Hydrogen bonds (H-bonds) are pivotal in various chemical and biological systems and exhibit complex behavior under external perturbations. This study investigates the structural, vibrational, and energetic properties of prototypical H-bonded dimers, water (H2O)2, hydrogen fluoride (HF)2, hydrogen sulfide (H2S)2, and ammonia (NH3)2 - and the respective monomers under static and homogeneous electric fields (EFs) using the accurate explicitly correlated singles and doubles coupled cluster method (CCSD) for equilibrium geometries and harmonic vibrational frequencies and the perturbative triples CCSD(T) method for energies. As for the vibrational response of the H2O, HF, H2S, and NH3 monomers, it turns out that dipole derivatives primarily govern the geometry relaxation. Perturbation theory including cubic anharmonicity can reproduce CCSD results on the vibrational Stark effect, except for NH3, where deviations arise due to its floppiness. The field-induced modifications in H-bond lengths, vibrational Stark effects, binding energies, and charge-transfer mechanisms in monomers and dimers are elucidated. Symmetry-adapted perturbation theory (SAPT) analysis on dimers reveals that electrostatics dominates the stabilization of H-bonds across all field strengths, while induction contributions increase significantly with stronger fields, particularly in systems with more polarizable atoms. Our results reveal a universal strengthening of intermolecular interactions at moderate to strong field intensities with significant variability among dimers due to inherent differences in molecular polarizability and charge distribution. Notably, a direct correlation is observed between the binding energies and the vibrational Stark effect of the stretching mode of the H-bond donor molecule, both in relation to the charge-transfer energy term, across all of the investigated dimers. All of these findings provide insights into the EF-driven modulation of H-bonds, highlighting implications for catalysis, hydrogen-based technologies, and biological processes.

• Publikační typ
• časopisecké články MeSH

Pseudouridine is the most frequently naturally occurring RNA modification, found in all classes of biologically functional RNAs. Compared to uridine, pseudouridine contains an additional hydrogen bond donor group and is therefore widely regarded as a structure stabilizing modification. However, the effects of pseudouridine modifications on the structure and dynamics of RNAs have so far only been investigated in a limited number of different structural contexts. Here, we introduced pseudouridine modifications into the U-turn motif and the adjacent U:U closing base pair of the neomycin-sensing riboswitch (NSR)-an extensively characterized model system for RNA structure, ligand binding, and dynamics. We show that the effects of replacing specific uridines with pseudouridines on RNA dynamics crucially depend on the exact location of the replacement site and can range from destabilizing to locally or even globally stabilizing. By using a combination of NMR spectroscopy, MD simulations and QM calculations, we rationalize the observed effects on a structural and dynamical level. Our results will help to better understand and predict the consequences of pseudouridine modifications on the structure and function of biologically important RNAs.

• Klíčová slova
• MD simulations, NMR, RNA structure, U-turn, U:U base pair, pseudouridine,
• MeSH
• konformace nukleové kyseliny MeSH
• párování bází MeSH
• pseudouridin * genetika   MeSH
• RNA * genetika   chemie   MeSH
• uridin MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• pseudouridin * MeSH
• RNA * MeSH
• uridin MeSH

Recognition of single-stranded RNA (ssRNA) by RNA recognition motif (RRM) domains is an important class of protein-RNA interactions. Many such complexes were characterized using nuclear magnetic resonance (NMR) and/or X-ray crystallography techniques, revealing ensemble-averaged pictures of the bound states. However, it is becoming widely accepted that better understanding of protein-RNA interactions would be obtained from ensemble descriptions. Indeed, earlier molecular dynamics simulations of bound states indicated visible dynamics at the RNA-RRM interfaces. Here, we report the first atomistic simulation study of spontaneous binding of short RNA sequences to RRM domains of HuR and SRSF1 proteins. Using a millisecond-scale aggregate ensemble of unbiased simulations, we were able to observe a few dozen binding events. HuR RRM3 utilizes a pre-binding state to navigate the RNA sequence to its partially disordered bound state and then to dynamically scan its different binding registers. SRSF1 RRM2 binding is more straightforward but still multiple-pathway. The present study necessitated development of a goal-specific force field modification, scaling down the intramolecular van der Waals interactions of the RNA which also improves description of the RNA-RRM bound state. Our study opens up a new avenue for large-scale atomistic investigations of binding landscapes of protein-RNA complexes, and future perspectives of such research are discussed.

• MeSH
• HuR protein metabolismus   MeSH
• motiv rozpoznávající RNA genetika   MeSH
• proteiny vázající RNA * metabolismus   MeSH
• RNA * chemie   MeSH
• RRM proteiny metabolismus   MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• HuR protein MeSH
• proteiny vázající RNA * MeSH
• RNA * MeSH
• RRM proteiny MeSH