ClC-0 is a chloride channel whose gating is sensitive to both voltage and chloride. Based on analysis of gating kinetics using single-channel recordings, a five-state model was proposed to describe the dependence of ClC-0 fast-gate opening on voltage and external chloride (Chen, T.-Y., and C. Miller. 1996. J. Gen. Physiol. 108:237-250). We aimed to use this five-state model as a starting point for understanding the structural changes that occur during gating. Using macroscopic patch recordings, we were able to reproduce the effects of voltage and chloride that were reported by Chen and Miller and to fit our opening rate constant data to the five-state model. Upon further analysis of both our data and those of Chen and Miller, we learned that in contrast to their conclusions, (a) the features in the data are not adequate to rule out a simpler four-state model, and (b) the chloride-binding step is voltage dependent. In order to be able to evaluate the effects of mutants on gating (described in the companion paper, see Engh et al. on p. 351 of this issue), we developed a method for determining the error on gating model parameters, and evaluated the sources of this error. To begin to mesh the kinetic model(s) with the known CLC structures, a model of ClC-0 was generated computationally based on the X-ray crystal structure of the prokaryotic homolog ClC-ec1. Analysis of pore electrostatics in this homology model suggests that at least two of the conclusions derived from the gating kinetics analysis are consistent with the known CLC structures: (1) chloride binding is necessary for channel opening, and (2) chloride binding to any of the three known chloride-binding sites must be voltage dependent.
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http://dx.doi.org/10.1085/jgp.200709759 | DOI Listing |
JCO Clin Cancer Inform
January 2025
Department of Radiology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi, India.
Purpose: To explore the perceived utility and effect of simplified radiology reports on oncology patients' knowledge and feasibility of large language models (LLMs) to generate such reports.
Materials And Methods: This study was approved by the Institute Ethics Committee. In phase I, five state-of-the-art LLMs (Generative Pre-Trained Transformer-4o [GPT-4o], Google Gemini, Claude Opus, Llama-3.
PLoS Comput Biol
January 2025
Department of Physics, University of Toronto, Toronto, Ontario, Canada.
Efflux pumps that transport antibacterial drugs out of bacterial cells have broad specificity, commonly leading to broad spectrum resistance and limiting treatment strategies for infections. It remains unclear how efflux pumps can maintain this broad spectrum specificity to diverse drug molecules while limiting the efflux of other cytoplasmic content. We have investigated the origins of this broad specificity using theoretical models informed by the experimentally determined structural and kinetic properties of efflux pumps.
View Article and Find Full Text PDFRecent advances in generative modeling enable efficient sampling of protein structures, but their tendency to optimize for designability imposes a bias toward idealized structures at the expense of loops and other complex structural motifs critical for function. We introduce SHAPES (Structural and Hierarchical Assessment of Proteins with Embedding Similarity) to evaluate five state-of-the-art generative models of protein structures. Using structural embeddings across multiple structural hierarchies, ranging from local geometries to global protein architectures, we reveal substantial undersampling of the observed protein structure space by these models.
View Article and Find Full Text PDFCPT Pharmacometrics Syst Pharmacol
January 2025
Department of Pharmacy, Uppsala University, Uppsala, Sweden.
Type 2 diabetes (T2D) is a progressive metabolic disorder that could be an underlying cause of long-term complications that increase mortality. The assessment of the probability of such events could be essential for mortality risk management. This work aimed to establish a framework for risk predictions of macrovascular complications (MVC) and diabetic kidney disease (DKD) in patients with T2D, using real-world data from the Swedish National Diabetes Registry (NDR), in the presence of mortality as a competing risk.
View Article and Find Full Text PDFWearable Technol
December 2024
Biorobotics Laboratory, EPFL, Lausanne, Vaud, Switzerland.
Neuromuscular controllers (NMCs) offer a promising approach to adaptive and task-invariant control of exoskeletons for walking assistance, leveraging the bioinspired models based on the peripheral nervous system. This article expands on our previous development of a novel structure for NMCs with modifications to the virtual muscle model and reflex modulation strategy. The modifications consist firstly of simplifications to the Hill-type virtual muscle model, resulting in a more straightforward formulation and reduced number of parameters; and second, using a finer division of gait subphases in the reflex modulation state machine, allowing for a higher degree of control over the shape of the assistive profile.
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