Force Field for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids

On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules

RNA molecules play a vital role in biological processes within the cell, with significant implications for science and medicine. Notably, the biological functions exerted by specific RNA molecules are often linked to the RNA conformational ensemble. However, the experimental characterization of such three-dimensional RNA structures is challenged by the structural heterogeneity of RNA and by its multiple dynamic interactions with binding partners such as small molecules, proteins, and metal ions. Consequently, our current understanding of the structure-function relationship of RNA molecules is still limited. In this context, we highlight molecular dynamics (MD) simulations as a powerful tool to complement experimental efforts on RNAs. Despite the recognized limitations of current force fields for RNA MD simulations, examining the dynamics of selected RNAs has provided valuable functional insights into their structures.

Unveiling the Mechanism of Phenamacril Resistance in F. graminearum: Computational and Experimental Insights into the C423A Mutation in FgMyoI

Phenamacril (PHA) is a highly selective fungicide for controlling fusarium head blight (FHB) mainly caused by F. graminearum and F. asiaticum. However, the C423A mutation in myosin I of F. graminearum (FgMyoI) leads to natural resistance to PHA. Here, based on the computational approaches and biochemical validation, we elucidate the atomic-level mechanism behind the natural resistance of F. graminearum to the fungicide PHA due to the C423A mutation in FgMyoI. The mutation leads to a rearrangement of pocket residues, resulting in increased size and flexibility of the binding pocket, which impairs the stable binding of PHA. MST experiments confirm that the mutant protein FgMyoIC423A exhibits significantly reduced affinity for PHA compared to wild-type FgMyoI and the nonresistant C423K mutant. This decreased binding affinity likely underlies the development of PHA resistance in F. graminearum. Conversely, the nonresistant C423K mutant retains sensitivity to PHA due to the introduction of a strong hydrogen bond donor, which facilitates stable binding of PHA in the pocket. These findings shed light on the molecular basis of PHA resistance and provide new directions for the creation of new myosin inhibitors.

Targeting the conserved active site of splicing machines with specific and selective small molecule modulators

The self-splicing group II introns are bacterial and organellar ancestors of the nuclear spliceosome and retro-transposable elements of pharmacological and biotechnological importance. Integrating enzymatic, crystallographic, and simulation studies, we demonstrate how these introns recognize small molecules through their conserved active site. These RNA-binding small molecules selectively inhibit the two steps of splicing by adopting distinctive poses at different stages of catalysis, and by preventing crucial active site conformational changes that are essential for splicing progression. Our data exemplify the enormous power of RNA binders to mechanistically probe vital cellular pathways. Most importantly, by proving that the evolutionarily-conserved RNA core of splicing machines can recognize small molecules specifically, our work provides a solid basis for the rational design of splicing modulators not only against bacterial and organellar introns, but also against the human spliceosome, which is a validated drug target for the treatment of congenital diseases and cancers.

RNA targeting and cleavage by the type III-Dv CRISPR effector complex

CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for destruction1-5. Target RNA cleavage at regular intervals is characteristic of type III effector complexes6-8. Here, we determine the structures of the Synechocystis type III-Dv complex, an apparent evolutionary intermediate from multi-protein to single-protein type III effectors9,10, in pre- and post-cleavage states. The structures show how multi-subunit fusion proteins in the effector are tethered together in an unusual arrangement to assemble into an active and programmable RNA endonuclease and how the effector utilizes a distinct mechanism for target RNA seeding from other type III effectors. Using structural, biochemical, and quantum/classical molecular dynamics simulation, we study the structure and dynamics of the three catalytic sites, where a 2'-OH of the ribose on the target RNA acts as a nucleophile for in line self-cleavage of the upstream scissile phosphate. Strikingly, the arrangement at the catalytic residues of most type III complexes resembles the active site of ribozymes, including the hammerhead, pistol, and Varkud satellite ribozymes. Our work provides detailed molecular insight into the mechanisms of RNA targeting and cleavage by an important intermediate in the evolution of type III effector complexes.

Influence of ion and hydration atmospheres on RNA structure and dynamics: insights from advanced theoretical and computational methods

RNA, a highly charged biopolymer composed of negatively charged phosphate groups, defies electrostatic repulsion to adopt well-defined, compact structures. Hence, the presence of positively charged metal ions is crucial not only for RNA's charge neutralization, but they also coherently decorate the ion atmosphere of RNA to stabilize its compact fold. This feature article elucidates various modes of close RNA-ion interactions, with a special emphasis on Mg2+ as an outer-sphere and inner-sphere ion. Through examples, we highlight how inner-sphere chelated Mg2+ stabilizes RNA pseudoknots, while outer-sphere ions can also exert long-range electrostatic interactions, inducing groove narrowing, coaxial helical stacking, and RNA ring formation. In addition to investigating the RNA's ion environment, we note that the RNA's hydration environment is relatively underexplored. Our study delves into its profound interplay with the structural dynamics of RNA, employing state-of-the-art atomistic simulation techniques. Through examples, we illustrate how specific ions and water molecules are associated with RNA functions, leveraging atomistic simulations to identify preferential ion binding and hydration sites. However, understanding their impact(s) on the RNA structure remains challenging due to the involvement of large length and long time scales associated with RNA's dynamic nature. Nevertheless, our contributions and recent advances in coarse-grained simulation techniques offer insights into large-scale structural changes dynamically linked to the RNA ion atmosphere. In this connection, we also review how different cutting-edge computational simulation methods provide a microscopic lens into the influence of ions and hydration on RNA structure and dynamics, elucidating distinct ion atmospheric components and specific hydration layers and their individual and collective impacts.

Surface-Accelerated String Method for Locating Minimum Free Energy Paths

We present a surface-accelerated string method (SASM) to efficiently optimize low-dimensional reaction pathways from the sampling performed with expensive quantum mechanical/molecular mechanical (QM/MM) Hamiltonians. The SASM accelerates the convergence of the path using the aggregate sampling obtained from the current and previous string iterations, whereas approaches like the string method in collective variables (SMCV) or the modified string method in collective variables (MSMCV) update the path only from the sampling obtained from the current iteration. Furthermore, the SASM decouples the number of images used to perform sampling from the number of synthetic images used to represent the path. The path is optimized on the current best estimate of the free energy surface obtained from all available sampling, and the proposed set of new simulations is not restricted to being located along the optimized path. Instead, the umbrella potential placement is chosen to extend the range of the free energy surface and improve the quality of the free energy estimates near the path. In this manner, the SASM is shown to improve the exploration for a minimum free energy pathway in regions where the free energy surface is relatively flat. Furthermore, it improves the quality of the free energy profile when the string is discretized with too few images. We compare the SASM, SMCV, and MSMCV using 3 QM/MM applications: a ribozyme methyltransferase reaction using 2 reaction coordinates, the 2'-O-transphosphorylation reaction of Hammerhead ribozyme using 3 reaction coordinates, and a tautomeric reaction in B-DNA using 5 reaction coordinates. We show that SASM converges the paths using roughly 3 times less sampling than the SMCV and MSMCV methods. All three algorithms have been implemented in the FE-ToolKit package made freely available.

Characterizing the Molecular Mechanism of the Lethal C423D Mutation in FgMyoI: A Molecular Perspective

The lethal mutation C423D in Fusarium graminearum myosin I (FgMyoI) occurs close to the binding pocket of the allosteric inhibitor phenamacril and causes severe inhibition on mycelial growth of F. graminearum strain PH-1. Here, based on extensive Gaussian accelerated molecular dynamics simulations and wet experiments, we elucidate the underlying molecular mechanism of the abnormal functioning of the FgMyoIC423D mutant at the atomistic level. Our results suggest that the damaging mutation C423D exhibits a synergistic allosteric inhibition mechanism similar to but more robust than that of phenamacril, including effects on the active site and actin binding. Unlike phenamacril-induced closure of Switch2, the mutation results in unfolding of the N-terminal relay helix with a partially opened Switch2 and blocks the structural rearrangement of the relay/SH1 helices, impairing the proper initiation of the recovery stroke. Due to the significant influence of C423D mutation on the function of FgMyoI, designing covalent inhibitors targeting this site holds tremendous potential.

DP/MM: A Hybrid Model for Zinc-Protein Interactions in Molecular Dynamics

Zinc-containing proteins are vital for many biological processes, yet accurately modeling them using classical force fields is hindered by complicated polarization and charge transfer effects. This study introduces DP/MM, a hybrid force field scheme that utilizes a deep potential model to correct the atomic forces of zinc ions and their coordinated atoms, elevating them from MM to QM levels of accuracy. Trained on the difference between MM and QM atomic forces across diverse zinc coordination groups, the DP/MM model faithfully reproduces structural characteristics of zinc coordination during simulations, such as the tetrahedral coordination of Cys4 and Cys3His1 groups. Furthermore, DP/MM allows water exchange in the zinc coordination environment. With its unique blend of accuracy, efficiency, flexibility, and transferability, DP/MM serves as a valuable tool for studying structures and dynamics of zinc-containing proteins and also represents a pioneering approach in the evolving landscape of machine learning potentials for molecular modeling.

Modeling Lanthanide Ions in Solution: A Versatile Force Field in Aqueous and Organic Solvents

In this paper, we propose a new nonpolarizable force field for describing the Ln3+ (Ln = lanthanide) series based on a 12-6-4 Lennard-Jones potential. The development of the force field was performed in pure water by adjusting both the ion-oxygen distance and the hydration free energy. This force field accurately reproduces the Ln3+ hydration properties through the series, especially the coordination number that is hardly accessible using a nonpolarizable force field. Then, the validity and the transferability of the current force field were evaluated for two different systems containing Ln3+ in various solvents, namely, 0.1 mol L-1 La(NO3)3 salts in methanol and Eu(NO3)3 salts in solvent organic phases composed of DMDOHEMA molecules in n-heptane. The good agreement between our simulations and the data available in the literature confirms the accuracy of the force field for describing the lanthanide cations in both aqueous and nonaqueous media.

Allosteric inhibition of myosin by phenamacril: a synergistic mechanism revealed by computational and experimental approaches

BACKGROUND

Myosin plays a crucial role in cellular processes, while its dysfunction can lead to organismal malfunction. Phenamacril (PHA), a highly species-specific and non-competitive inhibitor of myosin I (FgMyoI) from Fusarium graminearum, has been identified as an effective fungicide for controlling plant diseases caused by partial Fusarium pathogens, such as wheat scab and rice bakanae. However, the molecular basis of its action is still unclear.

RESULTS

This study used multiple computational approaches first to elucidate the allosteric inhibition mechanism of FgMyoI by PHA at the atomistic level. The results indicated the increase of adenosine triphosphate (ATP) binding affinity upon PHA binding, which might impede the release of hydrolysis products. Furthermore, simulations revealed a broadened outer cleft and a significantly more flexible interface for actin binding, accompanied by a decrease in signaling transduction from the catalytic center to the actin-binding interface. These various effects might work together to disrupt the actomyosin cycle and hinder the ability of motor to generate force. Our experimental results further confirmed that PHA reduces the enzymatic activity of myosin and its binding with actin.

CONCLUSION

Therefore, our findings demonstrated that PHA might suppress the function of myosin through a synergistic mechanism, providing new insights into myosin allostery and offering new avenues for drug/fungicide discovery targeting myosin. © 2023 Society of Chemical Industry.

Discovery of potent pyrrolo-pyrimidine and purine HDAC inhibitors for the treatment of advanced prostate cancer

The development of drugs for the treatment of advanced prostate cancer (PCA) remains a challenging task. In this study we have designed, synthesized and tested twenty-nine novel HDAC inhibitors based on three different zinc binding groups (trifluoromethyloxadiazole, hydroxamic acid, and 2-mercaptoacetamide). These warheads were conveniently tethered to variously substituted phenyl linkers and decorated with differently substituted pyrrolo-pyrimidine and purine cap groups. Remarkably, most of the compounds showed nanomolar inhibitory activity against HDAC6. To provide structural insights into the Structure-Activity Relationships (SAR) of the investigated compounds, docking of representative inhibitors and molecular dynamics of HDAC6-inhibitor complexes were performed. Compounds of the trifluoromethyloxadiazole and hydroxamic acid series exhibited promising anti-proliferative activities, HDAC6 targeting in PCA cells, and in vitro tumor selectivity. Representative compounds of the two series were tested for solubility, cell permeability and metabolic stability, demonstrating favorable in vitro drug-like properties. The more interesting compounds were subjected to migration assays, which revealed that compound 13 and, to a lesser extent, compound 15 inhibited the invasive behaviour of androgen-sensitive and -insensitive advanced prostate cancer cells. Compound 13 was profiled against all HDACs and found to inhibit all members of class II HDACs (except for HDAC10) and to be selective with respect to class I and class IV HDACs. Overall, compound 13 combines potent inhibitory activity and class II selectivity with favorable drug-like properties, an excellent anti-proliferative activity and marked anti-migration properties on PCA cells, making it an excellent lead candidate for further optimization.

Mechanism of Fluoride Ion Encapsulation by Magnesium Ions in a Bacterial Riboswitch

Riboswitches sense various ions in bacteria and activate gene expression to synthesize proteins that help maintain ion homeostasis. The crystal structure of the aptamer domain (AD) of the fluoride riboswitch shows that the F- ion is encapsulated by three Mg2+ ions bound to the ligand-binding domain (LBD) located at the core of the AD. The assembly mechanism of this intricate structure is unknown. To this end, we performed computer simulations using coarse-grained and all-atom RNA models to bridge multiple time scales involved in riboswitch folding and ion binding. We show that F- encapsulation by the Mg2+ ions bound to the riboswitch involves multiple sequential steps. Broadly, two Mg2+ ions initially interact with the phosphate groups of the LBD using water-mediated outer-shell coordination and transition to a direct inner-shell interaction through dehydration to strengthen their interaction with the LBD. We propose that the efficient binding mode of the third Mg2+ and F- is that they form a water-mediated ion pair and bind to the LBD simultaneously to minimize the electrostatic repulsion between three Mg2+ bound to the LBD. The tertiary stacking interactions among the LBD nucleobases alone are insufficient to stabilize the alignment of the phosphate groups to facilitate Mg2+ binding. We show that the stability of the whole assembly is an intricate balance of the interactions among the five phosphate groups, three Mg2+, and the encapsulated F- ion aided by the Mg2+ solvated water. These insights are helpful in the rational design of RNA-based ion sensors and fast-switching logic gates.

The inhibitory mechanism of echinacoside against Staphylococcus aureus Ser/Thr phosphatase Stp1 by virtual screening and molecular modeling

CONTEXT

Stp1 is a new potential target closely related to the pathogenicity of Staphylococcus aureus (S. aureus). In this study, effective Stp1 inhibitors were screened via virtual screening and enzyme activity experiments, and the inhibition mechanism was analyzed using molecular dynamics simulation.

METHODS

AutoDock Vina 4.0 software was used for virtual screening. The molecular structures of Stp1 and ligands were obtained from the RCSB Protein Data Bank and Zinc database, respectively. The molecular dynamics simulation used the Gromacs 4.5.5 software package with the Amberff99sb force field and TIP3P water model. AutoDock Tools was used to add polar hydrogen atoms to Stp1 and distribute part of the charge generated by Kollman's combined atoms. The binding free energies were calculated using the Amber 10 package.

RESULTS

The theoretical calculation results are consistent with the experimental results. We found that echinacoside (ECH) substantially inhibits the hydrolytic activity of Stp1. ECH competes with the substrate by binding to the active center of Stp1, resulting in a decrease in Stp1 activity. In addition, Met39, Gly41, Asp120, Asn162, and Ile163 were identified to play key roles in the binding of Stp1 to ECH. The benzene ring of ECH also plays an important role in complex binding. These findings provide a robust foundation for the development of innovative anti-infection drugs.

The Modulation of Sucrose Nonfermenting 1-Related Protein Kinase 2.6 State by Persulfidation and Phosphorylation: Insights from Molecular Dynamics Simulations

SnRK2.6 (SUCROSE NONFERMENTING 1-RELATED PROTEIN KINASE2.6) has been characterized as a molecular switch for the intracellular abscisic acid (ABA) signal-transduction pathway. Normally, SnRK2.6 is kept in an "off" state, forming a binary complex with protein phosphatase type 2Cs (PP2Cs). Upon stressful conditions, SnRK2.6 turns into an "on" state by its release from PP2Cs and then phosphorylation at Ser175. However, how the "on" and "off" states for SnRK2.6 are fine-tuned, thereby controlling the initiation and braking processes of ABA signaling, is still largely unclear. SnRK2.6 activity was tightly regulated through protein post-translational modifications (PTM), such as persulfidation and phosphorylation. Taking advantage of molecular dynamics simulations, our results showed that Cys131/137 persulfidation on SnRK2.6 induces destabilized binding and weakened interactions between SnRK2.6 and HAB1 (HYPERSENSITIVE TO ABA1), an important PP2C family protein. This unfavorable effect on the association of the SnRK2.6-HAB1 complex suggests that persulfidation functions are a positive regulator of ABA signaling initiation. In addition, Ser267 phosphorylation in persulfidated SnRK2.6 renders a stable physical association between SnRK2.6 and HAB1, a key characterization for SnRK2.6 inhibition. Rather than Ser175, HAB1 cannot dephosphorylate Ser267 in SnRK2.6, which implies that the retained phosphorylation status of Ser267 could ensure that the activated SnRK2.6 reforms the binary complex to cease ABA signaling. Taken together, our findings expand current knowledge concerning the regulation of persulfidation and phosphorylation on the state transition of SnRK2.6 and provide insights into the fine-tuned mechanism of ABA signaling.

Microcalorimetry reveals multi-state thermal denaturation of G. stearothermophilus tryptophanyl-tRNA synthetase

Mechanistic studies of Geobacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) afford an unusually detailed description-the escapement mechanism-for the distinct steps coupling catalysis to domain motion, efficiently converting the free energy of ATP hydrolysis into biologically useful alternative forms of information and work. Further elucidation of the escapement mechanism requires understanding thermodynamic linkages between domain configuration and conformational stability. To that end, we compare experimental thermal melting of fully liganded and apo TrpRS with a computational simulation of the melting of its fully liganded form. The simulation also provides important structural cameos at successively higher temperatures, enabling more confident interpretation. Experimental and simulated melting both proceed through a succession of three transitions at successively higher temperature. The low-temperature transition occurs at approximately the growth temperature of the organism and so may be functionally relevant but remains too subtle to characterize structurally. Structural metrics from the simulation imply that the two higher-temperature transitions entail forming a molten globular state followed by unfolding of secondary structures. Ligands that stabilize the enzyme in a pre-transition (PreTS) state compress the temperature range over which these transitions occur and sharpen the transitions to the molten globule and fully denatured states, while broadening the low-temperature transition. The experimental enthalpy changes provide a key parameter necessary to convert changes in melting temperature of combinatorial mutants into mutationally induced conformational free energy changes. The TrpRS urzyme, an excerpted model representing an early ancestral form, containing virtually the entire catalytic apparatus, remains largely intact at the highest simulated temperatures.

Comparison of force fields to study the zinc-finger containing protein NPL4, a target for disulfiram in cancer therapy

Molecular dynamics (MD) simulations are a powerful approach to studying the structure and dynamics of proteins related to health and disease. Advances in the MD field allow modeling proteins with high accuracy. However, modeling metal ions and their interactions with proteins is still challenging. NPL4 is a zinc-binding protein and works as a cofactor for p97 to regulate protein homeostasis. NPL4 is of biomedical importance and has been proposed as the target of disulfiram, a drug recently repurposed for cancer treatment. Experimental studies proposed that the disulfiram metabolites, bis-(diethyldithiocarbamate)‑copper and cupric ions, induce NPL4 misfolding and aggregation. However, the molecular details of their interactions with NPL4 and consequent structural effects are still elusive. Here, biomolecular simulations can help to shed light on the related structural details. To apply MD simulations to NPL4 and its interaction with copper the first important step is identifying a suitable force field to describe the protein in its zinc-bound states. We examined different sets of non-bonded parameters because we want to study the misfolding mechanism and cannot rule out that the zinc may detach from the protein during the process and copper replaces it. We investigated the force-field ability to model the coordination geometry of the metal ions by comparing the results from MD simulations with optimized geometries from quantum mechanics (QM) calculations using model systems of NPL4. Furthermore, we investigated the performance of a force field including bonded parameters to treat copper ions in NPL4 that we obtained based on QM calculations.

Benchmarking biomolecular force field-based Zn2+ for mono- and bimetallic ligand binding sites

Zn²⁺ is one of the most versatile biologically available metal ions, but accurate modeling of Zn²⁺ -containing metalloproteins at the biomolecular force field level can be challenging. Since most Zn²⁺ models are parameterized in bulk solvent, in-depth knowledge about their performance in a protein environment is limited. Thus, we systematically investigate here the behavior of non-polarizable Zn²⁺ models for their ability to reproduce experimentally determined metal coordination and ligand binding in metalloproteins. The benchmarking is performed in challenging environments, including mono- (carbonic anhydrase II) and bimetallic (metallo-β-lactamase VIM-2) ligand binding sites. We identify key differences in the performance between the Zn²⁺ models with regard to the preferred ligating atoms (charged/non-charged), attraction of water molecules, and the preferred coordination geometry. Based on these results, we suggest suitable simulation conditions for varying Zn²⁺ site geometries that could guide the further development of biomolecular Zn²⁺ models.

Machines on Genes through the Computational Microscope

Macromolecular machines acting on genes are at the core of life's fundamental processes, including DNA replication and repair, gene transcription and regulation, chromatin packaging, RNA splicing, and genome editing. Here, we report the increasing role of computational biophysics in characterizing the mechanisms of "machines on genes", focusing on innovative applications of computational methods and their integration with structural and biophysical experiments. We showcase how state-of-the-art computational methods, including classical and ab initio molecular dynamics to enhanced sampling techniques, and coarse-grained approaches are used for understanding and exploring gene machines for real-world applications. As this review unfolds, advanced computational methods describe the biophysical function that is unseen through experimental techniques, accomplishing the power of the "computational microscope", an expression coined by Klaus Schulten to highlight the extraordinary capability of computer simulations. Pushing the frontiers of computational biophysics toward a pragmatic representation of large multimegadalton biomolecular complexes is instrumental in bridging the gap between experimentally obtained macroscopic observables and the molecular principles playing at the microscopic level. This understanding will help harness molecular machines for medical, pharmaceutical, and biotechnological purposes.

Comparison of Empirical Zn2+ Models in Protein–DNA Complexes

Zinc ions are the second most abundant ions found in humans. Their role in proteins can be merely structural but also catalytic, owing to their transition metal character. Modelling their geometric–coordination versatility by empirical force fields is, thus, a challenging task. In this work, we evaluated three popular models, specifically designed to represent zinc ions with regard to their capability of preserving structural integrity. To this end, we performed molecular dynamics simulations of two zinc-containing protein–DNA complexes, which differed in their zinc coordination, i.e., four cysteines or two cysteines and two histidines. The most flexible non-bonded 12-6-4 Lennard–Jones-type model shows a preference for six-fold coordination of the Zn2+-ions in contradiction to the crystal structure. The cationic dummy atom model favours tetrahedral geometry, whereas the bonded extended zinc AMBER force field model, by construction, best preserves the initial geometry of a regular or slightly distorted tetrahedron. Our data renders the extended zinc AMBER force field the best model for structural zinc ions in a given geometry. In more complicated cases, though, more flexible models may be advantageous.

RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations

The distribution of cations around nucleic acids is essential for a broad variety of processes ranging from DNA condensation and RNA folding to the detection of biomolecules in biosensors. Predicting the exact distribution of ions remains challenging since the distribution and, hence, a broad variety of nucleic acid properties depend on the salt concentration, the valency of the ions, and the ion type. Despite the importance, a general theory to quantify ion-specific effects for highly charged biomolecules is still lacking. Moreover, recent experiments reveal that despite their similar building blocks, DNA and RNA duplexes can react differently to the same ionic conditions. The aim of our current work is to provide a comprehensive set of molecular dynamics simulations using more than 180 μs of simulation time. For the mono- and divalent cations Li⁺, Na⁺, K⁺, Cs⁺, Ca²⁺, Sr²⁺, and Ba²⁺, the simulations allow us to reveal the ion-specific distributions and binding patterns for DNA and RNA duplexes. The microscopic insights from the simulations display the origin of ion-specificity and shed light on the question of why DNA and RNA show opposing behavior in the same ionic conditions. Finally, the detailed binding patterns from the simulations reveal why RNA can capture more cations than DNA.

RNA as a Major-Groove Ligand: RNA-RNA and RNA-DNA Triplexes Formed by GAA and UUC or TTC Sequences

Friedreich's ataxia is associated with noncanonical nucleic acid structures that emerge when GAA:TTC repeats in the first intron of the FXN gene expand beyond a critical number of repeats. Specifically, the noncanonical repeats are associated with both triplexes and R-loops. Here, we present an in silico investigation of all possible triplexes that form by attaching a third RNA strand to an RNA:RNA or DNA:DNA duplex, complementing previous DNA-based triplex studies. For both new triplexes results are similar. For a pyridimine UUC⁺ third strand, the parallel orientation is stable while its antiparallel counterpart is unstable. For a neutral GAA third strand, the parallel conformation is stable. A protonated GA⁺A third strand is stable in both parallel and antiparallel orientations. We have also investigated Na⁺ and Mg²⁺ ion distributions around the triplexes. The presence of Mg²⁺ ions helps stabilize neutral, antiparallel GAA triplexes. These results (along with previous DNA-based studies) allow for the emergence of a complete picture of the stability and structural characteristics of triplexes based on the GAA and TTC/UUC sequences, thereby contributing to the field of trinucleotide repeats and the associated unusual structures that trigger expansion.

RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis

Electrostatic interactions are fundamental to RNA structure and function, and intimately influenced by solvation and the ion atmosphere. RNA enzymes, or ribozymes, are catalytic RNAs that are able to enhance reaction rates over a million-fold, despite having only a limited repertoire of building blocks and available set of chemical functional groups. Ribozyme active sites usually occur at junctions where negatively charged helices come together, and in many cases leverage this strained electrostatic environment to recruit metal ions in solution that can assist in catalysis. Similar strategies have been implicated in related artificially engineered DNA enzymes. Herein, we apply Poisson-Boltzmann, 3D-RISM, and molecular simulations to study a set of metal-dependent small self-cleaving ribozymes (hammerhead, pistol, and Varkud satellite) as well as an artificially engineered DNAzyme (8-17) to examine electrostatic features and their relation to the recruitment of monovalent and divalent metal ions important for activity. We examine several fundamental roles for these ions that include: (1) structural integrity of the catalytically active state, (2) pKa tuning of residues involved in acid-base catalysis, and (3) direct electrostatic stabilization of the transition state via Lewis acid catalysis. Taken together, these examples demonstrate how RNA electrostatics orchestrates the site-specific and territorial binding of metal ions to play important roles in catalysis.

Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme

The pistol ribozyme (Psr) is one among the most recently discovered classes of small nucleolytic ribozymes that catalyze site-specific RNA self-cleavage through 2'-O-transphosphorylation. The Psr contains a conserved guanine (G40) that in crystal structures is in a position suggesting it plays the role of the general base to abstract a proton from the nucleophile to activate the reaction. Although some functional data is consistent with this mechanistic role, a notable exception is 2-aminopurine (2AP) substitution which has no effect on the rate, unlike similar substitutions across other so-called "G + M" and "G + A" ribozyme classes. Herein we postulate that an alternate conserved guanine, G42, is the primary general base, and provide evidence from molecular simulations that the active site of Psr can undergo local refolding into a structure that is consistent with the common "L-platform/L-scaffold" architecture identified in G + M and G + A ribozyme classes with Psr currently the notable exception. We summarize the key currently available experimental data and present new classical and combined quantum mechanical/molecular mechanical simulation results that collectively suggest a new hypothesis. We hypothesize that there are two available catalytic pathways supported by different conformational states connected by a local refolding of the active site: (1) a primary pathway with an active site architecture aligned with the L-platform/L-scaffold framework where G42 acts as a general base, and (2) a secondary pathway with the crystallographic active site architecture where G40 acts as a general base. We go on to make several experimentally testable predictions, and suggest specific experiments that would ultimately bring closure to the mystery as to "who stole the proton in the pistol ribozyme?".

Twisting DNA by salt

The structure and properties of DNA depend on the environment, in particular the ion atmosphere. Here, we investigate how DNA twist -one of the central properties of DNA- changes with concentration and identity of the surrounding ions. To resolve how cations influence the twist, we combine single-molecule magnetic tweezer experiments and extensive all-atom molecular dynamics simulations. Two interconnected trends are observed for monovalent alkali and divalent alkaline earth cations. First, DNA twist increases monotonously with increasing concentration for all ions investigated. Second, for a given salt concentration, DNA twist strongly depends on cation identity. At 100 mM concentration, DNA twist increases as Na+ < K+ < Rb+ < Ba2+ < Li+ ≈ Cs+ < Sr2+ < Mg2+ < Ca2+. Our molecular dynamics simulations reveal that preferential binding of the cations to the DNA backbone or the nucleobases has opposing effects on DNA twist and provides the microscopic explanation of the observed ion specificity. However, the simulations also reveal shortcomings of existing force field parameters for Cs+ and Sr2+. The comprehensive view gained from our combined approach provides a foundation for understanding and predicting cation-induced structural changes both in nature and in DNA nanotechnology.

Consistent Picture of Phosphate-Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization

The binding of divalent cations to the ubiquitous phosphate group is essential for a number of key biological processes, such as DNA compaction, RNA folding, or interactions of some proteins with membranes. Yet, probing their binding sites, modes, and associated binding free energy is a challenge for both experiments and simulations. In simulations, standard force fields strongly overestimate the interaction between phosphate groups and divalent cations. Here, we examine how different strategies to include electronic polarization effects in force fields─implicitly, through the use of scaled charges or pair-specific Lennard-Jones parameters, or explicitly, with the polarizable force fields Drude and AMOEBA─capture the interactions of a model phosphate compound, dimethyl phosphate, with calcium and magnesium divalent cations. We show that both implicit and explicit approaches, when carefully parameterized, are successful in capturing the overall binding free energy and that common trends emerge from the comparison of different simulation approaches. Overall, the binding is very moderate, slightly weaker for Ca²⁺ than Mg²⁺, and the solvent-shared ion pair is slightly more stable than the contact monodentate ion pair. The bidentate ion pair is higher in energy (or even fully unstable for Mg²⁺). Our results thus suggest practical ways to capture the divalent cations with biomolecular phosphate groups in complex biochemical systems. In particular, the computational efficiency of implicit models makes them ideally suited for large-scale simulations of biological assemblies, with improved accuracy compared to state-of-the-art fixed-charge force fields.

Force Field Parameterization of Actinyl Molecular Cations Using the 12-6-4 Model

In this work, a set of 12-6-4 force fields (FFs) parameters were developed for the actinyl molecular cations, AnO2n+ (n = 1, 2), from uranium to plutonium for classical molecular dynamics (MD) for four water models: TIP3P, SPC/E, OPC3, and TIP4Pew. Such a non-bonded potential model taking into account the induced dipole between the metallic center and the surrounding molecules has shown better performances for various cations than the classic 12-6 non-bonded potentials. The parametrization method proposed elsewhere for metallic cations has been extended to these molecular cations. In contrast to the actinyl 12-6 FFs from the literature, the new models reproduce correctly both solvation and thermodynamic properties, thanks to the inclusion of the induced dipole term (C4). The transferability of such force fields was assessed by performing MD simulations of carbonato actinyl species, which are highly implicated in actinide migration or actinide extraction from seawater. A highly satisfying agreement was found when comparing the EXAFS signals computed from our MD simulation to the experimental ones. The set of FFs developed here opens new possibilities for the study of actinide chemistry.

Chelator-Based Parameterization of the 12-6-4 Lennard-Jones Molecular Mechanics Potential for More Realistic Metal Ion-Protein Interactions

Metal ions are associated with a variety of proteins and play critical roles in a wide range of biochemical processes. There are multiple ways to study and quantify protein–metal ion interactions, including molecular dynamics simulations. Recently, the AMBER molecular mechanics forcefield was modified to include a 12-6-4 Lennard-Jones potential, which allows for a better description of nonbonded terms through the additional pairwise C_ij coefficients. Here, we demonstrate a method of generating C_ij parameters that allows parametrization of specific metal ion-ligating groups in order to tune binding energies computed by thermodynamic integration. The new C_ij coefficients were tested on a series of chelators: ethylenediaminetetraacetic acid, nitrilotriacetic acid, egtazic acid, and the EF1 loop peptides from the proteins lanmodulin and calmodulin. The new parameters show significant improvements in computed binding energies relative to existing force fields and produce coordination numbers and ion-oxygen distances that are in good agreement with experimental values. This parametrization method should be extensible to a range of other systems and could be readily adapted to tune properties other than binding energies.

Magnesium Force Fields for OPC Water with Accurate Solvation, Ion-Binding, and Water-Exchange Properties: Successful Transfer from SPC/E

Magnesium plays a vital role in a large variety of biological processes. To model such processes by molecular dynamics simulations, researchers rely on accurate force field parameters for Mg2+ and water. OPC is one of the most promising water models yielding an improved description of biomolecules in water. The aim of this work is to provide force field parameters for Mg2+ that lead to accurate simulation results in combination with OPC water. Using twelve different Mg2+ parameter sets, that were previously optimized with different water models, we systematically assess the transferability to OPC based on a large variety of experimental properties. The results show that the Mg2+ parameters for SPC/E are transferable to OPC and closely reproduce the experimental solvation free energy, radius of the first hydration shell, coordination number, activity derivative, and binding affinity toward the phosphate oxygens on RNA. Two optimal parameter sets are presented: MicroMg yields water exchange in OPC on the microsecond timescale in agreement with experiments. NanoMg yields accelerated exchange on the nanosecond timescale and facilitates the direct observation of ion binding events for enhanced sampling purposes.

Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D

Magnesium is essential in many vital processes. To correctly describe Mg2+ in physiological processes by molecular dynamics simulations, accurate force fields are fundamental. Despite the importance, force fields based on the commonly used 12-6 Lennard-Jones potential showed significant shortcomings. Recently progress was made by an optimization procedure that implicitly accounts for polarizability. The resulting microMg and nanoMg force fields (J. Chem. Theory Comput. 2021, 17, 2530-2540) accurately reproduce a broad range of experimental solution properties and the binding affinity to nucleic acids in TIP3P water. Since countless simulation studies rely on available water models and ion force fields, we here extend the optimization and provide Mg2+ parameters in combination with the SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D water models. For each water model, the Mg2+ force fields reproduce the solvation free energy, the distance to oxygens in the first hydration shell, the hydration number, the activity coefficient derivative in MgCl2 solutions, and the binding affinity and distance to the phosphate oxygens on nucleic acids. We present two parameter sets: MicroMg yields water exchange on the microsecond time scale and matches the experimental exchange rate. Depending on the water model, nanoMg yields accelerated water exchange in the range of 106 to 108 exchanges per second. The nanoMg parameters can be used to enhance the sampling of binding events, to obtain converged distributions of Mg2+, or to predict ion binding sites in biomolecular simulations. The parameter files are freely available at https://github.com/bio-phys/optimizedMgFFs.

Rational Design of Nonbonded Point Charge Models for Divalent Metal Cations with Lennard-Jones 12-6 Potential

Exploring a metal-involved biochemical process at a molecular level often requires a reliable description of metal properties in aqueous solution by classical nonbonded models. An additional C₄ term for considering ion-induced dipole interactions was previously proposed to supplement the widely used Lennard-Jones 12-6 potential (known as the 12-6-4 LJ-type model) with good accuracy. Here, we demonstrate an alternative to modeling divalent metal cations (M²⁺) with the traditional 12-6 LJ potential by developing nonbonded point charge models for use with 11 water models: TIP3P, SPC/E, SPC/E_b, TIP4P-Ew, TIP4P-D, and TIP4P/2005 and the more recent OPC3, TIP3P-FB, OPC, TIP4P-FB, and a99SB-disp. Our designed models simultaneously reproduce the experimental hydration free energy, ion-oxygen distance, and coordination number in the first hydration shell accurately for most of the metal cations, an accuracy equivalent to that of the complex 12-6-4 LJ-type and double exponential potential models. A systematic comparison with the existing M²⁺ models is presented as well in terms of effective ion radii, diffusion constants, water exchange rates, and ion-water interactions. Molecular dynamics simulations of metal substitution in Escherichia coli glyoxalase I variants show the great potential of our new models for metalloproteins.

Controlled Trafficking of Multiple and Diverse Cations Prompts Nucleic Acid Hydrolysis

Recent in crystallo reaction intermediates have detailed how nucleic acid hydrolysis occurs in the RNA ribonuclease H1 (RNase H1), a fundamental metalloenzyme involved in maintaining the human genome. At odds with the previous characterization, these in crystallo structures unexpectedly captured multiple metal ions (K⁺ and Mg²⁺) transiently bound in the vicinity of the two-metal-ion active site. Using multi-microsecond all-atom molecular dynamics and free-energy simulations, we investigated the functional implications of the dynamic exchange of multiple K⁺ and Mg²⁺ ions at the RNase H1 reaction center. We found that such ions are timely positioned at non-overlapping locations near the active site, at different stages of catalysis, being crucial for both reactants' alignment and leaving group departure. We also found that this cation trafficking is tightly regulated by variations of the solution's ionic strength and is aided by two conserved second-shell residues, E188 and K196, suggesting a mechanism for the cations' recruitment during catalysis. These results indicate that controlled trafficking of multi-cation dynamics, opportunely prompted by second-shell residues, is functionally essential to the complex enzymatic machinery of the RNase H1. These findings revise the current knowledge on the RNase H1 catalysis and open new catalytic possibilities for other similar metalloenzymes including, but not limited to, CRISPR-Cas9, group II intron ribozyme and the human spliceosome.

Developing and Assessing Nonbonded Dummy Models of Magnesium Ion with Different Hydration Free Energy References

A large diversity in the targeted hydration free energies (HFEs) during model parameterization of metal ions was reported in the literature with a difference by dozens of kcal/mol. Here, we developed a series of nonbonded dummy models of the Mg²⁺ ion targeting different HFE references in TIP3P water, followed by assessments of the designed models in the simulations of MgCl₂ solution and biological systems. Together with the comparison of existing models, we conclude that the difference in the targeted HFEs has a limited influence on the model performance, while the usability of these models differs from case to case. The feasibility of reproducing more properties of Mg²⁺ such as diffusion constants and water exchange rates using a nonbonded dummy model is demonstrated. Underestimated activity derivative and osmotic coefficient of MgCl₂ solutions in high concentration reveal a necessity for further optimization of ion-pair interactions. The developed dummy models are applicable to metal coordination with Asp, Glu, and His residues in metalloenzymes, and the performance in predicting monodentate or bidentate binding modes of Asp/Glu residues depends on the complexity of metal centers and the choice of protein force fields. When both the binding modes coexist, the nonbonded dummy models outperform point charge models, probably in need of considering polarization of metal-binding residues by, for instance, charge calibration in classical force fields. This work is valuable for the use and further development of magnesium ion models for simulations of metal-containing systems with good accuracy.

Structure and Dynamics of Meprin β in Complex with a Hydroxamate-Based Inhibitor

The astacin protease Meprin β represents an emerging target for drug development due to its potential involvement in disorders such as acute and chronic kidney injury and fibrosis. Here, we elaborate on the structural basis of inhibition by a specific Meprin β inhibitor. Our analysis of the crystal structure suggests different binding modes of the inhibitor to the active site. This flexibility is caused, at least in part, by movement of the C-terminal region of the protease domain (CTD). The CTD movement narrows the active site cleft upon inhibitor binding. Compared with other astacin proteases, among these the highly homologous isoenzyme Meprin α, differences in the subsites account for the unique selectivity of the inhibitor. Although the inhibitor shows substantial flexibility in orientation within the active site, the structural data as well as binding analyses, including molecular dynamics simulations, support a contribution of electrostatic interactions, presumably by arginine residues, to binding and specificity. Collectively, the results presented here and previously support an induced fit and substantial movement of the CTD upon ligand binding and, possibly, during catalysis. To the best of our knowledge, we here present the first structure of a Meprin β holoenzyme containing a zinc ion and a specific inhibitor bound to the active site. The structural data will guide rational drug design and the discovery of highly potent Meprin inhibitors.

Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis

We redevelop the variational free energy profile (vFEP) method using a cardinal B-spline basis to extend the method for analyzing free energy surfaces (FESs) involving three or more reaction coordinates. We also implemented software for evaluating high-dimensional profiles based on the multistate Bennett acceptance ratio (MBAR) method which constructs an unbiased probability density from global reweighting of the observed samples. The MBAR method takes advantage of a fast algorithm for solving the unbinned weighted histogram (UWHAM)/MBAR equations which replaces the solution of simultaneous equations with a nonlinear optimization of a convex function. We make use of cardinal B-splines and multiquadric radial basis functions to obtain smooth, differentiable MBAR profiles in arbitrary high dimensions. The cardinal B-spline vFEP and MBAR methods are compared using three example systems that examine 1D, 2D, and 3D profiles. Both methods are found to be useful and produce nearly indistinguishable results. The vFEP method is found to be 150 times faster than MBAR when applied to periodic 2D profiles, but the MBAR method is 4.5 times faster than vFEP when evaluating unbounded 3D profiles. In agreement with previous comparisons, we find the vFEP method produces superior FESs when the overlap between umbrella window simulations decreases. Finally, the associative reaction mechanism of hammerhead ribozyme is characterized using 3D, 4D, and 6D profiles, and the higher-dimensional profiles are found to have smaller reaction barriers by as much as 1.5 kcal/mol. The methods presented here have been implemented into the FE-ToolKit software package along with new methods for network-wide free energy analysis in drug discovery.

Extended magnesium and calcium force field parameters for accurate ion-nucleic acid interactions in biomolecular simulations

Magnesium and calcium play an essential role in the folding and function of nucleic acids. To correctly describe their interactions with DNA and RNA in biomolecular simulations, an accurate parameterization is crucial. In most cases, the ion parameters are optimized based on a set of experimental solution properties such as solvation free energies, radial distribution functions, water exchange rates, and activity coefficient derivatives. However, the transferability of such bulk-optimized ion parameters to quantitatively describe biomolecular systems is limited. Here, we extend the applicability of our previous bulk-optimized parameters by including experimental binding affinities toward the phosphate oxygen on nucleic acids. In particular, we systematically adjust the combination rules that are an integral part of the pairwise interaction potentials of classical force fields. This allows us to quantitatively describe specific ion binding to nucleic acids without changing the solution properties in the most simple and efficient way. We show the advancement of the optimized Lorentz combination rule for two representative nucleic acid systems. For double-stranded DNA, the optimized combination rule for Ca²⁺ significantly improves the agreement with experiments, while the standard combination rule leads to unrealistically distorted DNA structures. For the add A-riboswitch, the optimized combination rule for Mg²⁺ improves the structure of two specifically bound Mg²⁺ ions as judged by the experimental distance to the binding site. Including experimental binding affinities toward specific ion binding sites on biomolecules, therefore, provides a promising perspective to develop a more accurate description of metal cations for biomolecular simulations.

Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties

Magnesium ions play an essential role in many vital processes. To correctly describe their interactions in molecular dynamics simulations, an accurate parametrization is crucial. Despite the importance and considerable scientific effort, current force fields based on the commonly used 12-6 Lennard-Jones interaction potential fail to reproduce a variety of experimental solution properties. In particular, no parametrization exists so far that simultaneously reproduces the solvation free energy and the distance to the water oxygens in the first hydration shell. Moreover, current Mg2+ force fields significantly underestimate the rate of water exchange leading to unrealistically slow exchange kinetics. In order to make progress in the development of improved models, we systematically optimize the Mg2+ parameters in combination with the TIP3P water model in a much larger parameter space than previously done. The results show that a long-ranged interaction potential and modified Lorentz-Berthelot combination rules allow us to accurately reproduce multiple experimental properties including the solvation free energy, the distances to the oxygens of the first hydration shell, the hydration number, the activity coefficient derivative in MgCl2 solutions, the self-diffusion coefficient, and the binding affinity to the phosphate oxygen of RNA. Matching this broad range of thermodynamic properties, we present two sets of optimal parameters: MicroMg yields water exchange on the microsecond timescale in agreement with experiments. NanoMg yields water exchange on the nanosecond timescale facilitating the direct observation of ion-binding events. As shown for the example of the add A-riboswitch, the optimized parameters correctly reproduce the structure of specifically bound ions and permit the de novo prediction of Mg2+-binding sites in biomolecular simulations.

Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models

Commonly seen in rare-earth chemistry and materials science, highly charged metal ions play key roles in many chemical processes. Computer simulations have become an important tool for scientific research nowadays. Meaningful simulations require reliable parameters. In the present work, we parametrized 18 M(III) and 6 M(IV) metal ions for four new water models (OPC3, OPC, TIP3P-FB, TIP4P-FB) in conjunction with each of the 12-6 and 12-6-4 nonbonded models. Similar to what was observed previously, issues with the 12-6 model can be fixed by using the 12-6-4 model. Moreover, the four new water models showed comparable performance or considerable improvement over the previous water models (TIP3P, SPC/E, and TIP4P_EW) in the same category (3-point or 4-point water models, respectively). Finally, we reported a study of a metalloprotein system demonstrating the capability of the 12-6-4 model to model metalloproteins. The reported parameters will facilitate accurate simulations of highly charged metal ions in aqueous solution.

The structure of Prp2 bound to RNA and ADP-BeF3- reveals structural features important for RNA unwinding by DEAH-box ATPases

Noncoding intron sequences present in precursor mRNAs need to be removed prior to translation, and they are excised via the spliceosome, a multimegadalton molecular machine composed of numerous protein and RNA components. The DEAH-box ATPase Prp2 plays a crucial role during pre-mRNA splicing as it ensures the catalytic activation of the spliceosome. Despite high structural similarity to other spliceosomal DEAH-box helicases, Prp2 does not seem to function as an RNA helicase, but rather as an RNA-dependent ribonucleoprotein particle-modifying ATPase. Recent crystal structures of the spliceosomal DEAH-box ATPases Prp43 and Prp22, as well as of the related RNA helicase MLE, in complex with RNA have contributed to a better understanding of how RNA binding and processivity might be achieved in this helicase family. In order to shed light onto the divergent manner of function of Prp2, an N-terminally truncated construct of Chaetomium thermophilum Prp2 was crystallized in the presence of ADP-BeF3- and a poly-U12 RNA. The refined structure revealed a virtually identical conformation of the helicase core compared with the ADP-BeF3-- and RNA-bound structure of Prp43, and only a minor shift of the C-terminal domains. However, Prp2 and Prp43 differ in the hook-loop and a loop of the helix-bundle domain, which interacts with the hook-loop and evokes a different RNA conformation immediately after the 3' stack. On replacing these loop residues in Prp43 by the Prp2 sequence, the unwinding activity of Prp43 was abolished. Furthermore, a putative exit tunnel for the γ-phosphate after ATP hydrolysis could be identified in one of the Prp2 structures.

A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization

Molecular simulations can elucidate atomistic-level mechanisms of key biological processes, which are often hardly accessible to experiment. However, the results of the simulations can only be as trustworthy as the underlying simulation model. In many of these processes, interactions between charged moieties play a critical role. Current empirical force fields tend to overestimate such interactions, often in a dramatic way, when polyvalent ions are involved. The source of this shortcoming is the missing electronic polarization in these models. Given the importance of such biomolecular systems, there is great interest in fixing this deficiency in a computationally inexpensive way without employing explicitly polarizable force fields. Here, we review the electronic continuum correction approach, which accounts for electronic polarization in a mean-field way, focusing on its charge scaling variant. We show that by pragmatically scaling only the charged molecular groups, we qualitatively improve the charge-charge interactions without extra computational costs and benefit from decades of force field development on biomolecular force fields.

Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models

Monovalent ions play significant roles in various biological and material systems. Recently, four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB), with significantly improved descriptions of condensed phase water, have been developed. The pairwise interaction between the metal ion and water necessitates the development of ion parameters specifically for these water models. Herein, we parameterized the 12-6 and the 12-6-4 nonbonded models for 12 monovalent ions with the respective four new water models. These monovalent ions contain eight cations including alkali metal ions (Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺), transition-metal ions (Cu⁺ and Ag⁺), and Tl⁺ from the boron family, along with four halide anions (F^-, Cl^-, Br^-, I^-). Our parameters were designed to reproduce the target hydration free energies (the 12-6 hydration free energy (HFE) set), the ion-oxygen distances (the 12-6 ion-oxygen distance (IOD) set), or both of them (the 12-6-4 set). The 12-6-4 parameter set provides highly accurate structural features overcoming the limitations of the routinely used 12-6 nonbonded model for ions. Specifically, we note that the 12-6-4 parameter set is able to reproduce experimental hydration free energies within 1 kcal/mol and experimental ion-oxygen distances within 0.01 Å simultaneously. We further reproduced the experimentally determined activity derivatives for salt solutions, validating the ion parameters for simulations of ion pairs. The improved performance of the present water models over our previous parameter sets for the TIP3P, TIP4P, and SPC/E water models (Li, P. et al J. Chem. Theory Comput. 2015 11 1645 1657) highlights the importance of the choice of water model in conjunction with the metal ion parameter set.

Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich's ataxia: DNA triplexes and RNA/DNA hybrids

Expansion of the GAA/TTC repeats in the first intron of the FXN gene causes Friedreich's ataxia. Non-canonical structures are linked to this expansion. DNA triplexes and R-loops are believed to arrest transcription, which results in frataxin deficiency and eventual neurodegeneration. We present a systematic in silico characterization of the possible DNA triplexes that could be assembled with GAA and TTC strands; the two hybrid duplexes [r(GAA):d(TTC) and d(GAA):r(UUC)] in an R-loop; and three hybrid triplexes that could form during bidirectional transcription when the non-template DNA strand bonds with the hybrid duplex (collapsed R-loops, where the two DNA strands remain antiparallel). For both Y·R:Y and R·R:Y DNA triplexes, the parallel third strand orientation is more stable; both parallel and antiparallel protonated d(GA+A)·d(GAA):d(TTC) triplexes are stable. Apparent contradictions in the literature about the R·R:Y triplex stability is probably due to lack of molecular resolution, since shifting the third strand by a single nucleotide alters the stability ranking. In the collapsed R-loops, antiparallel d(TTC+)·d(GAA):r(UUC) is unstable, while parallel d(GAA)·r(GAA):d(TTC) and d(GA+A)·r(GAA):d(TTC) are stable. In addition to providing new structural perspectives for specific therapeutic aims, our results contribute to a systematic structural basis for the emerging field of quantitative R-loop biology.

Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations

Mapping the route of nucleoside triphosphate (NTP) entry into the sequestered active site of RNA polymerase (RNAP) has major implications for elucidating the complete nucleotide addition cycle. Constituting a dichotomy that remains to be resolved, two alternatives, direct NTP delivery via the secondary channel (CH2) or selection to downstream sites in the main channel (CH1) prior to catalysis, have been proposed. In this study, accelerated molecular dynamics simulations of freely diffusing NTPs about RNAPII were applied to refine the CH2 model and uncover atomic details on the CH1 model that previously lacked a persuasive structural framework to illustrate its mechanism of action. Diffusion and binding of NTPs to downstream DNA, and the transfer of a preselected NTP to the active site, are simulated for the first time. All-atom simulations further support that CH1 loading is transcription factor IIF (TFIIF) dependent and impacts catalytic isomerization. Altogether, the alternative nucleotide loading systems may allow distinct transcriptional landscapes to be expressed.

Electrode surface modification of graphene-MnO2 supercapacitors using molecular dynamics simulations

In this study, molecular dynamics (MD) simulations have been performed to explore the variation of ion density and electric potential due to electrode surface modification. Two different surface morphologies, having planer and slit pore with different conditions of surface charge, have been studied for graphene-MnO₂ surface using LAMMPS. For different pore widths, the concentration of ions in the double layer is observed to be very low when the surface of the graphene-MnO₂ electrode is charged. With a view to identify the optimal pore size for the simulation domain considered, three different widths for the nano-slit type pores and the corresponding ion-ion interactions are examined. Though this effect is negligible for pores with 9.23 and 3.55 Å widths, a considerable increase in the ionic concentration within the 7.10 Å pores is observed when the electrode is kept neutral. The edge region of these nano-slit pores leads to effective energy storage by promoting ion separation and a significantly higher charge accumulation is found to occur on the edges compared to the basal planes. For the simulation domain of the present study, partition coefficient is maximum for a pore size of 7.10 Å, indicating that the ions' penetration and movement into nano-slit pores are most favorable for this optimum pore size for MnO₂-graphene electrodes with aqueous NaCl electrolyte. Graphical Abstract The importance of understanding the commercial feasibility of supercapacitor material has made qualitatively predicting the optimized electrode structure one of the main targets of energy related researches. While great progress has been made in recent years, a coherent theoretical picture of the optimized electrode structure remains elusive. This article discusses the most favorable design of supercapacitor electrode for ion-electrode interaction.

Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation

Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 Å and 2.65 Å-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1-exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1-sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.

Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins

We developed a novel force field in the context of AMBER parameterization for glutamate and aspartate zinc(II)-binding residues. The interaction between the zinc ion and the coordinating atoms is represented by a spherical nonbonded parameterization. The polarization effect due to the zinc ion has been taken into account by redefining the atomic charges on the residues through accurate quantum mechanical calculations. The new zinc-binding ASP and GLU residues, along with the CYS and HIS zinc-binding residues, parameterized in a recent work [Macchiagodena M.;J. Chem. Inf. Model.2019, 59, 3803-3816], allow users to reliably simulate 96% of the Zn-proteins available in the Protein Data Bank. The upgraded force field for zinc(II)-bound residues has been tested performing molecular dynamics simulations with an explicit solvent and comparing the structural information with experimental data for five different proteins binding zinc(II) with GLU, ASP, HIS, and CYS. We further validated our approach by evaluating the binding free energy of (R)-2-benzyl-3-nitropropanoic acid to carboxypeptidase A using a recently developed nonequilibrium alchemical method. We demonstrated that in this setting it is crucial to take into account polarization effects also on the metal-bound inhibitor.

Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models

Divalent metal ions play important roles in biological and materials systems. Molecular dynamics simulation is an efficient tool to investigate these systems at the microscopic level. Recently, four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB) have been developed and better represent the physical properties of water than previous models. Metal ion parameters are dependent on the water model employed, making it necessary to develop metal ion parameters for select new water models. In the present work, we performed parameter scanning for the 12-6 Lennard-Jones nonbonded model of divalent metal ions in conjunction with the four new water models as well as four previous water models (TIP3P, SPC/E, TIP4P, and TIP4P-Ew). We found that these new three-point and four-point water models provide comparable or significantly improved performance for the simulation of divalent metal ions when compared to previous water models in the same category. Among all eight water models, the OPC3 water model yields the best performance for the simulation of divalent metal ions in the aqueous phase when using the 12-6 model. On the basis of the scanning results, we independently parametrized the 12-6 model for 24 divalent metal ions with each of the four new water models. As noted previously, the 12-6 model still fails to simultaneously reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values even with these new water models. To solve this problem, we parametrized the 12-6-4 model for the 16 divalent metal ions for which we have both experimental HFE and IOD values for each of the four new water models. The final parameters are able to reproduce both the experimental HFE and IOD values accurately. To validate the transferability of our parameters, we carried out benchmark calculations to predict the energies and geometries of ion-water clusters as well as the ion diffusivity coefficient of Mg²⁺. By comparison to quantum chemical calculations and experimental data, these results show that our parameters are well designed and have excellent transferability. The metal ion parameters for the 12-6 and 12-6-4 models reported herein can be employed in simulations of various biological and materials systems when using the OPC3, OPC, TIP3P-FB, or TIP4P-FB water model.

Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics

A large variety of physicochemical properties involving RNA depends on the type of metal cation present in solution. In order to gain microscopic insight into the origin of these ion specific effects, we apply molecular dynamics simulations to describe the interactions of metal cations and RNA. For the three most common ion binding sites on RNA, we calculate the binding affinities and exchange rates of eight different mono- and divalent metal cations. Our results reveal that binding sites involving phosphate groups preferentially bind metal cations with high charge density (such as Mg²⁺) in inner-sphere conformations while binding sites involving N7 or O6 atoms preferentially bind cations with low charge density (such as K⁺). The binding affinity therefore follows a direct Hofmeister series at the backbone but is reversed at the nucleobases leading to a high selectivity of ion binding sites on RNA. In addition, the exchange rates for cation binding cover almost 5 orders of magnitude, leading to a vastly different time scale for the lifetimes of contact pairs. Taken together, the site-specific binding affinities and the specific lifetime of contact pairs provide the microscopic explanation of ion specific effects observed in a wide variety of macroscopic RNA properties. Finally, combining the results from atomistic simulations with extended Poisson-Boltzmann theory allows us to predict the distribution of metal cations around double-stranded RNA at finite concentrations and to reproduce the results of ion counting experiments with good accuracy.