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Proteins capable of switching between distinct active states in response to biochemical cues are ideal for sensing and controlling biological processes. Activatable CRISPR‐Cas systems are significant in precise genetic manipulation and sensitive molecular diagnostics, yet directly controlling Cas protein function remains challenging. Herein, we explore anti‐CRISPR (Acr) proteins as modules to create synthetic Cas protein switches (CasPSs) based on computational chemistry‐directed rational protein interface engineering. Guided by molecular fingerprint analysis, electrostatic potential mapping, and binding free energy calculations, we rationally engineer the molecular interaction interface between Cas12a and its cognate Acr proteins (AcrVA4 and AcrVA5) to generate a series of orthogonal protease‐responsive CasPSs. These CasPSs enable the conversion of specific proteolytic events into activation of Cas12a function with high switching ratios (up to 34.3‐fold). These advancements enable specific proteolysis‐inducible genome editing in mammalian cells and sensitive detection of viral protease activities during virus infection. This work provides a promising strategy for developing CRISPR‐Cas tools for controllable gene manipulation and regulation and clinical diagnostics. [ABSTRACT FROM AUTHOR]

The enzyme complex IκB kinase (IKK) is an essential activator of NF-κB signaling pathway involved in propagating the cellular response to inflammation. The complex contains two functional subunits IKKαand IKKβ, which are structurally conserved kinases and selective inhibition of them would result in distinct biological effects. However, most existing IKK inhibitors show moderate or high promiscuity for the two homologous kinases. Understanding of the molecular mechanism and biological implication underlying the specific interactions in IKK–ligand recognition is thus fundamentally important for the rational design of selective IKK inhibitors. In the current work, we integrated molecular docking, quantum mechanics/molecular mechanics calculation and Poisson–Boltzmann/surface area analysis to investigate the structural basis and energetic property of the selective binding of small-molecule ligands to IKKαand IKKβ. It was found that the selectivity is primarily determined by the size and topology difference in ATP-binding pocket of IKKαand IKKβkinase domains; bulky inhibitor molecules commonly have, respectively, low and appropriate affinities towards IKKαand IKKβ, and thus exhibit relatively high selectivity for IKKβover IKKα, whereas small ligands can only bind weakly to both the two kinases with low selectivity. In addition, the conformation, arrangement and distribution of residues in IKK pockets are also responsible for constituting the exquisite specificity of ligand binding to KKαand IKKβ. Next, a novel quantitative structure–selectivity relationship model was developed to characterize the relative contribution of each kinase residue to inhibitor selectivity and to predict the selectivity and specificity for a number of known IKK inhibitors. Results showed that the active-site residues contribute significantly to the selectivity by directly interacting with inhibitor ligands, while those protein portions far away from the kinase active sites may also play an important role in determining the selectivity through long-range non-bonded forces and indirect allosteric effect. [ABSTRACT FROM PUBLISHER]

The uplift of the Tibetan Plateau (TP) during the late Cenozoic is thought to be one of crucial factors controlling Asian climate. However, the complex interaction between tectonics and climate change is still unclear. Here we present the first record of clay mineralogy and elemental geochemistry covering ~12.7–4.8 Ma in a fluvial‐lacustrine sequence in the Xining Basin. Geochemical provenance proxies (Th/Sc, Zr/Sc, and Cr/Zr) in the <2‐μm fraction show a significant provenance change at ~8.8 Ma. Silicate‐based weathering indexes (CIA, CIW, and PIA) displayed coeval changes with provenance but discrepant changes with regional climate. Since the clay mineralogy exhibits significant change at ~7.8 Ma uncorrelated with modifications in provenance, it can be employed to reveal regional climate change. The rise in illite and associated decrease in the sum of smectite and illite/smectite mixed layers reflect gradual and slow aridification since ~12.7 Ma with intensified drying since ~7.8 Ma until approaching the modern climate status. Our results, together with other regional climatic and tectonic records, clearly illustrate that accelerated uplift of the northeastern TP since ~8–9 Ma has mainly modulated the regional erosion, weathering, transportation, and sedimentation and amplified the global cooling and drying trend toward the regional climate of modern conditions. Our study suggests that in the tectonically active northeastern TP, a comprehensive mineralogical and geochemical investigation of the fine‐grained fraction of the basin sediments could retrieve the interactions between tectonics and climate behind the complex change in exhumed lithology and sedimentary routing systems. Key Points: A long‐term gradual aridification since 12.7 Ma and an enhanced drying event since ~7.8 Ma occurred in the Xining BasinUplift of the northeastern Tibetan Plateau was the major driver of the evolution of regional climate and landscape since the late MioceneClay minerals are well‐used potential proxies for paleoclimatic reconstructions in complex sedimentary routing systems [ABSTRACT FROM AUTHOR]