Assessing the mechanism of facilitated proton transport across GUVs trapped in a microfluidic device Thursday, July 25, 2024 Proton transport across lipid membranes is one of the most fundamental reactions that make up living organisms. In vitro, however, the study of proton transport reactions can be very challenging due to limitations imposed by proton concentrations, compartment size, and unstirred layers as well as buffer exchange and buffer capacity. In this study, we have developed a proton permeation assay based on the microfluidic trapping of giant vesicles enclosing the pH-sensitive dye pyranine to address some of these challenges. Read more
A Mechanism for Slow Rhythms in Coordinated Pancreatic Islet Activity Thursday, July 25, 2024 Insulin levels in the blood oscillate with a variety of periods, including rapid ( 5 – 10 min), ultradian (50 – 120 min), and circadian (24 h). Oscillations of insulin are beneficial for lowering blood glucose and disrupted rhythms are found in people with type 2 diabetes and their close relatives. These in vivo secretion dynamics imply that the oscillatory activity of individual islets of Langerhans are synchronized, although the mechanism for this is not known. One mechanism by which islets may synchronize is negative feedback of insulin on whole body glucose levels. Read more
Interior pH Sensing Residue of Human Voltage-Gated Proton Channel Hv1 is Histidine 168 Wednesday, July 24, 2024 The molecular mechanisms governing the human voltage-gated proton channel hHv1 remain elusive. Here we used membrane-enabled hybrid-solvent continuous constant pH molecular dynamics (CpHMD) simulations with pH replica exchange to further evaluate the recently obtained structural models of hHv1 in the closed (hyperpolarized) and open (depolarized) states (Geragotelis, Tobias et al., Proc. Natl. Acad. Sci. USA 2020) and explore potential pH-sensing residues. The CpHMD titration at a set of symmetric pH conditions revealed three residues that can gain or lose protons upon channel depolarization. Read more
Receptor binding and tortuosity explain morphogen local-to-global diffusion coefficient transition Tuesday, July 23, 2024 Morphogens are intercellular signaling molecules providing spatial information to cells in developing tissues to coordinate cell fate decisions. The spatial information is encoded within long-ranged concentration gradients of the morphogen. Direct measurement of morphogen dynamics in a range of systems suggests that local and global diffusion coefficients can differ by orders of magnitude. Further, local diffusivity can be large, which would potentially abolish any concentration gradient rapidly. Read more
Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning Monday, July 22, 2024 Protein-DNA interactions and protein-mediated DNA compaction play key roles in a range of biological processes. The length scales typically involved in DNA bending, bridging, looping, and compaction (≥ 1 kbp) are challenging to address experimentally or by all-atom molecular dynamics simulations, making coarse-grained simulations a natural approach. Here we present a simple and generic coarse-grained model for the DNA-protein and protein-protein interactions, and investigate the role of the latter in the protein-induced compaction of DNA. Read more
Evidence for a transfer-to-trap mechanism of fluorophore concentration quenching in lipid bilayers Sunday, July 21, 2024 It is important to understand the behaviours of fluorescent molecules because, firstly, they are often utilized as probes in biophysical experiments and, secondly, they are crucial cofactors in biological processes such as photosynthesis. A phenomenon called “fluorescence quenching” occurs when fluorophores are present at high concentrations but the mechanisms for quenching are debated. Here, we used a technique called “in-membrane electrophoresis” to generate concentration gradients of fluorophores within a supported lipid bilayer (SLB), across which quenching was expected to occur. Read more
Locking the hERG channel into place: Using a photoreactive unnatural amino acid to study voltage-gated channel movement Friday, July 19, 2024 The voltage-gated K+ channel, hERG, is a member of the Ether-a-go-go family and plays a critical role in heart physiology by repolarizing cardiac myocytes (1-4). The functional channel is comprised of four subunits, each including six transmembrane domains with large intracellular domains, a Per-ARNT-Sim (PAS) domain in the amino terminus, and the cyclic nucleotide-binding homology domain (CNBHD) in the carboxy terminus. Interactions between the PAS domain and CNBHD have been implicated in hERG channel deactivation (5-7), but how these domains interact during channel gating remains largely unknown. Read more
Inferring Cellular Contractile Forces and Work using Deep Morphology Traction Microscopy Friday, July 19, 2024 Traction Force Microscopy (TFM) has emerged as a widely used standard methodology to measure cell-generated traction forces and determine their role in regulating cell behavior. While TFM platforms have enabled many discoveries, their implementation remains limited due to complex experimental procedures, specialized substrates, and the ill-posed inverse problem where low magnitude high-frequency noise in the displacement field severely contaminates the resulting traction measurements. Here, we introduce Deep Morphology Traction Microscopy (DeepMorphoTM), a Deep Learning alternative to conventional TFM approaches. Read more
Elucidating the Role of Lipid Interactions in Stabilizing the Membrane Protein KcsA Wednesday, July 17, 2024 The significant effects of lipid binding on the functionality of potassium channel KcsA have been validated by brilliant studies. However, the specific interactions between lipids and KcsA, such as binding parameters for each binding event, have not been fully elucidated. In this study, we employed native mass spectrometry to investigate the binding of lipids to KcsA and their effects on the channel. The tetrameric structure of KcsA remains intact even in the absence of lipid binding. However, the subunit architecture of the E71A mutant, which is constantly open at low pH, relies on tightly associated copurified lipids. Read more
The phase behavior of skin-barrier lipids: a combined approach of experiments and simulations Wednesday, July 17, 2024 Skin barrier function is localized in its outermost layer, the stratum corneum (SC), which is comprised of corneocyte cells embedded in an extracellular lipid matrix containing ceramides (CERs), cholesterol (CHOL), and free fatty acids (FFAs). The unique structure and composition of this lipid matrix are important for skin barrier function. In this study, experiments and molecular dynamics simulation were combined to investigate the structural properties and phase behavior of mixtures containing nonhydroxy sphingosine CER (CER NS), CHOL, and FFA. Read more
2D Electrical Admittance Lattice Model Of Biological Cellular System For Modeling Electroporation Tuesday, July 16, 2024 In this work, a new modeling approach has been presented to obtain a two-dimensional transport lattice of a biological cellular system for the calculation of the potential distribution throughout the system and investigation of the corresponding membrane electroporation. The presented model has been obtained by a modified bilayer model of the cell membrane. This modified membrane model allows for an effective inclusion of the shape of the cell membrane in the potential calculation. The results of the model have shown good agreement with the results of the well-known Schwan equation and COMSOL Multiphysics for the circular cell. Read more