Article
Biochemistry & Molecular Biology
Sevde Puza, Shima Asfia, Ralf Seemann, Jean-Baptiste Fleury
Summary: Lipid droplets (LD) locate in the endoplasmic reticulum membrane and play important roles in biological functions. A protein called ADRP surrounds LDs along with phospholipid monolayers and is involved in storing neutral lipids. This article focuses on the influence of ADRP on the 3D shape of LDs embedded in bilayers and the diffusion of phospholipids on LD surfaces. The study shows that ADRP significantly affects the 3D structure of LDs. Rating: 9/10.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Yang Liu, Xu Zheng, Dongshi Guan, Xikai Jiang, Guoqing Hu
Summary: In this study, the impact of heterogeneous nanostructures on anomalous diffusion in dipalmitoylphosphatidylcholine (DPPC) monolayers is investigated. The existence of condensed nanodomains and their influence on diffusion are identified. The findings reveal a universal characteristic of multistage mean square displacement (MSD) and an anomalous double-peaked displacement probability distribution (DPD) phenomenon.
Article
Biophysics
Rafael G. Oliveira, Mariana Paolorossi, Leide Passos Cavalcanti, Antonio Malfatti-Gasperini, Guillermo G. Montich
Summary: The study found that when beta 2GPI binds with anionic phospholipids, it forms a lamellar stacking with a periodicity, and the interactions between membranes mediated by beta 2GPI are favored when the membranes are in the liquid crystalline state.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2021)
Article
Biochemistry & Molecular Biology
Diana Priyadarshini, Josip Ivica, Frances Separovic, Maurits R. R. de Planque
Summary: Many antimicrobial peptides (AMPs) are cationic host defence peptides (HDPs) that interact with microbial membranes, potentially serving as therapeutics to combat antibiotic resistance. Studying the effects of four AMPs and a bee toxin on different phospholipid membranes highlights the importance of using appropriate bilayer compositions and peptide concentrations for AMP research. The research confirms existing peptide-bilayer interaction models and emphasizes the significance of understanding AMP behavior in relation to lipid bilayers mimicking bacterial and human cell membranes.
BIOPHYSICAL CHEMISTRY
(2022)
Article
Polymer Science
Kirsten Ullmann, Lea Fachet, Hermann Nirschl, Gero Leneweit
Summary: Phospholipids exhibit different behaviors at different temperatures, with faster adsorption process in the liquid crystalline state than in the gel state. Concentration-dependent results show no significant difference between DPPC and DSPC. The addition of cholesterol stabilizes the liposomal conformation in the mixture.
Article
Chemistry, Multidisciplinary
One-Sun Lee, Mohamed E. Madjet, Khaled A. Mahmoud
Summary: The study conducted molecular dynamics simulations to investigate the interaction between MXene nanosheets and a model bacterial membrane, revealing that MXene adsorption could induce a local phase transition in the membrane and lead to cell lysis. This proposed bactericidal mechanism of MXenes provides a useful model for designing new antibacterial nanomaterials.
Article
Engineering, Environmental
Yiping Feng, Jiayong Lao, Jiale Zou, Zhiyu Zhu, Daguang Li, Guoguang Liu, Liang Mao
Summary: Understanding the interactions between nanomaterials and cell membranes is important for ecotoxicology and human health. In this study, the interaction between graphitic carbon nitride (CN) and red blood cells was investigated. It was found that CN causes rapid cell membrane rupture through a physical interaction mechanism rather than chemical oxidation. Additionally, CN was found to extract phospholipids, particularly phosphatidylcholine, from cell membranes.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Erwin London
Summary: Lipid asymmetry, an important feature of eukaryotic plasma membranes, can induce or suppress the ability of membranes to form ordered domains (rafts). Studies have shown that a loss of asymmetry can also induce the formation of ordered domains.
Review
Biochemistry & Molecular Biology
Hamdi Nsairat, Abed Alqader Ibrahim, Areej M. Jaber, Sharif Abdelghany, Randa Atwan, Naeem Shalan, Hiba Abdelnabi, Fadwa Odeh, Mohamed El-Tanani, Walhan Alshaer
Summary: This review aims to provide a perspective and a clear understanding of the main factors regulating the colloidal and bilayer stability of liposomes, with a focus on the role of cholesterol and its potential alternatives. Furthermore, strategies for achieving more stable in vitro and in vivo liposomes with improved drug release and encapsulation efficiencies are analyzed.
JOURNAL OF LIPOSOME RESEARCH
(2023)
Article
Food Science & Technology
Mingyu Yin, Ryosuke Matsuoka, Yinci Xi, Xichang Wang
Summary: The study found that phospholipids derived from egg yolk and soya bean exhibited significant antioxidant and lipid-lowering abilities in a high-fat-and-sucrose diet model, reducing liver burden and improving blood lipid and inflammation markers, with egg yolk phospholipids showing more effective therapeutic benefits.
Article
Biochemistry & Molecular Biology
Tatyana Rokitskaya, Elena A. Kotova, Yuri N. Antonenko
Summary: By investigating the generation of potentials on a planar bilayer lipid membrane induced by usnic acid in the presence of concentration gradients of hydrogen, magnesium, or calcium ions, it was found that usnic acid could generate abnormal membrane potentials, potentially through ionophore-mediated coupled fluxes of multiple ions across the membrane.
BIOELECTROCHEMISTRY
(2021)
Article
Food Science & Technology
Limin Man, Wei Ren, Huaxiu Qin, Mengqi Sun, Shumao Yuan, Mingxia Zhu, Guiqin Liu, Changfa Wang, Mengmeng Li
Summary: In this study, the lipid and volatile organic compound (VOC) profiles of donkey, bovine, and sheep meat were analyzed and compared using UHPLC-ESI-MS and SPME-GC-MS. Potential markers were identified to distinguish between different meats, and the flavor differences were related to the fatty acid profile in lipids.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Materials Science, Multidisciplinary
Tun Naw Sut, Bo Kyeong Yoon, Won-Yong Jeon, Joshua A. Jackman, Nam-Joon Cho
Summary: Supported lipid bilayer (SLB) coatings, versatile cell-membrane-mimicking biointerfaces, have been expanded for medical and biotechnology applications, facilitating various studies and applications like biosensors, diagnostics, and antifouling surfaces.
APPLIED MATERIALS TODAY
(2021)
Article
Chemistry, Physical
Xue Lai, Hanjian Lai, Mengzhen Du, Hui Chen, Dongsheng Qiu, Yulin Zhu, Mingrui Pu, Yiwu Zhu, Erjun Zhou, Feng He
Summary: Quasiplanar heterojunction organic solar cells, with efficient exciton dissociation and charge transfer, have gained attention. In this study, a co-acceptor-based Q-PHJ OSC with enhanced crystallinity was achieved using two compatible acceptors. The co-Q-PHJ device exhibited improved thermal stability and efficiency.
CHEMISTRY OF MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Megan Wood, Michael Morales, Elizabeth Miller, Samuel Braziel, Joseph Giancaspro, Patrick Scollan, Juan Rosario, Alyssa Gayapa, Michael Krmic, Sunghee Lee
Summary: The study showed that the presence of neutral ibuprofen increases the water permeability of lipid membranes composed of DOPC, but this effect is not observed when cholesterol is present in the DOPC. This suggests a potential competition between ibuprofen and cholesterol on the hydrocarbon core environment of the phospholipid assembly, influencing water transport phenomena.
Article
Biochemistry & Molecular Biology
Larisa Chernyaeva, Giorgio Ratti, Laura Teirila, Satoshi Fudo, Uni Rankka, Anssi Pelkonen, Paula Korhonen, Katarzyna Leskinen, Salla Keskitalo, Kari Salokas, Christina Gkolfinopoulou, Katrina E. Crompton, Matti Javanainen, Lotta Happonen, Markku Varjosalo, Tarja Malm, Ville Leinonen, Angeliki Chroni, Paivi Saavalainen, Seppo Meri, Tommi Kajander, Adam J. M. Wollman, Eija Nissila, Karita Haapasalo
Summary: By studying the interaction between apoE4 and FH, it was found that this interaction affects the neurotoxicity and clearance of A beta 1-42, which is related to AD pathogenesis. ApoE and FH reduce the binding of A beta 1-42 to CR3 and the subsequent phagocytosis by microglia, leading to changes in gene expression related to AD. FH forms complement-resistant oligomers with apoE/A beta 1-42 complexes, and the formation of these complexes is isoform specific, with apoE2 and apoE3 having higher affinity to FH than apoE4. These complexes reduce A beta 1-42 oligomerization and toxicity, and colocalize with C1q on A beta plaques in the brain, providing important insights into AD pathogenesis and how the strongest genetic risk factor for AD predisposes to neuroinflammation in the early stages of the disease pathology.
Article
Physics, Multidisciplinary
Kiril Zelenkovski, Trifce Sandev, Ralf Metzler, Ljupco Kocarev, Lasko Basnarkov
Summary: We present a refined approach to explore complex networks with stochastic resetting based on node centrality measures. This approach allows a random walker to jump not only to a deliberately chosen resetting node, but also to a node that can reach all other nodes faster. By considering the resetting site as the geometric center, we calculate the Global Mean First Passage Time (GMFPT) using Markov chain theory to determine the search performance of the random walk with resetting. We compare different nodes as resetting sites by comparing their GMFPT values.
Article
Chemistry, Physical
Balazs Fabian, Ilpo Vattulainen, Matti Javanainen
Summary: The shear viscosity of lipid membranes is crucial for determining the rates of diffusion-limited reactions and the movement of lipids, proteins, and other membrane constituents. This study uses molecular dynamics simulations to extract the shear viscosities of lipid membranes under various conditions. The results demonstrate the significant effects of protein concentration, cholesterol concentration, and temperature on membrane viscosity.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Semen Yesylevskyy, Hector Martinez-Seara, Pavel Jungwirth
Summary: This study investigates the influence of membrane curvature on Ca2+ binding to phospholipid bilayers using molecular dynamics simulations. The results show that Ca2+ ions preferentially bind to the concave surfaces of both zwitterionic and anionic bilayers. The membrane curvature also leads to significant changes in binding, including differences in ion concentrations, lipid coordination distributions, and binding patterns to different chemical groups of lipids. The effects of curvature differ between the concave and convex monolayers, and charge scaling is found to reduce Ca2+ binding to curved phosphatidylserine bilayers.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Vojtech Kostal, Philip E. Mason, Hector Martinez-Seara, Pavel Jungwirth
Summary: We conducted ab initio molecular dynamics simulations based on density functional theory to investigate the hydration structure of common alkali and alkali earth metal cations. Our findings suggest that the widely used atom pairwise dispersion correction scheme D3 leads to inaccuracies in the hydration structures of these cations by assigning dispersion coefficients based on the neutral form of the atom rather than its actual oxidation state. To address this issue, we propose disabling the D3 correction specifically for all cation-including pairs, resulting in a significantly improved agreement with experimental data.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Physics, Multidisciplinary
Timo J. Doerries, Ralf Metzler, Aleksei Chechkin
Summary: This article examines the transport of diffusive particles switching between mobile and immobile states with finite rates. The study focuses on the impact of advection on density functions and mean squared displacements (MSDs). Significant anomalous diffusion with cubic scaling in time of the MSD is found at intermediate time scales for high Peclet numbers. This cubic scaling is present for both short and long mean residence times in the immobile state. The study also reveals the newly observed phenomenon of advection-induced subdiffusion for immobilized tracers in the presence of high Peclet numbers. Additionally, the effective advection velocity is reduced in the long-time limit, while the MSD is enhanced by advection. The physical mechanisms behind the emergence of non-Gaussian density functions and the characteristics of the MSD are explored.
NEW JOURNAL OF PHYSICS
(2023)
Article
Physics, Multidisciplinary
Philipp G. Meyer, Ralf Metzler
Summary: In this study, we investigate the overdamped dynamics of various stochastic processes under confinement of an harmonic potential. We analyze the impact of both static and dynamic noise on the dynamics of pure processes and find that noise poses challenges for process inference. We observe that static noise leads to subdiffusive behavior, while dynamic noise results in superdiffusive behavior.
NEW JOURNAL OF PHYSICS
(2023)
Article
Mathematics, Applied
Joanna Janczura, Marcin Magdziarz, Ralf Metzler
Summary: Modern experiments often generate extensive data on the diffusive dynamics of tracer particles, many of which deviate from the laws of Brownian motion. In this study, we focus on the anomalous dynamics of confined tracer particles and propose new estimators for the parameters. By calculating the empirical quadratic variation of a single trajectory, we are able to recover the subordination process governing the particle motion and use it for parameter estimation.
Article
Mathematics, Interdisciplinary Applications
Petar Jolakoski, Arnab Pal, Trifce Sandev, Ljupco Kocarev, Ralf Metzler, Viktor Stojkoski
Summary: Detailed knowledge of individual income dynamics is crucial for investigating the existence of the American dream and understanding the potential for improving income during one's working life. This study develops a framework that disaggregates the temporal properties of income at the individual level, overcoming the limitations of previous methods that rely on transition matrices. The framework, based on the concept of First Passage Time in a stochastic process, provides improved and more granular estimates of income dynamics. The results contribute to our understanding of income dynamics in real economies and offer tools for policy interventions.
CHAOS SOLITONS & FRACTALS
(2023)
Article
Physics, Condensed Matter
Ekrem Aydiner, Andrey G. Cherstvy, Ralf Metzler, Igor M. Sokolov
Summary: In this study, we examine the behavior of a kinetic exchange-trading model under various initial distributions of money using Monte-Carlo simulations. Our findings indicate that the Pareto laws and their exponents show little sensitivity to the initial conditions, regardless of whether the system is closed or open.
EUROPEAN PHYSICAL JOURNAL B
(2023)
Article
Chemistry, Physical
Denys Biriukov, Matti Javanainen
Summary: The routinely used periodic boundary conditions for molecular simulations of asymmetric lipid membranes and solvent environments are complicated. This study presents a method to efficiently model lipid membrane and solvent asymmetry using a single lipid bilayer and an inverted flat-bottom potential to restrain ions and solutes to only interact with the relevant leaflet. The method is validated and discussed in terms of limitations, computational efficiency, and a step-by-step guide for simulation setup.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Matti Javanainen, Peter Heftberger, Jesper J. Madsen, Markus S. Miettinen, Georg Pabst, O. H. Samuli Ollila
Summary: Cholesterol plays a critical role in biomembranes, affecting their structure and dynamics. Molecular dynamics simulations are important tools for studying these effects; however, different force fields yield different predictions. In this study, we systematically evaluated the performance of commonly used force fields in describing the structure and dynamics of binary mixtures of palmitoyloleoylphosphatidylcholine (POPC) and cholesterol, using quantitative quality measures.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Physics, Multidisciplinary
Jakub Slezak, Ralf Metzler
Summary: We introduce a stochastic process called incremental multifractional Brownian motion (IMFBM), which behaves locally like fractional Brownian motion with varying Hurst exponent and diffusivity. We derive formulas for the mean squared displacement and correlations of IMFBM, which are simple and elementary. We also provide simulation comparisons and estimation methods for IMFBM. This mathematically simple process is valuable in understanding anomalous diffusion dynamics in changing environments, such as viscoelastic systems or actively moving particles.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2023)
Article
Chemistry, Physical
Petro Khoroshyy, Hector Martinez-Seara, Jitka Myskova, Josef Lazar
Summary: This study investigates the dynamics of transition dipole moments (TDMs) in fluorescent proteins (FPs) using time-resolved fluorescence polarization measurements and molecular dynamics simulations. The results show significant differences in the orientation of the excitation and emission TDMs in the investigated FPs, but these differences are largely attributed to the rapid motions of fluorophores within the FP molecular framework. These findings provide insights for improved determinations of orientational distributions of FP molecules and more accurate interpretations of fluorescence resonance energy transfer (FRET) observations.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Sudeep Karki, Matti Javanainen, Shahid Rehan, Dale Tranter, Juho Kellosalo, Juha Huiskonen, Lotta Happonen, Ville Paavilainen
Summary: This study reveals the mechanism by which TRAP assists in polypeptide translocation by presenting the structure of the core Sec61/TRAP complex bound to a mammalian ribosome using cryo-EM.
