Review
Biochemistry & Molecular Biology
Anna Ananchenko, Toka O. K. Hussein, Deepansh Mody, Mackenzie J. Thompson, John E. Baenziger
Summary: Pentameric ligand-gated ion channels (pLGICs) play a crucial role in synaptic communication and are considered important targets for treating neurological disorders. Lipids and lipophilic compounds modulate pLGIC function, and recent structural and biophysical data have identified binding sites for lipids on pLGICs.
Review
Physiology
Wayland W. L. Cheng, Mark J. Arcario, John T. Petroff
Summary: Lipids modulate the function of ion channels through direct lipid-protein interactions. Cryo-EM studies have identified lipid binding sites on ion channels, but the role of these sites in lipid modulation is not fully understood. These binding sites also coincide with sites for other allosteric modulators or drugs, suggesting that lipids act as endogenous allosteric modulators. This review focuses on lipid-drug binding sites in pentameric ligand-gated ion channels and transient receptor potential channels, highlighting the shared sites for phospholipids, sterols, anesthetics, and vanilloids. The implications of lipid binding at these sites, such as potential changes in drug potency and guiding drug design through protein-lipid interactions, are discussed. However, further studies are needed to fully understand the mechanisms of lipid modulation at these sites.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Marie Lycksell, Urska Rovsnik, Anton Hanke, Anne Martel, Rebecca J. Howard, Erik Lindahl
Summary: This study characterized the structure and dynamics of DeCLIC using cryo-EM, SANS, and MD simulations, revealing alternative conformations of the NTD and calcium-binding site and expanding the conformational landscape of the pLGIC family. Moreover, it demonstrated the power of combining low-resolution scattering, high-resolution structural, and MD simulation data to elucidate highly conserved interfacial interactions in the pLGIC family.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Cathrine Bergh, Stephanie A. Heusser, Rebecca Howard, Erik Lindahl
Summary: The study utilized enhanced sampling to simulate the pH-gated channel GLIC and construct Markov state models of gating, revealing differential effects of protonation and mutation on channel states, estimation of open probabilities and transition rates, as well as state- and protonation-dependent symmetrization.
Article
Biology
Noah M. Dietzen, Mark J. Arcario, Lawrence J. Chen, John T. Petroff, K. Trent Moreland, Kathiresan Krishnan, Grace Brannigan, Douglas F. Covey, Wayland W. L. Cheng
Summary: Polyunsaturated fatty acids (PUFAs) inhibit pentameric ligand-gated ion channels (pLGICs), but the specific mechanism of inhibition is unclear. This study found that docosahexaenoic acid (DHA), a type of PUFA, is more effective at inhibiting the ELIC receptor's response to agonists compared to other fatty acids. Using experiments and simulations, the researchers identified two binding sites for fatty acids in the outer transmembrane domain (TMD) of ELIC, and demonstrated that DHA selectively binds to these sites and inhibits ELIC by binding to a specific intrasubunit site.
Article
Biochemistry & Molecular Biology
Filip Koniuszewski, Florian D. Vogel, Konstantina Bampali, Jure Fabjan, Thomas Seidel, Petra Scholze, Philip B. Schmiedhofer, Thierry Langer, Margot Ernst
Summary: This study explores the potential for polypharmacology among pLGICs, revealing that ligands can interact with homologous sites in many members of the superfamily and multiple pockets in distinct localizations of individual receptor subtypes share common ligands. This poses challenges for the development of selective agents.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
John T. Petroff, Noah M. Dietzen, Ezry Santiago-McRae, Brett Deng, Maya S. Washington, Lawrence J. Chen, K. Trent Moreland, Zengqin Deng, Michael Rau, James A. J. Fitzpatrick, Peng Yuan, Thomas T. Joseph, Jerome Henin, Grace Brannigan, Wayland W. L. Cheng
Summary: The model pLGIC ELIC is positively modulated by the anionic phospholipid phosphatidylglycerol, which stabilizes the activated, open-channel state of the pLGIC.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Shuo Han, Xiang-Ping Chu, Ryan Goodson, Prae Gamel, Sophia Peng, Joshua Vance, Shizhen Wang
Summary: Cholesterol inhibits the hHv1 channel by stabilizing the voltage-sensing S4 segment at resting conformations, providing a mechanism for the regulation of fertilization by the hHv1 channel.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Neurosciences
Sultan Mayar, Mina Memarpoor-Yazdi, Ahmad Makky, Romina Eslami Sarokhalil, Nazzareno D'Avanzo
Summary: This study examines the effects of cannabinoids on HCN1 channels and finds that CBD and THC have opposing effects on HCN1 current. The study also reveals that changes to membrane fluidity are not the primary mechanism of HCN1 regulation by cannabinoids. These findings are important for understanding the potential therapeutic role of cannabinoids in neurological disorders.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Ivan Felsztyna, Marcos A. Villarreal, Daniel A. Garcia, Virginia Miguel
Summary: This study evaluated the usability of homology models in virtual screening (VS) for the RDL receptor, a relevant protein target for insecticide molecules. The impact of template conformational states on VS performance was analyzed. Homology models based on different pLGIC templates representing closed, open, and desensitized states were obtained. Their performance in prioritizing active ligands was assessed, and the best-performing models were subjected to molecular dynamics simulations. The results showed that the structural properties of the binding site and the template conformational state influenced the VS performance. Models with more constricted binding cavities tended to have better performance, and the closed conformation template produced the best results. These findings provide guidance for the application of homology modeling in virtual screening for other proteins in the pLGIC family.
Article
Biology
Mykhaylo Slobodyanyuk, Mackenzie J. Thompson, Rebecca A. Dean, John E. Baenziger, Roberto A. Chica, Corrie J. B. DaCosta
Summary: A study on the prokaryotic ligand-gated ion channel ELIC provides insights into the origin of agonism and antagonism at nicotinic acetylcholine receptors. Acetylcholine acts as an agonist in acetylcholine receptors but as an antagonist in ELIC. By substituting important residues in the agonist-binding site of ELIC, the apparent affinity for acetylcholine is reduced, demonstrating different roles of these residues in different contexts. The study also highlights a mechanism of antagonism where agonists with appreciable affinity but no efficacy can act as competitive antagonists.
COMMUNICATIONS BIOLOGY
(2022)
Article
Physiology
Ainara Claveras Cabezudo, Asma Feriel Khoualdi, Nazzareno D'Avanzo
Summary: Protein-lipid interactions play a crucial role in regulating ion channel function, and phosphoinositides have been found to enhance the activation of HCN channels. Computational docking and simulations suggest that the binding of phosphoinositides to HCN1 channels is not well-coordinated and occurs over a broad surface of charged residues.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yipeng Cao, Rui Yang, Wei Wang, Shengpeng Jiang, Chengwen Yang, Qingxin Wang, Ningbo Liu, Yi Xue, Imshik Lee, Xiangfei Meng, Zhiyong Yuan
Summary: Protein-lipid interactions play a crucial role in the function of membrane ion-channel proteins, which should be considered along with the diversity and complexity of membrane lipid composition. In this study, the distribution of different lipids in the membrane and the structure and conductance properties of phospholamban (PLN) pentamers were investigated through molecular dynamics simulations. The results suggest that cholesterol enriches around the protein, stabilizing the structure of PLN pentamers. The absence of cholesterol increases the flexibility of the protein backbone and lowers the energy barrier for ion permeation.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Multidisciplinary Sciences
Williams E. Miranda, Jiqing Guo, Haydee Mesa-Galloso, Valentina Corradi, James P. Lees-Miller, D. Peter Tieleman, Henry J. Duff, Sergei Yu Noskov
Summary: Lipid regulation of mammalian ion channel function is crucial for controlling electrical signaling and transport specificity. This study used molecular dynamics simulations, mutagenesis, and electrophysiology to investigate the effects of ceramide-sphingolipid probe on hERG1 channels, revealing a mechanism of allosteric modulation through conformational selection.
NATURE COMMUNICATIONS
(2021)
Review
Health Care Sciences & Services
Grace Hey, Rohan Rao, Ashley Carter, Akshay Reddy, Daisy Valle, Anjali Patel, Drashti Patel, Brandon Lucke-Wold, Daniel Pomeranz Krummel, Soma Sengupta
Summary: Gliomas are aggressive and heterogeneous primary brain malignancies that are difficult to treat. Ligand-gated ion channels (LGICs) have been identified as valuable biomarkers and diagnostic tools in the pathogenesis of gliomas. Various LGICs, including P2X, SYT16, and PANX2, can be altered in glioma, disrupting neural homeostasis and worsening symptoms. LGICs, such as purinoceptors, glutamate-gated receptors, and Cys-loop receptors, are being targeted in clinical trials for potential therapeutic benefits in glioma diagnosis and treatment.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Article
Multidisciplinary Sciences
Vasyl Bondarenko, Marta M. Wells, Qiang Chen, Tommy S. Tillman, Kevin Singewald, Matthew J. Lawless, Joel Caporoso, Nicole Brandon, Jonathan A. Coleman, Sunil Saxena, Erik Lindahl, Yan Xu, Pei Tang
Summary: In this study, using a combination of experiments and computational methods, the full-length intracellular domain (ICD) structure of the human alpha 7 nicotinic acetylcholine receptor in a resting state was determined. It was found that a significant portion of the ICD residues are located in highly flexible regions, with a large loop (loop L) contributing to its stability by anchoring onto the MA helix. Known motifs for cytoplasmic binding, regulation, and signaling were observed in both helices and disordered flexible regions, highlighting the important role of ICD conformational plasticity in orchestrating various biological processes.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Cathrine Bergh, Stephanie A. Heusser, Rebecca Howard, Erik Lindahl
Summary: The study utilized enhanced sampling to simulate the pH-gated channel GLIC and construct Markov state models of gating, revealing differential effects of protonation and mutation on channel states, estimation of open probabilities and transition rates, as well as state- and protonation-dependent symmetrization.
Article
Chemistry, Multidisciplinary
Milosz Wieczor, Vito Genna, Juan Aranda, Rosa M. Badia, Josep Lluis Gelpi, Vytautas Gapsys, Bert L. de Groot, Erik Lindahl, Marti Municoy, Adam Hospital, Modesto Orozco
Summary: Exascale computing will revolutionize molecular simulations, improving their quality and quantity. This article reviews how the biomolecular simulations field is preparing for this change and showcases the power of these simulation strategies through the work done by the HPC simulation community.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Multidisciplinary Sciences
Shaotong Zhu, Akshay Sridhar, Jinfeng Teng, Rebecca J. Howard, Erik Lindahl, Ryan E. Hibbs
Summary: GABA(A) receptors are important drug targets in the central nervous system for treating anxiety, sleep disorders, and epilepsy. This study presents two high-resolution structures of GABA(A) receptors bound by the drugs zolpidem and DMCM, providing insights into receptor modulation.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Aujan Mehregan, Sergio Perez-Conesa, Yuxuan Zhuang, Ahmad Elbahnsi, Diletta Pasini, Erik Lindahl, Rebecca J. Howard, Chris Ulens, Lucie Delemotte
Summary: This article mainly introduces the characteristics and functions of the envelope (E) protein, one of the structural proteins of SARS-CoV-2. By combining experimental and computational methods, researchers have found that the E protein can multimerize independently and plays an important role in viral budding. The study also found that the E protein may promote viral replication by reducing intracellular Ca2+ levels.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2022)
Article
Biophysics
Magnus Lundborg, Christian Wennberg, Jack Lidmar, Berk Hess, Erik Lindahl, Lars Norlen
Summary: A molecular-level understanding of skin permeation can improve the prediction of skin permeability and the effects of chemical penetration enhancers. This approach can facilitate product development and safety assessment of cosmetics.
BIOPHYSICAL JOURNAL
(2022)
Article
Multidisciplinary Sciences
Marie Lycksell, Urska Rovsnik, Anton Hanke, Anne Martel, Rebecca J. Howard, Erik Lindahl
Summary: This study characterized the structure and dynamics of DeCLIC using cryo-EM, SANS, and MD simulations, revealing alternative conformations of the NTD and calcium-binding site and expanding the conformational landscape of the pLGIC family. Moreover, it demonstrated the power of combining low-resolution scattering, high-resolution structural, and MD simulation data to elucidate highly conserved interfacial interactions in the pLGIC family.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Vasyl Bondarenko, Qiang Chen, Kevin Singewald, Nandan Haloi, Tommy S. Tillman, Rebecca J. Howard, Erik Lindahl, Yan Xu, Pei Tang
Summary: This study reveals the binding details and structural changes induced by Ivermectin in the alpha 7nAChR using nuclear magnetic resonance, comparative modeling, and molecular dynamics simulations. The binding of Ivermectin to the alpha 7nAChR is stabilized by hydrophobic interactions between adjacent subunits, resulting in an expanded inter-subunit gap. The ion-permeation pathway shows a profile similar to the desensitized alpha 7nAChR, providing insights into cytoplasmic signaling under different functional states.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Multidisciplinary Sciences
Dagimhiwat H. Legesse, Chen Fan, Jinfeng Teng, Yuxuan Zhuang, Rebecca J. Howard, Colleen M. Noviello, Erik Lindahl, Ryan E. Hibbs
Summary: Legesse et al. present structural studies of a human GABAA receptor in complex with positive and negative modulator neurosteroids, uncovering mechanisms of potentiation and inhibition. Allopregnanolone, a positive modulator, binds at the receptor-bilayer interface, while inhibitory neurosteroids bind in the pore. MD simulations and electrophysiology support the mechanism of allopregnanolone potentiating channel activity and suggest pore block as the dominant mechanism for sulfated neurosteroid inhibition.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Christian Blau, Linnea Yvonnesdotter, Erik Lindahl
Summary: The high-resolution cryo-EM maps pose challenges in automatically fitting atoms to densities while maintaining a good fit and allowing protein secondary structure changes. This study presents a solution using a maximum likelihood approach to identify the most likely structure that produced the observed density map. The derived refinement potentials and adaptive force scaling algorithm demonstrate improved performance.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biology
Steven De Gieter, Casey I. Gallagher, Eveline Wijckmans, Diletta Pasini, Chris Ulens, Rouslan G. Efremov
Summary: Cys-loop receptors play critical roles in electrochemical signaling throughout the animal kingdom. Understanding the diversity of these receptors in invertebrates, particularly the expansion of nACh-like genes, provides insights into their evolution and functional divergence. In this study, the cryo-EM structure of the orphan receptor Alpo4 from a thermophile worm was solved, revealing unique features in the ligand binding site and channel pore. This structural basis enhances our understanding of Alpo4 and suggests new strategies for designing specific channel modulators.
Meeting Abstract
Biophysics
Anton Jansen, Paul Bauer, Rebecca J. Howard, Erik Lindahl, Berk Hess
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Christian Blau, Linnea Yvonnesdotter, Erik Lindahl
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Akshay Sridhar, Sarah C. Lummis, Erik Lindahl, Rebecca J. Howard, Chris Ulens
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Sebastian Wingbermuhle, Erik Lindahl
BIOPHYSICAL JOURNAL
(2022)