stomatal characteristics of 72 traditionally-bred varieties. We found significant variation in SS, SD and maximal stomatal conductance (gsmax) but did not identify any varieties with SD and gsmax as low as the genetically manipulated stomatal development mutant OsEPF1oe. C_LIO_LITraditionally-bred varieties with high SD and small SS (resulting in high gsmax) typically had lower biomasses, and these plants were more resilient to drought than low SD and large SS plants, which were physically larger. None of the varieties tested were as resilient to drought or salinity as low SD OsEPF1oe mutants. High SD and small SS rice displayed faster stomatal closure during rising VPD, but photosynthesis and plant cooling were reduced. C_LIO_LICompromises will be required when choosing rice SS and SD to tackle multiple future environmental stresses. C_LI

plant biology↗

bioRxiv2021

A type I interferon response defines a conserved microglial state required for effective phagocytosis

Microglia are brain resident phagocytes that can engulf synaptic components and extracellular matrix as well as whole neurons. However, whether there are unique molecular mechanisms that regulate these distinct phagocytic states is unknown. Here we define a molecularly distinct microglial subset whose function is to engulf neurons in the developing brain. We transcriptomically identified a cluster of Type I interferon (IFN-I) responsive microglia that expanded 20-fold in the postnatal day 5 somatosensory cortex after partial whisker deprivation, a stressor that accelerates neural circuit remodeling. In situ, IFN-I responsive microglia were highly phagocytic and actively engulfed whole neurons. Conditional deletion of IFN-I signaling (Ifnar1fl/fl) in microglia but not neurons resulted in dysmorphic microglia with stalled phagocytosis and an accumulation of neurons with double strand DNA breaks, a marker of cell stress. Conversely, exogenous IFN-I was sufficient to drive neuronal engulfment by microglia and restrict the accumulation of damaged neurons. IFN-I deficient mice had excess excitatory neurons in the developing somatosensory cortex as well as tactile hypersensitivity to whisker stimulation. These data define a molecular mechanism through which microglia engulf neurons during a critical window of brain development. More broadly, they reveal key homeostatic roles of a canonical antiviral signaling pathway in brain development.

neuroscience↗

bioRxiv2021

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours.

bioinformatics↗

bioRxiv2021

HaVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences

BackgroundSARS-CoV-2 related research has increased in importance worldwide since December 2019. Several new variants of SARS-CoV-2 have emerged globally, of which the most notable and concerning currently are the UK variant B.1.1.7, the South African variant B1.351 and the Brazilian variant P.1. Detecting and monitoring novel variants is essential in SARS-CoV-2 surveillance. While there are several tools for assembling virus genomes and performing lineage analyses to investigate SARS-CoV-2, each is limited to performing singular or a few functions separately. ResultsDue to the lack of publicly available pipelines, which could perform fast reference-based assemblies on raw SARS-CoV-2 sequences in addition to identifying lineages to detect variants of concern, we have developed an open source bioinformatic pipeline called HaVoC (Helsinki university Analyzer for Variants Of Concern). HaVoC can reference assemble raw sequence reads and assign the corresponding lineages to SARS-CoV-2 sequences. ConclusionsHaVoC is a pipeline utilizing several bioinformatic tools to perform multiple necessary analyses for investigating genetic variance among SARS-CoV-2 samples. The pipeline is particularly useful for those who need a more accessible and fast tool to detect and monitor the spread of SARS-CoV-2 variants of concern during local outbreaks. HaVoC is currently being used in Finland for monitoring the spread of SARS-CoV-2 variants. HaVoC user manual and source code are available at https://www.helsinki.fi/en/projects/havoc and https://bitbucket.org/auto_cov_pipeline/havoc, respectively.

bioinformatics↗

bioRxiv2020

A Molecular Taxonomy of Tumors Independent of Tissue-of-Origin

Cancer is a complex disease involving disrupted cellular metabolism, basic biochemical processes, and the microenvironment. However, despite some generally agreed upon unifying principles (Hanahan and Weinberg 2000, 2011), molecular signatures remain largely indistinguishable from tissue-of-origin, presenting a major barrier for precision health and individualized medicine. To address this challenge, we reduce mutation data to disruptions in a select set of pathways relevant to basic cell biology, from DNA replication to cellular communication. Using dimensionality reduction techniques, we assign tumor samples into ten clusters distinct from tissue-of-origin and largely free of bias from mutational burden or clinical stage. We show that the clusters vary in prognosis by modeling relative risk of death by cancer type and cluster. We identify cluster-specific mutations in different tissues, demonstrating that tissue-specific signatures contribute to common cellular phenotypes. Moreover, germline risk genes involved in replication fidelity and genome stability are equally distributed among clusters, contrary to the expectation that such genes are avatars of molecular subtype. We investigate metastatic and non-metastatic pathways, and show that most differences are cluster-specific. Some metastatic pathways from one cluster are cluster-specific pathways from non-metastatic tumors of another cluster, suggesting phenotypic convergence. Taken as a whole, our observations suggest that common driver genes combine with tissue-specific disruptions in tumor-promoting pathways to produce a limited number of distinct molecular phenotypes. Thus, we present a coherent view of global tumor biology, and explain how common cellular dysfunction might arise from tissue-specific mutations.

cancer biology↗

bioRxiv2018

Structural Basis for Antiarrhythmic Drug Interactions with the Human Cardiac Sodium Channel

The human voltage-gated sodium channel, hNav1.5, is responsible for the rapid upstroke of the cardiac action potential and is target for antiarrhythmic therapy. Despite the clinical relevance of hNav1.5 targeting drugs, structure-based molecular mechanisms of promising or problematic drugs have not been investigated at atomic scale to inform drug design. Here, we used Rosetta structural modeling and docking as well as molecular dynamics simulations to study the interactions of antiarrhythmic and local anesthetic drugs with hNav1.5. These calculations revealed several key drug binding sites formed within the pore lumen that can simultaneously accommodate up to two drug molecules. Molecular dynamics simulations identified a hydrophilic access pathway through the intracellular gate and a hydrophobic access pathway through a fenestration between domains III and IV. Our results advance the understanding of molecular mechanisms of antiarrhythmic and local anesthetic drug interactions with hNav1.5 and will be useful for rational design of novel therapeutics.

biophysics↗