Cations are known to mediate diverse interactions in nucleic acids duplexes but they are critical in the arrangement of four-stranded structures. Here, we use all-atom molecular dynamics simulations with explicit solvent to analyse the mechanical unfolding of representative intramolecular G-quadruplex structures: a parallel, a hybrid and an antiparallel DNA and a parallel RNA, in the presence of stabilising cations. We confirm the stability of these conformations in the presence of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\rm {K}^+$\end{document} central ions and observe distortions from the tetrad topology in their absence. Force-induced unfolding dynamics is then investigated. We show that the unfolding events in the force-extension curves are concomitant to the loss of coordination between the central ions and the guanines of the G-quadruplex. We found lower ruptures forces for the parallel configuration with respect to the antiparallel one, while the behaviour of the force pattern of the parallel RNA appears similar to the parallel DNA. We anticipate that our results will be essential to interpret the fine structure rupture profiles in stretching assays at high resolution and will shed light on the mechanochemical activity of G-quadruplex-binding machinery.

Employing X-ray photon correlation spectroscopy, we measure the kinetics and dynamics of a pressure-induced liquid−liquid phase separation (LLPS) in a water−lysozyme solution. Scattering invariants and kinetic information provide evidence that the system reaches the phase boundary upon pressure-induced LLPS with no sign of arrest. The coarsening slows down with increasing quench depths. The g 2 functions display a two-step decay with a gradually increasing nonergodicity parameter typical for gelation. We observe fast superdiffusive (γ ≥ 3/2) and slow subdiffusive (γ < 0.6) motion associated with fast viscoelastic fluctuations of the network and a slow viscous coarsening process, respectively. The dynamics age linearly with time τ ∝ t w , and we observe the onset of viscoelastic relaxation for deeper quenches. Our results suggest that the protein solution gels upon reaching the phase boundary.

Water plays a fundamental function in life and technology. To gain a deeper knowledge to the problem of the hydration of biomolecules, the dynamics of water around a 89-residue protein of interest in molecular recognition, cancer cell research and amyloid fribrils investigations is analyzed. The biomolecule is the ribonuclease inhibitor barstar wild-type. The dynamics of the protein and the 7430 water molecules of the bath in which is immersed, is monitored during a period of 7 ns by using all-atom molecular dynamics simulations. The results confirm the existence of multiple time scales in the dynamics of water (10 -1 to 10 3 ps) at atomic level. That heterogeneity of residence times is not lost if the system of reference is just one atom of the inhibitor. The dehydration process of barstar is considered through the analysis of time correlation functions obtaining an averaged decay time of τ = 84.0 ± 0.3 ps. A power law distribution, with scaling exponent α = 0.57 ± 0.04, suggests that this hydration water exhibits a scale free dynamics (with respect to the residence time of solvent molecules). Most of the water molecules located on the surface of the protein spend times smaller than the picosecond while only about 1% of them stay for periods of time on the nanosecond scale.