Article
Chemistry, Multidisciplinary
Haleh Alimohamadi, Jaime de Anda, Michelle W. Lee, Nathan W. Schmidt, Taraknath Mandal, Gerard C. L. Wong
Summary: Peptide-induced transmembrane pore formation is common in biology, but directly observing the structure of these pores is difficult. Experimental determination of the structure and phase behavior of peptide-lipid systems, particularly the geometric parameters of cubic phases, is relatively straightforward. By leveraging the theory of anisotropic inclusions, researchers have developed a simple method to estimate the size of transmembrane pores and found that the estimates align well with known pore sizes. Antimicrobial peptides are able to induce stable pores, while cell-penetrating peptides form highly unstable pores.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Cell Biology
Joannalyn B. Delacruz, Satyan Sharma, Shailendra Singh Rathore, Meng Huang, Joan S. Lenz, Manfred Lindau
Summary: The study found that very narrow fusion pores are cation selective, while more dilated fusion pores are anion permeable. The narrow fusion pores' cation selectivity accelerates the release of positively charged transmitters, while the release of glutamate may require more dilated fusion pores.
Article
Multidisciplinary Sciences
Prabhat Tripathi, Arash Firouzbakht, Martin Gruebele, Meni Wanunu
Summary: Translocation of proteins is influenced by structural fluctuations and electric fields at the solid-state nanopore can control this process. By studying the change in occupancy of protein conformations as a function of electric field, we can determine the number of accessible conformational states and evaluate the ruggedness of their free energy landscapes. We also found that translocation becomes faster at higher electric fields, while folding rates are not correlated with ease of translocation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Materials Science, Multidisciplinary
Shinya Iwata, Hiroaki Uehara, Tatsuki Okamoto, Tatsuo Takada
Summary: The effects of an external electric field on the rupture of molecules in polymeric materials were evaluated at the molecular level using quantum chemical calculations. It was found that oxidation and impurities have an impact on the rupture force of molecules, as well as the decomposition of cross-linking agents in polyethylene leading to the formation of water trees.
MATERIALS TODAY COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Meng Wang, Xin Yi
Summary: In this study, a comprehensive theoretical investigation was conducted on the mechanical behaviors of lipid droplets. It was found that various factors such as membrane bending rigidity, tension, spontaneous curvature, lipid droplet size, and interfacial energy collectively play essential roles in regulating the growth and budding transition of lipid droplets. The study established budding phase diagrams to account for the characteristic interaction states, and analytical solutions on the bulge profiles were obtained to estimate the value of interfacial energy. This research uncovers the fundamental mechanics of lipid droplet formation and budding, with implications for the stability of echogenic liposomes and cellular incorporation of nanoparticles.
Article
Multidisciplinary Sciences
Shyamal Mosalaganti, Agnieszka Obarska-Kosinska, Marc Siggel, Reiya Taniguchi, Beata Turonova, Christian E. Zimmerli, Katarzyna Buczak, Florian H. Schmidt, Erica Margiotta, Marie-Therese Mackmull, Wim J. H. Hagen, Gerhard Hummer, Jan Kosinski, Martin Beck
Summary: This study combines artificial intelligence-based structure prediction with in situ structural biology to reveal the structure and function of the human nuclear pore complex (NPC) scaffold. The findings demonstrate the importance of linker nucleoporins in establishing the higher-order structure of the scaffold and suggest that it widens the central pore rather than stabilizing the fusion of the inner and outer nuclear membranes.
Article
Biochemistry & Molecular Biology
Ishan Goswami, Robert Bielitz, Scott S. Verbridge, Michael R. von Spakovsky
Summary: Experimental evidence shows that pulsed electric fields can alter mammalian cell behavior. A scaling law based on the Ising model is introduced to predict the behavior of lipid membranes under different pulse parameters, demonstrating the robustness of the computational methodology.
BIOELECTROCHEMISTRY
(2021)
Article
Chemistry, Applied
Tian Tian, Farah Zaaboul, Shipeng Yin, Zhan Ye, Yanwen Sun, Jialiang Zhao, Yuanfa Liu
Summary: This study analyzed the oxidative stability of pecan kernels and the behavior of oleosomes during storage. The results showed that the oxidation index of pecan oil increased significantly after 20 days of storage. There was a relationship between the damage of oleosomes in pecans and their oxidative stability. The rupture of oleosomes increased the contact between oil and oxygen, accelerating the oxidation process. Further analysis revealed that the oil content of oleosomes decreased during storage, while their particle size increased significantly. It is likely that the hydrolysis of endogenous proteins, particularly oleosins, caused the rupture of oleosomes. This led to an increase in the content of free fatty acids and oxidized triacylglycerols, while the content of polyunsaturated fatty acids decreased significantly. An in-vitro model confirmed that the rupture of oleosomes resulted in oil leakage and accelerated the oxidation of endogenous oil.
Article
Chemistry, Physical
Yangyang Zhang, Donghui Liu, Yiyang Zhang, Yachong Guo, Wenfei Li, Fabrice Thalmann
Summary: This article describes a coarse-grained model of POPC and DOPC lipid peroxides and discusses their predicted structure and the influence of hydration. In addition, electron and neutron scattering length density profiles of the simulated bilayers are provided.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Microbiology
Klara Latrova, Tereza Dolejsova, Lucia Motlova, Gabriela Mikusova, Juraj Bosak, Kateiina Snopkova, David Smajs, Ivo Konopasek, Radovan Fiser
Summary: Fonticins are phage tail-like bacteriocins produced by the Gram-negative bacterium Pragia fontium. They can penetrate sensitive cells and form large pores. This research reveals the structural properties of Fonticins and their potential application as a nanodevice.
JOURNAL OF BACTERIOLOGY
(2023)
Article
Multidisciplinary Sciences
Zhuang Liu, Arun Yethiraj, Qiang Cui
Summary: Biomolecular phase separation is an important mechanism for cellular organization, and lipid membranes have been recognized as a regulatory center for biomolecular condensation. However, the interplay between membrane phase behaviors and surface biopolymers in the regulation of surface condensation remains unclear.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Engineering, Environmental
Yue Yang, Sen Qiao, Mingmei Zheng, Qinqin Han, Ruiyu Wang, Jiti Zhou, Xie Quan
Summary: An electro-enhanced membrane bioreactor (EMBR) was constructed using a polyaniline-based carbon (PAC) separation membrane as a membrane-electrode for in-situ electro-generation and activation of H2O2 to ·OH without the use of metal catalyst. The EMBR showed improved resistance to membrane fouling compared to the control membrane, with a 77.41% fouling rate. The EMBR also achieved satisfactory wastewater treatment with low levels of chemical oxygen demand and NH4+-N in the effluent.
Article
Engineering, Environmental
Yuchen Yuan, Chang Tian, Jiadong Liu
Summary: The organic conductive membrane prepared by chemical vapor deposition on a PVDF membrane surface showed stable chemical properties and anti-fouling performance after modification, with a slight decrease in adsorption capacity. Additionally, the presence of an electric field further enhanced the anti-fouling properties of the modified membrane compared to the blank and modified membranes without electric field.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2021)
Article
Environmental Sciences
Pu Li, Chao Yang, Feiyun Sun, Xiao-yan Li
Summary: Membrane fouling is a major challenge in water and wastewater treatment using membrane technology. This study developed an electrically assisted technique involving a conductive ceramic membrane coated with dopamine and carbon nanotubes, which effectively reduced fouling rates by applying a negative charge. The use of an imposed electric field was found to greatly decrease the amount of foulants attached to the membrane surface and pores.
Article
Engineering, Mechanical
Choon-Peng Chng, Yoel Sadovsky, K. Jimmy Hsia, Changjin Huang
Summary: The physico-mechanical properties of nanoscale lipid vesicles play a crucial role in their interaction with biological systems. The interplay between vesicle size and stiffness is essential for understanding their biological functions and optimizing diagnostics and therapeutics. Molecular dynamics simulations reveal that the softening of nano-vesicles is closely related to changes in membrane structure, providing a valuable insight for further exploration in biophysics and biomedical applications of nano-vesicles.
EXTREME MECHANICS LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Jiajun Wang, Jayesh Arun Bafna, Satya Prathyusha Bhamidimarri, Mathias Winterhalter
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2019)
Article
Chemistry, Multidisciplinary
Jiajun Wang, Remi Terrasse, Jayesh Arun Bafna, Lorraine Benier, Mathias Winterhalter
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Article
Chemistry, Medicinal
Jigneshkumar Dahyabhai Prajapati, Crystal Mele, Mehmet Alphan Aksoyoglu, Mathias Winterhalter, Ulrich Kleinekathoefer
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
Biology
Julia Vergalli, Alessio Atzori, Jelena Pajovic, Estelle Dumont, Giuliano Malloci, Muriel Masi, Attilio Vittorio Vargiu, Mathias Winterhalter, Matthieu Refregiers, Paolo Ruggerone, Jean-Marie Pages
COMMUNICATIONS BIOLOGY
(2020)
Article
Chemistry, Multidisciplinary
Sushil Pangeni, Jigneshkumar Dahyabhai Prajapati, Jayesh Bafna, Mohamed Nilam, Werner M. Nau, Ulrich Kleinekathoefer, Mathias Winterhalter
Summary: This study focused on quantifying the passage of the large peptide protamine (Ptm) across CymA, a passive channel for cyclodextrin uptake. Results showed that the kinetics of Ptm entry through CymA was independent of its concentration, with about 1-2 events per second and long dwell times observed per channel. Additionally, voltage-dependent entry of single Ptm peptide molecules into the channel was resolved, with extrapolation to zero voltage revealing a translocation rate of about one molecule per second per channel.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Chemistry, Multidisciplinary
Jigneshkumar Dahyabhai Prajapati, Ulrich Kleinekathoefer, Mathias Winterhalter
Summary: Traditional antibiotics are facing the challenge of Gram-negative bacteria developing resistance, prompting the urgent need for new antibacterial agents. Designing new antibiotic molecules that can rapidly penetrate Gram-negative bacteria and achieve lethal intracellular drug accumulation is a major challenge. The lack of simple experimental techniques to measure antibiotic uptake and local concentrations in subcellular compartments is a limiting factor.
Article
Multidisciplinary Sciences
Samira Sadeghi, Siddharth Deshpande, Girish Vallerinteavide Mavelli, Alphan Aksoyoglu, Jayesh Bafna, Mathias Winterhalter, R. Manjunatha Kini, David P. Lane, Chester L. Drum
Summary: In vitro protein folding often leads to aggregation and low yields. Researchers have used nanoscale exoshells to enhance soluble yield, functional yield, and specific activity of folded proteins.
NATURE COMMUNICATIONS
(2021)
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)
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
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)
Article
Chemistry, Multidisciplinary
Jiajun Wang, Jigneshkumar Dahyabhai Prajapati, Ulrich Kleinekathoefer, Mathias Winterhalter
