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Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural changes caused by PTMs equate to altered physiological function has not been maintained. In this Perspective, we cover the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs. We distinguish results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization. Lastly, we offer insights into how opportunities for modern research efforts on in silico PTM characterization may proceed given current state-of-the-art computing capabilities and methodological advancements. 

Improving nitrogen use efficiency is critical to enhancing agricultural productivity and to mitigate environmental pollution. To overcome the fluctuations in soil nitrate concentration, plants have evolved an elaborate nitrate transporting mechanism that switches between high and low affinity. In plants, NRT1.1, a root-associated nitrate transporter, switches its affinity upon phosphorylation at Thr101. However, the molecular basis of this unique functional behavior known as dual-affinity switching remains elusive. Crystal structures of the NRT1.1 nitrate transporter have provided evidence for the two competing hypotheses to explain the origin of dual-affinity switching. It is not known how the interplay between transporter phosphorylation and dimerization regulates the affinity switching. To reconcile the different hypotheses, we have performed extensive simulations of nitrate transporter in conjunction with Markov state models to elucidate the molecular origin for a dual-affinity switching mechanism. Simulations of monomeric transporter reveal that phosphorylation stabilizes the outward-facing state and accelerates dynamical transitions for facilitating transport. On the other hand, phosphorylation of the transporter dimer decouples dynamic motions of dimer into independent monomers and thus facilitates substrate transport. Therefore, the phosphorylation-induced enhancement of substrate transport and dimer decoupling not only reconcile the competing experimental results but also provide an atomistic view of how nitrate transport is regulated in plants. 

Abstract Electro‐responsive functional materials can play a critical role in selective metal recovery and recycling due to the need for molecular differentiation between transition metals in complex mixtures. Redox‐active metallopolymers are a promising platform for electrochemical separations, offering versatile structural tuning and fast electron transfer. First, through a judicious selection of polymer structure between a main‐chain metallopolymer (polyferrocenylsilane) and a pendant‐group metallopolymer (polyvinylferrocene), charge‐transfer interactions and binding strength toward competing metal ions are tuned, which as a result, dictate selectivity. For example, almost an order of magnitude increase in separation factor between chromate and meta‐vanadate can be achieved, depending on polymer structure. Second, these metallopolymer electrodes exhibit potential‐dependent selectivity that can even flip ion preference, based solely on electrical means—indicating a control parameter that is orthogonal to structural modifications. Finally, this work presents a framework for evaluating electrochemical separations in multicomponent ion mixtures and elucidates the underlying charge‐transfer mechanisms resulting in molecular selectivity through a combination of spectroscopy and electronic structure calculations. The findings demonstrate the applicability of redox‐metallopolymers in tailored electrochemical separations for environmental remediation, value‐added metal recovery, waste recycling, and even mining processing.