Article
Chemistry, Physical
Abhishek Acharya, Jigneshkumar Dahyabhai Prajapati, Ulrich Kleinekathoefer
Summary: Understanding the molecular mechanisms underlying the transport of antibiotics into bacterial cells is crucial for the development of effective antibacterial drugs. Accurate determination of free energy surfaces for antibiotic translocation is necessary for meaningful comparisons between different classes of antibiotics. Two sampling methods combining umbrella sampling and metadynamics-style biasing schemes with temperature acceleration have been employed to improve sampling and convergence in this study, showing promising results for the ciprofloxacin-OmpF system.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Multidisciplinary Sciences
James Osei-Owusu, Ekaterina Kots, Zheng Ruan, Ljubica Mihaljevic, Kevin Hong Chen, Ami Tamhaney, Xinyu Ye, Wei Lu, Harel Weinstein, Zhaozhu Qiu
Summary: In response to acidic pH, the proton-activated chloride (PAC) channel opens to transport anions across cellular membranes, playing important roles in cellular physiology and acidosis-related diseases. Through mutagenesis and electrophysiological studies, this research identifies critical residues, including histidine and aspartic acid, as potential pH sensors for human PAC. The study also reveals that the beta 12 strand and the joint region between upper and lower extracellular domains allosterically regulate proton-dependent PAC activation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Neurosciences
Jianyong Ma, Xiaoqian Gao, Yutian Li, Thomas E. DeCoursey, Gary E. Shull, Hong-Sheng Wang
Summary: Regulation of intracellular pH is crucial for cardiac function. The HVCN1 proton channel, expressed in canine ventricular myocytes, provides an energetically efficient mechanism for H+ extrusion, contributing to pH regulation and potentially facilitating CO2 disposal.
JOURNAL OF PHYSIOLOGY-LONDON
(2022)
Article
Chemistry, Physical
Vinaya Kumar Golla, Jigneshkumar Dahyabhai Prajapati, Ulrich Kleinekathoefer
Summary: A numerically efficient hybrid Brownian and molecular dynamics approach has been developed and evaluated for studying the translocation of antibiotics through the outer membrane of Gram-negative bacteria. Results suggest that this approach accurately reproduces experimental and simulation findings, making it a promising tool for screening new antibiotics.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Review
Biochemistry & Molecular Biology
Yoshifumi Okochi, Yasushi Okamura
Summary: The voltage-gated proton channel Hv1, also known as VSOP, regulates reactive oxygen species (ROS) production and phagosomal pH maintenance, while promoting calcium influx at the plasma membrane in phagocytes. It serves as both a positive and negative regulator of ROS generation in neutrophils, inhibiting hypochlorous acid production and ERK signaling to reduce inflammation upon fungal infection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Physical
Maria Queralt-Martin, D. Aurora Perini, Antonio Alcaraz
Summary: This study investigates the adsorption dynamics of trace amounts of different salts of trivalent cations in biological nanopores, revealing differential modulation of ion conduction and selectivity inversion. The research systematically compares the effect of three trivalent electrolytes on OmpF current-voltage relationships and analyzes open channel current noise to determine the existence of equilibrium/non-equilibrium mechanisms of ion adsorption. The study provides fundamental information relevant to different biological and electrochemical systems where transport phenomena involve ion adsorption in charged surfaces under nanoscale confinement.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Wen-Long Huang, Xu-Dong Wang, Yu-Fei Ao, Qi-Qiang Wang, De-Xian Wang
Summary: Based on the structure and function of natural ClC selectivity filter, a ClC-type single channel molecule with high ion transport activity and excellent Cl-/K+ selectivity was designed. It exhibited a permeability ratio of P Cl /PKthorn up to 12.31, comparable to natural ClC proteins, and showed high anion/anion selectivity and pH-dependent conductance and ion selectivity. The ClC-like transport behavior was achieved through hydrogen bonding, anion-pi interactions, and pH-responsive terminal phenylalanine residues in the central macrocyclic skeleton.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(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)
Review
Biochemistry & Molecular Biology
Laxmicharan Samineni, Bibek Acharya, Harekrushna Behera, Hyeonji Oh, Manish Kumar, Ratul Chowdhury
Summary: Proteins are crucial for cellular functions and their structures can be engineered for industrial applications. This article reviews successful cases of protein engineering in pore-forming proteins and discusses their applications in nucleotide/peptide sequencing, single-molecule sensing, and molecular separations.
Article
Cell Biology
Jae Won Kwon, Young Keul Jeon, Sung Joon Kim
Summary: This study investigates the effects of extracellular and intracellular pH on human CALHM1 and reveals the remarkable pH sensitivity of CALHM1, which might contribute to the pH-dependent modulation of neuronal excitability or taste sensation.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2023)
Review
Pharmacology & Pharmacy
Juan J. Alvear-Arias, Antonio Pena-Pichicoi, Christian Carrillo, Miguel Fernandez, Tania Gonzalez, Jose A. Garate, Carlos Gonzalez
Summary: The acid-base characteristics of tumor cells and the tumor microenvironment have attracted scientific interest. The voltage-gated proton channel (Hv1) plays a crucial role in maintaining pH balance and has been found to be overexpressed in acidic tumor environments. Evidence suggests that the Hv1 channel is involved in the development of malignancy features in solid tumors, making it a potential therapeutic target.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Weicheng Peng, Caden C. Maydew, Hiu Kam, Jacob K. Lynd, Jasmine N. Tutol, Shelby M. Phelps, Sameera Abeyrathna, Gabriele Meloni, Sheel C. Dodani
Summary: Chloride is crucial for all forms of life and recent research has demonstrated the potential of chloride-sensitive fluorescent proteins for cellular applications. This study presents a bioinformatics strategy to efficiently identify and design new chloride-sensitive fluorescent proteins, using GFPxm163 as an example.
Article
Biochemistry & Molecular Biology
Paul Linsdell
Summary: The study found that the chloride conductance of the CFTR channel is mainly determined by the ability of anions to bind in the pore already occupied by chloride ions, rather than by anion:anion interactions within the pore. Although anion binding is necessary for high conductance, mutations that strengthen anion binding have little effect on conductance, indicating that the wild-type CFTR pore is already close to saturated with chloride ions.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2021)
Article
Plant Sciences
Zhenguo Zhou, Sheng Zheng, Syed Inzimam Ul Haq, Dianfeng Zheng, Quan-Sheng Qiu
Summary: This review summarizes the current advances in understanding the function and mechanisms of cellular pH and ions in regulating pollen tube growth. It is found that ions such as Ca2+, K+, and Cl-, as well as cellular pH, play important physiological roles in pollen tube growth. Ca2+ is particularly crucial in regulating cytoskeletons and cell wall development. Furthermore, pH regulation of ion flow, cell wall development, auxin signaling, and cytoskeleton function also contribute to pollen tube growth. Unanswered questions regarding the interplay of ion homeostasis and pH dynamics, as well as the regulation of pollen tube growth by proton pumps and ion transporters in the trans-Golgi network, need to be addressed in the future.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Food Science & Technology
Nan Li, Xingbin Yang, Dehui Lin
Summary: This study developed konjac glucomannan-based intelligent films by incorporating curcumin and bacterial cellulose nanofibers. The results showed that the addition of curcumin improved the microstructure, physical properties, and fresh-keeping performance of the films. Films loaded with 3% curcumin exhibited the best properties, including improved mechanical strength, barrier properties, antioxidant activity, and antibacterial properties. Furthermore, the films could also act as a pH colorimetric indicator for meat.
FOOD PACKAGING AND SHELF LIFE
(2022)
Article
Chemistry, Physical
Maria Queralt-Martin, Jose J. Perez-Grau, Laidy M. Alvero Gonzalez, D. Aurora Perini, Javier Cervera, Vicente M. Aguilella, Antonio Alcaraz
Summary: Ion permeation across nanoscopic structures differs considerably from microfluidics due to steric constraints, transformed solvent properties, and charge-regulation effects. Little is known about nanofluidics in moderately concentrated solutions, which are important for industrial applications. Our study shows that nanoconfinement triggers biphasic concentration patterns in ion transport properties, revealing the contributions of ion-ion correlations and ion-surface interactions.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
D. Aurora Perini, Elisa Parra-Ortiz, Inmaculada Varo, Maria Queralt-Martin, Martin Malmsten, Antonio Alcaraz
Summary: The interaction between nanoplastics and phospholipid membranes can affect membrane integrity and lead to toxic effects.
Article
Virology
Wahyu Surya, Maria Queralt-Martin, Yuguang Mu, Vicente M. Aguilella, Jaume Torres
Summary: The accessory protein 7b of SARS-CoV-2 is involved in virus-host interactions and has been hypothesized to form ion channels. However, our study shows that while 7b forms various oligomers, they do not function as bona fide ion channels. Disulfide-linked dimers are not essential for tetramer formation.
Article
Biology
Amaia Gonzalez-Magana, Jon Altuna, Maria Queralt-Martin, Eneko Largo, Carmen Velazquez, Itxaso Montanchez, Patricia Bernal, Antonio Alcaraz, David Albesa-Jove
Summary: This study reveals the molecular mechanism of Tse5-CT, the toxic product of the Pseudomonas aeruginosa T6SS. Tse5-CT is a pore-forming toxin that depolarizes the bacterial membrane, leading to bacterial death. This finding highlights the importance of membrane depolarization as a competitive strategy in polymicrobial environments.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Aurelio J. Dregni, Matthew J. McKay, Wahyu Surya, Maria Queralt-Martin, Joao Medeiros-Silva, Harrison K. Wang, Vicente Aguilella, Jaume Torres, Mei Hong
Summary: The E protein of SARS-CoV-2 forms a pentameric ion channel in the ERGIC membrane of the infected cell. The cytoplasmic domain of the protein plays a role in virus pathogenicity and assembly. Solid-state NMR analysis revealed that the cytoplasmic domain adopts a β-sheet conformation and forms an umbrella-shaped bundle. The structure of the cytoplasmic domain may be influenced by the concentration of the protein in lipid bilayers.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Wahyu Surya, Ernesto Tavares-Neto, Andrea Sanchis, Maria Queralt-Martin, Antonio Alcaraz, Jaume Torres, Vicente M. Aguilella
Summary: This study discusses the claim that the E protein in coronaviruses forms cation-selective channels, but found that the selectivity of these channels is very mild and depends on the lipid environment. The study also found no evidence that the E protein forms specific calcium channels or requires specific conditions for activation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Laidy M. Alvero-Gonzalez, D. Aurora Perini, Maria Queralt-Martin, Alex Peralvarez-Marin, Clara Vinas, Antonio Alcaraz
Summary: DynA is an endogenous neuropeptide that has non-opioid pathophysiological properties and can induce cell permeability similar to cell-penetrating peptides. The interaction of DynA with cellular membrane is modulated by lipid charge distribution, enabling passive ionic transport via membrane remodeling and pore formation, as well as peptide direct internalization independent of cellular transduction pathways.
BIOELECTROCHEMISTRY
(2023)
Article
Materials Science, Biomaterials
Miquel Nuez-Martinez, Maria Queralt-Martin, Amanda Munoz-Juan, Vicente M. Aguilella, Anna Laromaine, Francesc Teixidor, Clara Vinas, Catarina G. Pinto, Teresa Pinheiro, Joana F. Guerreiro, Filipa Mendes, Catarina Roma-Rodrigues, Pedro Baptista, Alexandra R. Fernandes, Srecko Valic, Fernanda Marques
Summary: This study explores the potential use of ferrabis(dicarbollides) as radiosensitizers for GBM radiotherapy. The results show that this radiation therapy can reduce the viability and survival of tumor cells, and proton boron fusion radiation therapy combined with boron-rich compounds is a promising treatment modality.
JOURNAL OF MATERIALS CHEMISTRY B
(2022)
Meeting Abstract
Biophysics
Deborah Aurora Perini, Marcel Aguilella-Arzo, Antonio Alcaraz, Alex Peralvarez-Marin, Maria Queralt-Martin
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Deborah Aurora Perini, Laidy M. Alvero-Gonzalez, Maria Lidon Lopez-Peris, Antonio Alcaraz, Maria Queralt-Martin
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Deborah Aurora Perini, Elisa Parra-Ortiz, Inmaculada Varo, Maria Queralt-Martin, Martin Malmsten, Antonio Alcaraz
BIOPHYSICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Philipp Grad, Katarina Edwards, Lars Gedda, Victor Agmo Hernandez
Summary: This study investigates the effects of polyethylene glycol-(PEG) modified lipids and gangliosides on the Ca2+ induced interaction between liposomes composed of palmitoyl-oleoyl phosphatidylethanolamine (POPE) and palmitoyl-oleoyl phosphatidylserine (POPS) at physiological ionic strength. The results show that naked liposomes tend to adhere, rupture, and collapse on each other's surfaces upon addition of Ca2+, eventually resulting in the formation of large multilamellar aggregates and bilayer sheets. However, the presence of gangliosides or PEGylated lipids leads to the formation of small, long-lived bilayer fragments/disks. PEGylated lipids seem to be more effective than gangliosides at stabilizing these structures. The study suggests that direct liposome-liposome fusion is not the dominating process triggered by Ca2+ in the systems studied.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Saurabh Saraswat, Archana Chugh
Summary: Cell penetrating peptides (CPP) are important tools for intracellular delivery of molecules. In this study, a novel marine-derived CPP from Engraulis japonicus, called Engraulisin, was reported. Engraulisin demonstrated successful cellular uptake and selective antimicrobial activity against Methicillin-resistant Staphylococcus aureus (MRSA), making it a potential candidate for drug delivery.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Emanuela Efodili, Ashlynn Knight, Maryem Mirza, Cedric Briones, Il-Hyung Lee
Summary: This study demonstrates the spontaneous transfer of small membrane-bound peptides between a supported lipid bilayer and giant unilamellar vesicles in vitro. The transfer occurs through the formation of hemi-fusion stalks and is limited to small peptides due to the highly curved structure of the stalk. This system provides a synthetic platform for studying peptide trafficking between synthetic membranes.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Yueqi Niu, Si Jia Chen, Jeffery B. Klauda
Summary: Macrophage membranes in the activated state are more tightly packed, exhibit increased chain order across lipid species, and form specific lipid clusters. These findings provide physiologically accurate models for future computational studies of macrophage membranes and their proteins.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Niki Baccile, Vincent Chaleix, Ingo Hoffmann
Summary: This study measured the bending rigidity of self-assembled structures formed by a new biobased glucolipid bioamphiphile using neutron spin-echo (NSE) technology. The results showed that the bending rigidity of these structures is lower or higher compared to phospholipid membranes, providing a new theoretical basis for the application of these new molecular systems.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Alain Bolano Alvares, Pablo E. A. Rodriguez, Gerardo D. Fidelio
Summary: The behavior of amphiphilic molecules at the air/water interface was studied to evaluate the arrangement formed in a confined area. The surface properties of zwitterionic DPPC lipid and A beta(1-40) amyloid peptide in mixed films were investigated at different temperatures. DPPC undergoes a phase transition depending on temperature and lateral pressure, which allows for the study of its influence on amyloid structure formation.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Lukasz Plachta, Marzena Mach, Magdalena Kowalska, Pawel Wydro
Summary: Resveratrol, a popular phytoalexin found in grapes and red wine, has beneficial effects on the cardiovascular system, exhibits antiviral, antibacterial, and antifungal properties, and may have therapeutic effects against cancer. This study investigates the interaction of resveratrol with model cell membranes, demonstrating changes in their physicochemical parameters and highlighting the role of cholesterol content in resveratrol incorporation. The findings suggest that the molecular mechanism of action of resveratrol may involve interactions with lipid rafts.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Edurne Rujas, Beatriz Apellaniz, Johana Torralba, David Andreu, Jose M. M. Caaveiro, Shixia Wang, Shan Lu, Jose L. Nieva
Summary: This study investigates the role of fusion peptide and Trp-rich membrane proximal external region in HIV-1 fusion and demonstrates that liposome-based formulations containing FP-MPER hybrid peptides can induce the production of specific neutralizing antibodies in rabbits. The results support the use of liposomes as vaccine carriers and the inclusion of lipid membranes in immunogens to elicit specific humoral responses.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Dailin Li, Dingyuan Shi, Lei Wang
Summary: G protein-gated inwardly rectifying potassium (GIRK) channels play a significant role in regulating cell excitability. This study investigated the ion permeation mechanism in GIRK2 mutants using molecular dynamic simulations and QM/MM methods. The results revealed the importance of a multi-ion distribution for ion conduction.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Max J. den Uijl, Arnold J. M. Driessen
Summary: Membrane protein insertion into and translocation across the bacterial cytoplasmic membrane are essential processes facilitated by the Sec translocon. The phospholipid dependence of membrane protein insertion has remained mostly unknown. This study reveals that the insertion of the mannitol permease MtlA into the membrane depends on the presence of phosphatidylglycerol and is stimulated by phosphatidylethanolamine.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Patrick Allen, Adam C. Smith, Vernon Benedicto, Abbas Abdulhasan, Vasanthy Narayanaswami, Enrico Tapavicza
Summary: We explore the stability, size, and structure of nanodiscs formed by the N-terminal domain of apolipoprotein E3 and a variable number of 1,2-dimyristoyl-sn-glycero-3-phosphocholine molecules. Our simulations suggest that nanodiscs containing 240 to 420 DMPC molecules are stable. The antiparallel configuration shows more protein-protein interactions and ionic contacts, as well as greater stability and rigidity compared to the parallel configuration.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Patrick M. Keating, Nicholas P. Schifano, Xinrui Wei, Matthew Y. Kong, Jinwoo Lee
Summary: Lassa virus (LASV) infection is dependent on the fusion of its viral membrane with the host cell membrane, and our study reveals that this fusion process involves pH-dependent conformational changes in the transmembrane domain of LASV. These findings provide valuable insights into the fusion mechanism of LASV and can be utilized in the design of therapeutics to combat Lassa virus infections and prevent its potential spread.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Ashley L. Bennett, Kristen N. Cranford, Austin L. Bates, Christopher R. Sabatini, Hee-Seung Lee
Summary: This study employed molecular dynamics simulations to elucidate the binding, folding, and insertion details of TP10W in the cell membrane. The simulations revealed that TP10W can translocate across the lipid membrane as a monomer, and the charged amino acid side chains can move between lipid leaflets. Comparison with point mutated variants demonstrated significant conformational changes due to charge distribution.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Jessica H. van Wonderen, Jason C. Crack, Marcus J. Edwards, Thomas A. Clarke, Gerhard Saalbach, Carlo Martins, Julea N. Butt
Summary: Electrogenic bacteria transfer excess respiratory electrons to metal oxide particles and electrodes through the MtrCAB complex. The crystal structure of MtrCAB from S. baltica OS185 was resolved, and liquid chromatography mass spectrometry was used to determine the mass values of the three proteins in purified MtrCAB complexes.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Review
Biochemistry & Molecular Biology
Yi-Ming Chen, Ching-Tai Lu, Chia-Wen Wang, Wolfgang B. Fischer
Summary: A series of dye ligands were ranked based on docking experiments, selecting the most suitable ligands for binding with different proteins. Additionally, a comparison study was conducted on a series of repurposing drugs and known antivirals.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
