Biology subjects

Mlynsky, V.

Publications and source records attributed to Mlynsky, V..

18 recordsLinked to original sources

bioRxiv2026

From gHBfix to NBfix: Reweighting-Driven Refinement of Hydrogen-Bond Interactions in RNA Force Fields

Understanding RNA structural dynamics is essential for elucidating its biological functions, and molecular dynamics (MD) simulations provide an important atomistic complement to experimental approaches. However, the predictive power of MD is fundamentally limited by the accuracy of the underlying empirical Force Fields (FFs), particularly in capturing the delicate balance of non-bonded interactions. Here, we present a systematic reparameterization strategy that replaces the external gHBfix19 hydrogen-bond (H-bond) correction potential with an equivalent set of NBfix Lennard-Jones modifications within a state-of-the-art RNA FF. Using a quantitatively converged temperature replica-exchange MD ensemble of the GAGA tetraloop, we employed a reweighting-based optimization protocol to derive NBfix parameters that reproduce the thermodynamic effects of the original gHBfix19 terms. Sequential optimization of individual gHBfix19 components proved essential to ensure stable and transferable parameter refinement. The resulting fully reformulated NBfix-based variant, termed OL3CP-NBfix19, was validated on a representative set of RNA motifs, including tetranucleotides, A-form duplexes, and tetraloops. Across all tested systems, its performance is comparable to that of the reference gHBfix19 FF. By embedding the H-bond corrections directly into the standard non-bonded framework, the NBfix formulation eliminates external biasing potentials, simplifies practical deployment, and reduces computational overhead. Beyond this specific reparameterization, our results demonstrate a practical workflow for translating targeted H-bond corrections into native FF terms for efficient biomolecular simulations.

biophysics↗

bioRxiv2026

Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampling Methods for Force Field Benchmarking

Biologically functional RNAs operate near marginal stability, and their rugged free-energy landscapes and profound structural dynamics - typically not captured by structural biology experiments - play decisive roles. Atomistic molecular dynamics (MD) simulations provide a unique means to characterize these features. However, the applicability of atomistic MD is currently limited by accessible simulation timescales and, most importantly, by force-field (FF) accuracy. Folding free energies ({Delta}G{degrees}fold) of small RNA motifs represent well-defined targets for quantitative benchmarking of RNA FFs. In practice, however, obtaining thermodynamic estimates that are sufficiently robust for direct comparison with experimental data remains highly challenging, even for small RNA systems, and many published studies rely on sampling that is not fully converged. Here, we systematically assess the performance of widely used advanced enhanced-sampling techniques using the 8-mer r(gcGAGAgc) tetraloop as a representative benchmark system. We test temperature replica exchange (T-REMD), two solute-tempering variants of replica exchange (REST2 and REHT), as well as well-tempered metadynamics and on-the-fly probability enhanced sampling combined with solute tempering (ST-MetaD and ST-OPES). Among the tested approaches, T-REMD proves to be the most robust, yielding reproducible folding equilibria and consistent estimates of {Delta}G{degrees}fold after approximately 20 s of simulation time, independent of the initial folded or unfolded conformational ensemble. Our results provide practical guidelines for selecting sampling protocols suitable for quantitative RNA benchmarks and lay the foundation for systematic validation and future refinement of RNA FFs.

biophysics↗

bioRxiv2025

Destabilization of Structured RNAs by OPC and TIP4PD Water Models

The four-point OPC water model has recently gained reputation as the preferred choice for molecular dynamics (MD) simulations of nucleic acids and even proteins, providing more realistic reproduction of bulk physical properties of water than the older three-point models. It has been shown to improve for example simulations of unstructured biomolecules such as RNA tetranucleotides or intrinsically disordered proteins. However, the performance for folded RNA structures was not specifically explored. In this study, we present extensive testing of the OPC water model on three different RNAs with highly intricate tertiary structures - the ribosomal L1 stalk RNA-protein protuberance, the mini tetraloop-tetraloop receptor (miniTTR-6) folded RNA, and the GAAA tetraloop-tetraloop receptor homodimer. The OPC performance is directly compared against SPC/E, TIP3P, OPC3, and TIP4P-EW water models along with the common OL3 AMBER RNA force field (FF). We found substantial effect of the water model on simulation behavior. For all three systems, we observe large-scale unfolding of the RNA, and even loss of the L1 stalk protein-RNA interface, when simulated with the OPC. In contrast, the simulations are entirely stable with the three-point water models. The underlying cause seems to be the higher affinity of the OPC waters to H-bond donor and acceptor groups of the RNA, disrupting the native solute-solute interactions. An identical issue can be observed also for the similar and widely used TIP4PD water model combined with the DES-Amber RNA FF. Our findings suggest that caution is warranted when using the four-point OPC and TIP4PD water models for simulations of structured RNAs. In combination with the current AMBER RNA FFs, the three-point water models may provide more realistic alternatives.

biophysics↗

bioRxiv2025

The Kink-Turn Motif: A Powerful Test for Revealing Weaknesses in RNA Force Fields

The kink-turn is a recurrent RNA structural motif that induces a sharp bend (kink) in the A-form RNA helix. It is defined by key structural features, including consecutive sheared AG base pairs, an A-minor interaction, and multiple base-sugar interactions. Accurate representation of these densely packed non-canonical motifs in molecular dynamics simulations poses a significant challenge for contemporary force fields (FFs). Here, we present extended simulations of ribosomal kink-turn 7 (Kt-7) using a broad spectrum of pair-additive and polarizable RNA FFs. None of the tested FFs manage to flawlessly describe all the specific structural features of the Kt-7, which are described in detail in this work. Still, several FFs provide rather acceptable results and should not cause problems in simulations of larger RNAs containing a kink-turn. On aggregate, the widely used OL3 (ff99bsc0{chi}OL3) and polarizable AMOEBA FFs achieve the best performance. On the other hand, some more recently parametrized FF variants struggle to describe the Kt-7s tertiary A-minor interaction - an ubiquitous tertiary contact in RNA. This raises some concerns about the broader applicability of these FFs and suggests that they may be overfitted to small RNA model systems, such as RNA tetranucleotides. The difficulties manifest as either reversible local disruptions of the A-minor interaction and other tertiary contacts or, in some cases, irreversible unkinking of the entire motif. Based on our findings, we strongly suggest including the kink-turn motif in training and benchmarking datasets as the quintessential regression test to enhance the robustness and accuracy of RNA FF parametrization efforts.

biophysics↗

bioRxiv2025

RNA G-Quadruplex Emerges from a Coil-Like Ensemble via Multiple Pathways

RNA G-quadruplexes (rG4s) are vital structural elements in gene regulation and genome stability. In untranslated regions of mRNAs, rG4s influence translation efficiency and mRNA localization. Additionally, rG4s of long non-coding RNAs and telomeric RNA play roles in RNA processing and cellular aging. Despite their significance, atomic-level folding mechanisms of rG4s remain poorly understood due to their complexity. We used enhanced-sampling all-atom molecular dynamics simulations to model the folding of an r(GGGA)3GGG sequence into a parallel-stranded rG4. The folding pathways suggest that RNA initially adopts a compact coil- like ensemble, marked by dynamic guanine stacking and pairing. The three-quartet rG4 builds up gradually from the coil via diverse routes involving strand rearrangements and guanine incorporations. While the folding mechanism is multi-pathway, various two-quartet rG4s seem to be a common transitory ensemble for most routes. Our simulations also exposed force-field imbalances, with the predicted folding free energy of +12.5 kcal/mol deviating from experiments. Additionally, the enhanced sampling protocol, combining well-tempered metadynamics with solute tempering, faced productivity challenges on the multidimensional free-energy surface. Overall, this study provides atomistic insights into rG4 folding, emphasizing compact coil-like ensembles as key precursors, while revealing limitations in simulating non-canonical RNA structures.

biophysics↗

bioRxiv2024

Integrated Database of Force-Field Parameters, Experimental Measurements and Molecular Dynamics Simulations

Molecular Dynamic (MD) simulation is a vital theoretical tool for exploring nucleic acids (RNA, DNA), proteins and other (bio)molecular systems, generating vast amounts of data daily. Efficient storage and possible reuse of this data is a persistent challenge. Here, we introduce IDA (Integrated DAtabase of force fields and datasets from experiments and MD simulations), an innovative database scheme for datasets from various types of MD simulations. IDA supports outputs from different MD approaches, i.e., standard MD simulations, importance sampling techniques, simulated annealing, and other enhanced sampling methods including replica-exchange simulations. IDA also houses a collection of molecule-specific force fields (FFs) and experimental datasets. Uploaded MD outputs, FFs, and experimental data are integrated in a standardized format, allowing efficient data mining and extraction of valuable insights from the extensive data generated by diverse MD simulations. With the data and metadata holdings of IDA, and the prospective assignment of persistent identifiers, our work aims to make key steps towards making MD data FAIR (findable, accessible, interoperable, reusable).

bioinformatics↗

bioRxiv2024

Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of UUCG RNA Tetraloop and Other Systems.

Molecular dynamics (MD) simulations are an important and well-established tool for investigating RNA structural dynamics, but their accuracy relies heavily on the quality of the employed force field (ff). In this work, we present a comprehensive evaluation of widely used pair-additive and polarizable RNA ffs using the challenging UUCG tetraloop (TL) benchmark system. Extensive standard MD simulations, initiated from the NMR structure of the 14-mer UUCG TL, revealed that most ffs did not maintain the native state, instead favoring alternative loop conformations. Notably, three very recent variants of pair-additive ffs, OL3CP-gHBfix21, DESAMBER, and OL3R2.7, successfully preserved the native structure over a 10 x 20 {micro}s timescale. To further assess these ffs, we performed enhanced sampling folding simulations of the shorter 8-mer UUCG TL, starting from the single-stranded conformation. Estimated folding free energies ({Delta}G{degrees}fold) varied significantly among these three ffs, with values of 0.0 {+/-} 0.6 kcal/mol, 2.4 {+/-} 0.8 kcal/mol, and 7.4 {+/-} 0.2 kcal/mol for OL3CP-gHBfix21, DESAMBER, and OL3R2.7, respectively. The {Delta}G{degrees}fold value from OL3CP-gHBfix21 was closest to experimental data, while the higher {Delta}G{degrees}fold values from DESAMBER and OL3R2.7 were unexpected, suggesting an over- or underestimation of key interactions within the folded and mis(un)folded ensembles. These discrepancies led us to further test DESAMBER and OL3R2.7 ffs on additional RNA and DNA systems, where further performance issues were observed. Our results emphasize the complexity of accurately modeling RNA dynamics and suggest that creating an RNA ff capable of reliably performing across a wide range of RNA motifs remains extremely challenging. In conclusion, our study provides valuable insights into the capabilities of current RNA ffs and highlights key areas for future ff development.

biophysics↗

bioRxiv2024

Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes

Mixed double helices formed by RNA and DNA strands, commonly referred to as hybrid duplexes or hybrids, are essential in biological processes like transcription and reverse transcription. They are also important for their applications in CRISPR gene editing and nanotechnology. Yet, despite their significance, the hybrids have been seldom modeled by atomistic molecular dynamics methodology, and there is no benchmark study systematically assessing the force-field performance. Here, we present an extensive benchmark study of the hybrids using contemporary and commonly utilized pairwise additive and polarizable nucleic acid force fields. Our findings indicate that none of the available force-field choices accurately reproduces all the characteristic structural details of the hybrids. The AMBER force fields are unable to populate the C3'-endo (north) pucker of the DNA strand and underestimate inclination. CHARMM force field accurately describes the C3'-endo pucker and inclination but shows base pair instability. The polarizable force fields struggle with accurately reproducing the helical parameters. Some force-field combinations even demonstrate a discernible conflict between the RNA and DNA parameters. In this work, we offer a candid assessment of the force-field performance for mixed DNA/RNA duplexes. We provide guidance on selecting utilizable force-field combinations, as well as highlight potential pitfalls and best practices for obtaining optimal performance.

biophysics↗

bioRxiv2024

Mechanical stability and unfolding pathways of parallel tetrameric G-quadruplexes probed by pulling simulations

Guanine-quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, many aspects of which remain elusive, despite being important for understanding of structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy - Steered Molecular Dynamics (SMD) simulations - combined with standard Molecular Dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. The vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event and it usually started at the 3-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.

biophysics↗

bioRxiv2023

Parallel G-quadruplex folds via multiple paths involving G-tract stacking and structuring from coil ensemble

G-quadruplexes (G4s) are non-canonical nucleic acid structures that fold through complex processes. Characterization of G4 folding landscape contributes to comprehending G4 roles in gene regulation but is challenging for experiments and computations. Here we investigate the folding of a three-quartet parallel DNA G4 with (GGGA)3GGG sequence using all-atom explicit-solvent enhanced-sampling molecular dynamics (MD) simulations. We suggest an early formation of guanine stacks in the G-tracts, which behave as semi-rigid blocks in the folding process. The parallel G4 folding is initiated by the formation of a collapsed compact coil-like ensemble. Structuring of the G4 from the coil then proceeds via various cross-like, hairpin, slip-stranded, and two-quartet ensembles and can bypass the G-triplex structure. While parallel G-hairpins are extremely unstable when isolated, they are more stable inside the coil structure. Folding of parallel G4 does not appear to involve any salient intermediates and, instead, it is an extremely multiple-pathway process. On the methodology side, we show that the AMBER DNA force field predicts the folded G4 to be less stable than the unfolded ensemble, uncovering substantial force-field issues. Overall, we provide unique atomistic insights into the folding landscape of parallel-stranded G4 but also reveal limitations of the state-of-the-art MD techniques.

molecular biology↗

bioRxiv2023

Simple Adjustment of Intra-nucleotide Base-phosphate Interaction in OL3 AMBER Force Field Improves RNA Simulations

Molecular dynamics (MD) simulations represent an established tool to study RNA molecules. Outcome of MD studies depends, however, on the quality of the used force field (ff). Here we suggest a correction for the widely used AMBER OL3 ff by adding a simple adjustment of nonbonded parameters. The reparameterization of Lennard-Jones potential for the -H8...O5- and -H6...O5- atom pairs addresses an intra-nucleotide steric clash occurring in the type 0 base-phosphate interaction (0BPh). The non-bonded fix (NBfix) modification of 0BPh interactions (the NBfix0BPh modification) was tuned via reweighting approach and, subsequently, tested using extensive set of standard and enhanced sampling simulations of both unstructured and folded RNA motifs. The modification corrects minor but visible intra-nucleotide clash for the anti nucleobase conformation. We observed that structural ensembles of small RNA benchmark motifs simulated with the NBfix0BPh modification provide better agreement with experiments. No side-effects of the modification were observed in standard simulations of larger structured RNA motifs. We suggest that the combination of OL3 RNA ff and NBfix0BPh modification is a viable option to improve RNA MD simulations.

biophysics↗

bioRxiv2023

Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations

Guanine quadruplexes (GQs) are non-canonical nucleic acid structures involved in many biological processes. GQs formed in single-stranded regions often need to be unwound by cellular machinery, so their mechanochemical properties are important. Here, we performed steered molecular dynamics simulations of human telomeric GQs to study their unfolding. We examined four pulling regimes, including very slow setup with pulling velocity and force load accessible to high-speed atomic force microscopy. We identified multiple factors affecting the unfolding mechanism. The more the direction of force was perpendicular to the GQ channel axis (determined by GQ topology), the more the base unzipping mechanism happened. If the GQ had either all-anti or all-syn pattern in a strand, strand slippage mechanism was more likely to occur. Importantly, slower pulling velocity led to richer unfolding pathways including partial refolding attempts. We show that GQ may eventually unfold after force drop under forces smaller than those the GQ withstood before the drop. This suggests that proteins in vivo might resolve GQs even if their stall forces are smaller than GQ rupture force. Finally, we found out that different unfolding intermediates may have very similar chain end-to-end distance, which reveals some limitations of structural interpretations of single-molecule spectroscopic data.

biophysics↗

bioRxiv2022

Spontaneous binding of single-stranded RNAs to RRM proteins visualised by unbiased atomistic simulations with rescaled RNA force field

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 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 (MD) 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 millisecond-scale aggregate ensemble of unbiased simulations we were able to observe a few dozens of binding events. The 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. The SRFS1 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 vdW interactions of the RNA which also improves description of the RNA-RRM bound state. Our study opens a new avenue for large-scale atomistic investigations of binding landscapes of protein-RNA complexes and future perspectives of such research are discussed.

molecular biology↗

bioRxiv2021

Towards Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Corrections

Atomistic molecular dynamics (MD) simulations represent established technique for investigation of RNA structural dynamics. Despite continuous development, contemporary RNA simulations still suffer from suboptimal accuracy of empirical potentials (force fields, ffs) and sampling limitations. Development of efficient enhanced sampling techniques is important for two reasons. First, they allow to overcome the sampling limitations and, second, they can be used to quantify ff imbalances provided they reach a sufficient convergence. Here, we study two RNA tetraloops (TLs), namely the GAGA and UUCG motifs. We perform extensive folding simulations and calculate folding free energies ({Delta}Gfold) with the aim to compare different enhanced sampling techniques and to test several modifications of the nonbonded terms extending the AMBER OL3 RNA ff. We demonstrate that replica exchange solute tempering (REST2) simulations with 12-16 replicas do not show any sign of convergence even when extended to time scale of 120 s per replica. However, combination of REST2 with well-tempered metadynamics (ST-MetaD) achieves good convergence on a time-scale of 5-10 s per replica, improving the sampling efficiency by at least two orders of magnitude. Effects of ff modifications on {Delta}Gfold energies were initially explored by the reweighting approach and then validated by new simulations. We tested several manually-prepared variants of gHBfix potential which improve stability of the native state of both TLs by up to ~2 kcal/mol. This is sufficient to conveniently stabilize the folded GAGA TL while the UUCG TL still remains under-stabilized. Appropriate adjustment of van der Waals parameters for C-H...O5 base-phosphate interaction are also shown to be capable of further stabilizing the native states of both TLs by ~0.6 kcal/mol.

biophysics↗

bioRxiv2020

W-RESP: Well-Restrained Electrostatic Potential Derived Charges. Revisiting the Charge Derivation Model.

Representation of electrostatic interactions by a Coulombic pair-wise potential between atom-centered partial charges is a fundamental and crucial part of empirical force fields used in classical molecular dynamics simulations. The broad success of the AMBER force field family originates mainly from the restrained electrostatic potential (RESP) charge model, which derives partial charges to reproduce the electrostatic field around the molecules. However, description of the electrostatic potential around molecules by standard RESP may be biased for some types of molecules. In this study, we modified the RESP charge derivation model to improve its description of the electrostatic potential around molecules, and thus electrostatic interactions in the force field. In particular, we re-optimized the atomic radii for definition of the grid points around the molecule, redesigned the restraining scheme and included extra point charges. The RESP fitting was significantly improved for aromatic heterocyclic molecules. Thus, the suggested W-RESP(-EP) charge derivation model showed clear potential for improving the performance of the nucleic acid force fields, for which poor description of nonbonded interactions, such as underestimated base pairing, makes it difficult to describe the folding free energy landscape of small oligonucleotides.

biophysics↗

bioRxiv2020

UNCG RNA tetraloop as a formidable force-field challenge for MD simulations

Explicit solvent atomistic molecular dynamics (MD) simulations represent an established technique to study structural dynamics of RNA molecules and an important complement for diverse experimental methods. However, performance of molecular mechanical (MM) force fields (ffs) remains far from satisfactory even after decades of development, as apparent from a problematic structural description of some important RNA motifs. Actually, some of the smallest RNA molecules belong to the most challenging systems for MD simulations and, among them, the UNCG tetraloop is saliently difficult. We report a detailed analysis of UNCG MD simulations, depicting the sequence of events leading to the loss of the UNCG native state during MD simulations. We identify molecular interactions, backbone conformations and substates that are involved in the process. The total amount of MD simulation data analyzed in this work is close to 1.3 millisecond. Then, we unravel specific ff deficiencies using diverse quantum mechanical/molecular mechanical (QM/MM) and QM calculations. Comparison between the MM and QM methods shows discrepancies in the description of the 5-flanking phosphate moiety and both signature sugar-base interactions. Our work indicates that poor behavior of the UNCG tetraloop in simulations is a complex issue that cannot be attributed to one dominant and straightforwardly correctable factor. Instead, there is a concerted effect of multiple ff inaccuracies that are coupled and amplifying each other. We attempted to improve the simulation behavior by some carefully-tailored interventions but the results are still far from satisfactory, underlying the difficulties in development of accurate nucleic acids ffs.

biophysics↗

bioRxiv2020

Fine-tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides

Determination of RNA structural-dynamic properties is challenging for experimental methods. Thus atomistic molecular dynamics (MD) simulations represent a helpful technique complementary to experiments. However, contemporary MD methods still suffer from limitations of force fields (ffs), including imbalances in the non-bonded ff terms. We have recently demonstrated that some improvement of state-of-the-art AMBER RNA ff can be achieved by adding a new term for H-bonding called gHBfix, which increases tuning flexibility and reduces the risk of side-effects. Still, the first gHBfix version did not fully correct simulations of short RNA tetranucleotides (TNs). TNs are key benchmark systems due to availability of unique NMR data, although giving too much weight on improving TN simulations can easily lead to over-fitting to A-form RNA. Here we combine the gHBfix version with another term called tHBfix, which separately treats H-bond interactions formed by terminal nucleotides. This allows to refine simulations of RNA TNs without affecting simulations of other RNAs. The approach is in line with adopted strategy of current RNA ffs, where the terminal nucleotides possess different parameters for the terminal atoms than the internal nucleotides. The combination of gHBfix with tHBfix significantly improves the behavior of RNA TNs during well-converged enhanced-sampling simulations. TNs mostly populate canonical A-form like states while spurious intercalated structures are largely suppressed. Still, simulations of r(AAAA) and r(UUUU) TNs show some residual discrepancies with the primary NMR data which suggests that future tuning of some other ff terms might be useful.

biophysics↗

bioRxiv2018

IMPROVING THE PERFORMANCE OF THE RNA AMBER FORCE FIELD BY TUNING THE HYDROGEN-BONDING INTERACTIONS

Molecular dynamics (MD) simulations became a leading tool for investigation of structural dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force fields, ffs), RNA ffs have persisting deficiencies, which hamper their utilization in quantitatively accurate simulations. Previous studies have shown that at least two salient problems contribute to difficulties in description of free-energy landscapes of small RNA motifs: (i) excessive stabilization of the unfolded single-stranded RNA ensemble by intramolecular base-phosphate and sugar-phosphate interactions, and (ii) destabilization of the native folded state by underestimation of stability of base pairing. Here, we introduce a general ff term (gHBfix) that can selectively fine-tune non-bonding interaction terms in RNA ffs, in particular the H-bonds. gHBfix potential affects the pair-wise interactions between all possible pairs of the specific atom types, while all other interactions remain intact, i.e., it is not a structure-based model. In order to probe the ability of the gHBfix potential to refine the ff non-bonded terms, we performed an extensive set of folding simulations of RNA tetranucleotides and tetraloops. Based on these data we propose particular gHBfix parameters to modify the AMBER RNA ff. The suggested parametrization significantly improves the agreement between experimental data and the simulation conformational ensembles, although our current ff version still remains far from being flawless. While attempts to tune the RNA ffs by conventional reparametrizations of dihedral potentials or non-bonded terms can lead to major undesired side effects as we demonstrate for some recently published ffs, gHBfix has a clear promising potential to improve the ff performance while avoiding introduction of major new imbalances.

biochemistry↗