Article
Biochemistry & Molecular Biology
Lisa M. Petti, Benjamin N. Koleske, Daniel DiMaio
Summary: Most eukaryotic transmembrane and secreted proteins contain N-terminal signal peptides that facilitate membrane insertion and subsequent degradation. A small hydrophobic protein can act as a signal peptide while retaining transforming activity, interacting with target protein transmembrane domains. This finding suggests that naturally occurring signal peptides may have additional biological activities.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Sante Roperto
Summary: Bovine Deltapapillomavirus genus is highly pathogenic and commonly found in bladder tumors of adult cattle and water buffaloes. These viruses are associated with specific gene mutations that may lead to abnormal cell proliferation and differentiation, particularly in animals grazing on pastures rich in bracken fern.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Qingshan Fu, James J. Chou
Summary: The study identified the structure of the TMD of the S protein of SARS-CoV-2, revealing it as a transmembrane alpha-helix trimer that spontaneously assembles in the membrane, with a strong hydrophobic core. The research also found that, despite being highly stable, single mutations can completely dissociate this trimer.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Immunology
R. Hoikhman, D. Molinkova, D. Pillarova, P. Linhart, A. Kopecka, P. Jahn
Summary: Equine sarcoids (ES) are the most common skin tumor in horses, affecting their economic value and welfare. Bovine papillomavirus (BPV) is the cause of this tumor, with the E5 protein downregulating MHC I to escape immune reaction and allow viral infected cells to proliferate into ES. By using an ELISA test, antibodies to the E5 oncoprotein were found in ES positive horses, indicating an immune response to this protein.
VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY
(2023)
Article
Chemistry, Organic
Michael B. Pastor, Chao Feng, Yi-Ju Tsai, Amelia Watson, Qinliang Zhao
Summary: X-ray crystal structures of four substituted N,N'-diarylformamidines reveal the formation of cyclic dimers in solid state, while steric hindrance from substituents affects the coexistence of s-trans and s-cis isomers in solution. The distribution of isomers in solution depends on solvent choice, concentration, and addition of acid or coordinating solvent.
Article
Biochemistry & Molecular Biology
Nikolaus M. Loening, Elisar Barbar
Summary: Swallow, a 62 kDa multidomain protein, plays a critical role in the proper localization of several mRNAs involved in Drosophila oocyte development. Dimerization of Swallow is dependent on a 71-residue self-association domain and is stabilized by its binding interaction with dynein light chain (LC8). The structure of the self-association domain has been characterized using solution-state nuclear magnetic resonance spectroscopy, revealing a parallel coiled-coil structure and providing insight into the regulation of dimerization stability.
Article
Biochemistry & Molecular Biology
Jian Xie, Daniel DiMaio
Summary: Historically, genetic analysis of mammalian cells involved isolating randomly arising mutant cell lines to identify the mutant gene responsible for altered properties. Recent advancements in somatic cell genetics have introduced functional genomics screens which systematically perturb the expression of every protein-coding gene to determine the resulting phenotype. A novel functional genomics screening strategy has been outlined where libraries of artificial transmembrane proteins, called traptamers, are expressed to select rare cells with desired phenotypes that can help dissect complex biological processes. By using this new strategy, insights into the process of how human papillomaviruses enter cells have been gained.
Article
Infectious Diseases
Anna Cutarelli, Francesca De Falco, Valeria Uleri, Canio Buonavoglia, Sante Roperto
Summary: The present study used liquid biopsy to investigate highly pathogenic bovine deltapapillomavirus DNA in blood samples of goats, revealing varying infection rates and genotype distributions. The findings suggest that animal husbandry practices may contribute to cross-species transmission of BPVs.
TRANSBOUNDARY AND EMERGING DISEASES
(2021)
Article
Immunology
Yannick D. Muller, Duy P. Nguyen, Leonardo M. R. Ferreira, Patrick Ho, Caroline Raffin, Roxxana Valeria Beltran Valencia, Zion Congrave-Wilson, Theodore L. Roth, Justin Eyquem, Frederic Van Gool, Alexander Marson, Laurent Perez, James A. Wells, Jeffrey A. Bluestone, Qizhi Tang
Summary: This study revealed a fundamental difference between CD28-TMD and CD8-TMD, indicating that CD28-TMD can modulate CAR T-cell activities by engaging endogenous partners.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Francesca De Falco, Anna Cutarelli, Adriana Florinela Catoi, Barbara Degli Uberti, Bianca Cuccaro, Sante Roperto
Summary: Persistent infection and tumorigenesis by papillomaviruses require manipulation of cellular processes involved in innate immune responses. A study found that a pathway essential for innate immune sensing, the cGAS-STING pathway, is impaired in bovine papillomavirus (BPV) infection, leading to persistent viral infection and tumorigenesis.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Deborah E. Shalev
Summary: Metal chelation plays an important role in providing structural stability and forming reactive centers in metalloproteins. Peptide-metal complexes, which exist in nature, offer a way to study protein binding regions and control experimental variables effectively.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Meng Tang, Ruiyu Cao, Lingyu Du, Jikang Xu, Bin Wu, Bo OuYang
Summary: The study successfully produced small TMD peptides using a combination of TrpLE fusion protein and SNAC-tag under mild conditions, avoiding the usage of toxic reagents and simplifying downstream protein purification and reconstitution. High-quality NMR spectra were obtained for two representative TMDs, demonstrating a more efficient and practical approach for structural characterization of small TM proteins.
Article
Biochemistry & Molecular Biology
Monica L. Fernandez-Quintero, Eugene F. DeRose, Scott A. Gabel, Geoffrey A. Mueller, Klaus R. Liedl
Summary: In this study, the conformational diversity of an anti-GFP-binding nanobody was characterized using molecular dynamics simulations and experimental data from NMR spectroscopy. The results showed excellent agreement between the distance maps obtained from NMR and MD simulations, as well as similar conformational spaces for simulations with and without time-averaged restraints. The motions observed in the ps-ns timescale, particularly in the CDR3 loop, also showed good agreement between measured and calculated order parameters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Alison N. Roth, Yunhua Chen, Marquix A. S. Adamson, Eunbyeol Gi, Molly Wagner, Aaron J. Rossini, Javier Vela
Summary: This study presents a colloidal synthesis method for alkaline-earth chalcogenide nanocrystals using the reaction of metal carboxylates with carbon disulfide or selenourea. The particle sizes of the nanocrystals can be tuned by exploring the synthetic phase space, and the phase purity of the selenide compositions are confirmed using solid-state NMR spectroscopy. Additionally, barium di- and triselenides, rare nanocrystalline alkaline-earth polychalcogenides, are successfully synthesized using this method, and electronic structure calculations reveal their semiconducting properties.
Article
Biochemistry & Molecular Biology
Qingxin Li, Qiwei Huang, Congbao Kang
Summary: In this study, the TM domain of SARS-CoV-2 spike protein was analyzed using solution NMR spectroscopy. The results revealed a helical structure, an unstructured linker, and important amino acid residues. These findings provide valuable insights into the function of the spike protein.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Ann M. Dixon, Syamal Roy
Article
Education, Scientific Disciplines
Hugo A. van den Berg
Article
Education, Scientific Disciplines
Joseph R. Dunford, E. Josiah Lutton, Jolene Atia, Andrew M. Blanks, Hugo A. van den Berg
Article
Education, Scientific Disciplines
Hugo A. van den Berg
Article
Biochemistry & Molecular Biology
Rhiannon L. Brooks, Ann M. Dixon
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2020)
Article
Immunology
Thomas Whalley, Garry Dolton, Paul E. Brown, Aaron Wall, Linda Wooldridge, Hugo van den Berg, Anna Fuller, Jade R. Hopkins, Michael D. Crowther, Meriem Attaf, Robin R. Knight, David K. Cole, Mark Peakman, Andrew K. Sewell, Barbara Szomolay
FRONTIERS IN IMMUNOLOGY
(2020)
Article
Multidisciplinary Sciences
Christine Lockey, Richard J. Edwards, David Roper, Ann M. Dixon
SCIENTIFIC REPORTS
(2020)
Article
Multidisciplinary Sciences
Rhiannon L. Brooks, Chandni S. Mistry, Ann M. Dixon
Summary: The study found that the reticulons closely related to RTNLB13 in Arabidopsis thaliana contain curvature-sensing amphipathic helices (APH) with sequence conservation, playing an important role in ER membrane curvature. In contrast, a more distantly related branch of reticulons developed a linker between the transmembrane domain and APH, which may enhance functional flexibility.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Eleanor S. Jayawant, Jack Hutchinson, Dorota Gasparikova, Christine Lockey, Lidon Prunonosa Lara, Ciaran Guy, Rhiannon L. Brooks, Ann M. Dixon
Summary: Antibiotic resistance poses a significant threat to human health, but antimicrobial peptides show great potential for clinical use. Lynronne-1, identified in the rumen microbiome, has broad-spectrum activity against pathogens and has been studied for its structure and design of new peptides with improved activity.
Article
Multidisciplinary Sciences
Mathew Clement, Lea Knezevic, Tamsin Dockree, James E. McLaren, Kristin Ladell, Kelly L. Miners, Sian Llewellyn-Lacey, Anzelika Rubina, Ore Francis, David K. Cole, Andrew K. Sewell, John S. Bridgeman, David A. Price, Hugo A. van den Berg, Linda Wooldridge
Summary: This study investigates how CD8(+) T cells modulate antigen sensitivity through interactions with MHCI and CD8, showing that this interaction can reorder the agonist hierarchy of peptide ligands with different affinities for the TCR.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Christine Lockey, Hannah Young, Jessica Brown, Ann M. Dixon
Summary: The transmembrane domains of human BCR are sites of strong protein-protein interactions that may play a crucial role in BCR functionality.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
James P. C. Coverdale, Hugo A. van den Berg, Siavash Khazaipoul, Hannah E. Bridgewater, Alan J. Stewart, Claudia A. Blindauer
Summary: This study quantitatively explores the role of the extracellular medium in influencing metal uptake into cells. Utilizing a chemically-defined model system, the researchers found that zinc influx into endothelial cells is correlated with the extracellular free zinc concentration. Additionally, allosteric inhibition of zinc-binding to albumin by free fatty acids was shown to increase zinc flux.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Christopher M. Miles, Pin-Chia Hsu, Ann M. Dixon, Syma Khalid, Gabriele C. Sosso
Summary: This paper investigates the role of cellular membranes in facilitating ice nucleation during cryopreservation and elucidates the factors affecting their ability to act as ice nucleating agents, through molecular dynamics simulations.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Eleanor S. Jayawant, Jonathan D. Beadle, Ina Wilkening, Piotr Raubo, Michael Shipman, Rebecca Notman, Ann M. Dixon
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2020)
Article
Chemistry, Multidisciplinary
Stefan Roesner, George J. Saunders, Ina Wilkening, Eleanor Jayawant, Joanna V. Geden, Paul Kerby, Ann M. Dixon, Rebecca Notman, Michael Shipman
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)