SignificanceThe complex and often highly dynamic 3D structures of RNA molecules are central to their diverse cellular functions. Molecular dynamics (MD) simulations have played a major role in characterizing the structure and dynamics of proteins, but the physical models (“force fields”) used for simulating nucleic acids are substantially less accurate overall than those used in protein simulations, creating a major challenge for MD studies of RNA. Here, we report an RNA force field capable of describing the structural and thermodynamic properties of RNA molecules with accuracy comparable to state-of-the-art protein force fields. This force field should facilitate the use of MD simulation as a tool for the study of biologically significant RNA molecules and protein–RNA complexes.

The accuracy of atomistic physics-based force fields for the simulation of biological macromolecules has typically been benchmarked experimentally using biophysical data from simple, often single-chain systems. In the case of proteins, the careful refinement of force field parameters associated with torsion-angle potentials and the use of improved water models have enabled a great deal of progress toward the highly accurate simulation of such monomeric systems in both folded and, more recently, disordered states. In living organisms, however, proteins constantly interact with other macromolecules, such as proteins and nucleic acids, and these interactions are often essential for proper biological function.Here, we show that state-of-the-art force fields tuned to provide an accurate description of both ordered and disordered proteins can be limited in their ability to accurately describe protein−protein complexes. This observation prompted us to perform an extensive reparameterization of one variant of the Amber protein force field. Our objective involved refitting not only the parameters associated with torsion-angle potentials but also the parameters used to model nonbonded interactions, the specification of which is expected to be central to the accurate description of multicomponent systems. The resulting force field, which we call DES-Amber, allows for more accurate simulations of protein−protein complexes, while still providing a state-of-the-art description of both ordered and disordered single-chain proteins. Despite the improvements, calculated protein−protein association free energies still appear to deviate substantially from experiment, a result suggesting that more fundamental changes to the force field, such as the explicit treatment of polarization effects, may simultaneously further improve the modeling of single-chain proteins and protein−protein complexes.

Metazoan replication-dependent histone mRNAs have a conserved stem-loop (SL) at their 3′-end. The stem–loop binding protein (SLBP) specifically recognizes the SL to regulate histone mRNA metabolism, and the 3′-5′ exonuclease 3′hExo trims its 3′-end after processing. We report the crystal structure of a ternary complex of human SLBP RNA binding domain, human 3′hExo, and a 26-nucleotide SL RNA. Only one base of the SL is recognized specifically by SLBP, and the two proteins primarily recognize the shape of the RNA. SLBP and 3′hExo have no direct contact with each other, and induced structural changes in the loop of the SL mediate their cooperative binding. The 3′ flanking sequence is positioned in the 3′hExo active site, but the ternary complex limits the extent of trimming.

A conserved stem-loop motif of the constitutive decay element (CDE) in the 3′ UTR of mRNAs is recognized by the ROQ domain of Roquin, which mediates their degradation. Here we report two crystal structures of the Homo sapiens ROQ domain in complex with CDE RNA. The ROQ domain has an elongated shape, with three sub-domains. The 19-nt Hmgxb3 CDE is bound as a stem-loop to domain III. The 23-nt TNF RNA is bound as a duplex, to a separate site at the interface between domains I and II. Mutagenesis studies confirm that the ROQ domain has two separate RNA binding sites, one for stem-loop RNA (A site) and the other for dsRNA (B site). Mutation in either site perturbs the Roquin-mediated degradation of HMGXB3 and IL-6 mRNAs in human cells, demonstrating the importance of both sites for mRNA decay.

Although molecular dynamics (MD) simulations have been used extensively to study the structural dynamics of proteins, the role of MD simulation in studies of nucleic acid based systems has been more limited. One contributing factor to this disparity is the historically lower level of accuracy of the physical models used in such simulations to describe interactions involving nucleic acids. By modifying nonbonded and torsion parameters of a force field from the Amber family of models, we recently developed force field parameters for RNA that achieve a level of accuracy comparable to that of state-of-the-art protein force fields. Here we report force field parameters for DNA, which we developed by transferring nonbonded parameters from our recently reported RNA force field and making subsequent adjustments to torsion parameters. We have also modified the backbone charges in both the RNA and DNA parameter sets to make the treatment of electrostatics compatible with our recently developed variant of the Amber protein and ion force field. We name the force field resulting from the union of these three parameter sets (the new DNA parameters, the revised RNA parameters, and the existing protein and ion parameters) DES-Amber . Extensive testing of DES-Amber indicates that it can describe the thermal stability and conformational flexibility of single- and double-stranded DNA systems with a level of accuracy comparable to or, especially for disordered systems, exceeding that of state-of-the-art nucleic acid force fields. Finally, we show that, in certain favorable cases, DES-Amber can be used for long-timescale simulations of protein–nucleic acid complexes.