A deep dive into the molecular dynamics and membrane interaction of EGFR, revealing distinct active and inactive conformations, the role of lipid environment, and subtle structural regulation.
Notes on a 2003 Nature Structural Biology paper introducing the concept of evolutionarily conserved residue networks that mediate allosteric communication. Using sequence-based statistical coupling analysis (SCA), the authors map sparse, functionally critical networks in GPCRs, proteases, and hemoglobins, highlighting a fundamental mechanism of long-range communication in protein structures.
Notes on a 2003 Nature Structural Biology paper introducing the concept of evolutionarily conserved residue networks that mediate allosteric communication. Using sequence-based statistical coupling analysis (SCA), the authors map sparse, functionally critical networks in GPCRs, proteases, and hemoglobins, highlighting a fundamental mechanism of long-range communication in protein structures.
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 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 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 2006_PNAS paper exploring conserved structural mechanisms of kinase activation via surface comparison.
Notes on a 2014 PNAS paper analyzing PKA dynamics through community analysis.
Notes on 2008_PNAS paper revealing F-helix as a hub for regulatory and catalytic spine anchoring in protein kinases.
Notes on 2008_PNAS paper revealing F-helix as a hub for regulatory and catalytic spine anchoring in protein kinases.
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.
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 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 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.
