An in-depth review of CaMKK signaling, including structural, regulatory, and functional insights into its activation, downstream effects, and implications for disease.
Notes on 2014 ACS paper introducing DFGmodel, a computational approach to predict kinase inactive structures for type-II inhibitor discovery. Includes insights on DFG-flip and kinase conformational analysis.
Notes on 2004 Molecular Cell review analyzing how activation segment conformation regulates protein kinase activity, including insights into RD pocket, anchor residues, and alternative activation mechanisms.
Notes on 2012 FEBS Review about how phosphorylation controls protein stability via phosphodegrons and phospho-inhibited degrons, integrating ubiquitin-mediated degradation in cell cycle regulation.
Notes on 2005 Biophysical Journal article analyzing atomistic pathways of Ca²⁺ binding to calmodulin, highlighting stepwise binding, dehydration coupling, and residue dynamics.
Notes on 2024_ACS paper discussing the kinetic and structural principles of phosphorylation-driven protein switches and their biosensor applications.
Notes on 2004 Elsevier article discussing how weak links stabilize complex networks, with insights into phosphorylation, metabolic flux, and protein folding.
Notes on 2010_PNAS study exploring how multisite phosphorylation of p53 modulates its interaction with CBP and transcriptional activation.
Notes on 2010 Cell Review article exploring the structural and evolutionary principles that shape the dynamic regulatory mechanisms of protein kinases.
Notes on 2002 Cell review discussing conformational plasticity of protein kinases, highlighting key structural elements, activation mechanisms, and pseudosubstrate regulation. Includes insights on αC helix, activation loop, and therapeutic implications (e.g., Gleevec binding).
Notes on 2008_PNAS paper revealing F-helix as a hub for regulatory and catalytic spine anchoring in protein kinases.
Comprehensive notes on AKAPs as molecular scaffolds that regulate spatial and temporal signaling by anchoring PKA and other enzymes, enabling precise phosphorylation events in response to cellular stimuli.
The study redefines CASK as an active Mg²⁺-independent kinase that phosphorylates neurexin, integrating scaffolding and enzymatic functions, challenging its previous classification as a pseudokinase.
Notes on the 2023 TIBS review proposing that intrinsically disordered regions (IDRs), with their sequence-dependent structural biases, are well-suited to act as sensors and actuators of cellular physicochemistry. Discusses physical principles, molecular mechanisms, and experimental strategies for investigating IDR sensitivity and highlights their potential biological roles.
Notes on the 2014 PNAS paper using single-molecule FRET to analyze the conformational response of intrinsically disordered proteins (IDPs) to molecular crowding. Highlights how IDP compaction depends not only on crowder concentration but also on crowder size, challenging traditional crowding models and introducing polymer-specific effects.
