Article
Biophysics
Abhishek Acharya, Kalyanashis Jana, Dominik Gurvic, Ulrich Zachariae, Ulrich Kleinekathofer
Summary: Predicting molecular permeability and evaluating the effect of molecular transformations on permeation rates are critical for the development of effective antibiotics. In this study, a computational approach using Brownian dynamics is proposed to obtain estimates of molecular permeability through a porin channel within hours. The method is significantly faster compared with previous approaches and shows good correlation with experimental results. The potential applications of this method in high-throughput screening for fast permeators are discussed.
BIOPHYSICAL JOURNAL
(2023)
Article
Infectious Diseases
Rajaguru Arivuselvam, Ayed A. Dera, Syed Parween Ali, Yasser Alraey, Ahmed Saif, Umme Hani, Sivaa Arumugam Ramakrishnan, Mohamed Sheik Tharik Abdul Azeeze, Raman Rajeshkumar, Aishwarya Susil, Haritha Harindranath, B. R. Prashantha Kumar
Summary: This report presents a bioactive compound, prodigiosin, isolated from a new strain of Serratia marcescens JSSCPM1. The compound's structure and antibacterial activity were determined using chromatographic methods, nuclear magnetic resonance analysis, and in silico studies. The results showed that prodigiosin has a strong binding affinity towards specific drug targets.
Article
Multidisciplinary Sciences
Oliver F. Harder, Sarah V. Barrass, Marcel Drabbels, Ulrich J. Lorenz
Summary: Microsecond time-resolved cryo-EM allows for observation of fast protein dynamics, as demonstrated by the contraction of the CCMV capsid induced by a pH jump.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Mengqi Wang, Yimeng Zhao, Yoshiki Hayashi, Koichi Ito, Motoyuki Hattori
Summary: MgtE is a Mg2+-selective channel regulated by intracellular Mg2+ concentration and plays an important role in cellular Mg2+ homeostasis. Multiple Mg2+ binding sites in MgtE family proteins have been identified, showing the conservation and diversity of the cytoplasmic Mg2+ binding site in these proteins.
ACTA BIOCHIMICA ET BIOPHYSICA SINICA
(2023)
Article
Engineering, Biomedical
Yasin Ozturk, Aliakbar Ebrahimi, Araz Norouz Dizaji, Ozge Kaygusuz, Jayesh Arun Bafna, Mathias Winterhalter, Guven Cankaya, Cihan Darcan, Fatma Dogan Guzel
Summary: The study investigates the reproducible generation of micropores in the range of 50-100 microns in diameter in a Teflon film. The multi-pulse method is more convenient for lipid bilayer formation and has a higher success rate. Experimental results show that the lipid bilayer on Teflon pores can last for more than 33 hours.
BIOMEDICAL MICRODEVICES
(2021)
Article
Chemistry, Multidisciplinary
Kenichi Umeda, Kei Kobayashi, Hirofumi Yamada
Summary: A local solvation measurement technique based on three-dimensional frequency-modulation atomic force microscopy has been successfully developed and used to investigate the molecular nanomechanics in the formation and disruption of micelles on a hydrophobic surface. It has been found that the nanomechanics depends on the form of the molecular assembly, and the hemifusion and disruption processes on the micellar surface result in higher energy dissipation compared to the monolayer surface.
Article
Chemistry, Multidisciplinary
Leonard Desvignes, Vasily S. Stolyarov, Marco Aprili, Freek Massee
Summary: The text highlights the importance of manipulating individual atoms and molecules using a scanning tunneling microscope for the development of atomic-scale devices and structures, particularly molecular motors. It also introduces the controlled manipulation of a rotor in Fe doped Bi2Se3, where current into the rotor is finely tuned with voltage to achieve directional switching.
Article
Engineering, Electrical & Electronic
Qiuyuan Wang, Yi Zeng, Kai Yuan, Qingqi Zeng, Pingfan Gu, Xiaolong Xu, Hanwen Wang, Zheng Han, Kentaro Nomura, Wenhong Wang, Enke Liu, Yanglong Hou, Yu Ye
Summary: The efficiency of spintronic devices can be improved by generating higher effective magnetic fields with lower working currents. Spin-transfer torques can drive magnetic domain wall motion in a device composed of a single material. Here, we report magnetism modulation in Co3Sn2S2-a magnetic Weyl semimetal-via spin-transfer-torque-driven domain wall motion. The threshold current density for driving domain wall motion is less than 5.1 x 10(5) A cm(-2) at zero external field and less than 1.5 x 10(5) A cm(-2) at a moderate external field (0.2 kOe). The spin-transfer-torque effective field can reach as high as 2.4-5.6 kOe MA(-1) cm(2) at 150 K.
NATURE ELECTRONICS
(2023)
Article
Polymer Science
Li Qian, Yaxian Wang, Ying Lu, Yongfeng Men
Summary: Research on the crystallization behaviors of two impact copolymer polypropylenes (ICP) revealed differences in their crystallization peaks at different cooling rates, with ICP-A and ICP-B showing distinct behaviors. These differences can be attributed to their different chain microstructures.
Article
Astronomy & Astrophysics
Li-Jia Liu, Bo Peng, Lei Yu, Bin Liu, Ji-Guang Lu, Ye-Zhao Yu, Hong-Wei Xi, Ming Xiong, O. Chang
Summary: The Five-hundred-meter Aperture Spherical radio Telescope (FAST) conducted a series of Interplanetary Scintillation (IPS) observations and obtained significant scientific results. The observations revealed a linear decrease in solar wind velocity with increasing frequency, a finding that has not been reported in literature. Additionally, variations in solar wind velocity on a time-scale of 3-5 minutes were detected.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2022)
Article
Engineering, Electrical & Electronic
Mingjin Hu, Wei Hua, Huafeng Xiao, Zheng Wang, Kai Liu, Kun Cai, Yi Wang
Summary: The proposed method minimizes latency in current control for AC drives, reducing computational delay without sacrificing modulation index and increasing stability margin or system bandwidth. The technique has been validated through experimental investigations on a permanent magnet synchronous motor.
IEEE TRANSACTIONS ON POWER ELECTRONICS
(2021)
Article
Polymer Science
Ce Shi, Yujing Tang, Ying Lu, Yongfeng Men
Summary: The translation mentions that Ethylene vinyl alcohol copolymer (EVOH) is widely used in the packaging industry and its crystallization behavior plays a significant role in production properties. Through the study on the crystallization kinetics and crystalline structure of EVOH, it is discovered that the crystallization rate of EVOH has a bimodal dependence on the crystallization temperature with a preference for different phases at different temperature ranges. The trend of crystallinity and crystallization enthalpy matches as the crystallization temperature increases.
Article
Engineering, Electrical & Electronic
Ruiqi Cheng, Yingjie He, Chao Lei, Yue Wang, Jinjun Liu
Summary: This article presents a method to achieve equivalent modulation of multilevel current converters, allowing for direct control of switch states by constructing an equivalent relationship between output levels and switch states. The method is generalized to n-level topologies and modulation strategies, ensuring correctness and universality. Simulation and experiment results validate the effectiveness of the method.
IEEE TRANSACTIONS ON POWER ELECTRONICS
(2021)
Article
Neurosciences
Lena Henke, Ashley G. Lewis, Lars Meyer
Summary: Neural oscillations are found to be synchronized with eye movements during naturalistic reading, indicating that speech and language processing impose preferred processing time scales onto reading, largely independent of actual physical rhythms in the stimulus.
JOURNAL OF NEUROSCIENCE
(2023)
Article
Multidisciplinary Sciences
Robert Law, Poul Christoffersen, Bryn Hubbard, Samuel H. Doyle, Thomas R. Chudley, Charlotte M. Schoonman, Marion Bougamont, Bas des Tombe, Bart Schilperoort, Cedric Kechavarzi, Adam Booth, Tun Jan Young
Summary: Measurements of ice temperature are crucial for understanding ice viscosity and thermodynamic processes within glaciers. Researchers advanced their understanding of glacier thermodynamics by obtaining a high-vertical-resolution temperature-sensing profile from a deep borehole in Greenland. The findings reveal notable spatial heterogeneity in conditions facilitating the fast motion of marine-terminating glaciers in Greenland, both vertically and at the catchment scale.
Review
Physics, Multidisciplinary
Joao Luis Carvalho-de-Souza, Andrea Saponaro, C. A. Z. Bassetto, Oliver Rauh, Indra Schroeder, Fabio Franciolini, Luigi Catacuzzeno, Francisco Bezanilla, Gerhard Thiel, Anna Moroni
Summary: This article summarizes recent advancements in understanding the mechanisms of ion permeation and gating in channel proteins, focusing on the elementary steps of ion transport through the pore and non-canonical modes of intramolecular communication between peripheral sensory domains and the central channel pore.
ADVANCES IN PHYSICS-X
(2022)
Article
Biochemistry & Molecular Biology
Oliver Rauh, Jennifer Opper, Maximilian Sturm, Nils Drexler, Deborah D. D. Scheub, Ulf-P. Hansen, Gerhard Thiel, Indra Schroeder
Summary: Most potassium channels have two gate locations, an inner gate and a filter gate, and the function of these gates is coupled in many channels. This study focuses on the filter gate of the viral channel KcvNTS and investigates its opening and closing mechanisms through single-channel recordings and gating analysis. The results show that mutations can affect the closing speed of the filter gate, and the coupling between the filter gate and surrounding structures may rely on different modes of interaction. Quantitative analysis suggests a concerted action of subunits in the energy barrier for filter closure.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tanzir Ahmed, Jayesh Arun Bafna, Roland Hemmler, Karsten Gall, Richard Wagner, Mathias Winterhalter, Michael J. Vellekoop, Sander van den Driesche
Summary: This work presents a microsystem setup for sensitive biological membrane translocation measurements. Thin free-standing synthetic bilayer lipid membranes (BLM) are constructed in microfabricated silicon nitride apertures and used for electrophysiological measurements of pore proteins. The integration of pore-forming proteins is achieved through direct reconstitution or reconstitution via outer membrane vesicles (OMVs) released from Gram-negative bacteria. This microsystem allows for investigation of fast gating events, pore blocking, and gating events of small pores.
Article
Chemistry, Multidisciplinary
Jiajun Wang, Jigneshkumar Dahyabhai Prajapati, Fan Gao, Yi-Lun Ying, Ulrich Kleinekathoefer, Mathias Winterhalter, Yi-Tao Long
Summary: Chirality is important but often overlooked in biological and chemical processes due to technical limitations. Researchers have used an electrostatically asymmetric membrane channel to successfully identify chiral amino acids in single peptides. This study provides a new approach for developing chiral recognition and protein sequencing methods.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biology
Muriel Masi, Julia Vergalli, Ishan Ghai, Andrea Barba-Bon, Therese Schembri, Werner M. Nau, Daniel Lafitte, Mathias Winterhalter, Jean-Marie Pages
Summary: This study investigated the translocation and killing effects of different cephalosporins on Gram-negative bacteria. The results revealed that the activity and efficiency of the drugs were influenced by the expression of specific porins. Through experimentation and analysis, it was found that the net negative charge of one of the cephalosporins contributed to its higher permeation through less cation-selective porins. These findings provide insights into the susceptibility of specific bacteria strains to cephalosporins.
COMMUNICATIONS BIOLOGY
(2022)
Editorial Material
Biology
Neil L. Harrison, Geoffrey W. Abbott, Martina Gentzsch, Andrei Aleksandrov, Anna Moroni, Gerhard Thiel, Stephen Grant, Colin G. Nichols, Henry A. Lester, Andreas Hartel, Kenneth Shepard, David Cabrera Garcia, Masayuki Yazawa
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Igor V. Bodrenko, Tsedenia Alemu Zewdie, Jiajun Wang, Eshita Paul, Susanne Witt, Mathias Winterhalter
Summary: This study investigates protein-protein interaction using electrophysiology, focusing on the structure of the TolC-AcrA-AcrB complex and the inhibitory effect of potential efflux pump inhibitors. The findings suggest that the fluctuation of ion current and the average current through the TolC channel can be used as complementary measures to assess the interaction of the complex.
Article
Chemistry, Medicinal
Abhishek Acharya, Ishan Ghai, Claudio Piselli, Jigneshkumar Dahyabhai Prajapati, Roland Benz, Mathias Winterhalter, Ulrich Kleinekathoefer
Summary: In this study, the molecular mechanism of an antibiotic permeating through a bacterial channel is revealed, with a focus on the role of conformational dynamics of the constriction loop. The dynamics of the L3 loop, specifically the F118 to S125 segment, at the constriction regions of the OmpF porin is investigated using temperature accelerated sliced sampling approach. The importance of hydrogen-bond stabilization in the conformational dynamics of the L3 loop is demonstrated through single channel electrophysiology experiments and applied-field simulations. The findings suggest that conformational dynamics of the constriction loop may play a general role in antibiotic permeation through porins.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Multidisciplinary
Yao Chen, Andrea Barba-Bon, Bohumir Gruner, Mathias Winterhalter, M. Alphan Aksoyoglu, Sushil Pangeni, Maryam Ashjari, Klaudia Brix, Giulia Salluce, Yeray Folgar-Camean, Javier Montenegro, Werner M. Nau
Summary: Cobalt bisdicarbollides (COSANs) are used as selective and efficient molecular carriers to transport hydrophilic oligopeptides through membranes. They can permeate lipid bilayer membranes without causing membrane damage. COSANs transport arginine-rich and lysine-rich peptides effectively, but cannot transport small molecules or anionic cargos. The transportation mechanism is a molecular carrier mechanism, and living cell experiments show that a fluorescent peptide cargo can be delivered into the cytosol.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Physiology
Jan H. Krumbach, Daniel Bauer, Atiyeh Sadat Sharifzadeh, Andrea Saponaro, Rene Lautenschlaeger, Kristina Lange, Oliver Rauh, Dario DiFrancesco, Anna Moroni, Gerhard Thiel, Kay Hamacher
Summary: The authors used molecular dynamics simulations to study the interactions between monovalent cations and the HCN4 channel, and found that cation selectivity is determined by an adaptation of the cations to the filter structure. This study is important for understanding biological processes such as heartbeat and neuronal firing.
JOURNAL OF GENERAL PHYSIOLOGY
(2023)
Article
Cell Biology
Anja J. Engel, Steffen Paech, Markus Langhans, James L. van Etten, Anna Moroni, Gerhard Thiel, Oliver Rauh
Summary: When the K+ channel-like protein Kesv from Ectocarpus siliculosus virus 1 is expressed in mammalian cells, it is targeted to the mitochondria. By altering codon usage or inserting hydrophobic amino acids into the protein's C-terminal transmembrane domain, the targeting can be redirected to the endoplasmic reticulum (ER). Positive charge in the inserted amino acid triplet serves as a strong signal for mitochondria sorting, while a combination of hydrophilic amino acids and rarely used codons favors mitochondria sorting in cases of neutral amino acid triplets. Sorting to the ER is influenced by the inverse dependency. The data suggest that local changes in elongation velocity and co-translational folding in the C-terminal transmembrane domain can influence intracellular protein sorting.
Article
Chemistry, Physical
Stefan Milenkovic, Jiajun Wang, Silvia Acosta-Gutierrez, Mathias Winterhalter, Matteo Ceccarelli, Igor V. Bodrenko
Summary: Transmembrane beta-barrel proteins are versatile candidates for various technological applications and their behavior is influenced by environmental conditions. Comparing two highly homologous porins, OmpF and OmpC, we observed subtle amino acid substitutions that can modulate mass transport properties. These differences can be attributed to the disparities in the environmental conditions under which the porins are expressed. Our analysis not only highlights the advantages of enhanced sampling methods, but also provides valuable insights into the biological function and technical applications of these proteins.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Meeting Abstract
Biophysics
Andrea Saponaro, Daniel Bauer, Hunter Giese, Paolo Swuec, Alessandro Porro, Federica Gasparri, Atiyeh Sadat Sharifzadeh, Antonio Chaves-Sanjuan, Ermanno Uboldi, Anastasia Polyakova, Martino Bolognesi, Gerhard Thiel, Bina Santoro, Anna Moroni
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2021)
Article
Biophysics
Michael Schmidt, Indra Schroeder, Daniel Bauer, Gerhard Thiel, Kay Hamacher
Summary: Coarse-grained protein models approximate physical potentials through relative entropy framework, which adjusts model parameters by minimizing entropy to maximize likelihood of reproducing observations. This study extends the optimization process to identify optimal mappings to dimension-reduced topologies, evaluating findings by comparing anisotropic network models of ion channels to experimental results.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2021)