# DNA Nanodevices as Mechanical Probes of Protein Structure and Function
## 5 Future Enabling Technologies for Protein-DNA Nanodevices
### Computational Simulation of Protein-DNA Nanostructures
There are ongoing efforts to further improve the force fields to capture both the properties of nucleic acids as well as proteins, and to quantitatively reproduce free-energies of their interactions [75]. An alternative to atomistic simulation is to use coarse-grained models, which represent groups of atoms as a single particle, with interactions between them parameterized to reproduce a particular set of properties of the system: e.g., thermodynamics, structural motifs or mechanical properties. The trade-off in reduced accuracy is balanced by the models' ability to study larger systems (up to hundreds of thousands of nucleotides for the model oxDNA) and longer timescales, including processes that happen on the order of seconds. Examples of models that can represent both proteins and nucleic acids include the MARTINI [76] 3 SPN.2 DNA model with the incorporated AWSEM protein model, [77] and the recently introduced ANM-oxDNA model [78] (Figure 7). These coarse-grained models differ in terms of the detail of their representation as well as the set of properties their parameters are fitted to reproduce. ANM-oxDNA, which uses the established oxDNA model [79; 80; 81] for DNA nanotechnology and combines it with an anisotropic network model (ANM) of proteins [82], has been used to simulate an experimentally realized DNA-protein hybrid nanocage reported by the [PERSON] lab [57]. The ANM model represents the protein as a string of rigid beads connected by a parametrized spring potential. The ANM-oxDNA further parametrizes the linkers connecting the proteins and DNA by a potential function that reproduces the behavior of a linker in a fully atomistic simulation. The use of other coarse-grained models that support nucleic acids as well as proteins has so far been limited to biomolecular systems, and it would be interesting to benchmark them against DNA-protein structures. Most current modeling approaches for DNA-protein systems have focused on biological problems, such as the estimation of DNA-protein interaction energies, docking or the effect of proteins binding to DNA [75]. As a result, these methods rarely address the same behavior relevant to DNA-protein hybrid nanosystems, like the mechanical effect of pulling a protein attached to a nanostructure, the protein-DNA nanostructure response to change in temperature, and the accurate representation of linkers are necessary to realistically capture the experimental behavior of hybrid nanosystems. New experimental datasets would greatly help in benchmarking existing models, as well as developing new ones with fine-tuned parameters to better represent the protein-hybrid nanostructures. Examples of data that would be useful to the modeling community include cryo-EM imaging of protein-DNA hybrid constructs, studies of assembly yield as a function of temperature, and imaging nanostructures where the protein and DNA are subject to mechanical stresses. Not only can such experiments provide important data on parametrization of the properties of the linkers, but can also help uncover properties of proteins that can further improve model parameters, also benefiting their accuracy for biomolecular simulations. As was the case with the emergence of DNA nanotechnology, we can expect that further examples of successful experimental realization of DNA nanostructures interacting with proteins will lead to development of more accurate models, which will, in turn, enable design of more complex nanodevices. New modeling and design tools can help to interpret data produced from interactions between protein and DNA, be used for more accurate reconstruction of nanostructures with bound proteins via cryo-EM and also probe designs for optimal placements of protein interacting sites in the nanostructures. [PERSON] primarily wrote Sections 1-4 and Section 5.1. [PERSON] primarily wrote Section 5.2. Both authors edited the final manuscript. The authors gratefully acknowledge [PERSON] for help preparing Figures 1 and 6. All authors have read and agreed to the published version of the manuscript.