Review
Biochemistry & Molecular Biology
Bankala Krishnarjuna, Ayyalusamy Ramamoorthy
Summary: Atomic-resolution structural studies of membrane-associated proteins and peptides in a membrane environment are important for understanding their biological function and disease pathology. Recent advancements in NMR spectroscopy, cryoEM approaches, and the development of novel membrane mimetics have overcome the complexity of the cell membrane and enabled reconstitution and investigation of membrane proteins.
Article
Biochemistry & Molecular Biology
Renato Bruni, Aisha Laguerre, Anna-Maria Kaminska, Sean McSweeney, Wayne A. Hendrickson, Qun Liu
Summary: Membrane proteins play important roles in cellular function and metabolism, but their study is often hindered by difficulties in expression and purification. This study presents a high-throughput screening workflow for eukaryotic membrane protein targets using cell-free protein synthesis in various lipidic mimetics, showing that 57% of the tested membrane proteins can be expressed in soluble form. The results demonstrate the utility of using cell-free systems for screening and production of eukaryotic membrane proteins.
Article
Biochemistry & Molecular Biology
Laura R. Blackholly, Nicola J. Harris, Heather E. Findlay, Paula J. Booth
Summary: The majority of alpha helical membrane proteins fold co-translationally during their synthesis on the ribosome. Cell-free translation of membrane proteins is emerging as a useful tool to address folding during translation by a ribosome. The bacterial leucine transporter, LeuT can be synthesised and inserted into lipid membranes using a variety of in vitro transcription translation systems. LeuT is considered a paradigm for neurotransmitter transporters and possesses a knotted structure that is characteristic of this transporter family.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Physical
Bankala Krishnarjuna, Gaurav Sharma, Sang-Choul Im, Richard Auchus, G. M. Anantharamaiah, Ayyalusamy Ramamoorthy
Summary: Lipid-bilayer nanodiscs provide a stable membrane environment for the study of membrane proteins. In this study, the formation of peptide-based nanodiscs using the anti-inflammatory and tumor-suppressing peptide AEM28 was investigated. The results showed that AEM28 and 2F-based nanodiscs are suitable for studying membrane proteins and can solubilize E. coli cell membranes.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2024)
Article
Biochemistry & Molecular Biology
Sarah Dallo, Jeehae Shin, Shanwen Zhang, Qian Ren, Huan Bao
Summary: Signal transduction at the synapse relies on protein-lipid interactions for the regulation of synaptic vesicle biogenesis, neurotransmitter release, and postsynaptic receptor activation. Recent advances in nanodiscs have greatly enhanced our ability to study and manipulate these interactions, offering new opportunities for understanding synaptic transmission.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lauren E. Ball, Liam J. Riley, Waled Hadasha, Rueben Pfukwa, Corinne J. Smith, Timothy R. Dafforn, Bert Klumperman
Summary: Polymer-based lipid nanoparticles, such as DIBMA, have shown significant advancements in the study of membrane proteins. Research indicates that DIBMA exhibits excellent performance in lipid nanodisc formation and membrane protein extraction, with better solubilization efficiency and cleaner separation compared to SMA and commercially available DIBMA.
Article
Multidisciplinary Sciences
Ved P. Tiwari, Yuki Toyama, Debajyoti De, Lewis E. Kay, Pramodh Vallurupalli
Summary: Conformational dynamics in protein folding are critical, and NMR spectroscopy is a valuable tool for studying the different conformational states. Using chemical exchange saturation transfer, invisible minor states on the energy landscape of the A39G mutant FF domain were detected and analyzed, showing that the folding mechanism involves four-state exchange processes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Stephen G. Sligar, Ilia G. Denisov
Summary: Membrane proteins play crucial roles in biological processes, but are often challenging to study. The NanoDisc platform offers a self-assembled system that solubilizes membrane proteins in water while maintaining their functional activity. NanoDiscs have utility in studying cellular signaling complexes and delivering drugs, showcasing their versatility in biochemistry and pharmacology.
Review
Biotechnology & Applied Microbiology
Yixin Rong, Sheila Ingemann Jensen, Kresten Lindorff-Larsen, Alex Toftgaard Nielsen
Summary: The expression of correctly folded and functional heterologous proteins is crucial in biotechnological production processes. Bacterial platform organisms like E. coli are commonly used due to their proven suitability at an industrial scale, but can suffer from protein aggregation and low functional protein levels. This review explores cellular mechanisms influencing protein folding and expression across different organisms, and discusses experimental methods to improve protein folding, such as codon optimization and chaperone co-production.
BIOTECHNOLOGY ADVANCES
(2023)
Review
Biochemistry & Molecular Biology
Nicola J. Harris, Grant A. Pellowe, Laura R. Blackholly, Samuel Gulaidi-Breen, Heather E. Findlay, Paula J. Booth
Summary: This review discusses various methods for studying the folding of membrane proteins in different lipid environments, including in vitro folding methods and single-molecule force spectroscopy studies. It also highlights recent advances in co-translational folding studies using different lipid systems or native membranes.
Article
Biochemistry & Molecular Biology
Hannah Welte, Pia Sinn, Michael Kovermann
Summary: This study investigates the binding affinity between proteins and nucleic acids using fluorine labeling technology, and proposes a reliable experimental approach to determine the affinity between single stranded DNA molecules and target proteins in complex biological environments. By applying high-resolution F-19 NMR spectroscopy, this research advances the identification of intermolecular interactions in native surroundings, offering a potent platform for future studies in cell applications.
Article
Biochemistry & Molecular Biology
Kenichi Ataka, Axel Baumann, Jheng-Liang Chen, Aoife Redlich, Joachim Heberle, Ramona Schlesinger
Summary: The folding process of transmembrane domains of microbial rhodopsins during cell-free expression was investigated using SEIRAS, revealing that the unsuccessful expression of certain rhodopsins is not due to translation process but rather the folding process post-translation. It was also found that retinal chromophore plays a crucial role in compacting the polypeptide into its tertiary structure and forming a fully functional protein.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Marie-Laure Fogeron, Lauriane Lecoq, Laura Cole, Matthias Harbers, Anja Bockmann
Summary: CFPS systems are versatile tools for basic research and product development, with WG-CFPS offering high yields for synthesizing complex eukaryotic proteins. The separation of translation reactions from cellular processes provides flexibility to adapt to protein needs. These systems have the potential to become widely used tools for recombinantly preparing challenging eukaryotic proteins.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
David R. Jacobson, Thomas T. Perkins
Summary: By using an atomic-force-microscope assay optimized for mechanical force to reversibly unfold local regions of an individual protein, researchers overcame limitations of chemical denaturation assays in understanding the energetics of membrane proteins. This approach provided quantitative insight into the Delta Delta G of single amino acid mutations in membrane proteins and highlighted the contribution of membrane protein-lipid contacts to folding energetics. The platform established allows for determining Delta Delta G for fully folded membrane proteins embedded in their native bilayers.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Nicolai Tidemand Johansen, Frederik Gronbaek Tidemand, Martin Cramer Pedersen, Lise Arleth
Summary: We have witnessed significant progress in the design, optimization, and utilization of carrier particle systems for studying membrane proteins in near-native environments over the past decade. New and improved systems continue to emerge, pushing the boundaries of existing carrier systems, while specific carrier systems establish themselves as the preferred choice for certain types of target membrane proteins. This review covers the most commonly used carrier systems, highlighting their similarities and differences, as well as current trends and future directions in the field. Special attention is given to the biophysical properties and membrane mimicking ability of each system, and how they may impact the study of embedded membrane proteins and their structure or function.
Article
Materials Science, Biomaterials
Maxim B. Gongalsky, Daniela A. Muftieva, Jukka K. S. Saarinen, Antti Isomaki, Nikolay V. Pervushin, Gelina S. Kopeina, Leena J. Peltonen, Clare J. Strachan, Boris Zhivotovsky, Helder A. Santos, Liubov A. Osminkina
Summary: Coherent anti-Stokes Raman scattering (CARS) is a powerful optical method for rapid visualization of biological objects. In this study, efficient nonresonant CARS imaging of silicon nanoparticles (SiNPs) in human cells was demonstrated. SiNPs can be visualized without specific labels due to their high third-order nonlinear susceptibility. CARS microscopy provides localization of SiNPs within biological structures at the cellular level and can be used to monitor various bioprocesses.
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2022)
Article
Oncology
Viacheslav V. Senichkin, Nikolay V. Pervushin, Alexey V. Zamaraev, Elena V. Sazonova, Anton P. Zuev, Alena Y. Streletskaia, Tatiana A. Prikazchikova, Timofei S. Zatsepin, Olga V. Kovaleva, Elena M. Tchevkina, Boris Zhivotovsky, Gelina S. Kopeina
Summary: Apoptosis is a programmed cell death process regulated by genes and proteins, including the Bcl-2 protein family. Resistance of cancer cells to apoptosis is often associated with overexpression of antiapoptotic proteins. This study found that Bak and Bcl-xL protein regulate the sensitivity and resistance of cancer cells to Mcl-1 inhibition. BH3 mimetics targeting Mcl-1 have shown promise in cancer treatment.
Article
Biochemistry & Molecular Biology
Maxim M. M. Zaigraev, Ekaterina N. N. Lyukmanova, Alexander S. S. Paramonov, Zakhar O. O. Shenkarev, Anton O. O. Chugunov
Summary: Ly6/uPAR proteins with GPI-anchors have various positions and orientations on the membrane surface, regardless of the linker length between the LU domain and GPI-anchor. The proteins interact with the membrane through polypeptide parts and glycans. Different proteins have different contact regions with the membrane and unique orientations, indicating that GPI-anchoring does not determine the optimal pre-orientation for receptor interaction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Irina S. Panina, Sergey V. Balandin, Andrey V. Tsarev, Anton O. Chugunov, Andrey A. Tagaev, Ekaterina I. Finkina, Daria V. Antoshina, Elvira V. Sheremeteva, Alexander S. Paramonov, Jasmin Rickmeyer, Gabriele Bierbaum, Roman G. Efremov, Zakhar O. Shenkarev, Tatiana V. Ovchinnikova
Summary: To date, several lantibiotics have been found to target lipid II, a peptidoglycan precursor in bacterial cytoplasmic membrane. The alpha-component of lichenicidin, a two-component lantibiotic, contains potential lipid II binding sites. NMR spectroscopy and MD simulations provided evidence that the C-terminal domain of lichenicidin interacts with lipid II. The contact area of lipid II includes pyrophosphate, disaccharide residues, and bactoprenol's first isoprene units.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Vladislav V. Motov, Erik F. Kot, Alexandra V. Shabalkina, Sergey A. Goncharuk, Alexander S. Arseniev, Marina V. Goncharuk, Konstantin S. Mineev
Summary: Membrane proteins are essential in molecular biology, but studying their structures requires finding suitable membranes and refolding protocols. Isotropic bicelles are commonly used as membrane mimetics, but the refolding process is still not well understood. To find the best refolding methods for helical membrane proteins, we studied the interactions between proteins, lipids, and detergents in trifluoroethanol-water mixtures. Using NMR spectroscopy and light scattering, we determined key states of the compounds and proposed optimal protocols. These protocols were tested on various membrane domains with successful results.
JOURNAL OF BIOMOLECULAR NMR
(2023)
Article
Biochemistry & Molecular Biology
Eugene P. Kramarova, Sophia S. Borisevich, Edward M. Khamitov, Alexander A. Korlyukov, Pavel Dorovatovskii, Anastasia D. Shagina, Konstantin S. Mineev, Dmitri Tarasenko, Roman A. Novikov, Alexey A. Lagunin, Ivan Boldyrev, Aiarpi A. Ezdoglian, Natalia Yu Karpechenko, Tatiana A. Shmigol, Yuri Baukov, Vadim V. Negrebetsky
Summary: The synthesis of products from the interaction of 1,3-propanesultone ring with amides of pyridinecarboxylic acids was investigated. The position of the substituent in the heteroaromatic fragment and temperature condition influenced the yield of the reaction products. A mechanism and transition-state model were proposed based on spectroscopic, X-Ray, and quantum-chemical calculation data. The synthesized compounds showed promising pharmacological effects and low acute toxicity.
Review
Pharmacology & Pharmacy
Vladislav S. S. Rybchenko, Teimur K. K. Aliev, Anna A. A. Panina, Mikhail P. P. Kirpichnikov, Dmitry A. A. Dolgikh
Summary: The anti-tumor properties of various cytokines have been studied extensively in experiments and clinical trials, but their toxicity and lack of tumor specificity have limited their clinical applications. Utilizing tumor-specific monoclonal antibodies or their fragments to deliver fused cytokines to tumors can minimize side effects and increase therapeutic effectiveness. This review provides an overview of different formats of antibody-cytokine fusion proteins, their targets, mechanisms of action, and biological effects, with a focus on formats that prevent off-target cytokine-receptor interactions to minimize side effects. The efficacy of antibody-mediated cytokine delivery, either as a monotherapy or in combination with other agents, is discussed based on preclinical and clinical data.
Article
Biophysics
Bruno Hargittay, Konstantin S. Mineev, Christian Richter, Sridhar Sreeramulu, Hendrik R. A. Jonker, Krishna Saxena, Harald Schwalbe
Summary: We report the NMR chemical shift assignment of FGF8b, an important regulator of brain embryonic development in humans. The obtained chemical shifts agree with X-ray data, except for the N-terminal gN helix which forms only when complexed with the receptor. This data serves as a starting point for investigating the interaction of FGF8b with its receptors and potential drugs or inhibitors.
BIOMOLECULAR NMR ASSIGNMENTS
(2023)
Article
Biochemistry & Molecular Biology
Lada E. Petrovskaya, Evgeniy P. Lukashev, Mahir D. Mamedov, Elena A. Kryukova, Sergei P. Balashov, Dmitry A. Dolgikh, Andrei B. Rubin, Mikhail P. Kirpichnikov, Sergey A. Siletsky
Summary: Microbial rhodopsins are diverse membrane proteins that convert light energy to ion transport or sensory signals. We aimed to obtain proteoliposomes with unidirectional orientation using a proton-pumping retinal protein from Exiguobacterium sibiricum (ESR) as a model. Three ESR hybrids with soluble protein domains were obtained and characterized. Our experiments show that the hybrid with Caf1M promotes the unidirectional orientation of ESR in proteoliposomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yulia A. Bogdanova, Elvira R. Zaitseva, Alexander Yu. Smirnov, Nadezhda S. Baleeva, Alexey S. Gavrikov, Ivan N. Myasnyanko, Sergey A. Goncharuk, Erik F. Kot, Konstantin S. Mineev, Alexander S. Mishin, Mikhail S. Baranov
Summary: In this study, we demonstrated that NanoLuc luciferase, a well-known enzyme, can serve as a fluorogen activating protein for arylidene-imidazolones analogs of the Kaede protein chromophore. We showed that these compounds can be utilized as fluorescent sensors for this particular protein and can also be employed alongside it as a genetically encoded tag in fluorescent microscopy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Fedor D. Kornilov, Yury B. Slonimskiy, Daria A. Lunegova, Nikita A. Egorkin, Anna G. Savitskaya, Sergey Yu. Kleymenov, Eugene G. Maksimov, Sergey A. Goncharuk, Konstantin S. Mineev, Nikolai N. Sluchanko
Summary: This study explains the ligand promiscuity of AstaPo1 by determining its NMR structure and validating it through various experiments. The FAS1 domain of AstaPo1 binds carotenoids by embracing their polyene structure, but cannot cap the beta-ionone rings to dictate specificity. This research also suggests the neofunctionalization of FAS1 in a subset of AstaP-like proteins in green algae.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Medicinal
Alix Troster, Nathalie Jores, Konstantin S. Mineev, Sridhar Sreeramulu, Michael DiPrima, Giovanna Tosato, Harald Schwalbe
Summary: This concept paper describes the general strategies for EPHA2 inhibition with small molecules and summarizes the potential of targeting EPHA2 in CRC. EPHA2 plays a crucial role in the development and resistance mechanisms of CRC.
Article
Biochemistry & Molecular Biology
Renata I. Zagitova, Konstantin V. Purtov, Aleksandr S. Shcheglov, Konstantin S. Mineev, Maxim A. Dubinnyi, Ivan N. Myasnyanko, Olga A. Belozerova, Vera G. Pakhomova, Valentin N. Petushkov, Natalia S. Rodionova, Vladislav A. Lushpa, Elena B. Guglya, Sergey Kovalchuk, Valeri B. Kozhemyako, Jeremy D. Mirza, Anderson G. Oliveira, Ilia V. Yampolsky, Zinaida M. Kaskova, Aleksandra S. Tsarkova
Summary: In this study, three compounds were isolated and structurally elucidated from the Chaetomorpha linum algae. These compounds showed bioluminescence activity with Chaetopterus luciferase in the presence of Fe2+ ions. They are derivatives of polyunsaturated fatty acid peroxides. The study also confirmed the broad substrate specificity of the luciferase by obtaining and demonstrating the activity of their structural analogues in the bioluminescence reaction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Anna S. Gorbunova, Alexey V. Zamaraev, Maria A. Yapryntseva, Olga V. Kovaleva, Elena M. Tchevkina, Maria V. Turkina, Boris Zhivotovsky, Gelina S. Kopeina
Summary: Lung cancer, especially lung adenocarcinoma (LUAD), is a major cause of cancer-related deaths worldwide. Dysregulation of mitochondrial quality control proteins (MQCPs) in lung cancer cells may impact mitochondrial maintenance and integrity. This study developed a novel MQCP signature to predict overall survival in LUAD patients and successfully stratified patients into high- and low-risk groups.
CELL DEATH DISCOVERY
(2023)
Article
Infectious Diseases
Nelli F. Khabibullina, Daria M. Kutuzova, Irina A. Burmistrova, Irina Lyadova
Summary: Tuberculosis (TB) is a serious global public health problem, with about one quarter of the world's population infected with Mtb and having a latent TB infection (LTBI). The diagnosis and treatment of LTBI are still under discussion due to the broad range of conditions it involves. This review emphasizes the complexity of LTBI and discusses issues such as phenotypic insusceptibility, diagnoses, chemoprophylaxis, and the necessity of treatment.
TROPICAL MEDICINE AND INFECTIOUS DISEASE
(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)