Article
Chemistry, Multidisciplinary
Devika Vikraman, R. Smrithi Krishnan, Remya Satheesan, Anjali Devi Das, Kozhinjampara R. Mahendran
Summary: In this study, the natural membrane protein CymA was engineered as a nanopore sensor and was found to selectively translocate cationic polypeptides with specific charge and voltage dependence. Additionally, the dynamic segment of the pore was found to play a significant role in molecular transport.
CHEMISTRY-AN ASIAN JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Abdul Basit, Rakesh Kumar Mishra, Pradipta Bandyopadhyay
Summary: Binding of calcium ion to calcium-binding proteins triggers various biological processes, but calculating the binding affinity remains challenging. Implicit polarization method improves agreement between calculated and experimental results, indicating further improvement is necessary for quantitative match.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Review
Physics, Multidisciplinary
Mahmoud Moqadam, Thibault Tubiana, Emmanuel E. Moutoussamy, Nathalie Reuter
Summary: Peripheral membrane proteins temporarily bind to biological membranes but their interface with membrane lipids is hard to observe directly. Molecular dynamics simulations help fill knowledge gaps but due to high computational costs, different levels of membrane models are often used for simulations.
ADVANCES IN PHYSICS-X
(2021)
Article
Infectious Diseases
Teerasit Techawiwattanaboon, Praparat Thaibankluay, Chahya Kreangkaiwal, Suwitra Sathean-Anan-Kun, Prasong Khaenam, Jiradej Makjaroen, Trairak Pisitkun, Kanitha Patarakul
Summary: This study identified surface-exposed outer membrane proteins of pathogenic Leptospira interrogans serovar Pomona using surface biotinylation and proteinase K shaving methods, followed by LC-MS/MS analysis. Analysis revealed known and predicted SE-OMPs, with some of them potentially playing important roles in virulence and infection of leptospires.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Chemistry, Analytical
Durga Devi Khanal, Sajad Tasharofi, Mohammadmehdi Azizi, Morteza G. Khaledi
Summary: The new supramolecular biphasic systems containing fluoroalcohol-induced coacervates (FAiC) offer concomitant fractionation and high solubilizing power for proteins, especially membrane proteins, leading to enrichment of low-abundance proteins. When used in bottom-up proteomics workflow, these systems significantly increase coverage of the whole proteome, various subproteomes, post-translationally modified proteins, and low-abundance proteins compared to conventional methodologies, with a particular impact on integral membrane proteins and proteins with alpha-helices.
ANALYTICAL CHEMISTRY
(2021)
Article
Cell Biology
Qixin Chen, Liu-Yi Liu, Zhiqi Tian, Zhou Fang, Kang-Nan Wang, Xintian Shao, Chengying Zhang, Weiwei Zou, Fiona Rowan, Kangqiang Qiu, Baohua Ji, Jun-Lin Guan, Dechang Li, Zong-Wan Mao, Jiajie Diao
Summary: In this study, a dual-color fluorescent probe called mtGLP was developed to monitor the dynamics of mitochondrial membrane and mtDNA simultaneously. Through experiments and simulations, it was discovered that nucleoid condensates utilize peripheral fission to maintain mitochondrial homeostasis.
Article
Chemistry, Multidisciplinary
Precious Jolugbo, Thomas Willott, Wei-Hsiang Lin, Thomas Maisey, Dermott O'Callaghan, Mark A. Green, David G. Jayne, M. Ibrahim Khot
Summary: We developed a CEA-conjugated polymer nanoparticle probe for targeting CEA-expressing CRC cells in vitro. Its efficacy was evaluated in 2D and 3D cultures of LS174T, LoVo, and HT29 CRC cell lines. CPN510-CEA-Af demonstrated higher fluorescent signal intensity than unconjugated particles, indicating its potential as a probe for image-guided colorectal cancer surgery.
Article
Chemistry, Multidisciplinary
Pengfei Zhang, Jiapei Jiang, Xinyu Zhou, Jayeeta Kolay, Rui Wang, Zijian Wan, Shaopeng Wang
Summary: The optical approach of plasmonic scattering microscopy (PSM) allows label-free imaging and quantification of protein markers on exosomes. PSM provides improved spatial resolution and distortion-free images, similar signal-to-noise ratio to objective coupled surface plasmon resonance (SPR) microscopy, and millimeter-scale field of view for high throughput exosome size distribution analysis.
Article
Biochemical Research Methods
Ke Yan, Hongwu Lv, Yichen Guo, Yongyong Chen, Hao Wu, Bin Liu
Summary: In this study, an adaptive multi-view method is proposed for predicting different types of therapeutic peptides. Experimental results show that the proposed method performs well in predicting multiple types of therapeutic peptides.
Review
Chemistry, Multidisciplinary
Barbara Blanco-Fernandez, Vitor M. Gaspar, Elisabeth Engel, Joao F. Mano
Summary: This article discusses the current landscape of intrinsically bioactive protein and peptide hydrogels employed for 3D tumor modeling, showcasing the importance of recreating the tumor microenvironment and the main considerations for generating ECM-mimetic 3D hydrogel in vitro tumor models.
Review
Chemistry, Multidisciplinary
Enrico Falcone, Christelle Hureau
Summary: This study reports on a concept that explains the formation of reactive oxygen species by copper ions bound to the amyloid-β peptide involved in Alzheimer's disease. The concept is based on a refined and extended in-between state mechanism that was first described a decade ago for pure electron transfer.
CHEMICAL SOCIETY REVIEWS
(2023)
Review
Chemistry, Multidisciplinary
Enrico Falcone, Christelle Hureau
Summary: This article reports on the refinement and extension of a decade-old concept for pure electron transfer to explain the formation of reactive oxygen species by copper ions bound to the Aβ peptide in Alzheimer's disease. The coordination of copper in intrinsically disordered peptides is versatile, and instead of direct electron transfer, an in-between state (IBS) mechanism is proposed. The IBS in copper-bound intrinsically disordered proteins (IDPs) is accessible due to the flexibility of IDPs and fast exchange between coordination sites, and it accounts for the formation of reactive oxygen species (ROS).
CHEMICAL SOCIETY REVIEWS
(2023)
Article
Biochemical Research Methods
Alexios Chatzigoulas, Zoe Cournia
Summary: Abnormal protein-membrane attachment plays a role in cellular pathway dysfunction and diseases. Modulating protein-membrane interactions through machine learning algorithms offers a promising therapeutic strategy for previously undruggable peripheral membrane proteins. This study presents an ensemble machine learning methodology for predicting membrane-penetrating amino acids, achieving high accuracy in identifying these amino acids and providing potential insights for designing drug-like molecules.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Stanislaw Knutelski, Mona Awad, Natalia Lukasz, Michal Bukowski, Justyna Smialek, Piotr Suder, Grzegorz Dubin, Pawel Mak
Summary: The study isolated and identified 17 antibacterial proteins and peptides from the immunized hemolymph of the red palm weevil, describing their nucleotide coding sequences through bioinformatic analysis. The compounds showed bactericidal or bacteriostatic effects, including well-known factors and unexpected findings that require further investigation.
Article
Chemistry, Multidisciplinary
Lilin Feng, Liang Gao, Daniel F. Sauer, Yu Ji, Haiyang Cui, Ulrich Schwaneberg
Summary: This study presents a facile and reversible method to immobilize a wide range of His(6)-tagged proteins on the E. coli cell surface through Fe(iii)-metal complexes. Successfully, an eGFP and four enzymes with His(6)-tag were immobilized on the cell surface. Moreover, a hydrogel sheath around E. coli cells was generated by immobilizing the His(6)-tagged HRP.
CHEMICAL COMMUNICATIONS
(2021)