Article
Biochemical Research Methods
Alican Gulsevin, Jens Meiler
Summary: The AmphiScan protocol is a tool developed to predict the interaction of amphipathic helices with membranes, with features of fast, accurate, and highly customizable.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Chemistry, Physical
Masanori Hashimoto, Koichi Miyagawa, Manish Singh, Kota Katayama, Mitsuo Shoji, Yuji Furutani, Yasuteru Shigeta, Hideki Kandori
Summary: Heliorhodopsins (HeRs), a recently discovered family of rhodopsins, have an inverted membrane topology compared to other rhodopsins. ATR-FTIR spectroscopy studies have demonstrated the binding of Zn2+ to HeR, specifically affecting the structure and function. The specific binding site of Zn2+ was found to be located at the cytoplasmic side of TaHeR.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Engineering, Chemical
Na Sui, Shukai Miao, Kaihui Cui, Tong Li, Haitao Zhou, Kun Huang
Summary: Efficient separation of Pr3+/Nd3+ was achieved in this study by implementing a kinetic extraction strategy in systems with different salting-out agents. The experimental results showed that the separation coefficient can be higher than 8. The enhancing effect on separation of Pr3+/Nd3+ from different salting-out agents was related to the salting-out effect, which was influenced by the type and concentration of the agents.
SEPARATION AND PURIFICATION TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yaxin Wang, Binghong Xu, Sen Ma, Hao Wang, Luqing Shang, Cheng Zhu, Sheng Ye
Summary: This study presents the design and examination of five new inhibitors targeting the 3C-Like protease of SARS-CoV-2. The inhibitors showed nanomolar inhibitory capacity and reduced viral loads, highlighting their potential as broad-spectrum antiviral drugs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biophysics
Gabriel C. A. da Hora, John D. M. Nguyen, Jessica M. J. Swanson
Summary: This study investigates the association and permeation of Mycolactone through models of the mammalian endoplasmic reticulum (ER) and plasma membranes (PMs). The research reveals that Mycolactone exhibits different binding and permeation mechanisms in the ER membrane compared to the PMs. Increased order and interactions with unsaturated lipid tails stabilize the toxin in the ER membrane, while disruption of lipid packing destabilizes it in the PMs.
BIOPHYSICAL JOURNAL
(2022)
Article
Biophysics
Yuliang Sun, Zhixiong Deng, Xukai Jiang, Bing Yuan, Kai Yang
Summary: The study revealed that PMB has a preference for specific lipid species in its interaction with different membrane systems, leading to complex membrane interaction states. These findings provide insights into the action mechanism of PMB at a membrane level, laying the foundation for developing novel and safer polymyxin strategies for better clinical use.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2022)
Article
Chemistry, Physical
Natasha H. Rhys, David J. Barlow, M. Jayne Lawrence, Christian D. Lorenz
Summary: This study used molecular dynamics simulations to investigate the interactions between different diols with varying carbon chain lengths and hydroxylation patterns and a DMPC monolayer, finding that shorter diols can penetrate deeper into the lipid monolayer and disrupt its structure, while all diols studied formed hydrogen-bonded networks with DMPC head groups.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Tanusree Mookherjee, Angshuman Bagchi, Rita Ghosh
Summary: This study reveals a possible molecular mechanism of how the peptide circPPP1R12A can promote cancer by interfering with the Mst pathway. The peptide was found to bind to Mst1/2 proteins, preventing their interactions with Sav1 and inhibiting the activation of the Mst pathway.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Ainara Claveras Cabezudo, Christina Athanasiou, Alexandros Tsengenes, Rebecca C. Wade
Summary: Reducing the nonbonded interactions between protein and water enables protein encapsulation in phospholipid micelles and bilayers.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Physics, Multidisciplinary
D. Minogue, M. R. Eskildsen, C. Reichhardt, C. J. O. Reichhardt
Summary: Numerical simulations were conducted to investigate the transition dynamics between metastable and ground state vortex lattice phases in a system with combined sixfold and twelvefold vortex-vortex interactions. The study revealed that the metastable state can decay by changing the vortex-vortex interaction and applying a drive that mimics an oscillating magnetic field.
NEW JOURNAL OF PHYSICS
(2023)
Article
Multidisciplinary Sciences
N. Gao, Z. W. Yao, G. H. Lu, H. Q. Deng, F. Gao
Summary: The study found a new diffusion mechanism for <100> interstitial dislocation loops in BCC iron using self-adaptive accelerated molecular dynamics, which represents a significant step towards understanding the mechanical behavior and microstructure evolution of the material.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Sergio Perez-Conesa, Eric G. Keeler, Dongyu Zhang, Lucie Delemotte, Ann E. McDermott
Summary: The pH-gated prokaryotic channel KcsA has been extensively studied as the first potassium channel with an x-ray structure determined, but questions related to the allosteric coupling between its gates remain open. Solid-state nuclear magnetic resonance (SSNMR) can provide insights into the molecular basis of activation mechanisms by studying the wild-type protein under activating conditions, and simulation techniques such as molecular dynamics (MD) simulations can help determine the activated state captured in SSNMR experiments.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Materials Science, Paper & Wood
Bing Zhang, Jie-qin Yang, Ying Liu, Bin Hu, Yang Yang, Li Zhao, Qiang Lu
Summary: This study investigates the characteristics of cellulose-lignin and lignin-lignin interactions at different temperatures using molecular dynamics simulations. The results reveal that the temperature plays a crucial role in these interactions, which are influenced by the degree of cellulose surface solvation and lignin self-aggregation.
Article
Chemistry, Physical
Antonia Statt, Devon C. Kleeblatt, Wesley F. Reinhart
Summary: This study applies unsupervised machine learning to analyze soft matter systems, providing new insights into the structure of large-scale, disordered aggregates formed by sequence-defined macromolecules. By classifying the global aggregate structure directly using descriptions of local environments, a deeper understanding of the possible self-assembled structures and their relationships is obtained.
Article
Chemistry, Physical
Delin Sun, Stewart He, W. F. Drew Bennett, Camille L. Bilodeau, Olaf S. Andersen, Felice C. Lightstone, Helgi I. Ingolfsson
Summary: Research on gramicidin A (gA) subunit dimerization in lipid bilayers revealed a dimer structure with two subunits connected by six hydrogen bonds, as well as two additional dimer structures stabilized by four or two hydrogen bonds. The temporal evolution study found that the dimer can form directly with six hydrogen bonds, or through paths involving two or four hydrogen bonds.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Biochemistry & Molecular Biology
David A. Collu, Cristina Carucci, Marco Piludu, Drew F. Parsons, Andrea Salis
Summary: Ultra-thin nanosheets of two Aurivillius oxides, BWO and BMO, were synthesized and a new procedure for efficient photocatalytic BMO nanosheets was developed. Both BWO and BMO demonstrated effective degradation of the water pollutant dye MG, with BMO showing higher removal rates and stability. Additionally, adsorption contributed to MG removal differently for the two photocatalysts, indicating distinct degradation mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Federico Fiori, Hind Moukham, Federico Olia, Davide Piras, Sergio Ledda, Andrea Salis, Luigi Stagi, Luca Malfatti, Plinio Innocenzi
Summary: This study synthesized two carbon dots and tested their cellular uptake and bioimaging performance in vitro. The results showed that these carbon dots are highly biocompatible, exhibit high photostability, and can effectively be taken up by cells for bioimaging purposes.
Article
Multidisciplinary Sciences
H. Jonathan G. Lindstrom, Ran Friedman
Summary: Targeted therapies for CML are effective but rarely curative. Drug resistance is a major cause of death in CML, and preventing resistance is crucial. Drug rotation has been theorized as a way to delay resistance, and in vitro testing has shown some promising results in a CML cell line.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Baswanth Oruganti, Erik Lindahl, Jingmei Yang, Wahid Amiri, Rezwan Rahimullah, Ran Friedman
Summary: This study explores the effectiveness of combination therapies using the recently developed allosteric inhibitor asciminib with the ATP-competitive inhibitors nilotinib and dasatinib in inhibiting the BCR-Abl1 kinase activity in CML cell lines. The results show that asciminib significantly enhances the inhibitory activity of nilotinib, but not of dasatinib.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Yuan Xu, Shu Zhang, Erik Lindahl, Ran Friedman, Wei Wu, Peifeng Su
Summary: In this work, a general tight-binding based energy decomposition analysis (EDA) scheme is proposed for intermolecular interactions. The scheme, known as DFTB-EDA, is capable of performing interaction analysis with different self-consistent charge (SCC) type DFTB methods. By dividing the total interaction energy into frozen, polarization, and dispersion terms, the performance of DFTB-EDA with SCC-DFTB2/3 and GFN1/2-xTB for various interaction systems is discussed and assessed.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Luisa Moretto, Marko Usaj, Oleg Matusovsky, Dilson E. Rassier, Ran Friedman, Alf Mansson
Summary: Release of Pi from the myosin active site is essential for force generation, but the mechanism behind it is not well understood. This study presents evidence for a multistep Pi-release model that reconciles conflicting views and reveals potential functional complexities.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Ran Friedman
Summary: The use of actinides for medical, scientific and technological purposes is gaining importance. Understanding their interactions with biomolecules and designing agents with high affinities require accurate reference values for actinide hydration. This study developed a set of ionic radii that enables calculations of binding energies for actinides and biomolecules.
Article
Biochemistry & Molecular Biology
Magdalena Szota, Pawel Wolski, Cristina Carucci, Flaminia Cesare Marincola, Jacek Gurgul, Tomasz Panczyk, Andrea Salis, Barbara Jachimska
Summary: This study investigates the effect of the protonation degree of G4PAMAM dendrimer and the anticancer drug 5-fluorouracil (5FU) on the efficiency of complex formation. The most favorable conditions for constructing the G4PAMAM-5FU complex are a low degree of protonation of the dendrimer molecule with the drug simultaneously present in a deprotonated form. The formation of the stable complex is confirmed by fluorine components in the XPS spectra.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Monica Mura, Cristina Carucci, Flaminia Cesare Marincola, Maura Monduzzi, Drew F. Parsons, Andrea Salis
Summary: This study evaluates the specific effects of buffers on the thermal stability of DNA, showing that increasing buffer concentration enhances DNA stability and different buffer types have different influences.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Chemistry, Physical
Thales Souza Freire, Ignez Caracelli, Julio Zukerman-Schpector, Ran Friedman
Summary: Gilteritinib is effective in treatment of acute myeloid leukaemia (AML) by inhibiting the FLT3/ITD mutated protein. However, tumour cells develop resistance to gilteritinib due to mutations in the drug target. We used a computer-aided approach to understand the resistance mechanism and found that the mutations F691L and D698N lead to higher activation energy barrier, making mutant enzymes more active. This suggests that tyrosine kinases contribute to resistance against type 1 and type 2 kinase inhibitors.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biophysics
Monica Mura, Ben Humphreys, Jennifer Gilbert, Andrea Salis, Tommy Nylander
Summary: Knowledge of DNA-lipid layer interactions is crucial for various applications. The ionic composition of the solvent greatly affects these interactions. Through experimental measurements, it was found that pH, buffers, and alkali metal chloride salts have an impact on the interaction between DNA and lipid bilayers.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2023)
Article
Chemistry, Physical
Davide Tocco, David Chelazzi, Rosangela Mastrangelo, Andrea Casini, Andrea Salis, Emiliano Fratini, Piero Baglioni
Summary: In this study, the location and conformational changes of proteins in Metal Organic Frameworks (MOFs) were investigated. Bovine serum albumin (BSA) was immobilized in two different zeolitic imidazolate frameworks (ZIF-zni and ZIF-8), forming micro-to nanoscale domains. The secondary structure of BSA also changed, with an increase in β-sheets and α-helices and a decrease in β-turns.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Chemistry, Inorganic & Nuclear
Giulia Rossella Delpiano, Alessandra Garau, Vito Lippolis, Joanna Izabela Lachowicz, Andrea Salis
Summary: Silica-based mesoporous materials, with metal-chelating properties, have great potential in metal recovery, sensing, and controlled storage of metal ions in industrial and mining processes.
DALTON TRANSACTIONS
(2022)
Article
Chemistry, Physical
Drew F. Parsons, Cristina Carucci, Andrea Salis
Summary: Buffer solutions not only regulate pH, but also affect the properties of protein molecules. The zeta potential of lysozyme changes significantly with different buffer solutions. Citrate buffer even causes a change in the sign of zeta potential. A theoretical model has been proposed to explain these buffer-specific effects, including the role of small cosmotropic ions. Experimental zeta potentials can be satisfactorily reproduced using this model.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Thermodynamics
Gabriele Olla, Daniela Meloni, Andrea Salis, Guido Ennas, Alessandra Piras, Silvia Porcedda
Summary: This study investigated mixtures containing 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide and ethanol or N-methy1-2-pyrrolidone, revealing the changes in excess molar enthalpies and excess partial molar enthalpies of components over the entire mole fraction range, as well as the thermal effects under extreme dilution conditions.
JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY
(2022)