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Articles by Ben Corry
When can AlphaFold predict the oligomeric states of proteins?
1 INTRODUCTION Between 30% and 50% of all proteins are thought to self-associate into stable complexes consisting of multiple copies of themselves (Levy & Teichmann, 2013; Schweke et al., 2024). This oligomerisation process is important for the structural and functional properties of these proteins, as it enables the formation of repetitive structural elements, catalytic interfaces in enzymes and the central pore in many membrane proteins.
2′-O-Methyl-guanosine RNA fragments antagonize TLR7 and TLR8 to limit autoimmunity - Nature Immunology
Abstract Recognition of RNA fragments by Toll-like receptor 7 (TLR7) and TLR8 helps to initiate the innate immune response against pathogens. An outstanding question is why RNA fragments generated during clearance of apoptotic cells fail to activate TLR7 and TLR8 signaling. Here we show that select 2′-O-methyl (2′-OMe) guanosine RNA fragments, including those derived from host RNAs, function as potent TLR7 and TLR8 antagonists and reduce TLR7 sensing in vivo.
Thermophobic diffusion becomes dominant in ultra-dilute alkali halide aqueous solutions - Communications Chemistry
Abstract Under the influence of a temperature gradient, particles diffuse to their more favourable temperature, inducing a concentration gradient, a phenomenon termed thermodiffusion. The shift between thermophobic and thermophilic transport occurs at the inversion temperature T0. Previous theories imply that only thermophobic behaviour, i.e. the absence of T0, occurs at infinite dilution due to the absence of ion–ion interactions, but this has yet to be confirmed.
KIDINS220 and InsP8 safeguard the stepwise regulation of phosphate exporter XPR1
Keywords inorganic phosphate homeostasis XPR1 SLC53A1 KIDINS220 primary familial brain calcification Cryo-EM Get full text access Log in, subscribe or purchase for full access. References 1. Berndt, T. ∙ Kumar, R. Phosphatonins and the regulation of phosphate homeostasis Annu. Rev. Physiol. 2007; 69:341-359 2. Peacock, M. Phosphate metabolism in health and disease Calcif. Tissue Int. 2021; 108:3-15 3. Wagner, C.A. The basics of phosphate metabolism Nephrol. Dial. Transplant. 2024; 39:190-201 4.
AlphaFold2 captures conformational transitions in the voltage-gated channel superfamily
Get full text access Log in, subscribe or purchase for full access. References 1. Yu, F.H. ∙ Catterall, W.A. The VGL-chanome: a protein superfamily specialized for electrical signaling and ionic homeostasis Sci. STKE. 2004; 2004, re15 2. Armstrong, C.M. ∙ Bezanilla, F. Currents related to movement of the gating particles of the sodium channels Nature. 1973; 242:459-461 3. Perozo, E. ∙ MacKinnon, R. ...
Molecular basis of the functional conflict between chloroquine and peptide transport in the Malaria parasite chloroquine resistance transporter PfCRT - Nature Communications
Abstract The Plasmodium falciparum chloroquine resistance transporter (PfCRT) is a key protein contributing to resistance against the antimalarial chloroquine (CQ). Mutations such as K76T enable PfCRT to transport CQ away from its target in the parasite’s digestive vacuole, but this comes at a cost to its natural peptide transport function. This creates fitness costs which can drive changes to drug susceptibility in parasite populations, but the molecular basis of this is not well understood.
AlphaFold2 captures conformational transitions in the voltage-gated channel superfamily
Abstract Voltage-gated ion channels are crucial membrane proteins responsible for the electrical activity in excitable cells. These channels respond to changes in the membrane potential via conformational changes in their voltage-sensing domains (VSDs) that leads to the opening and closing of the ion conduction pore.
Simulations of TamB suggest it facilitates lipid transport from the bacterial inner membrane
Abstract Gram-negative bacteria possess a double-membrane envelope that serves as a robust barrier against environmental stress and antibiotics. While the transport of phospholipids synthesized at the inner membrane (IM) to the outer membrane (OM) is critical for maintaining OM integrity and functionality, the molecular mechanisms governing this process remain incompletely understood. Members of the AsmA-like protein family in E.
AlphaFold can be used to predict the oligomeric states of proteins
Abstract Homooligomerisation is a prevalent and important process that many proteins undergo to form the quaternary structure required to carry out their biological functions. However, determining the oligomeric states and structures of some proteins through experimental methods remains technically challenging and time consuming.
Publisher Correction: Thermodiffusive desalination - Nature Communications
Correction to: Nature Communications https://doi.org/10.1038/s41467-024-47313-5, published online 08 April 2024 The original version of this Article contained an error in the citation of reference [19] which was incorrectly given as “Soret, C. Sur l’ćtat d’ćquilibre que prend, au point de vue de sa concentration, une dissolution saline primitivement homogc`ne, dont deux parties sont portćes à des tempćratures diffćrentes; Archives de Genc`ve, 3e Periode, t. II, p. 48; 1879. J. Phys. Theor. Appl.
Thermodiffusive desalination - Nature Communications
Abstract Desalination could solve the grand challenge of water scarcity, but materials-based and conventional thermal desalination methods generally suffer from scaling, fouling and materials degradation. Here, we propose and assess thermodiffusive desalination (TDD), a method that operates entirely in the liquid phase and notably excludes evaporation, freezing, membranes, or ion-adsorbing materials.
Mechanical activation opens a lipid-lined pore in OSCA ion channels - Nature
Abstract OSCA/TMEM63 channels are the largest known family of mechanosensitive channels1,2,3, playing critical roles in plant4,5,6,7 and mammalian8,9 mechanotransduction. Here we determined 44 cryogenic electron microscopy structures of OSCA/TMEM63 channels in different environments to investigate the molecular basis of OSCA/TMEM63 channel mechanosensitivity. In nanodiscs, we mimicked increased membrane tension and observed a dilated pore with membrane access in one of the OSCA1.2 subunits.
A binding site for phosphoinositides described by multiscale simulations explains their modulation of voltage-gated sodium channels
eLife assessment This important study employs multiscale simulations to show that PIP2 lipids bind to DIV S4-S5 linkers within the inactivated state of a voltage-gated sodium channel, affecting the coupling of voltage sensors to the ion-conducting pore.
A binding site for phosphoinositides described by multiscale simulations explains their modulation of voltage gated sodium channels
Abstract Voltage gated sodium channels (Nav) are membrane proteins which open to facilitate the inward flux of sodium ions into excitable cells. In response to stimuli, Nav channels undergo a transition from the resting, closed state to an open state which allows ion influx, before rapidly inactivating. Dysregulation of this functional cycle due to mutations leads to diseases including epilepsy, pain conditions and cardiac disorders, making Nav channels a significant pharmacological target.
A binding site for phosphoinositide modulation of voltage-gated sodium channels described by multiscale simulations
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A G358S mutation in the Plasmodium falciparum Na+ pump PfATP4 confers clinically-relevant resistance to cipargamin - Nature Communications
Abstract Diverse compounds target the Plasmodium falciparum Na+ pump PfATP4, with cipargamin and (+)-SJ733 the most clinically-advanced. In a recent clinical trial for cipargamin, recrudescent parasites emerged, with most having a G358S mutation in PfATP4. Here, we show that PfATP4G358S parasites can withstand micromolar concentrations of cipargamin and (+)-SJ733, while remaining susceptible to antimalarials that do not target PfATP4.
Mechanistic basis for multidrug resistance and collateral drug sensitivity conferred to the malaria parasite by polymorphisms in PfMDR1 and PfCRT
Fig 5. Correlations between rates of drug transport via PfMDR1 in Xenopus oocytes and in vitro parasite drug resistance indices. The rates of PfMDR1-mediated transport of lumefantrine, mefloquine, chloroquine, and quinine (Figs 2 and 4, and S1 Data) were plotted against the in vitro resistance index for the relevant drug and parasite strain (S3 Table). Where not shown, error bars fall within the symbols.
TLR7 gain-of-function genetic variation causes human lupus - Nature
Abstract Although circumstantial evidence supports enhanced Toll-like receptor 7 (TLR7) signalling as a mechanism of human systemic autoimmune disease1,2,3,4,5,6,7, evidence of lupus-causing TLR7 gene variants is lacking. Here we describe human systemic lupus erythematosus caused by a TLR7 gain-of-function variant. TLR7 is a sensor of viral RNA8,9 and binds to guanosine10,11,–12.
Characterising fenestration size in sodium channel subtypes and their accessibility to inhibitors Nav fenestration size and drug access
ABSTRACT Voltage-gated sodium channels (Nav) underlie the electrical activity of nerve and muscle cells. Humans have nine different subtypes of these channels, which are the target of small molecule inhibitors commonly used to treat a range of conditions. Structural studies have identified four lateral fenestrations within the Nav pore module that have been shown to influence Nav pore blocker access during resting-state inhibition.
Differences in local anaesthetic and antiepileptic binding in the inactivated state of human sodium channel Nav1.4
Abstract Voltage-gated sodium channels play a vital role in nerve and muscle cells, enabling them to encode and transmit electrical signals. Currently, there exist several classes of drugs that aim to inhibit these channels for therapeutic purposes, including local anesthetics, antiepileptics and antiarrhythmics. However, sodium-channel-inhibiting drugs lack subtype specificity; instead, they inhibit all sodium channels in the human body.
FRET-Modulated Multihybrid Nanoparticles for Brightness-Equalized Single-Wavelength Barcoding
Semiconductor quantum dots (QDs) are the most versatile fluorophores for Förster resonance energy transfer (FRET) because they can function as both donors and acceptors for a multitude of fluorophores. However, a complete understanding of multidonor–multiacceptor FRET networks on QDs and their full employment into advanced fluorescence sensing and imaging have not been accomplished.
The naked truth about K<sup>+</sup> selectivity
Potassium channels rapidly move K+ ions across cell membranes while blocking Na+, but how these two effects are achieved simultaneously has remained unclear. Now, extensive molecular simulations show a single mechanism that features fully dehydrated ions can explain both rapid transport and impeccable selectivity.
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