Article
Chemistry, Multidisciplinary
Han-Wen Chang, Ho- Ma, Yi-Shan Wu, Ming-Che Lee, Eric Chung-Yueh Yuan, Shing-Jong Huang, Yu-Sheng Cheng, Meng-Hsin Wu, Ling-Hsien Tu, Jerry Chun Chung Chan
Summary: This study successfully prepared high molecular-weight oligomeric aggregates of A beta with uniform size and monomorphic structure by incubating A beta peptides in reverse micelles. The A beta Os-40 adopted the structural motif of beta-loop-beta and the A beta Os-42 accelerated the fibrillization of A beta(40) monomers. Cross-seeding experiments showed that A beta Os-42 had an impact on the chemical states of certain residues in A beta Os-40.
Article
Environmental Sciences
Samal Kaumbekova, Mehdi Amouei Torkmahalleh, Masakazu Umezawa, Yanwei Wang, Dhawal Shah
Summary: The impact of air pollutants, specifically ultrafine particles (UFPs), on human health is a growing concern. This study used molecular dynamics simulations to investigate the effects of carbonaceous UFPs on the structure and oligomerization of A beta 42 peptides, which are associated with the development of Alzheimer's disease (AD). The results showed that the presence of carbonaceous UFPs promoted the aggregation and unfolding of the A beta 42 peptides, suggesting a potential link between air pollution and the progression of AD.
ENVIRONMENTAL POLLUTION
(2023)
Article
Biochemistry & Molecular Biology
Clayton A. Whitmore, Mariam I. Boules, William J. Behof, Justin R. Haynes, Dmitry Koktysh, Adam J. Rosenberg, Mohammed N. Tantawy, Wellington Pham
Summary: This study reports the design and synthesis of a novel [C-11]promethazine PET radioligand for future in vivo studies, with high radiochemical purity and molar activity. The specificity of the probe was demonstrated through autoradiography using human hippocampal tissues.
Article
Biochemistry & Molecular Biology
Nadezhda N. Sheveleva, Irina I. Tarasenko, Mikhail A. Vovk, Mariya E. Mikhailova, Igor M. Neelov, Denis A. Markelov
Summary: This paper studies two lysine-based peptide dendrimers with Lys-His-Arg and Lys-Arg-His repeating units and terminal lysine groups. The combination of histidine and arginine in these dendrimers could be important for biomedical applications, such as preventing dendrimer aggregation and facilitating dendrimer penetration through cell membranes. The synthesis of these dendrimers is described, and their structure is confirmed using 1D and 2D Nuclear Magnetic Resonance (NMR) spectroscopy. NMR spectroscopy and relaxation are used to investigate the structural and dynamic properties of these dendrimers and compare them with previously studied dendrimers with Lys-2Arg and Lys-2His repeating units. The results show that both Lys-His-Arg and Lys-Arg-His dendrimers exhibit pH-sensitive conformation and dynamics. The Lys-His-Arg dendrimer, which has a similar conformation to the more hydrophobic Lys-2His dendrimer, could be a more suitable candidate as a pH-sensitive nanocontainer for drug delivery compared to Lys-2His and Lys-Arg-His dendrimers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Lucia De Rosa, Donatella Diana, Rossella Di Stasi, Alessandra Romanelli, Michele F. M. Sciacca, Danilo Milardi, Carla Isernia, Roberto Fattorusso, Luca D. D'Andrea
Summary: Replacing leucine 10 in the QK peptide with different hydrophobic amino acids leads to changes in helical content and thermal stability, depending on the type of interaction that could be established between Leu7 and the residue in position 10. Interestingly, the changes in helical content and thermal stability are not always correlated, highlighting the complex nature of these interactions.
BIOORGANIC CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Andrea Fagagnini, Miguel Garavis, Irene Gomez-Pinto, Sabrina Fasoli, Giovanni Gotte, Douglas V. Laurents
Summary: Protein oligomerization is crucial for various physiological processes and diseases, with human Angiogenin (h-ANG) playing a significant role in this process. Mutations in h-ANG can affect the surrounding residues and active site residues differently. Additionally, there is ongoing debate regarding the structure adopted by RNA fragments after cleavage by h-ANG.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Michele F. M. Sciacca, Irina Naletova, Maria Laura Giuffrida, Francesco Attanasio
Summary: Alzheimer's disease, characterized by the aggregation of amyloid beta protein (A beta), is a common form of dementia. The aggregation and toxicity of A beta are strongly influenced by metal ions and phospholipidic membranes, particularly Cu2+ ions. Currently, there are no available treatments for this disease, but multifunctional compounds that can inhibit A beta fibrillogenesis and prevent the formation of A beta:Cu2+ complexes are of great interest.
ACS CHEMICAL NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Alexander S. Paramonov, Ekaterina N. Lyukmanova, Alexander G. Tonevitsky, Alexander S. Arseniev, Zakhar O. Shenkarev
Summary: Thionins are small cationic cysteine-rich peptides involved in plant immune response, with Viscotoxin A3 (VtA3) from mistletoe demonstrating antimicrobial and cytotoxic activity. The structure of VtA3 in membrane-mimicking media was studied, showing stability and potential ion channel formation. VtA3 interacts with membranes and can form oligomers in certain conditions, with potential implications for membrane disruption mechanisms.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Review
Neurosciences
Theodoros K. Karamanos, Arnout P. Kalverda, Sheena E. Radford
Summary: The early stages of protein misfolding and aggregation involve dynamic disorder and present challenges in capturing atomic level visualization. Identifying specific conformers on-pathway to aggregation within large pools of rapidly moving molecules is complex. This article describes experimental and computational approaches for studying the dynamic nature of protein misfolding and aggregation, and discusses challenges in describing these species due to ensemble averaging of experimental restraints. The potential of machine learning methods in extracting aggregation-relevant sub-ensembles is also explored.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Yang Gao, Stefan Wennmalm, Bengt Winblad, Sophia Schedin-Weiss, Lars O. Tjernberg
Summary: Through FRET imaging, Aβ42 oligomerization was successfully detected in primary neurons, showing that Aβ42 oligomerized in lysosomes/late endosomes in a concentration-dependent manner. These findings contribute to a better understanding of Aβ42 oligomerization in neurons.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Parvathy Jayan, Arshad A. Vahid, Safwa T. Kizhakkeduth, Shafeek O. H. Muhammed, Ajmala B. Shibina, Vinesh Vijayan
Summary: This study revealed the self-aggregation of truncated tau segment R3R4 peptide without the need for heparin induction. Specific regions in R3 and R4 were identified as the initiation sites of protein aggregation, and both R3 and R4 residues were found in the fibril filaments after self-aggregation, suggesting a resemblance to the in vivo aggregation process.
Article
Biochemistry & Molecular Biology
Minseon Kim, Jinyoung Son, Yongae Kim
Summary: This study focused on deriving a new antibacterial peptide with improved activity and less toxicity based on a naturally derived antibacterial peptide, investigating its structure-function relationship through spectroscopic analysis and measurement of minimal inhibitory concentration, as well as studying the structure and mechanism of the antibacterial peptide analog in the cell membrane through nuclear magnetic resonance (NMR) spectroscopy. The study aims to establish a system for the development of novel antibacterial peptides and provide a theoretical basis for research into antibiotic substitutes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Medicine, Research & Experimental
Camille Doyen, Eric Larquet, Pierre-Damien Coureux, Oriane Frances, Frederic Herman, Serge Sable, Jean-Pierre Burnouf, Christina Sizun, Ewen Lescop
Summary: This study utilized NMR spectroscopy to investigate peptide drugs in liposomal delivery systems, characterizing their structural, dynamic, and self-association properties, as well as interactions with liposomes. By studying liposome compositions and preparation methods, and using NMR to characterize membrane fluidity and thermotropic phase transitions, the localization and quantification of peptides within liposomes was achieved.
MOLECULAR PHARMACEUTICS
(2021)
Article
Biochemistry & Molecular Biology
Lennart Nicke, Philip Horx, Ronny Mueller, Sylvia Els-Heindl, Armin Geyer
Summary: A generalized synthetic strategy is proposed for asymmetric beta-indoylated amino acids by 8-aminoquinoline (8AQ)-directed C(sp(3))-H functionalization. The peptides with (indol-3-yl)-3-phenylalanine at position 2 have shown a wide range of activities as ghrelin receptor inverse agonists, demonstrating the potential for systematic variation of indole group position in bioactive peptides.
Article
Chemistry, Multidisciplinary
Renuka Ranjan, Nidhi Tiwari, Arvind M. Kayastha, Neeraj Sinha
Summary: The study utilizes mutant polypeptide as a model to gain insights into the mechanism of domain-swapped aggregation through real-time monitoring, showing the transition of dimer into monomeric intermediates and the presence of other species during aggregation via UV monitoring, DLS profiles, and NMR spectra. Diffusion NMR reveals changes in mobility of dimeric species, indicating the formation of lower molecular weight species during aggregation. This preliminary study explores the possibility of using biophysical methods to understand different stages of aggregation at an atomistic level.
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)