Coarse-grained dynamic RNA titration simulations

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.

Theory of Charge Regulation of Colloidal Particles in Electrolyte Solutions

We present a theory that enables us to (i) calculate the effective surface charge of colloidal particles and (ii) efficiently obtain titration curves for different salt concentrations. The theory accounts for the shift of pH of solution due to the presence of 1:1 electrolyte. It also accounts self-consistently for the electrostatic potential produced by the deprotonated surface groups. To examine the accuracy of the theory, we have performed extensive reactive Monte Carlo simulations, which show excellent agreement between theory and simulations without any adjustable parameters.

Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule

Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein-protein systems under different physical-chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pK_as for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This "RBD charge rule" should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.

Computer-aided comprehensive explorations of RNA structural polymorphism through complementary simulation methods

While RNA folding was originally seen as a simple problem to solve, it has been shown that the promiscuous interactions of the nucleobases result in structural polymorphism, with several competing structures generally observed for non-coding RNA. This inherent complexity limits our understanding of these molecules from experiments alone, and computational methods are commonly used to study RNA. Here, we discuss three advanced sampling schemes, namely Hamiltonian-replica exchange molecular dynamics (MD), ratchet-and-pawl MD and discrete path sampling, as well as the HiRE-RNA coarse-graining scheme, and highlight how these approaches are complementary with reference to recent case studies. While all computational methods have their shortcomings, the plurality of simulation methods leads to a better understanding of experimental findings and can inform and guide experimental work on RNA polymorphism.

Engineering of the XY Magnetic Layered System with Adeninium Cations: Monocrystalline Angle-Resolved Studies of Nonlinear Magnetic Susceptibility

An original example of modular crystal engineering involving molecular magnetic {Cu^II[W^V(CN)₈]}^- bilayers and adeninium cations (AdeH⁺) toward the new layered molecular magnet (AdeH){Cu^II[W^V(CN)₈]}·2H₂O (1) is presented. 1 crystallizes within the monoclinic C2 space group (a = 41.3174(12), b = 7.0727(3), c = 7.3180(2) Å, β = 93.119(3)°, and V = 2135 ų). The bilayer topology is based on a stereochemical matching between the square pyramidal shape of Cu^II moiety and the bicapped trigonal prismatic shape of [W^V(μ-CN)₅(CN)₃], and the separation between bilayers is significantly increased (by ∼50%; from ca. 9.5 to ca. 14.5 Å) compared to several former analogues in this family. This was achieved via a unique combination of (i) a 1D ribbonlike hydrogen bond system {AdeH⁺···H₂O···AdeH⁺···}_∞ exploiting planar water-assisted Hoogsteen···Sugar synthons with (ii) parallel 1D π-π stacks {AdeH⁺···AdeH⁺}_∞. In-plane 2D XY magnetism is characterized by a T_c close to 33 K, H_c,in-plane = 60 Oe, and H_{c,out-of-plane} = 750 Oe, high values of in-plane γ critical exponents (γ_b = 2.34(6) for H||b and γ_c = 2.16(5) for H||c), and a Berezinskii-Kosterlitz-Thouless (BKT) topological phase transition, deduced from crystal-orientation-dependent scaling analysis. The obtained values of in-plane ν critical exponents, ν_b = 0.48(5) for H||b and ν_c = 0.49(3) for H||c, confirm the BKT transition (ν_BKT = 0.5). Full-range angle-resolved monocrystalline magnetic measurements supported by dedicated calculations indicated the occurrence of nonlinear susceptibility performance within the easy plane in a magnetically ordered state. We refer the occurrence of this phenomenon to spontaneous resolution in the C2 space group, a tandem not observed in studies on previous analogues and rarely reported in the field of molecular materials. The above magneto-supramolecular strategy may provide a novel means for the design of 2D molecular magnetic networks and help to uncover the inherent phenomena.

Titr-DMD-A Rapid, Coarse-Grained Quasi-All-Atom Constant pH Molecular Dynamics Framework

The pH-dependence of enzyme fold stability and catalytic activity is a fundamentally dynamic, structural property which is difficult to study. The challenges and expense of investigating dynamic, atomic scale behavior experimentally means that computational methods, particularly constant pH molecular dynamics (CpHMD), are well situated tools for this. However, these methods often struggle with affordable sampling of sufficiently long time scales while also obtaining accurate pKa prediction and verifying the structures they generate. We introduce Titr-DMD, an affordable CpHMD method that combines the quasi-all-atom coarse-grained discrete molecular dynamics (DMD) method for conformational sampling with Propka for pKa prediction, to circumvent these issues. The combination enables rapid sampling on limited computational resources, while simulations are still performed on the atomic scale. We benchmark the method on a set of proteins with experimentally attested pKa and on the pH triggered conformational change in a staphylococcal nuclease mutant, a rare experimental study of such behavior. Our results show Titr-DMD to be an effective and inexpensive method to study pH-coupled protein dynamics.

Coarse-Grained Models of RNA Nanotubes for Large Time Scale Studies in Biomedical Applications

In order to describe the physical properties of large time scale biological systems, coarse-grained models play an increasingly important role. In this paper we develop Coarse-Grained (CG) models for RNA nanotubes and then, by using Molecular Dynamics (MD) simulation, we study their physical properties. Our exemplifications include RNA nanotubes of 40 nm long, equivalent to 10 RNA nanorings connected in series. The developed methodology is based on a coarse-grained representation of RNA nanotubes, where each coarse bead represents a group of atoms. By decreasing computation cost, this allows us to make computations feasible for realistic structures of interest. In particular, for the developed coarse-grained models with three bead approximations, we calculate the histograms for the bond angles and the dihedral angles. From the dihedral angle histograms, we analyze the characteristics of the links used to build the nanotubes. Furthermore, we also calculate the bead distances along the chains of RNA strands in the nanoclusters. The variations in these features with the size of the nanotube are discussed in detail. Finally, we present the results on the calculation of the root mean square deviations for a developed RNA nanotube to demonstrate the equilibration of the systems for drug delivery and other biomedical applications such as medical imaging and tissue engineering.

Multi-resolution simulations of intracellular processes

This is an introduction to the Thematic Issue of Interface Focus containing papers by speakers of the Theo Murphy International Scientific Meeting on ‘Multi-resolution simulations of intracellular processes’