Review
Biochemistry & Molecular Biology
Tomonori Tamura, Itaru Hamachi
Summary: Membrane biology studies have shown that organelle membranes play a crucial role in addition to providing structural support. Various chemical biology tools have been developed to understand the functions, properties, and dynamics of organelle membranes. This review focuses on the latest molecular probes for organelle membrane studies, highlighting chemical strategies for visualizing and quantitatively analyzing the dynamic properties of organelle membranes and lipids, and discussing the current limitations and future directions of this challenging research area.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Tomas Sabirovas, Ausra Valiuniene, Gintaras Valincius
Summary: In this study, biomimetic electrodes suitable for probing protein/phospholipid interactions were created on metallurgically polished aluminum surfaces. The fusion of multilamellar vesicles on the aluminum surface formed a hybrid bilayer lipid membrane (hBLM), with its complex capacitance being typical for intact phospholipid bilayers. The presence of cholesterol in hBLMs inhibited membrane damage caused by the peptide melittin, which showed a concentration-dependent interaction with the hBLMs.
SCIENTIFIC REPORTS
(2021)
Article
Physics, Multidisciplinary
N. Maridi, M. Benhamou, D. Khalil
Summary: This work investigates the structure and thermodynamic properties of a bilayer membrane composed of peptide molecules forming nanopores. The study reveals the existence of both repulsive and attractive forces between the nanopores. It is found that there is a critical nanopore density below which the nanopores do not coagulate.
CHINESE JOURNAL OF PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Yusuke Shimizu, Kohei Sato, Kazushi Kinbara
Summary: Inspired by natural calcium-induced reversible assembly and disassembly of membrane proteins, a phosphorylated amphiphile (PA) containing an oligo(phenylene-ethynylene) unit as a hydrophobic unit and a phosphate ester group as a hydrophilic calcium-binding unit was developed. The study demonstrated that PA can reversibly assemble and disassemble within lipid bilayer membranes in response to the sequential addition of calcium chloride and ethylene-diaminetetraacetic acid as a synthetic molecule for the first time.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Elisa Aranda, Jose A. Teruel, Antonio Ortiz, Maria Dolores Perez-Carceles, Jose N. Rodriguez-Lopez, Francisco J. Aranda
Summary: The anticarcinogenic properties of catechins, their interaction with lipids, and their potential site of action in membranes were studied. Experimental and computational research showed that catechins can modify lipid polymorphism and membrane structure and dynamics. These findings provide insights into the molecular effects of catechins and their potential impact on membrane function.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Review
Biochemical Research Methods
Rananjaya S. Gamage, Jordan L. Chasteen, Bradley D. Smith
Summary: This article summarizes the different ways that proteins are anchored in cell membranes and the strategies used to label membrane proteins in living cells. It also describes the methods used to produce lipidated proteins. A three-component synthetic construct composed of a lipophilic membrane anchor, hydrophilic linker, and exposed functional component is used to anchor the payload on the cell surface. Hydrocarbon chains are commonly used as the membrane anchor and amphiphilic fluorescent dyes with a zwitterionic linker have high persistence in living cell membranes. A new advance is the development of switchable membrane anchors for fundamental studies and applied biomaterials.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Chemistry, Medicinal
Irina D. Pogozheva, Grant A. Armstrong, Lingyang Kong, Timothy J. Hartnagel, Carly A. Carpino, Stephen E. Gee, Danielle M. Picarello, Amanda S. Rubin, Jumin Lee, Soohyung Park, Andrei L. Lomize, Wonpil Im
Summary: We conducted a comparative study using molecular dynamics simulations to investigate the effects of sterols and lipid unsaturation on the structural and mechanical properties of biomembranes. The study provides valuable insights into water permeation and the correlation between membrane properties and composition. The findings are important for understanding the behavior and function of biomembranes.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Review
Biochemistry & Molecular Biology
Muhammad Arifur Rahman, Ravinder Kumar, Enrique Sanchez, Taras Y. Nazarko
Summary: Originally seen as passive structures for lipid storage, lipid droplets (LDs) have been found to be dynamic organelles with important cellular functions. LDs are degraded through a process called lipophagy, where they are broken down within cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Physical
Ricki Chairil, Noah Malmstadt
Summary: Curvature-mediated lipid-protein interactions play a crucial role in cellular reactions and mechanisms. This study investigates the membrane curvature partitioning behavior of cube-shaped CsPbBr3 quantum dots (QDs) embedded within deformed giant unilamellar vesicles (GUVs). The results show that the distribution of CsPbBr3 QDs differs significantly from that of conventional fluorophores and quasispherical CdSe core/ZnS shell QDs, suggesting that the geometry of both QDs and lipid membranes affect the curvature preferences of QDs. These findings provide insights into the aggregation of proteins induced by curvature and the interactions between lipid membranes and intercalating particles.
Article
Biochemistry & Molecular Biology
Evan J. G. van Aalst, Collin J. Borcik, Benjamin Wylie
Summary: Membrane proteins and polycyclic lipids coordinate phospholipid bilayer ordering, resulting in the partitioning of liquid crystalline phase. This ordering plays important roles in signal transduction in eukaryotes and pathogenicity and antimicrobial resistance in prokaryotes. Experimental evidence indicates microdomain formation and lipid ordering in native membranes.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2022)
Review
Chemistry, Multidisciplinary
Agnes P. Girard-Egrot, Ofelia Maniti
Summary: Membrane proteins are crucial for cellular functions and understanding their functions is important for drug target development. However, studying membrane proteins is challenging as they require their native environment. Tethered-Bilayer Lipid Membranes (tBLMs) have emerged as a promising model for reconstituting membrane proteins due to their ability to provide a suitable environment and allow investigation through various analytical techniques.
APPLIED SCIENCES-BASEL
(2021)
Article
Optics
Haoning Tang, Fan Du, Stephen Carr, Clayton DeVault, Olivia Mello, Eric Mazur
Summary: This study demonstrates a twisted bilayer photonic crystal with ultra-flat photonic bands and extreme slow-light behavior. By adjusting the device geometry, the band structure of the photonic system can be easily engineered, providing significant freedom in device design. The research provides a fundamental understanding of the photonic properties of twisted bilayer photonic crystals and opens up new possibilities for enhancing nonlinear effects based on the nanoscale.
LIGHT-SCIENCE & APPLICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Roman S. Kirsanov, Ljudmila S. Khailova, Tatyana I. Rokitskaya, Iliuza R. Iaubasarova, Pavel A. Nazarov, Alisa A. Panteleeva, Konstantin G. Lyamzaev, Lyudmila B. Popova, Galina A. Korshunova, Elena A. Kotova, Yuri N. Antonenko
Summary: This article describes a new method of proton transport across lipid membranes using a synthesized precursor of triphenylphosphonium ylide. The precursor was found to release protons in mitochondrial, chloroplast, and artificial lipid membranes, suggesting its potential as a proton carrier. The new ylide-type protonophores show promising therapeutic properties as uncouplers.
BIOELECTROCHEMISTRY
(2023)
Article
Biochemical Research Methods
Nandan Kumar, G. Narahari Sastry
Summary: This study investigates the composition and structure-function relationships of lipids in human cell membranes. It was found that membranes enriched with cholesterol exhibit increased compactness and thickness.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2021)
Review
Biochemistry & Molecular Biology
N. Dadina, J. Tyson, S. Zheng, L. Lesiak, A. Schepartz
Summary: The article discusses recent advances in the design and application of lipid-based tools for visualizing and interrogating organelles in live cells, especially at super resolution. Strategies rely on modification of natural lipids or lipid-like small molecules ex cellula, where organelle specificity is provided by the structure of the chemically modified lipid, or in cellula using cellular machinery, where an enzyme labels the lipid in situ. Recent improvements to the chemistry of lipid probes have broadened the scope of biological questions that can be addressed by imaging organelle membranes at the nanoscale.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2021)
Meeting Abstract
Biophysics
Viviana Monje-Galvan, Gregory A. Voth
BIOPHYSICAL JOURNAL
(2019)
Article
Thermodynamics
Viviana Monje-Galvan, Jeffery B. Klauda
FLUID PHASE EQUILIBRIA
(2020)
Article
Biology
Viviana Monje-Galvan, Gregory A. Voth
Article
Biophysics
Alvin Yu, Alexander J. Pak, Peng He, Viviana Monje-Galvan, Lorenzo Casalino, Zied Gaieb, Abigail C. Dommer, Rommie E. Amaro, Gregory A. Voth
Summary: This article presents the current status and ongoing development of a largely bottom-up coarse-grained (CG) model of the SARS-CoV-2 virion. The CG model was constructed using data from cryo-electron microscopy, x-ray crystallography, and computational predictions to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into the complete virion model. The CG model allows for capturing viral behavior that is difficult to observe in atomistic simulations and can be iteratively improved with new data.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Jinhui Li, Poornima Kalyanram, Seyedalireza Rozati, Viviana Monje-Galvan, Anju Gupta
Summary: This study investigates the interactions between the dye D112 and mixed lipid bilayers, providing insights into its binding and insertion mechanisms. The results show that initial electrostatic binding occurs between the positive charge of D112 and the negative charge of the lipid headgroups. The interactions are governed by enthalpy-driven nonclassical hydrophobic effects. Two possible insertion mechanisms, harpoon and flip, are identified. The size of D112 aggregates affects the orientation and degree of insertion.
Review
Biophysics
Oluwatoyin Campbell, Viviana Monje-Galvan
Summary: The mammalian cell membrane is composed of a wide variety of lipid species, which play a critical role in biological function. Alterations to lipid metabolism can have serious consequences and are observed in viral diseases, particularly those caused by Flaviviridae family viruses. These viruses interfere with lipid metabolism during liver disease, and their pathogenesis involves protein-lipid interactions that affect lipid sorting and metabolism. Molecular dynamics simulations can provide insights into these interactions at the molecular level. This review focuses on recent advancements and knowledge gaps in understanding the molecular mechanisms of lipid-mediated liver disease caused by Flaviviridae viruses, specifically dengue, zika, and hepatitis C.
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Ricardo X. Ramirez, Oluwatoyin Campbell, Apoorva J. Pradhan, G. Ekin Atilla-Gokcumen, Viviana Monje-Galvan
Summary: Lipids, the structural part of membranes, play crucial roles in biological functions. However, our understanding of their involvement in key cellular processes and protein-lipid interactions is still limited. In this study, molecular dynamics simulations were performed to investigate the interaction between mixed lineage kinase domain-like (MLKL) protein and mammalian cell plasma membrane models. The results indicate that electrostatic interactions initially drive the binding of the protein, while the conformation of the bound protein modulates lipid recruitment and changes the local lipid environment. These findings enhance our knowledge of protein-lipid interactions at the membrane interface and provide insights into the molecular mechanisms of necroptotic pathway, which is being explored as a potential target for cancer and inflammatory diseases.
FRONTIERS IN CHEMISTRY
(2023)
Article
Nanoscience & Nanotechnology
Jinhui Li, Viviana Monje-Galvan
Summary: Triterpenoid saponins are organic compounds with antibacterial activity against both Gram-negative and Gram-positive bacteria. Their interaction with bacterial membrane lipids is important for their antibacterial activity. Understanding the mechanisms to disrupt bacterial lipid bilayers can help mitigate antibiotic resistance.
ACS APPLIED BIO MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Oluwatoyin Campbell, Viviana Monje-Galvan
Summary: This study investigates the interaction between Hepatitis C virus protein p7 and lipid membranes, as well as the mechanism of membrane reorganization. The results show that p7 is sensitive to its lipid environment, leading to different remodeling patterns in membranes. Helix 1 plays a crucial role in peptide insertion, while helix 2 and the adjacent loop prompt the recruitment of specific lipids to the protein binding site.
JOURNAL OF STRUCTURAL BIOLOGY
(2023)
Review
Engineering, Chemical
Jinhui Li, Viviana Monje-Galvan
Summary: This review highlights the potential antibacterial mechanisms of saponins from both experimental and molecular simulation perspectives and presents the current progress in the development and repurposing of natural-product antibiotics.
Meeting Abstract
Biophysics
Jinhui Li, Viviana Monje-Galvan
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Oluwatoyin Campbell, Viviana Monje-Galvan
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Physical
Viviana Monje-Galvan, Gregory A. Voth
Summary: Specific lipid-protein interactions are essential for cellular processes and pathogen replication. COVID-19 has caused significant global impact, with urgent need to understand the virus mechanisms during different life stages. Research on SARS-CoV-2 membrane proteins reveals their crucial role in viral assembly and infectivity.
FARADAY DISCUSSIONS
(2021)
Article
Biochemistry & Molecular Biology
Apoorva J. Pradhan, Daniel Lu, Laura R. Parisi, Shichen Shen, Ilyas A. Berhane, Samuel L. Galster, Kiana Bynum, Viviana Monje-Galvan, Omer Gokcumen, Sherry R. Chemler, Jun Qu, Jason G. Kay, G. Ekin Atilla-Gokcumen
Summary: Research has shown that during Necroptosis, protein acylation occurs on key players like MLKL and phosphoMLKL, with VLCFAs playing a crucial role in membrane recruitment. Additionally, disruption of endosomal trafficking may contribute to increased cell viability during Necroptosis.
CELL CHEMICAL BIOLOGY
(2021)
Meeting Abstract
Biophysics
Viviana Monje-Galvan, Alexander Pak, Gregory A. Voth
BIOPHYSICAL JOURNAL
(2021)