Article
Biochemistry & Molecular Biology
Magdalena Przybylo, Dominik Drabik, Joanna Doskocz, Ales Iglic, Marek Langner
Summary: The study found that the spontaneous formation of lipid pores is correlated with the mechanical properties of the membrane, depending on the composition of the lipid bilayer and the concentration of osmotically active compounds. Using liposomes as a model, it was demonstrated that the probability of lipid pores opening is correlated with membrane bending rigidity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Valerij S. Sokolov, Vsevolod Yu. Tashkin, Darya D. Zykova, Yulia V. Kharitonova, Timur R. Galimzyanov, Oleg V. Batishchev, Maria Joao Moreno
Summary: The lateral transport and release of protons at the water-membrane interface are important for cell bioenergetics. In this study, the kinetics of protons released from MNPS at the surface of a BLM were experimentally measured. A theoretical model describing the binding and release of protons at the membrane surface was developed. The results showed that the concentration of protons in the unstirred water layer near the BLM plays a crucial role in the rate-limiting step of proton release.
Article
Materials Science, Multidisciplinary
Orion Shih, Yi-Qi Yeh, Kuei-Fen Liao, Kun-Mou Li, Jia-Yin Tsai, Chieh-Chin Li, Yun-Wei Chiang, Richard K. Heenan, Yuh-Ju Sun, U-Ser Jeng
Summary: This study reveals the conformations and compositions of a proton-translocating pyrophosphatase Vigna radiata H+-PPase (VrPPase) in either detergent molecules or lipid nanodisc using SEC-SAXS, providing a deeper understanding of membrane-protein complexes.
MATERIALS CHEMISTRY AND PHYSICS
(2023)
Article
Electrochemistry
ZhangFei Su, Barbara Goodall, J. Jay Leitch, Jacek Lipkowski
Summary: The ion channel properties of gramicidin A in a model floating bilayer lipid membrane were studied, showing that the transport of Na+ across the membrane is independent of the transport of the counterion and the conductivity of the gA sodium channel depends on the transmembrane potential, with more gA molecules inserting into the bilayer as the transmembrane potential decreases.
ELECTROCHIMICA ACTA
(2021)
Article
Green & Sustainable Science & Technology
Qingting Liu, Xiaohe Wang, Xiaoxiao Zhang, Zhiwei Ling, Wenzhuo Wu, Xudong Fu, Rong Zhang, Shengfei Hu, Xiao Li, Feng Zhao, Xujin Bao
Summary: Polyethyleneimine-filled sepiolite nanorods (PEI@SNR)-embedded poly(2,5-benzimidazole) composites (ABPBI/PEI@SNR) were synthesized to enhance the proton conductivity and stability of proton-exchange membrane fuel cells (PEMFCs). The composite membranes showed improved thermal stability and achieved high proton conductivities from room temperature to 200 degrees C. The cell performance of the composite membrane-based PEMFCs was significantly better than previously reported zeolite-embedded membranes.
JOURNAL OF CLEANER PRODUCTION
(2022)
Article
Chemistry, Physical
Liming Guan, Beidou Guo, Xinrui Jia, Guancai Xia, Jian Ru Gong
Summary: Graphene monolayers exhibit permeability to thermal protons and impermeability to other atoms, showing potential applications in fuel cell technologies and hydrogen isotope separation. The giant photoeffect in proton transport through catalytically activated graphene membranes is attributed to the synergy between illumination and catalytically active metals, as well as the presence of long-lived hot electrons and a fast proton transport rate. Additionally, the metal catalyst increases the rate of the reaction by increasing the number of successful collisions between the reactants, leading to a significant photoeffect in improving the efficiency of photo(electro)catalytic reactions.
ACTA PHYSICO-CHIMICA SINICA
(2021)
Article
Biophysics
Olivier Soubias, Alexander J. Sodt, Walter E. Teague, Kirk G. Hines, Klaus Gawrisch
Summary: We investigated the influence of cholesterol-induced changes in bilayer thickness on the function of G-protein-coupled receptor (GPCR) rhodopsin. The equilibrium between metarhodopsin-I (MI) and metarhodopsin-II (MII) was monitored using UV-visible spectroscopy, and the ordering of hydrocarbon chains was probed using 2H-NMR. Addition of cholesterol shifted the equilibrium towards MII for thinner bilayers and towards MI for thicker bilayers, and small changes in bilayer thickness within the protein hydrophobic thickness range had drastic effects on MII formation. The interplay between bilayer and protein thickness, induced by cholesterol, resulted in significant swings of the MI-MII equilibrium in membranes of physiological thickness.
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Physical
Sungyu Choi, Sang-Hun Shin, Dong-Hyun Lee, Gisu Doo, Dong Wook Lee, Jonghyun Hyun, Jang Yong Lee, Hee-Tak Kim
Summary: The study introduces a radical-scavenger-embedded interlocking interfacial layer (IIL) to address delamination issue between hydrocarbon membranes and Nafion-based catalyst layers. The ball-socket joint structure of the IIL enables mechanical interlocking at the interface, with cerium oxide acting as a radical scavenger to prevent hydrothermal degradation of the IIL. The IIL-based PEMWE system operates for more than 500 hours with lower polarization compared to state-of-the-art hydrocarbon-based and Nafion-based PEMWE systems, marking an important milestone for cost-effective PEMWE system development.
JOURNAL OF MATERIALS CHEMISTRY A
(2022)
Review
Physiology
Manuel A. Anderegg, Gergely Gyimesi, Tin Manh Ho, Matthias A. Hediger, Daniel G. Fuster
Summary: This review summarizes the structure, function, and expression regulation of the SLC9B subfamily members, focusing primarily on the better-studied SLC9B paralog, NHA2. The potential of the SLC9B subfamily as drug targets is also reviewed.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Chemistry, Physical
Shubo Wang, Yuan Lin, Jian Yang, Lei Shi, Guang Yang, Xupin Zhuang, Zhenhuan Li
Summary: Composite PEMs with blend nanofibers of cellulose and UiO-66-NH2 embedded in sulfonated polysulfone matrix show high proton conductivity, low methanol permeability, and low swelling ratio. They have great potential for use as proton-conducting nanofillers in fuel cell PEMs.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2021)
Article
Engineering, Chemical
S. S. Melnikov, E. N. Nosova, E. D. Melnikova, V. Zabolotsky
Summary: This study demonstrates the potential of enhancing selectivity in ion separation using a bilayer membrane during electrodialysis, particularly in a mixed mode. The permselectivity coefficient can be significantly increased with the use of a bilayer membrane, showing specific selectivity between singly charged ions.
SEPARATION AND PURIFICATION TECHNOLOGY
(2021)
Review
Chemistry, Physical
Lin Chen, Yongwen Ren, Faying Fan, Tianyuan Wu, Zhe Wang, Yaojian Zhang, Jingwen Zhao, Guanglei Cui
Summary: Proton exchange membrane fuel cells are promising electrochemical energy conversion systems with high power density and minimal pollution. However, developing proton exchange membranes with satisfactory properties and competitive prices for commercialization remains a critical challenge. Constructing nanoscale artificial frameworks in PEMs contributes to the formation of proton transport channels. Yet, there is still a lack of adequate summary on this topic.
JOURNAL OF POWER SOURCES
(2023)
Article
Chemistry, Physical
Chen Qu, Riccardo Conte, Paul L. Houston, Joel M. Bowman
Summary: A full-dimensional potential energy surface for acetylacetone was presented using full and fragmented permutationally invariant polynomial approaches, showing tunneling splitting at different barrier heights. Calculations of electronic barrier height for H-atom transfer and splitting values were conducted using various methods, with results indicating fast evaluation of the fragmented surface.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Przemyslaw Jurczak, Kosma Szutkowski, Slawomir Lach, Stefan Jurga, Paulina Czaplewska, Aneta Szymanska, Igor Zhukov
Summary: Studying the mechanisms behind amyloid-based diseases can help identify future treatment targets, but the complexity and interactions of proteins responsible for fibril formation make it a challenging and time-consuming task. Human cystatin C, a cysteine-protease inhibitor, tends to form fibrils under certain stimuli, potentially regulated by cellular components with the cell membrane playing a key role in the oligomerization pathway. The use of phospholipid liposomes as membrane mimetics provides a promising alternative for studying protein-mimetic interactions.
Article
Chemistry, Multidisciplinary
Dawei Kang, Zheng-Wei Zuo, Zhaowu Wang, Weiwei Ju
Summary: By tuning the interlayer twist angle, a new degree of freedom is provided to explore the excellent properties of two dimensional layered materials, such as twisted bilayer SiC. The interplay of van der Waals interactions and strain induces dramatic displacements, while strain soliton networks separate stacking domains. The moire-pattern-induced properties of twisted bilayer SiC show promise for applications in nanoscale electronic and optical devices.
Article
Chemistry, Physical
Till Kirsch, Jogvan Magnus Haugaard Olsen, Viacheslav Bolnykh, Simone Meloni, Emiliano Ippoliti, Ursula Rothlisberger, Michele Cascella, Juergen Gauss
Summary: This study presents an interface of the wavefunction-based quantum chemical software CFOUR to the multiscale modeling framework MiMiC and validates its robustness and performance, including fast convergence and optimal energy conservation. The compatibility with the use of a QM/QM multiple time-step algorithm for reducing the cost of simulations using higher level wavefunction-based approaches is also pointed out.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Oscar Palomino-Hernandez, Carlo Santambrogio, Giulia Rossetti, Claudio O. Fernandez, Rita Grandori, Paolo Carloni
Summary: Mass spectrometry and single molecule force microscopy are experimental techniques that provide structural information on intrinsically disordered proteins (IDPs). This study analyzed molecular dynamics simulation data and experimental results to describe the main conformational ensemble of human alpha synuclein (AS) and shed light on its intramolecular interactions and overall compactness.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Medicinal
Mirko Paulikat, Daniele Vitone, Florian K. Schackert, Nils Schuth, Alessandra Barbanente, GiovanniMaria Piccini, Emiliano Ippoliti, Giulia Rossetti, Adam H. Clark, Maarten Nachtegaal, Michael Haumann, Holger Dau, Paolo Carloni, Silvano Geremia, Rita De Zorzi, Liliana Quintanar, Fabio Arnesano
Summary: This study elucidated the structural determinants of zinc-chloroquine interactions and zinc distribution in cells using computational and experimental methods. Chloroquine binds zinc through the quinoline ring nitrogen, forming tetrahedral complexes, but loses metal coordination at low pH. The findings have implications for other metal-targeting drugs and bioinorganic systems.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Ke Zuo, Riccardo Capelli, Giulia Rossetti, Rachel Nechushtai, Paolo Carloni
Summary: Human NEET proteins containing iron-sulfur clusters have been identified as potential drug targets for mitochondrial dysfunction-related diseases. However, the lack of understanding of ligand binding to the cytoplasmic domain of NEET protein has hindered rational drug design approaches.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Henri-Baptiste Marjault, Sohn Yang-Sung, Ke Zuo, Paolo Carloni, Ron Mittler, Rachel Nechushtai
Summary: This study identified a new human mitoNEET binding ligand (NTS-01) that specifically binds to the human mNT protein and stabilizes its [2Fe-2S] clusters under oxidative conditions in vitro. Treatment with NTS-01 induces mitochondrial fragmentation and reduces ovarian cancer cell proliferation. The NTS-01 molecule represents a promising lead compound for further drug design studies against ovarian cancer.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Mirko Paulikat, Juan Aranda, Emiliano Ippoliti, Modesto Orozco, Paolo Carloni
Summary: The authors used classical molecular dynamics and quantum mechanics/molecular mechanics methods to investigate proton transfer processes in N-ESI/IM-MS, and validated the simulation results with experimental data. The study revealed that the distribution of protons depends on the hydration level of the analytes and the size of droplets formed during electrospray experiments.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Medicinal
Bharath Raghavan, Mirko Paulikat, Katya Ahmad, Lara Callea, Andrea Rizzi, Emiliano Ippoliti, Davide Mandelli, Laura Bonati, Marco De Vivo, Paolo Carloni
Summary: Currently, in silico drug design in the initial stages of drug discovery can benefit from first-principle Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics (MD) simulations in explicit solvent, but many applications are limited by the short time scales that this approach can cover. The development of scalable first principle QM/MM MD interfaces that fully exploit current exascale machines is crucial in overcoming this problem and allowing for the study of ligand binding to protein with first principle accuracy. This study showcases the use of the Multiscale Modeling in Computational Chemistry (MiMiC) QM/MM framework, which demonstrates strong scaling and parallel efficiency of >70% up to >80,000 cores, making it a promising candidate for exascale applications.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Bharath Raghavan, Florian K. Schackert, Andrea Levy, Sophia K. Johnson, Emiliano Ippoliti, Davide Mandelli, Jogvan Magnus Haugaard Olsen, Ursula Rothlisberger, Paolo Carloni
Summary: MiMiC is a flexible and scalable multiscale modeling framework that combines quantum mechanics (QM) and molecular mechanics (MM) codes. The paragraph introduces MiMiCPy, a user-friendly tool written in Python 3 that automates the preparation of MiMiC input files. It also highlights the modular structure of MiMiCPy, allowing for easy extensions to new program formats.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Florian Karl Schackert, Johann Biedermann, Saeid Abdolvand, Sonja Minniberger, Chen Song, Andrew J. R. Plested, Paolo Carloni, Han Sun
Summary: This study investigates calcium conduction in calcium-permeable AMPAR using Molecular Dynamics (MD) simulations and multiscale Quantum Mechanics/Molecular Mechanics (QM/MM) simulations. The results explain the distinct calcium permeability in different RNA-edited forms of GluA2 and provide unprecedented insights into Ca(2+) permeation mechanisms in AMPARs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Benjamin Philipp Joseph, Verena Weber, Lisa Knuepfer, Alejandro Giorgetti, Mercedes Alfonso-Prieto, Sybille Krauss, Paolo Carloni, Giulia Rossetti
Summary: In this study, novel HuR inhibitors were identified using a combination of chemoinformatic methods, high-throughput virtual screening, and RNA-protein pulldown assays. The 4-(2-(2,4,6-trioxotetrahydropyrimidin-5(2H)-ylidene)hydrazineyl)benzoate ligand showed dose-dependent inhibition of HuR binding. This novel chemical scaffold provides a new avenue for the design of pharmaceutical agents targeting HuR.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Jin Zhang, Dan Song, Florian Karl Schackert, Juan Li, Shengqi Xiang, Changlin Tian, Weimin Gong, Paolo Carloni, Mercedes Alfonso-Prieto, Chaowei Shi
Summary: In this study, ssNMR and molecular dynamics simulations were used to investigate the fluoride channel Fluc-Ec1 in phospholipid bilayers. Previously unidentified fluoride binding sites and a water molecule binding site in the polar track were discovered. Additionally, a dynamic hotspot at loop 1 was observed, suggesting that loop 1 is a key determinant for channel gating.
Article
Chemistry, Multidisciplinary
Jonas Gossen, Rui Pedro Ribeiro, Dirk Bier, Bernd Neumaier, Paolo Carloni, Alejandro Giorgetti, Giulia Rossetti
Summary: This study presents an approach that combines structural data with a random forest agonist/antagonist classifier and a signal-transduction kinetic model to identify novel chemotype ligands. As a test case, the approach is applied to identify novel antagonists of the human adenosine transmembrane receptor type 2A, a target against Parkinson's disease and cancer.
Article
Chemistry, Physical
Ke Zuo, Agata Kranjc, Riccardo Capelli, Giulia Rossetti, Rachel Nechushtai, Paolo Carloni
Summary: This study introduces a new drug design approach that combines metadynamics free energy methods and experimental structural information to identify ligand poses on protein surfaces.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)