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N6-methyladenosine (m6A) is a prevalent RNA post-transcriptional modification that plays crucial roles in RNA stability, structural dynamics, and interactions with proteins. The YT521-B (YTH) family of proteins, which are notable m6A readers, function through their highly conserved YTH domain. Recent structural investigations and molecular dynamics (MD) simulations have shed light on the recognition mechanism of m6A by the YTHDC1 protein. Despite advancements, using MD to predict the stabilization induced by m6A on the free energy of binding between RNA and YTH proteins remains challenging, due to inaccuracy of the employed force field and limited sampling. For instance, simulations often fail to sufficiently capture the hydration dynamics of the binding pocket. This study addresses these challenges through an innovative methodology that integrates metadynamics, alchemical simulations, and force-field refinement. Importantly, our research identifies hydration of the binding pocket as giving only a minor contribution to the binding free energy and emphasizes the critical importance of precisely tuning force-field parameters to experimental data. By employing a fitting strategy built on alchemical calculations, we refine the m6A partial charges parameters, thereby enabling the simultaneous reproduction of N6 methylation on both the protein binding free energy and the thermodynamic stability of nine RNA duplexes. Our findings underscore the sensitivity of binding free energies to partial charges, highlighting the necessity for thorough parameterization and validation against experimental observations across a range of structural contexts.

The capability of current force fields to reproduce RNA structural dynamics is limited. Several methods have been developed to take advantage of experimental data in order to enforce agreement with experiments. We herein extend an existing framework, which allows arbitrarily chosen force-field correction terms to be fitted by quantification of the discrepancy between observables back-calculated from simulation and corresponding experiments. We apply a robust regularization protocol to avoid overfitting, and additionally introduce and compare a number of different regularization strategies, namely L1-, L2-, Kish Size-, Relative Kish Size- and Relative Entropy-penalties. The training set includes a GACC tetramer as well as more challenging systems, namely gcGAGAgc and gcUUCGgc RNA tetraloops. Specific intramolecular hydrogen bonds in the AMBER RNA force field are corrected with automatically determined parameters that we call gHBfix$_{opt}$. A validation involving a separate simulation of a system present in the training set (gcUUCGgc) and new systems not seen during training (CAAU and UUUU tetramers) displays improvements regarding native population of the tetraloop as well as good agreement with NMR-experiments for tetramers when using the new parameters. Then we simulate folded RNAs (a kink-turn and L1 stalk rRNA) including hydrogen bond types not sufficiently present in the training set. This allows a final modification of the parameter set which is named gHBfix21 and is suggested to be applicable to a wider range of RNA systems., Comment: Supporting information included in ancillary files

Ariel, the Atmospheric Remote-sensing Infrared Exoplanet Large-survey, was adopted as the fourth medium-class mission in ESA's Cosmic Vision programme to be launched in 2029. During its 4-year mission, Ariel will study what exoplanets are made of, how they formed and how they evolve, by surveying a diverse sample of about 1000 extrasolar planets, simultaneously in visible and infrared wavelengths. It is the first mission dedicated to measuring the chemical composition and thermal structures of hundreds of transiting exoplanets, enabling planetary science far beyond the boundaries of the Solar System. The payload consists of an off-axis Cassegrain telescope (primary mirror 1100 mm x 730 mm ellipse) and two separate instruments (FGS and AIRS) covering simultaneously 0.5-7.8 micron spectral range. The satellite is best placed into an L2 orbit to maximise the thermal stability and the field of regard. The payload module is passively cooled via a series of V-Groove radiators; the detectors for the AIRS are the only items that require active cooling via an active Ne JT cooler. The Ariel payload is developed by a consortium of more than 50 institutes from 16 ESA countries, which include the UK, France, Italy, Belgium, Poland, Spain, Austria, Denmark, Ireland, Portugal, Czech Republic, Hungary, the Netherlands, Sweden, Norway, Estonia, and a NASA contribution., Comment: Ariel Definition Study Report, 147 pages. Reviewed by ESA Science Advisory Structure in November 2020. Original document available at: https://www.cosmos.esa.int/documents/1783156/3267291/Ariel_RedBook_Nov2020.pdf/

Notwithstanding manufacture of complex organic molecules from impacting cometary and icy planet surface analogues is well-established, dust grain-grain collisions driven by turbulence in interstellar or circumstellar regions may represent a parallel chemical route toward the shock synthesis of prebiotically relevant species. Here we report on a study, based on the multi-scale shock-compression technique combined with ab initio molecular dynamics approaches, where the shock-waves-driven chemistry of mutually colliding isocyanic acid (HNCO) containing icy grains has been simulated by first-principles. At the shock wave velocity threshold triggering the chemical transformation of the sample (7 km/s), formamide is the first synthesized species representing thus the spring-board for the further complexification of the system. In addition, upon increasing the shock impact velocity, formamide is formed in progressively larger amounts. More interestingly, at the highest velocity considered (10 km/s), impacts drive the production of diverse carbon-carbon bonded species. In addition to glycine, the building block of alanine (i.e., ethanimine) and one of the major components of a plethora of amino-acids including, e.g., asparagine, cysteine, and leucine (i.e., vinylamine) have been detected after shock compression of samples containing the most widespread molecule in the universe (H2) and the simplest compound bearing all the primary biogenic elements (HNCO). The present results indicate novel chemical pathways toward the chemical complexity typical of interstellar and circumstellar regions., Comment: 9 pages, 4 figures

Radiationless deactivation channels of 2-thiocytosine in aqueous environment are revisited by means of quantum-chemical simulations of excited-state absorption spectra, and investigations of potential energy surfaces of the chromophore clustered with two water molecules using the algebraic diagrammatic construction method to the second-order (ADC(2)), and multireference configuration interaction with single and double excitations (MR-CISD) methods. We argue that interactions of explicit water molecules with thiocarbonyl group might enable water-chromophore electron transfer (WCET) which leads to formation of intersystem crossing that was not considered previously. This is the first example of a WCET process occurring in the triplet manifold of electronic states. This phenomenon might explain nonradiative decay of the triplet state population observed in thiopyrimidines in the absence of molecular oxygen. According to our calculations this WCET process might also entail a subsequent, virtually barrierless, electron-driven proton transfer (EDPT) resulting in the formation of hydroxyl radical which could further participate in photohydration or deamination reactions., Comment: 22 pages, 4 figures

Background: Guanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural studies, there is still limited knowledge on GQ folding. Scope of review: We review recent molecular dynamics (MD) simulation studies of the folding of GQs, with an emphasis paid to the human telomeric DNA GQ. We explain the basic principles and limitations of all types of MD methods used to study unfolding and folding in a way accessible to non-specialists. We discuss the potential role of G-hairpin, G-triplex and alternative GQ intermediates in the folding process. We argue that, in general, folding of GQs is fundamentally different from funneled folding of small fast-folding proteins, and can be best described by a kinetic partitioning (KP) mechanism. KP is a competition between at least two (but often many) well-separated and structurally different conformational ensembles. Major conclusions: The KP mechanism is the only plausible way to explain experiments reporting long time-scales of GQ folding and the existence of long-lived sub-states. A significant part of the natural partitioning of the free energy landscape of GQs comes from the ability of the GQ-forming sequences to populate a large number of syn-anti patterns in their G-tracts. The extreme complexity of the KP of GQs typically prevents an appropriate description of the folding landscape using just a few order parameters or collective variables. General significance: We reconcile available computational and experimental studies of GQ folding and formulate basic principles characterizing GQ folding landscapes, Comment: \c{opyright} 2016. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/

The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and RNA-protein interactions. Although state-of-the-art Molecular Dynamics (MD) force fields correctly describe the native state of these tetraloops as a stable free-energy basin on the microsecond time scale, enhanced sampling techniques reveal that the native state is not the global free energy minimum, suggesting yet unidentified significant imbalances in the force fields. Here, we tested our ability to fold the RNA tetraloops in various force fields and simulation settings. We employed three different enhanced sampling techniques, namely, temperature replica exchange MD (T-REMD), replica exchange with solute tempering (REST2), and well-tempered metadynamics (WT-MetaD). We aimed to separate problems caused by limited sampling from those due to force-field inaccuracies. We found that none of the contemporary force fields is able to correctly describe folding of the 5'-GAGA-3' tetraloop over a range of simulation conditions. We thus aimed to identify which terms of the force field are responsible for this poor description of TL folding. We showed that at least two different imbalances contribute to this behavior, namely, overstabilization of base-phosphate and/or sugar-phosphate interactions and underestimated stability of the hydrogen bonding interaction in base pairing. The first artifact stabilizes the unfolded ensemble, while the second one destabilizes the folded state. The former problem might be partially alleviated by reparametrization of the van der Waals parameters of the phosphate oxygens suggested by Case et al., while in order to overcome the latter effect we suggest local potentials to better capture hydrogen bonding interactions., Comment: Reprinted with permission from J. Chem. Theory Comput. 2016, 12 (9), pp 4534-4548. Copyright 2016 American Chemical Society

We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the folding free energy using parallel tempering in combination with well-tempered metadynamics. A key ingredient is the use of a recently developed metric distance, eRMSD, as a biased collective variable. We find that the native fold of both tetraloops is not the global free energy minimum using the Amber\c{hi}OL3 force field. The estimated folding free energies are 30.2kJ/mol for UUCG and 7.5 kJ/mol for GAGA, in striking disagreement with experimental data. We evaluate the viability of all possible one-dimensional backbone force field corrections. We find that disfavoring the gauche+ region of {\alpha} and {\zeta} angles consistently improves the existing force field. The level of accuracy achieved with these corrections, however, cannot be considered sufficient by judging on the basis of available thermodynamic data and solution experiments., Comment: Journal of Physical Chemistry Letters (2016)

DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting from the folded state and long T-REMD starting from the unfolded state, accumulating ~130 {\mu}s of atomistic simulations. Antiparallel G-hairpins should spontaneously form in all stages of the folding to support lateral and diagonal loops, with sub-{\mu}s scale rearrangements between them. We found no clear predisposition for direct folding into specific GQ topologies with specific syn/anti patterns. Our key prediction stemming from the T-REMD is that an ideal unfolded ensemble of the full GQ sequence populates all 4096 syn/anti combinations of its four G-stretches. The simulations can propose idealized folding pathways but we explain that such few-state pathways may be misleading. In the context of the available experimental data, the simulations strongly suggest that the GQ folding could be best understood by the kinetic partitioning mechanism with a set of deep competing minima on the folding landscape, with only a small fraction of molecules directly folding to the native fold. The landscape should further include nonspecific collapse processes where the molecules move via diffusion and consecutive random rare transitions, which could, e.g., structure the propeller loops., Comment: This article has been accepted for publication in Nucleic Acids Research Published by Oxford University Press