Biology subjects

Noyes, M.

Publications and source records attributed to Noyes, M..

4 recordsLinked to original sources

bioRxiv2024

The binding of Mint/X11 PDZ domains to CaV2 calcium channels predates bilaterian animals

PDZ domain mediated interactions with voltage-gated calcium (CaV) channel C-termini play important roles in localizing membrane Ca2+ signaling. The first such interaction was described between the scaffolding protein Mint-1 and CaV2.2 in mammals. In this study, we show through various in silico analyses that Mint is an animal-specific gene with a highly divergent N-terminus but a strongly conserved C-terminus comprised of a phosphotyrosine binding domain, two tandem PDZ domains (PDZ-1 and PDZ-2), and a C-terminal auto-inhibitory element that binds and inhibits PDZ-1. In addition to CaV2 channels, most genes that interact with Mint are also deeply conserved including amyloid precursor proteins, presenilins, neurexin, and CASK and Veli which form a tripartite complex with Mint in bilaterians. Through yeast and bacterial 2-hybrid experiments, we show that Mint and CaV2 channels from cnidarians and placozoans interact in vitro, and in situ hybridization revealed co-expression in dissociated neurons from the cnidarian Nematostella vectensis. Unexpectedly, the Mint orthologue from the ctenophore Hormiphora californiensis strongly binds the divergent C-terminal ligands of cnidarian and placozoan CaV2 channels, despite neither the ctenophore Mint, nor the placozoan and cnidarian orthologues, binding the ctenophore CaV2 channel C-terminus. Altogether, our analyses suggest that the capacity of Mint to bind CaV2 channels predates pre-bilaterian animals, and that evolutionary changes in CaV2 channel C-terminal sequences resulted in altered binding modalities with Mint.

evolutionary biology↗

bioRxiv2024

Brain and cancer associated binding domain mutations provide insight into CTCF's relationship with chromatin and its ability to act as a chromatin organizer

Here we used a series of CTCF mutations to explore CTCFs relationship with chromatin and its contribution to gene regulation. CTCFs impact depends on the genomic context of bound sites and the unique binding properties of WT and mutant CTCF proteins. Specifically, CTCFs signal strength is linked to changes in accessibility, and the ability to block cohesin is linked to its binding stability. Multivariate modelling reveals that both CTCF and accessibility contribute independently to cohesin binding and insulation, however CTCF signal strength has a stronger effect. CTCF and chromatin have a bidirectional relationship such that at CTCF sites, accessibility is reduced in a cohesin-dependent, mutant specific fashion. In addition, each mutant alters TF binding and accessibility in an indirect manner, changes which impart the most influence on rewiring transcriptional networks and the cells ability to differentiate. Collectively, the mutant perturbations provide a rich resource for determining CTCFs site-specific effects.

molecular biology↗

bioRxiv2022

Tandem Walk in Simulated Martian Gravity and Visual Environment

Astronauts returning from long-duration spaceflights experience visual-vestibular conflicts that causes motion sickness, perceptions that the environment is moving when it is not, problems with walking, and other functional tasks. To evaluate whether astronauts will have similar decrements associated with visual-vestibular conflicts after they land on Mars following exposure to weightlessness, participants were held by a device that offloads their weight; first entirely (0 G) for 10 minutes, and then partially (0.38 G) or not at all (1 G) for 15 minutes. Tandem (heel-to-toe) walk was used to assess the subjects walking performance. Ten subjects performed 2 trials of 10 steps on a medium-density foam surface. Four conditions were investigated: (a) 1 G in virtual reality (VR); (b) 1 G in VR with a superimposed disorienting optokinetic simulation (VR+DOS); (c) 0.38 G in VR; and (d) 0.38 G in VR+DOS. Tandem walk performance decreased in VR+DOS compared to VR in both 1 G and simulated 0.38 G. Tandem walking performance in VR+DOS was better in 0.38 G compared to 1 G. Tandem walking performance in VR+DOS in 1 G was not significantly different from tandem walking performance after spaceflight or bed rest. The increased tandem walking performance in 0.38 G compared to 1 G was presumably due to an increased cone of stability, allowing larger amplitude of body sway without resulting in a fall. Tandem walking on a compliant foam surface in VR+DOS is a potential analog for simulating postflight dynamic balance deficits in astronauts.

neuroscience↗

bioRxiv2019

A physics-based energy function allows the computational redesign of a PDZ domain

A powerful approach to understand protein structure and evolution is to perform computer simulations that mimic aspects of evolution. In particular, structure-based computational protein design (CPD) can address the inverse folding problem, exploring a large space of amino acid sequences and selecting ones predicted to adopt a given fold. Previously, CPD has been used to entirely redesign several proteins: all or most of the protein sequence was allowed to mutate freely; among sampled sequences, those with low computed folding energy were selected, and a few percent of them did indeed adopt the correct fold. Those studies used an energy function that was partly or largely knowledge-based, with several empirical terms. Here, we show that a PDZ domain can be entirely redesigned using a \"physics-based\" energy function that combines standard molecular mechanics and a recent, continuum electrostatic solvent model. Many thousands of sequences were generated by Monte Carlo simulation. Among the lowest-energy sequences, three were chosen for experimental testing. All three could be overexpressed and had native-like circular dichroism and 1D-NMR spectra. Two exhibited an increase in their thermal denaturation curves when a peptide ligand was present, indicating binding and suggesting correctly folded proteins. Evidently, the physical principles that govern molecular mechanics and continuum electrostatics are sufficient to perform whole-protein redesign. This is encouraging, since these methods provide physical insights, can be systematically improved, and are transferable to other biopolymers and ligands of medical or technological interest.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC=\"FIGDIR/small/790667v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@145ea28org.highwire.dtl.DTLVardef@10ffa2forg.highwire.dtl.DTLVardef@1f2460eorg.highwire.dtl.DTLVardef@d5691c_HPS_FORMAT_FIGEXP M_FIG Table of Contents Graphic\n\nC_FIG

biophysics↗