Article
Biochemistry & Molecular Biology
Gonzalo Ferreira, Axel Santander, Romina Cardozo, Luisina Chavarria, Lucia Dominguez, Nicolas Mujica, Milagros Benitez, Santiago Sastre, Luis Sobrevia, Garth L. Nicolson
Summary: Inwardly rectifying potassium (Kir) channels are important for maintaining membrane potential and potassium homeostasis. These channels have various subtypes and can be regulated by molecules found in nutrients, such as phosphoinositols, polyamines, and Mg2+. Changes in Kir channels can affect metabolism and the ability to absorb nutrients and electrolytes. The study of nutrigenomics of ion channels is crucial for understanding how diet and nutrients can impact ion channel function, expression, and lead to pathological conditions that affect diet and electrolyte intake.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2023)
Article
Multidisciplinary Sciences
Anu Tyagi, Tofayel Ahmed, Shi Jian, Saumya Bajaj, Seow Theng Ong, Stephanie Shee Min Goay, Yue Zhao, Igor Vorobyov, Changlin Tian, K. George Chandy, Shashi Bhushan
Summary: This study reports two structures of the human voltage-gated potassium channel Kv1.3 – apo-Kv1.3 and dalazatide-Kv1.3. Both structures are in an activated state and show remarkable rearrangements in the selectivity filter. In apo-Kv1.3, the aromatic residue Y447 adopts a unique position diverging from other K+ channels, while in dalazatide-Kv1.3, binding of dalazatide narrows the selectivity filter and stabilizes Y447 in a position similar to other K+ channels. These structural changes play a crucial role in Kv1.3's transition into the drug-blocked state.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Pengyang Xin, Linqi Xu, Wenpei Dong, Linlin Mao, Jingjing Guo, Jingjing Bi, Shouwei Zhang, Yan Pei, Chang-Po Chen
Summary: In this study, novel artificial K+ channels were developed by rebuilding the core modules of natural K+ channels in artificial systems. These channels exhibited high selectivity for K+ over Na+ and showed a selectivity sequence of K+≈Rb+ during the transport process, which is consistent with the cation permeability characteristics of natural K+ channels. Moreover, these artificial channels could efficiently insert into cell membranes, mediate K+ transmembrane transport, disrupt cellular K+ homeostasis, and trigger cell apoptosis. These findings demonstrate that the structures, transport behaviors, and physiological functions of natural K+ channels can be mimicked in synthetic channels by rebuilding their core modules in artificial systems.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Oncology
Martina Chirra, Hannah S. Newton, Vaibhavkumar S. Gawali, Trisha M. Wise-Draper, Ameet A. Chimote, Laura Conforti
Summary: Ion channels play a crucial role in regulating T cell function, and the tumor microenvironment can suppress the antitumor capabilities of T cells. Understanding the effects of the tumor microenvironment on ion channels in T cells can lead to the development of more effective immunotherapies.
Article
Chemistry, Physical
B. Wang, H. Yang, Y. Feng, S. Zeng, L. Tan, R. Xu, L. Wang, R. Hu, Y. Yu
Summary: The novel electrochemical milling process (EMP) is used to prepare ultrasmall-sized Bi nanoparticles embedded in a three-dimensional porous carbon framework (EMP-Bi@3DCF), showing excellent sodium/potassium storage performance at -20 degrees C. The ultrafast kinetics process is achieved through the ultrasmall sized Bi nanoparticles via EMP and 3D interconnected porous channels, leading to superior rate performances and long cycle life for both NIBs and KIBs at Low-T.
MATERIALS TODAY ENERGY
(2021)
Article
Cardiac & Cardiovascular Systems
Vahagn Ohanyan, Sean M. Raph, Marc M. Dwenger, Xuemei Hu, Thomas Pucci, Gregory Mack, Joseph B. Moore, William M. Chilian, Aruni Bhatnagar, Matthew A. Nystoriak
Summary: The Kv beta proteins play a crucial role in regulating vascular tone and blood flow in the heart. Kv beta 2 promotes oxygen sensitivity, while Kv beta 1.1 inhibits oxygen-dependent vasodilation.
CIRCULATION RESEARCH
(2021)
Article
Biochemical Research Methods
Jing Gong, Yu Gong, Ting Zou, Yuxiao Zeng, Cao Yang, Lingyue Mo, Jiahui Kang, Xiaotang Fan, Haiwei Xu, Jun Yang
Summary: A controllable perfusion microfluidic chip (CPMC) was designed to culture retinal organoids (ROs) derived from human pluripotent stem cells. The results demonstrated that this system allowed for expansion of retinal progenitor cell (RPC) pool, orchestration of retinal ganglion cell (RGC) specification, and axon growth. This study highlights the advantages of the CPMC in promoting RO growth and providing a controllable platform for the maturity of RGCs, with promising applications in modeling RGC-related disorders, drug screening, and cell transplantation.
Review
Biochemistry & Molecular Biology
Yevheniia Kravenska, Vanessa Checchetto, Ildiko Szabo
Summary: Potassium ions can enter and exit mitochondria through various channels in the outer and inner membranes, with the ATP-dependent potassium channel being the most studied and playing a crucial role in protecting cells against ischemic and neuronal damage.
Article
Biochemistry & Molecular Biology
Alba Vera-Zambrano, Mauro Lago-Docampo, Natalia Gallego, Juan Felipe Franco-Gonzalez, Daniel Morales-Cano, Alejandro Cruz-Utrilla, Marta Villegas-Esguevillas, Edgar Fernandez-Malave, Pilar Escribano-Subias, Jair Antonio Tenorio-Castano, Francisco Perez-Vizcaino, Diana Valverde, Teresa Gonzalez, Angel Cogolludo
Summary: Reduced expression and/or activity of Kv1.5 channels is a common feature in PAH. This study characterized seven KCNA5 variants found in PAH patients and found that two of them resulted in loss of channel function and reduced expression, affecting cell apoptosis. These findings suggest that KCNA5 variants may be causative or contributing factors for PAH.
AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY
(2023)
Article
Oncology
Jone Garate, Albert Maimo-Barcelo, Joan Bestard-Escalas, Roberto Fernandez, Karim Perez-Romero, Marco A. Martinez, M. Antonia Payeras, Daniel H. Lopez, Jose Andres Fernandez, Gwendolyn Barcelo-Coblijn
Summary: Colorectal cancer is preventable but deadly, and efforts to classify it using molecular features are ongoing. Imaging mass spectrometry allows visualization of molecular distribution in tissues, revealing changes in lipid compositions that may provide insights into potential drug targets for treatment.
Article
Chemistry, Multidisciplinary
Xin Li, Chenfei Zhuang, Junmin Xu, Liang Li, Tingting Xu, Shuge Dai, Xinchang Wang, Xinjian Li, Ye Wang
Summary: The K0.5V2O5/CNTs hybrid film offers fast kinetics for electron transfer and ion transportation, as well as providing an elastic medium to buffer the large volume change of the K0.5V2O5 nanobelts during cycling. As a cathode for KIBs, the K0.5V2O5/CNTs electrode exhibits reversible discharge capacity, good cycling stability, and excellent rate performance.
Review
Biochemistry & Molecular Biology
Karolina Nowicka-Bauer, Monika Szymczak-Cendlak
Summary: Sperm motility is closely linked to the sensitivity and specificity of ion channels, with different ion channels interacting to ensure timely and efficient fertilization. The activation and modulation of these channels play key roles in regulating sperm motility in animals.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Materials Science, Multidisciplinary
Minmin Li, Yuchen Cao, Yuting Xiong, Guangyan Qing
Summary: Biological ion channels have asymmetries in structure and charge distribution, which enable them to perform diverse activities such as signal transduction and cell motility. Inspired by this, researchers have been pursuing artificial ion channels with comparable functions. However, current homogeneous nanochannels have not been able to achieve similar rewards. Hierarchically engineered heterogeneous nanochannels, on the other hand, have shown promising properties such as ion selectivity and permeability, and have found applications in selective ion transport, energy conversion, biomolecular separation, and detection. In this article, recent advances in these hierarchically engineered nanochannel systems are reviewed, with a focus on pore-on-pore and pore-in-pore structures, and their potential applications are discussed.
NPG ASIA MATERIALS
(2023)
Review
Biochemistry & Molecular Biology
Eleonora Spekker, Gabor Nagy-Grocz, Laszlo Vecsei
Summary: Migraine is a primary headache disorder that imposes a significant burden on the healthcare system. Activation and sensitization of the trigeminovascular system are believed to be crucial in the pathogenesis of migraines. Ion channels play important roles in migraine pathophysiology, and dysfunction of these channels can lead to neuronal excitability and sensitization.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Flavio Costa, Carlo Guardiani, Alberto Giacomello
Summary: This study investigated the activation/deactivation mechanism of hERG, a voltage-gated potassium channel involved in severe inherited and drug-induced cardiac channelopathies, including Long QT Syndrome. The results revealed two distinct pathways connecting the voltage sensor domain with the pore domain, and identified LQTS-related mutations distributed along these pathways, providing a microscopic interpretation of their role. Additionally, it was found that the channel still functions as a gate even when a cut is introduced between the voltage sensor domain and the neighboring helix S5.
COMMUNICATIONS BIOLOGY
(2022)
Article
Immunology
Sheila F. Lumley, Gillian Rodger, Bede Constantinides, Nicholas Sanderson, Kevin K. Chau, Teresa L. Street, Denise O'Donnell, Alison Howarth, Stephanie B. Hatch, Brian D. Marsden, Stuart Cox, Tim James, Fiona Warren, Liam J. Peck, Thomas G. Ritter, Zoe de Toledo, Laura Warren, David Axten, Richard J. Cornall, E. Yvonne Jones, David Stuart, Gavin Screaton, Daniel Ebner, Sarah Hoosdally, Meera Chand, Derrick W. Crook, Anne-Marie O'donnell, Christopher P. Conlon, Koen B. Pouwels, A. Sarah Walker, Tim E. A. Peto, Susan Hopkins, Timothy M. Walker, Nicole E. Stoesser, Philippa C. Matthews, Katie Jeffery, David W. Eyre
Summary: Natural infection with detectable anti-spike antibodies and two doses of vaccine provide robust protection against SARS-CoV-2 infection, including the B.1.1.7 variant in healthcare workers. Single dose vaccination significantly reduces the risk of symptomatic infection.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Chemistry, Physical
Wanling Song, Robin A. Corey, T. Bertie Ansell, C. Keith Cassidy, Michael R. Horrell, Anna L. Duncan, Phillip J. Stansfeld, Mark S. P. Sansom
Summary: PyLipID is a Python package for identifying and characterizing lipid interactions on membrane proteins from molecular dynamics simulations. It utilizes community analysis for binding site detection and lipid residence time calculation, generates lipid poses using a density-based scoring function, and distinguishes lipid conformational rearrangements from full dissociation events. Additionally, PyLipID can analyze interactions of membrane proteins with other ligands, and facilitates systematic analysis of lipid interactions from large simulation data sets.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Multidisciplinary Sciences
Sebastian Jojoa-Cruz, Kei Saotome, Che Chun Alex Tsui, Wen-Hsin Lee, Mark S. P. Sansom, Swetha E. Murthy, Ardem Patapoutian, Andrew B. Ward
Summary: This study reports the structural and functional details of Flycatcher1 (FLYC1) and sheds light on its gating conformational transitions. FLYC1 is a candidate mechanosensitive channel involved in Venus flytrap touch-induced prey capture, and it is a larger protein with unique structural features. The results reveal novel structural features and conformational transitions that regulate the mechano-gating of FLYC1.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Nicolai Tidemand Johansen, Marta Bonaccorsi, Tone Bengtsen, Andreas Haahr Larsen, Frederik Gronbaek Tidemand, Martin Cramer Pedersen, Pie Huda, Jens Berndtsson, Tamim Darwish, Nageshewar Rao Yepuri, Anne Martel, Thomas Gunther Pomorski, Andrea Bertarello, Mark Sansom, Mikaela Rapp, Ramon Crehuet, Tobias Schubeis, Kresten Lindorff-Larsen, Guido Pintacuda, Lise Arleth
Summary: This study investigates the conformation and dynamic behavior of the Mg2+ channel CorA using small-angle neutron scattering, molecular dynamics simulations, and solid-state nuclear magnetic resonance spectroscopy. The researchers find that CorA undergoes conformational equilibria between multiple states and that conducting states become more populated in the absence of Mg2+. These findings are crucial for understanding the functional regulation of CorA.
Article
Biochemical Research Methods
Martin Hunt, Jeremy Swann, Bede Constantinides, Philip W. Fowler, Zamin Iqbal
Summary: The study developed a tool called ReadItAndKeep, which enables the removal of contaminating human reads from SARS-CoV-2 sequencing data on low-specification laptops. By excluding the polyA tail from the viral reference, the tool prevents the bleed-through of human reads.
Article
Biophysics
Linda X. Phan, Charlotte Lynch, Jason Crain, Mark S. P. Sansom, Stephen J. Tucker
Summary: Interactions between ions and water at hydrophobic interfaces within ion channels and nanopores are crucial for the movement of ions across biological membranes. Previous molecular-dynamics simulations showed that adding polarization effects can significantly affect the affinity of anions for aqueous/hydrophobic interfaces. Using a model biomimetic nanopore, molecular-dynamics simulations were performed to investigate the behavior of ions and water within the hydrophobic region. The results suggest that effective polarization is essential for an accurate description of ion and water behavior within hydrophobic nanoscale pores, especially for those that conduct Cl-.
BIOPHYSICAL JOURNAL
(2022)
Review
Biochemistry & Molecular Biology
Andreas H. Larsen, Laura H. John, Mark S. P. Sansom, Robin A. Corey
Summary: This article reviews recent attempts to characterize the interactions between peripheral membrane proteins (PMPs) and biological membranes. The article compares different methods used to identify and analyze lipid-binding sites from simulation data and highlights recent work on characterizing the energetics of these interactions using free energy calculations. The authors describe how improvements in methodologies and computing power will continue to contribute to the field of molecular dynamics simulations.
BIOSCIENCE REPORTS
(2022)
Article
Materials Science, Multidisciplinary
Enrique Abad, Santos Bravo Yuste, Vicente Garzo
Summary: This study focuses on the mean square displacement (MSD) of intruders in a freely cooling granular gas, revealing a logarithmic time dependence and complex mechanical parameter dependence.
Article
Biochemistry & Molecular Biology
Yao Meng, Sami Sanlidag, Sacha A. Jensen, Sean A. Burnap, Weston B. Struwe, Andreas H. Larsen Section, Xinyi Feng, Shruti Mittal, Mark S. P. Sansom, Cecilia Sahlgren, Penny A. Handford
Summary: The extracellular C2 domain of the Jagged/Serrate and Delta families of transmembrane ligands is important for optimal activation of the Notch receptor. Mutations affecting an N-glycosylation site in the C2 domain of JAGGED1 have been found in tumors, reducing the ligand's ability to activate Notch. Site-specific glycan analysis showed that a complex-type or high-mannose N-glycan at this site is required for full Notch activation. The presence of the N-glycan limits the orientation of JAG1 relative to the membrane, facilitating Notch binding.
Article
Multidisciplinary Sciences
Arvind Kumar, Kayla Kindig, Shanlin Rao, Afroditi-Maria Zaki, Sandip Basak, Mark S. P. Sansom, Philip C. Biggin, Sudha Chakrapani
Summary: This study reveals the structures of Glycine receptors (GlyRs) bound to Delta 9 -tetrahydrocannabinol (THC) using cryo-electron microscopy, providing insights into the therapeutic effects of cannabinoids.
NATURE COMMUNICATIONS
(2022)
Article
Infectious Diseases
Alice E. Brankin, Philip W. Fowler
Summary: Fluoroquinolone resistance is a threat to tuberculosis treatment, and Whole Genome Sequencing (WGS) with detection of catalogued resistance-associated mutations is a promising method for susceptibility testing. However, the sensitivity of this method is often less than 90% due to the masking of minor alleles. It is important to detect these minor resistance-conferring alleles in WGS or any sequencing-based approach for diagnosing fluoroquinolone resistance. Importance: rating 7/10.
JAC-ANTIMICROBIAL RESISTANCE
(2023)
Article
Biophysics
Ian M. Kenney, Oliver Beckstein
Summary: Kinetic and thermodynamic models are commonly used in biology to connect microscopic features to system function. However, the parameters of these models often come with uncertainties, making them violate fundamental statistical mechanical equalities. In this study, we develop a maximum likelihood approach named multibind to combine and correct these parameters, achieving thermodynamic consistency and data accuracy. Our approach is demonstrated with theoretical models and applied to solve the inverse problem of determining microscopic quantities from macroscopic measurements.
BIOPHYSICAL REPORTS
(2023)
Article
Multidisciplinary Sciences
Ken Sakamoto, Takuma Akimoto, Mayu Muramatsu, Mark S. P. Sansom, Ralf Metzler, Eiji Yamamoto
Summary: Cell membranes undergo phase separation into ordered Lo and disordered Ld domains, which regulate the localization of specific proteins related to cell signaling and trafficking. However, it is still unclear how the heterogeneity of the membranes affects the diffusion and localization of proteins in Lo and Ld domains.
Article
Physics, Fluids & Plasmas
F. Le Vot, S. B. Yuste, E. Abad, D. S. Grebenkov
Summary: In this study, the behavior of a two-particle system under confinement is investigated using Monte Carlo simulations. The survival probability and first-encounter time characteristics are comprehensively analyzed based on the simulation outcomes. Numerical estimates and empirical formulas are provided, and some surprising results are discovered.
Article
Chemistry, Multidisciplinary
Robin A. A. Corey, Noah Harrison, Philllp J. J. Stansfeld, Mark S. P. Sansom, Anna L. L. Duncan
Summary: The interaction between lipid components within the mitochondrial electron transport chain is crucial for maintaining the stability and function of supercomplexes, particularly the interaction between CL and MLCL. Accumulation of MLCL in individuals with BTHS disrupts supercomplex stability by forming relatively weak interactions at the interface lipid binding site.