Notes on the 2024 Nature paper exploring how sequence-dependent structural biases in intrinsically disordered proteins (IDPs) are preserved inside cells and how they respond to environmental changes. Using a combination of FRET, SAXS, SEC, and simulations, the study establishes glycine-serine repeats as model-free standards and demonstrates that IDP ensembles encode functional biases persistent in cellular contexts.
Notes on the 2020 ACS paper introducing a combined experimental, computational, and analytical framework to study how IDRs respond to changes in chemical environments. The work reveals sequence-dependent compaction and expansion of IDRs under different solutes and highlights the role of chemical sensitivity as an added layer of regulation in biology.
Notes on the 2018 Trends in Biochemical Sciences review covering diverse mechanisms by which protein kinases achieve substrate specificity. The paper explores recognition motifs, docking interactions, adaptor-mediated recruitment, and multisite phosphorylation, highlighting how these shape signaling networks. (Still can’t like this paper — 23.03.23)
Notes on the 1999 Cell paper describing crystal structures of spectrin repeats and introducing two models for spectrin’s flexibility: conformational rearrangement and linker bending. Provides insights into spectrin’s role as a flexible cytoskeletal scaffold.
Notes on the 2001 JMB paper introducing SOCKET, a computational tool that identifies coiled-coil motifs based on structural features rather than sequence patterns. Highlights the diversity of coiled-coil structures, the central role of knobs-into-holes packing, and applications in structural analysis and design.
Notes on the 1996 JMB paper introducing the Helical Lattice Superposition Model for analyzing helix-helix packing geometry in proteins. Explores mathematical formulations of optimal packing angles, comparing ‘knobs into holes’ and ‘ridges into grooves’ models, and provides insights into amino acid preferences and packing flexibility.
Notes on a 2002 JBC review dissecting CaMKII’s structure-function relationship, covering autoinhibition, isoform diversity, holoenzyme assembly, autophosphorylation, subunit exchange, and Ca2+/CaM frequency decoding — a foundational reference for understanding this multifunctional kinase as a calcium signal integrator.
Notes on a 2004 Plant Cell paper mapping Arabidopsis plasma membrane phosphoproteins and phosphorylation sites.
Notes on the fundamental roles and mechanisms of protein kinase autophosphorylation, including examples from PKA, PKC, MLCK, RTKs, and others. Functional effects and evolutionary perspectives are also discussed.
A study demonstrating that EGFR activation is not tightly coupled to specific transmembrane dimerization interfaces, suggesting a loose linkage between extracellular ligand binding and intracellular kinase activation.
Note on the evolutionary insights of CDPKs and CRKs through intron/exon analysis, proposing a monophyletic origin and highlighting the role of ancient intron-mediated gene fusion in the origin of CDPKs.
Notes on a 2015 Neuron paper revealing how CaMKII’s dual role as kinase and structural element regulates actin remodeling during synaptic plasticity, showing that autophosphorylation-mediated dissociation from F-actin provides a time window permissive for structural long-term potentiation (sLTP).
Comprehensive review on how PKA holoenzyme assembly provides unique insights into kinase regulation, highlighting regulatory-catalytic subunit interactions, anchoring proteins, and macromolecular scaffolds.
Notes on the mechanism by which PDK1 is activated via PIP3-mediated dimerization and trans-autophosphorylation, highlighting the role of PH domain autoinhibition, linker-mediated dimerization, and switch-like activation mechanisms.
Notes on a 2000 JBC paper dissecting the autoinhibitory mechanism of CaMKK, identifying Ile441 as critical for maintaining the inactive state, and showing that CaM-binding peptide orientation does not dictate relief from autoinhibition — a pivotal insight into CaMKK regulation.
