keyword
https://read.qxmd.com/read/38537131/analyzing-lipid-membrane-defects-via-a-coarse-grained-to-triangulated-surface-map-the-role-of-lipid-order-and-local-curvature-in-molecular-binding
#1
JOURNAL ARTICLE
Rianne W I van der Pol, Bregje W Brinkmann, G J Agur Sevink
Lipid packing defects are known to serve as quantitative indicators for protein binding to lipid membranes. This paper presents a protocol for mapping molecular lipid detail onto a triangulated continuum leaflet representation. Besides establishing the desired forward counterpart to the existing inverse TS2CG map, this coarse-grained to triangulated surface (CG2TS) map enables straightforward extraction of the defect characteristics for any membrane geometry found in nature. We have applied our protocol to investigate the role of local curvature and varying lipid packing on the defect constant π...
March 27, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38536965/nonadiabatic-conical-intersection-dynamics-in-the-local-diabatic-representation-with-strang-splitting-and-fourier-basis
#2
JOURNAL ARTICLE
Bing Gu
We develop and implement an exact conical intersection nonadiabatic wave packet dynamics method that combines the local diabatic representation, Strang splitting for the total molecular propagator, and discrete variable representation with uniform grids. By employing the local diabatic representation, this method captures all nonadiabatic effects, including nonadiabatic transitions, electronic coherences, and geometric phase. Moreover, it is free of singularities in the first and second derivative couplings and does not require the electronic wave function to be continuous with respect to the nuclear coordinates...
March 27, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38536659/sorcin-promotes-proliferation-of-hepatocellular-carcinoma-by-regulating-vegfa-b-via-pi3k-pathway
#3
JOURNAL ARTICLE
Huan Zhang, Shanshan Hu, Jaceline Gislaine Pires Sanches, Yizi Li, Yuanyi Wei, Chunwen Pu, Jun Zhang
Hepatocellular carcinoma (HCC) is a highly vascularized tumor, one of the most common and lethal cancer-related tumor deaths worldwide, with cell proliferation playing a key role. In this study our western blot results and data from TAGC demonstrate a strong association between Sorcin (SRI) overexpression and poor outcomes in HCC. Moreover, SRI overexpression was remarkably effective in promoting proliferation in vitro and increasing tumor growth in vivo, which were attenuated by knocking down SRI. Mechanistically, SRI regulated vascular endothelial growth factor A (VEGFA) and vascular endothelial growth factor B (VEGFB) through PI3K/Akt/FOXO1 signal pathway...
March 27, 2024: Journal of Physiology and Biochemistry
https://read.qxmd.com/read/38536144/free-energy-density-of-a-fluid-and-its-role-in-solvation-and-binding
#4
JOURNAL ARTICLE
Michael K Gilson, Tom Kurtzman
The concept that a fluid has a position-dependent free energy density appears in the literature but has not been fully developed or accepted. We set this concept on an unambiguous theoretical footing via the following strategy. <u>First</u>, we set forth four desiderata that should be satisfied by any definition of the position-dependent free energy density, f ( R ), in a system comprising only a fluid and a rigid solute: its volume integral, plus the fixed internal energy of the solute, should be the system free energy; it deviates from its bulk value, f bulk , near a solute but should asymptotically approach f bulk with increasing distance from the solute; it should go to zero where the solvent density goes to zero; and it should be well-defined in the most general case of a fluid made up of flexible molecules with an arbitrary interaction potential...
March 27, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38536125/overcoming-solubility-challenges-liposomal-isocoq-carbazole-as-a-promising-anti-tumor-agent-for-inoperable-and-radiation-insensitive-cancers
#5
JOURNAL ARTICLE
Diana Lamaa, Catherine Cailleau, Juliette Vergnaud, Julie Mougin, Jérôme Bignon, Mouad Alami, Elias Fattal, Abdallah Hamze, Nicolas Tsapis
This study evaluated the potential of isoCoQ-Carbazole, a diheterocyclic analog of isoCA-4, as an anti-tumor agent. To overcome its low aqueous solubility, liposomes were developed as a delivery system for the compound. In vitro experiments showed that loaded liposomes exhibited similar activity to the free form on multiple human tumor cell lines. In vivo experiments using a palliative intratumoral injection chemotherapy approach further demonstrated that isoCoQ-Carbazole loaded liposomes significantly reduced tumor growth in a CA-4-resistant HT29 cell model, without inducing any observable toxicity or weight loss in the treated mice...
March 27, 2024: Chembiochem: a European Journal of Chemical Biology
https://read.qxmd.com/read/38536122/investigating-the-potential-of-phenolic-compounds-and-carbohydrates-as-acceptor-substrates-for-levansucrasse-catalyzed-transfructosylation-reaction
#6
JOURNAL ARTICLE
Muriel Wong Min, Lan Liu, Salwa Karboune
This study characterizes the acceptor specificity of levansucrases (LSs) from Gluconobacter oxydans (LS1), Vibrio natriegens (LS2), Novosphingobium aromaticivorans (LS3), and Paraburkholderia graminis (LS4) using sucrose as fructosyl donor and selected phenolic compounds and carbohydrates as acceptors. Overall, V. natriegens LS2 proved to be the best biocatalyst for the transfructosylation of phenolic compounds. More than one fructosyl unit could be attached to fructosylated phenolic compounds. The transfructosylation of epicatechin by P...
March 27, 2024: Chembiochem: a European Journal of Chemical Biology
https://read.qxmd.com/read/38535244/toxicity-assessment-of-new-ag-zno-ago-nanocomposites-an-in-vitro-and-in-vivo-approach
#7
JOURNAL ARTICLE
José Rodrigues do Carmo Neto, Pablo Igor Ribeiro Franco, Yarlla Loyane Lira Braga, Jordana Fernandes de Oliveira, Hugo Felix Perini, Luís Fernando Duarte Albuquerque, Danieli Brolo Martins, Fernanda Rodrigues Helmo, Anderson Assunção Andrade, Marina Pacheco Miguel, Mara Rúbia Nunes Celes, Thiago Lopes Rocha, Anielle Christine Almeida Silva, Juliana Reis Machado, Marcos Vinícius da Silva
Zinc oxide nanoparticles (ZnO NPs) are metal oxide nanomaterials, which are important for several applications: antibacterial, anthelmintic, antiprotozoal and antitumoral, among others. These applications are mainly related to the ability to spontaneously produce and induce the production of reactive oxygen species that are important components for the destruction of pathogens and tumor cells. While trying to potentiate ZnO NPs, studies have associated these NPs with silver oxide (AgO) or silver (Ag) NPs. It has already been reported that this combination (Ag-ZnO/AgO NPs) is able to enhance the microbicidal potential...
February 20, 2024: Journal of Functional Biomaterials
https://read.qxmd.com/read/38533769/activin-e-is-a-tgf%C3%AE-ligand-that-signals-specifically-through-activin-receptor-like-kinase-7
#8
JOURNAL ARTICLE
Kylie A Vestal, Chandramohan Kattamuri, Muhasin Koyiloth, Luisina Ongaro, James A Howard, Aimee Deaton, Simina Ticau, Aditi Dubey, Daniel J Bernard, Thomas B Thompson
Activins are one of the three distinct subclasses within the greater Transforming Growth Factor β (TGFβ) superfamily. First discovered for their critical roles in reproductive biology, activins have since been shown to alter cellular differentiation and proliferation. At present, members of the activin subclass include activin A (ActA), ActB, ActC, ActE, and the more distant members myostatin and GDF11. While the biological roles and signaling mechanisms of most activins class members have been well-studied, the signaling potential of ActE has remained largely unknown...
March 27, 2024: Biochemical Journal
https://read.qxmd.com/read/38533528/silencing-of-circ_0088036-inhibits-growth-and-invasion-of-lung-adenocarcinoma-through-mir-203-sp1-axis
#9
JOURNAL ARTICLE
Xiuhua Liu, Yan Feng, Linna Wang, Lei Shi, Kunxiang Ji, Nan Hu, Yang Du, Mingyang Liu, Man Wang
Lung cancer is the leading cause of cancer-related deaths worldwide. Circular RNA (circRNA) circ_0088036 is a recently discovered circRNA known for its roles in rheumatoid arthritis. The study aimed to study the function of circ_0088036 in lung adenocarcinoma (LUAD). Circ_0088036 expressions were analyzed in the Gene Expression Omnibus (GEO) database. The relationship between circ_0088036 expressions and clinicopathological data of LUAD was assessed. The messenger RNA and protein levels were analyzed by quantitative real-time polymerase chain reaction and Western blot...
April 2024: Journal of Biochemical and Molecular Toxicology
https://read.qxmd.com/read/38532648/unraveling-hypothalamus-pituitary-dysregulation-hypergonadotropism-in-f-1-progeny-due-to-prenatal-exposure-to-hexavalent-chromium
#10
JOURNAL ARTICLE
Ajit Kumar Navin, Mariajoseph Michael Aruldhas, Kathiresh Kumar Mani, Shobana Navaneethabalakrishnan, Sankar Venkatachalam, Sakhila K Banu
The endocrine disruptor hexavalent chromium [Cr(VI)] is a proven reproductive toxicant. We recently demonstrated that prenatal Cr(VI) exposure causes testicular resistance to gonadotropins, resulting in hypergonadotropic hypoandrogenism in F1 rats. However, the mechanism driving hypergonadotropism in F1 rats exposed to Cr(VI) prenatally remains an enigma. Therefore, we hypothesized that 'Prenatal Cr(VI) exposure may disrupt steroid hormones-mediated negative feedback regulation of the hypothalamic GnRH, and its receptor in the pituitary of F1 rats, leading to hypergonadotropism...
April 2024: Journal of Biochemical and Molecular Toxicology
https://read.qxmd.com/read/38531828/first-principles-models-of-polymorphism-of-pharmaceuticals-maximizing-the-accuracy-to-cost-ratio
#11
JOURNAL ARTICLE
Jan Ludík, Veronika Kostková, Štefan Kocian, Petr Touš, Vojtěch Štejfa, Ctirad Červinka
Accuracy and sophistication of in silico models of structure, internal dynamics, and cohesion of molecular materials at finite temperatures increase over time. Applicability limits of ab initio polymorph ranking that would be feasible at reasonable costs currently represent crystals of moderately sized molecules (less than 20 nonhydrogen atoms) and simple unit cells (containing rather only one symmetry-irreducible molecule). Extending the applicability range of the underlying first-principles methods to larger systems with a real-life significance, and enabling to perform such computations in a high-throughput regime represent additional challenges to be tackled in computational chemistry...
March 26, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38531181/an-overview-of-aptamer-design-strategy-prominent-applications-and-potential-challenge-in-plants
#12
JOURNAL ARTICLE
Yanhui Yuan, Yi Li, Siying Liu, Pichang Gong, Jinxing Lin, Xi Zhang
Aptamers, serving as highly efficient molecular recognition and biotechnology tools, have garnered increasing interest in the realm of plant science in recent years. Aptamers are synthetic single-stranded short nucleotides or peptides, that bind targets with high specificity and affinity, triggering precise biological responses. As an alternative to antibodies, aptamers present promising avenues for advancement in biological researches. Aptamers function in a range of fields, encompassing cell signaling, drug development, biosensor technology, as well as botany, agricultural and forestry sciences...
March 19, 2024: Journal of Plant Physiology
https://read.qxmd.com/read/38531104/normal-clinical-laboratory-ranges-by-age-and-sex-and-impact-on-study-screening-outcomes-in-rural-mali
#13
JOURNAL ARTICLE
M'Bouye Doucoure, Amatigue Zeguime, Amadou Niangaly, Merepen A Guindo, Justin Y A Doritchamou, Mahamadoun H Assadou, Abdoulaye Katile, Moussa B Kanoute, Sidiki Perou, Adama Ouattara, Sintry Sanogo, Boucary Ouologuem, Souleymane Traore, Bakary Dao, Drissa Dembele, Mamady Kone, Bourama Kamate, Kourane Sissoko, Seydou Sankare, Sadio Diarra, Amagana Dolo, Mahamadou S Sissoko, Jennifer C C Hume, David Cook, Sara A Healy, J Patrick Gorres, Boubacar Traoré, Jordyn Gamiel, Patrick E Duffy, Issaka Sagara
The interpretation of a laboratory test result requires an appropriate reference range established in healthy subjects, and normal ranges may vary by factors such as geographic region, sex, and age. We examined hematological and clinical chemistry parameters in healthy residents at two rural vaccine trial sites: Bancoumana and Doneguebougou in Mali, West Africa. During screening of clinical studies in 2018 and 2019, peripheral blood samples from 1,192 apparently healthy individuals age 6 months to 82 years were analyzed at a laboratory accredited by the College of American Pathologists for a complete blood count, and creatinine and/or alanine aminotransferase levels...
March 26, 2024: American Journal of Tropical Medicine and Hygiene
https://read.qxmd.com/read/38530869/toward-post-hartree-fock-accuracy-for-protein-ligand-affinities-using-the-molecules-in-molecules-fragmentation-based-method
#14
JOURNAL ARTICLE
Ankur K Gupta, Sarah Maier, Bishnu Thapa, Krishnan Raghavachari
The complexity and size of large molecular systems, such as protein-ligand complexes, pose computational challenges for accurate post-Hartree-Fock calculations. This study delivers a thorough benchmarking of the Molecules-in-Molecules (MIM) method, presenting a clear and accessible strategy for layer/theory selections in post-Hartree-Fock computations on substantial molecular systems, notably protein-ligand complexes. An approach is articulated, enabling augmented computational efficiency by strategically canceling out common subsystem energy terms between complexes and proteins within the supermolecular equation...
March 26, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38530114/cysteine-independent-crispr-associated-protein-labeling-for-presentation-and-co-delivery-of-molecules-toward-genetic-and-epigenetic-regulations
#15
JOURNAL ARTICLE
Sadiya Tanga, Arpita Hota, Arkadeep Karmakar, Paramita Banerjee, Basudeb Maji
Labeling of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) associated proteins (Cas) is a huge challenge for their genome engineering applications. Cysteine-mediated bioconjugation is the most efficient strategy for labeling Cas proteins. Introducing a cysteine residue in the protein at the right place might be challenging without perturbing the enzymatic activity. We report a method that does not require cysteine residues for small molecule presentation on the CRISPR-associated protein SpCas9 for in vitro protein detection, probing cellular protein expression, and nuclear co-delivery of molecules in mammalian cells...
March 26, 2024: Chembiochem: a European Journal of Chemical Biology
https://read.qxmd.com/read/38530090/psl-chemical-biology-symposia-recent-progress-in-ferroptosis
#16
JOURNAL ARTICLE
Arthur Pereira, Leeroy Baron, Romain Bucci, Marina Plays, Giulia Bonasegale, Armel Picard-Bernes, Manuel Bibrowski, Nolwenn Morris, Sacha Marynberg, Fabien Sindikubwabo, Tatiana Cañeque, Sebastian Müller, Ludovic Colombeau, Stéphanie Solier, Yannick Bono, Christine Gaillet, Ludger Johannes, Alain Puisieux, Raphaël Rodriguez
This symposium is the 5th PSL (Paris Sciences & Lettres) Chemical Biology meeting (2015, 2016, 2019, 2023, 2024) held at Institut Curie. This initiative originally started at Institut de Chimie des Substances Naturelles (ICSN) in Gif-sur-Yvette, with a strong focus on chemistry. It was then continued at the Institut Curie (2015) covering a larger scope, before becoming the official PSL Chemical Biology meeting. This latest edition hosted around 150 participants and was focused on the burgeoning field of ferroptosis, its mechanism and implications in health and disease...
March 26, 2024: Chembiochem: a European Journal of Chemical Biology
https://read.qxmd.com/read/38530024/split-proteins-and-reassembly-modules-for-biological-applications
#17
JOURNAL ARTICLE
Jieun Bae, Jonghoon Kim, Jongdoo Choi, Hwiyeong Lee, Minseob Koh
Split systems, modular entities enabling controlled biological processes, have become instrumental in biological research. This review highlights their utility across applications like gene regulation, protein interaction identification, and biosensor development. Covering significant progress over the last decade, it revisits traditional split proteins such as GFP, luciferase, and inteins, and explores advancements in technologies like Cas proteins and base editors. We also examine reassembly modules and their applications in diverse fields, from gene regulation to therapeutic innovation...
March 26, 2024: Chembiochem: a European Journal of Chemical Biology
https://read.qxmd.com/read/38528898/the-canmeds-competency-framework-in-laboratory-medicine-a-phenomenographic-study-exploring-how-professional-roles-are-applied-outside-the-clinical-environment
#18
JOURNAL ARTICLE
Chloe Bogaty, Janneke Frambach
BACKGROUND: The CanMEDS Competency Framework is an internationally recognized model used to outline the proficiencies of a physician. It has predominantly been studied in clinical environments but not all medical specialties take part in direct patient contact. In laboratory medicine, the role of the physician is to promote and enhance patient diagnostics by managing and overseeing the functions of a diagnostic laboratory. METHODS: This phenomenographic study explores the lived experiences of biochemistry, microbiology, and pathology residency program directors to better understand how they utilize the CanMEDS competencies...
February 2024: Canadian Medical Education Journal
https://read.qxmd.com/read/38528715/low-density-lipoprotein-receptor-related-protein-5-6-promotes-endometrial-cancer-progression-and-cancer-cell-immune-escape
#19
JOURNAL ARTICLE
Lifan Shen, Chen Zhang, Genhai Zhu
The study investigated the potential association of the low-density lipoprotein (LDL) genome with endometrial cancer progression based on the Gene Expression Omnibus data set and The Cancer Genome Atlas data set. Differential and weighted gene coexpression network analysis was performed on endometrial cancer transcriptome datasets GSE9750 and GSE106191. The protein-protein interaction network was built using LDL-receptor proteins and the top 50 tumor-associated genes. Low-density lipoprotein-related receptors 5/6 (LRP5/6) in endometrial cancer tissues were correlated with oncogenes, cell cycle-related genes, and immunological checkpoints using Spearman correlation...
April 2024: Journal of Biochemical and Molecular Toxicology
https://read.qxmd.com/read/38528706/correlation-of-the-molecular-cross-sectional-area-of-organic-monofunctional-compounds-with-topological-descriptors
#20
JOURNAL ARTICLE
Didier Desmecht, Vincent Dubois
The molecular cross-sectional area (σ) has proved to be an interesting molecular measure not only in the field of adsorption phenomena on solids but also in biochemistry, physiology, or surfactant chemistry. The existing methods to estimate the cross-sectional areas are either not readily applicable or can only be applied to a limited number of compounds. The aim of this work was to describe a method, as general as possible, quick and easy to perform. To that end, the molecular cross-sectional areas were correlated with topological indices...
March 25, 2024: Journal of Chemical Information and Modeling
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