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Proteins achieve their complex functions, such as molecular recognition with high affinity and specificity, through intricate threedimensional geometries in functional sites. To engineer new protein functions, accurate positioning of amino acid functional groups is therefore critical but has remained difficult to achieve by computational methods because of current limitations in the design of new conformations with arbitrary user-defined geometries. Here, we introduce two computational methods capable of generating and predicting new local protein geometries: fragment kinematic closure (FKIC) and loophash kinematic closure (LHKIC). FKIC and LHKIC integrate two approaches: robotics-inspired kinematics of protein conformations and insertion of peptide fragments. We show that FKIC and LHKIC predict native-like conformations at atomic accuracy and with up to 140-fold improvements in sampling efficiency over previous approaches. We then use these methods to create a design protocol, pull into place (PIP), to position functionally important side chains via design of backbone conformations. We validate PIP by remodeling a sizeable active site region in an enzyme and confirming the engineered new conformations of two designs with crystal structures. The described methods can be applied broadly to the design of userdefined geometries for new protein functions. [ABSTRACT FROM AUTHOR]

Skeletal muscle atrophy is caused by various conditions, including aging, disuse related to a sedentary lifestyle and lack of physical activity, and cachexia. Our insufficient understanding of the molecular mechanism underlying muscle atrophy limits the targets for the development of effective pharmacologic treatments and preventions. Here, we identified Krüppel-like factor 5 (KLF5), a zinc-finger transcription factor, as a key mediator of the early muscle atrophy program. KLF5 was up-regulated in atrophying myotubes as an early response to dexamethasone or simulated microgravity in vitro. Skeletal muscle-selective deletion of Klf5 significantly attenuated muscle atrophy induced by mechanical unloading in mice. Transcriptomeand genome-wide chromatin accessibility analyses revealed that KLF5 regulates atrophy-related programs, including metabolic changes and E3-ubiquitin ligase-mediated proteolysis, in coordination with Foxo1. The synthetic retinoic acid receptor agonist Am80, a KLF5 inhibitor, suppressed both dexamethasone- and microgravityinduced muscle atrophy in vitro and oral Am80 ameliorated disuse- and dexamethasone-induced atrophy in mice. Moreover, in three independent sets of transcriptomic data from human skeletal muscle, KLF5 expression significantly increased with age and the presence of sarcopenia and correlated positively with the expression of the atrophy-related ubiquitin ligase genes FBXO32 and TRIM63. These findings demonstrate that KLF5 is a key transcriptional regulator mediating muscle atrophy and that pharmacological intervention with Am80 is a potentially preventive treatment. [ABSTRACT FROM AUTHOR]