Article
Materials Science, Multidisciplinary
Leonhard H. Urner, Ehsan Mohammadifar, Kai Ludwig, Denis Shutin, Francesco Fiorentino, Idlir Liko, Fernando G. Almeida, Daniel Kutifa, Rainer Haag, Carol Robinson
Summary: dPGS-PCL serves as a novel purification agent for membrane protein research, allowing for the study and purification of membrane proteins. Results demonstrate that protein yields and delipidation outcomes are influenced by the properties of membrane mimetics and membranes.
ACS APPLIED POLYMER MATERIALS
(2021)
Article
Engineering, Environmental
Anton Ribbenstedt, James M. Armitage, Felix Gunther, Jon A. Arnot, Steven T. J. Droge, Michael S. McLachlan
Summary: This study measured the bioconcentration factors (BCFs) of 10 anionic surfactants with different alkyl chain lengths and polar head groups in rainbow trout. The results showed that biotransformation was the dominant elimination mechanism, and there was a strong positive correlation between the BCF and the membrane lipid-water distribution ratio. The dataset is important for evaluating computational and experimental methods for assessing bioaccumulation.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jie Yang, Shilin Zhu, Hongli Zhang
Summary: This study presents a facile and patternable electrostatic assembly strategy to fabricate a highly permselective and anti-bacterial 2D nanofiltration membrane based on MXene. The Ti3C2Tx/PDDA composite membrane exhibits higher water permeance and rejection for MgCl2. It also demonstrates good resistance to swelling, long-term stability, high flux recovery ratio, and excellent anti-adhesive and anti-microbial activity against E. coli and S. aureus.
Article
Biochemistry & Molecular Biology
Kathleen W. Swana, Terri A. Camesano, Ramanathan Nagarajan
Summary: Supported lipid bilayers (SLBs) on quartz crystals are versatile model systems for studying cell membrane behavior. This study successfully formed entirely anionic SLBs by treating the quartz crystal, which provides valuable model systems for studying interactions with Gram-positive bacterial membranes.
Article
Biochemistry & Molecular Biology
Chad A. Sallaberry, Barbie J. Voss, William B. Stone, Fabiola Estrada, Advita Bhatia, J. Daniel Soto, Charles W. Griffin, Crystal M. Vander Zanden
Summary: This study investigates the effects of curcumin on amyloid beta (A beta) aggregation in Alzheimer's disease. The results show that curcumin can embed into anionic membranes, causing membrane thinning and reducing A beta accumulation on the membrane. Molecular simulations suggest that curcumin clusters near phenylalanine residues on the membrane-embedded A beta structure. Overall, curcumin inhibits A beta interactions with membranes through a combination of altered membrane structure and interactions with the A beta surface.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Biochemical Research Methods
Mckenna G. G. Hanson, Christian J. J. Grimme, Nicholas W. W. Kreofsky, Sidharth Panda, Theresa M. M. Reineke
Summary: Nucleic acid-based medicines and vaccines are playing an increasingly important role in our therapeutic toolbox. Antisense oligonucleotides (ASOs) are a key genetic medicine that can downregulate protein production. However, they need a delivery vehicle to enter cells. This study aimed to develop a method to rapidly discover new micelle formulations using mixed diblock polymers, which show improved delivery efficiency compared to linear nonmicelle variants.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Chemistry, Analytical
Sue Woon Tan, Won-Yong Jeon, Bo Kyeong Yoon, Joshua A. Jackman
Summary: Researchers used electrochemical impedance spectroscopy (EIS) to study the membrane-disruptive properties of antimicrobial lipids and surfactants. The results showed that glycerol monolaurate (GML) caused irreversible membrane damage, while lauric acid (LA) had mainly reversible effects on the membrane. Additionally, sodium dodecyl sulfate (SDS) could cause membrane solubilization in micellar form and membrane defect formation in monomeric form.
Review
Nanoscience & Nanotechnology
Koushik Debnath, Kevin Las Heras, Ambar Rivera, Stephen Lenzini, Jae-Won Shin
Summary: This Review discusses the role of extracellular vesicles (EVs) in the context of the extracellular matrix and how understanding their interactions inspires materials design for controlling EV release, retention, and production for various biological and therapeutic applications.
NATURE REVIEWS MATERIALS
(2023)
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)
Review
Biochemistry & Molecular Biology
Jie Gao, Ruihan Hou, Long Li, Jinglei Hu
Summary: Integral or peripheral membrane proteins, or protein oligomers often interact closely on cell membranes and perform biological tasks collectively. In addition to electrostatic and van der Waals interactions, these proteins also experience membrane-mediated interactions, which are crucial for their functionality and originate from perturbation of lipid membranes by protein inclusions. This type of interaction has been the subject of intensive research in membrane biophysics, with both theoretical and numerical studies conducted for membrane proteins and nanoparticles bound to lipid membranes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Cell Biology
Jagjeet Singh, Paulomi Sanghavi, Roop Mallik
Summary: Lipid droplets (LDs) are cellular organelles that store neutral lipids and play significant roles in protein sequestration, lipid supply, viral replication, and other important physiological functions. Motor protein-driven motion along microtubules facilitates LD-organelle interactions.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Cell Biology
Sabrina Chumpen Ramirez, Ruben Gomez-Sanchez, Pauline Verlhac, Ralph Hardenberg, Eleonora Margheritis, Katia Cosentino, Fulvio Reggiori, Christian Ungermann
Summary: During autophagy, Atg9 plays a critical role in establishing membrane contact sites and promoting lipid transfer. However, a specific mutation in Atg9 can impair autophagy progression by blocking phagophore expansion.
Article
Biochemistry & Molecular Biology
Bineet Sharma, Hossein Moghimianavval, Sung-Won Hwang, Allen P. Liu
Summary: This review discusses the importance of model membranes made of phospholipids for studying biological processes, focusing on key biological events involving membranes. The article also reviews different lipid bilayer platforms used for incorporating membrane proteins, methods for membrane fusion reconstitution, and the challenges and opportunities of intercellular communication between synthetic cells and natural cells.
Article
Chemistry, Physical
Nguyet-Minh Nguyen Le, Christian Steinbring, Bao Le-Vinh, Aamir Jalil, Barbara Matuszczak, Andreas Bernkop-Schnuerch
Summary: This study aimed to develop a drug delivery system that changes the zeta potential by decorating lipid-based nanocarriers with a polycationic cell penetrating peptide (CPP) and masking these cationic substructures with polyphosphates. The polyphosphate-coated PLL-decorated nanocarriers showed improved cellular uptake and significant conversion of zeta potential.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Akiko Yoshihara, Noriko Nagata, Hajime Wada, Koichi Kobayashi
Summary: The thylakoid membrane of cyanobacteria, plants, and algae mainly consists of uncharged galactolipids, but also includes anionic lipids such as sulfoquinovosyldiacylglycerol (SQDG) and phosphatidylglycerol (PG). Phosphatidylglycerol (PG) is essential for photosynthesis in all examined organisms, while the importance of SQDG varies. Additionally, plants produce another anionic lipid, glucuronosyldiacylglycerol (GlcADG), under phosphorus starvation, with its role still unclear. Studies on Arabidopsis mutants lacking PG and SQDG biosynthesis in plastids showed developmental defects in both photosynthetic and non-photosynthetic organs, indicating the pleiotropic role of these lipids. SQDG, but not GlcADG, is crucial for complementing PG in photosynthesis under PG-deficient conditions like phosphorus starvation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Correction
Chemistry, Analytical
Adrian Cernescu, Michal Szuwarzynski, Urszula Kwolek, Pawel Wydro, Mariusz Kepczynski, Szczepan Zapotoczny, Maria Nowakowska, Luca Quaroni
ANALYTICAL CHEMISTRY
(2021)
Article
Dentistry, Oral Surgery & Medicine
Wojciech Wilkonski, Lidia Jamroz-Wilkonska, Mariusz Kepczynski, Szczepan Zapotoczny, Urszula Maziarz, Luciano Giardino
Summary: The study showed that irrigation protocols ended with chlorhexidine resulted in deeper sealer penetration compared to alcohol.
AUSTRALIAN ENDODONTIC JOURNAL
(2022)
Article
Neurosciences
Lukasz Chrobok, Jasmin D. Klich, Anna M. Sanetra, Jagoda S. Jeczmien-Lazur, Kamil Pradel, Katarzyna Palus-Chramiec, Mariusz Kepczynski, Hugh D. Piggins, Marian H. Lewandowski
Summary: Short-term consumption of a high-fat diet increases daytime food intake and blunts daily rhythms in NTS neuronal discharge, while also decreasing responsiveness to metabolic neuropeptides and orexin immunoreactive fibres. These alterations occur without prominent body weight gain, suggesting that a high-fat diet initially reduces activity in the dorsal vagal complex to disinhibit mechanisms that suppress daytime feeding.
JOURNAL OF PHYSIOLOGY-LONDON
(2022)
Article
Chemistry, Medicinal
Vytautas Gapsys, David F. Hahn, Gary Tresadern, David L. Mobley, Markus Rampp, Bert L. de Groot
Summary: Currently, drug design projects can benefit from molecular dynamics simulations to predict protein-ligand binding free energy accurately. By utilizing workflows based on open source software packages, it is now possible to efficiently screen hundreds of compounds in a matter of days using pre-exascale computing resources.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Medicinal
Myeongkyu Kim, Jung-Hye Ha, Joonhyeok Choi, Bo-Ram Kim, Vytautas Gapsys, Ko On Lee, Jun-Goo Jee, Kalyan S. Chakrabarti, Bert L. de Groot, Christian Griesinger, Kyoung-Seok Ryu, Donghan Lee
Summary: This study focuses on Biliverdin IX beta reductase B (BLVRB) as a novel therapeutic target for thrombocytopenia, with the goal of repurposing drugs as new inhibitors of BLVRB. Through screening a library of FDA-approved compounds, 20 potential compounds were identified with high binding affinity to BLVRB's active site. The detailed binding modes, thermodynamic properties, and complex structures of water-soluble compounds provide a foundation for further research on the effects of BLVRB on ROS accumulation and megakaryocyte differentiation, potentially leading to new treatments for platelet disorders.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Marta Z. Pacia, Natalia Chorazy, Magdalena Sternak, Benedikt Fels, Michal Pacia, Mariusz Kepczynski, Kristina Kusche-Vihrog, Stefan Chlopicki
Summary: In this study, the role of Rac1 in TNF-induced vascular inflammation was investigated. It was found that Rac1 mediated the formation of lipid droplets and nanostructural alterations associated with vascular inflammation.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Chemistry, Medicinal
Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmueller, Bert L. de Groot, Vytautas Gapsys
Summary: This study assesses the costs and efficiency of cloud computing for atomistic simulations, comparing it to traditional on-premises compute clusters. The results show that, with the optimal cloud instances, cloud computing can be as cost-efficient as on-premises clusters for generating MD trajectories. Additionally, using global cloud resources can significantly accelerate high-throughput ligand-screening.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Medicine, Research & Experimental
Wojciech Wilkonski, Lidia Jamroz-Wilkonska, Mariusz Kepczynski, Szczepan Zapotoczny, Urszula Maziarz, Janusz Opila, Jolanta Pytko-Polonczyk
Summary: This study investigated the effect of three different irrigants on the penetration of an epoxy sealer into dentinal tubules. The results showed that final irrigation with chlorhexidine resulted in the deepest penetration of the sealer, while isopropyl alcohol had the most negative impact on sealer penetration.
ADVANCES IN CLINICAL AND EXPERIMENTAL MEDICINE
(2022)
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
Kalyan S. Chakrabarti, Simon Olsson, Supriya Pratihar, Karin Giller, Kerstin Overkamp, Ko On Lee, Vytautas Gapsys, Kyoung-Seok Ryu, Bert L. de Groot, Frank Noe, Stefan Becker, Donghan Lee, Thomas R. Weikl, Christian Griesinger
Summary: The study presents a theoretical and experimental framework to investigate protein binding mechanisms on sub-millisecond timescales. Using nuclear magnetic resonance and molecular dynamics simulations, the authors find that the binding mechanism between ubiquitin and the SH3 domain is based on conformational selection.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Yuriy Khalak, Gary Tresadern, David F. Hahn, Bert L. de Groot, Vytautas Gapsys
Summary: This research explores the combination of active learning protocol with first-principles based alchemical free energy calculations to identify high affinity PDE2 inhibitors. By explicitly evaluating only a small fraction of compounds in a large chemical library, we have successfully developed an efficient protocol.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Simon Boothroyd, Pavan Kumar Behara, Owen C. Madin, David F. Hahn, Hyesu Jang, Vytautas Gapsys, Jeffrey R. Wagner, Joshua T. Horton, David L. Dotson, Matthew W. Thompson, Jessica Maat, Trevor Gokey, Lee-Ping Wang, Daniel J. Cole, Michael K. Gilson, John D. Chodera, Christopher I. Bayly, Michael R. Shirts, David L. Mobley
Summary: We introduce the OpenFF 2.0.0 small molecule force field Sage, an improved version of Parsley. It features improved LJ parameters and fitting to a larger database of quantum chemical calculations. Force field benchmarks show improved performance and estimation of physical properties. Complete data and training results are available at https://github.com/openforcefield/openff-sage.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Agata Zak, Natan Rajtar, Waldemar Kulig, Mariusz Kepczynski
Summary: This study investigates the molecular organization and properties of lipid bilayers composed of phosphatidylcholines with saturated and unsaturated acyl chains. Experimental results show that the miscibility of DOPC/DPPC bilayers is very limited below the DPPC phase transition temperature. Molecular dynamics simulations reveal that electrostatic interactions for lipid like-pairs are much stronger than that for mixed pairs, while the entropic component increases significantly with temperature. Therefore, the miscibility of phospholipids is driven by entropy.
Article
Chemistry, Physical
Carter J. Wilson, Mikko Karttunen, Bert L. de Groot, Vytautas Gapsys
Summary: The stability, solubility, and function of a protein are determined by its net charge and the protonation states of its individual residues. The study demonstrates the applicability of a nonequilibrium alchemical free energy method for accurately predicting pK(a) values, which is comparable to current state-of-the-art predictors. The research also highlights the performance disparity associated with lysine partial charges in certain models and mentions an underused fix for this issue.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Wojciech Wilkonski, Marcin Krupinski, Lidia Jamroz-Wilkonska, Mariusz Kepczynski, Szczepan Zapotoczny, Urszula Maziarz, Janusz Opila, Piotr Wychowanski, Katarzyna Brus-Sawczuk
Summary: This study compared the effect of three irrigation protocols on the penetration of epoxy sealer into dentinal tubules and two dyes used to stain the sealer. The results showed that the longest resin tags were observed in group 2, while the shortest ones were found in group 1. There were significant differences among the groups in different sections of the roots. The isopropyl alcohol at the end of the irrigating protocol did not affect the higher sealer penetration into the dentinal tubules. The hydrophobic porphyrin may be considered as the favorable dye choice for staining endodontic sealers in further studies.
APPLIED SCIENCES-BASEL
(2023)