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The HIV-1 envelope glycoprotein (Env) is expressed at the surface of infected cells and as such can be targeted by non-neutralizing antibodies (nnAbs) that mediate antibody-dependent cellular cytotoxicity (ADCC). Previous single-molecule Förster resonance energy transfer (smFRET) studies demonstrated that Env from clinical isolates predominantly adopt a "closed" conformation (State 1), which is resistant to nnAbs. After interacting with the cellular receptor CD4, the conformational equilibrium of Env shifts toward States 2 and 3, exposing the coreceptor binding site (CoRBS) and permitting binding of antibodies targeting this site. We showed that the binding of anti-CoRBS Abs enables the engagement of other nnAbs that target the cluster A epitopes on Env. Anti-cluster A nnAbs stabilize an asymmetric Env conformation, State 2A, and have potent ADCC activity. CRF01_AE strains were suggested to be intrinsically susceptible to ADCC mediated by nnAbs. This may be due to the presence of a histidine at position 375, known to shift Env towards more "open" conformations. In this work, through adaptation of an established smFRET imaging approach, we report that the conformational dynamics of native, unliganded HIV-1 Env indicates frequent sampling of the State 2A conformation. This is in striking contrast with Envs from clades A and B, for example HIV-1, which do not transition to State 2A in the absence of ligands. These findings inform on the conformational dynamics of HIV-1 Env, which are relevant for structure-based design of both synthetic inhibitors of receptor binding, and enhancers of ADCC as therapeutic alternatives.
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http://dx.doi.org/10.1101/2024.08.22.609179 | DOI Listing |
J Phys Chem A
September 2025
Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States.
Ionization of alkanes to form radical cations activates their otherwise unreactive C-H bonds, facilitating important chemical processes such as hydrocarbon cracking. This work investigates the radical cation dissociation dynamics of hexane (CH) structural isomers by using femtosecond time-resolved mass spectrometry and quantum chemical calculations. All five isomers exhibit competition between the yields of fragment ions arising from direct C-C bond cleavage or dissociative rearrangement with hydrogen migration on dynamical time scales of ∼50-300 fs, suggesting that hydrogen migration in the metastable cations operates on such short time scales.
View Article and Find Full Text PDFAnal Chim Acta
November 2025
School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China; Anhui Provincial International Science and Technology Cooperation Base for Major Metabolic Diseases and Nutritional Interventions, Hefei, 230009, China; Intelligent Interconnected Systems Laboratory of A
Background: Copper is a vital trace element that plays a crucial role in various physiological processes due to its ability to exist in multiple oxidation states. Inspired by natural enzymes, researchers have developed copper-based nanozymes that mimic enzyme functions, offering cost-effective and stable alternatives to traditional enzymes. Despite their promising properties, the design and synthesis of these nanozymes can be complex and challenging.
View Article and Find Full Text PDFComput Biol Med
September 2025
Institute of Biotechnology, Department of Medical Biotechnology, SIMATS Engineering, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 602105, Tamil Nadu, India. Electronic address:
Small humanin-like peptide-6 (SHLP6), is derived from the mitochondrial genome. The 3D structure of SHLP6 was evaluated using PEPstr, with homology modeling predicting a Cyt-C structure with a DOPE score of -645.717 and a GA341 score of 0.
View Article and Find Full Text PDFBiophys J
September 2025
Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB, T1K 3M4, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton T6G 2E1, Alberta, Canada; Department of Microbiology, Immunology
The dengue virus (DENV) poses a significant threat to human health, accounting for approximately 400 million infections each year. Its genome features a circular structure that facilitates replication through long-range RNA-RNA interactions, utilizing cyclization sequences located in the untranslated regions (UTRs). To gain new insights into the organization of the DENV genome, we purified the 5' and 3' UTRs of DENV in vitro and examined their structural and binding properties using various biophysical techniques combined with computational methods.
View Article and Find Full Text PDFDrug Discov Today
September 2025
Department of Pharmaceutical and Artificial-Intelligence Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Cen
The landscape of allosteric drug discovery is undergoing a transformative shift, driven by the integration of three computational approaches: machine learning (ML), molecular dynamics (MD) simulations, and network theory. ML identifies potential allosteric sites from multidimensional biological datasets; MD simulations, empowered by enhanced sampling algorithms, reveal transient conformational states; and network analyses uncover communication pathways, further aiding in site identification. Their synergy enables rational allosteric modulator design.
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