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LL37 is a cathelicidin-derived antimicrobial peptide (AMP) with a broad spectrum of antimicrobial activity and wound-healing potential. The enhancement of these characteristics was recently demonstrated for a cysteine (CYS)-modified cathelicidin-derived LL37-SH conjugated with gold nanoparticles (AuNPs). Considering the potential of this peptide, we hereby report a computational study in which well-tempered metadynamics was applied to unveil the interaction of LL37-SH and LL37 with a AuNP with atomistic detail. A structural analysis combined with the free energy surface (FES) characterization allowed the assessment of the role of CYS residue during the formation of the conjugate, as well as to understand how the AuNP improves the antimicrobial activity of the peptide. It was found that CYS promotes a lower conformational entropy (before and after adsorption onto the AuNP) and a faster adsorption process when compared to the LL37 without CYS. The FES for LL37-SH is characterized by one global minimum, while for LL37 a potential metastable state was found. The presence of the AuNP leads to an elongation of the peptides along with the adsorption, which translates into the increase of the solvent-accessible surface area. This elongation combined with the greater availability of positively charged residues upon adsorption rationalizes the observed enhancement of the activity of the LL37-SH/AuNP conjugate.
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http://dx.doi.org/10.1021/acs.jpcb.8b05717 | DOI Listing |
Nucleic Acids Res
September 2025
Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic.
RNA G-quadruplexes (rG4s) are emerging as vital structural elements involved in processes like gene regulation, translation, and genome stability. Found in untranslated regions of messenger RNAs (mRNAs), they influence translation efficiency and mRNA localization. Additionally, rG4s of long noncoding RNAs and telomeric RNA play roles in RNA processing and cellular aging.
View Article and Find Full Text PDFJ Comput Chem
August 2025
Département de Chimie Moléculaire, UMR CNRS 5250/Université Grenoble Alpes, Grenoble Cedex, France.
Organolithium compounds play a pivotal role in organic synthesis, yet their high reactivity and extreme moisture sensitivity-due to the polar carbon-lithium bond-typically necessitate strictly anhydrous conditions. Intriguingly, recent studies have demonstrated that the addition of water can facilitate certain organolithium reactions, such as the efficient synthesis of 2,2-disubstituted tetrahydrofurans via the reaction of methyllithium (MeLi) with 4-chloro-1-phenylbutan-1-one under "on-water" conditions. Despite the success of such transformations, the underlying reaction mechanisms and the behavior of MeLi in aqueous environments remain poorly understood.
View Article and Find Full Text PDFJ Phys Chem B
August 2025
School of Chemical Engineering, National Technical University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, Athens, GR 15780, Greece.
We present an study of the deintercalation of berubicin from two double-stranded oligonucleotide DNA sequences using well-tempered metadynamics (WT-MetaD), an enhanced sampling method widely employed for biomolecular systems. In our recent study (Mikaelian, G. 2024, 128(26), 6291-6307), the thermodynamics of DNA-berubicin complexes in the intercalated state was examined in detail.
View Article and Find Full Text PDFJ Chem Phys
August 2025
Division of Energy, Matter and Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA.
Equilibrium and biased multi-atomic cluster expansion (MACE) accelerated molecular dynamics (MD) simulations in aqueous solutions are performed to investigate the ion capture and transport mechanisms of the {P5W30} Preyssler anion (PA) as the smallest representative member of the extended polyoxometalate (POM) family with an internal cavity. The unique interatomic interactions present in the internal cavity vs the exterior of PA are carefully investigated using equilibrium MACE MD simulations for two representative Na(H2O)@PA and Na@PA complexes in aqueous solutions. Our careful analyses of radial distribution functions and coordination numbers show that the presence of confined water in Na(H2O)@PA has profound modulating effects on the nature of the interactions of the encapsulated ion with the oxygens of the PA cavity.
View Article and Find Full Text PDFbioRxiv
July 2025
Department of Chemical and Biomedical Engineering, University of Wyoming, Laramie, WY 82071, United States.
The dynamic coupling between chromatin organization and biomolecular condensates is governed by chromatin-binding proteins, yet the structural mechanisms by which these proteins modulate nucleosome interactions across spatial and organizational scales remain poorly understood. In this work, using high-resolution sequence-specific coarse-grained models combined with well-tempered metadynamics and parallel tempering, we investigate how heterochromatin protein 1α (HP1α) and a truncated construct of Polyhomeotic-like protein (tPHC3) influence the stability and folding pathways of tetra-nucleosomes, a minimal yet functionally informative chromatin model, under dilute and dense-phase conditions. While these proteins are known to drive distinct nuclear condensates their differential impact on chromatin topology and folding dynamics remains unclear.
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