A highly recommended, advanced-level book on statistical thermodynamics applied to chemistry and biology — a natural follow-up to Protein Actions. Includes my annotated version and a clean copy for download.
Notes on 2002 Protein Science review on how proteins with specificity bind multiple diverse ligands through pre-existing conformational populations and hinge-bending motions.
Notes on 2017 review discussing how intrinsically disordered proteins (IDPs) form various types of complexes including fuzzy complexes, with implications for flexible signaling and dynamic regulation.
Highly recommended read on protein structure, dynamics, and modeling — accessible, like reading a novel. Includes my annotated version and a clean copy for download.
Notes on a 2021 Frontiers review discussing how proteome-wide protein pI distributions are linked to subcellular localization. The paper highlights how environmental conditions and compartment-specific features shape protein pI profiles, offering insights into protein solubility, function, and adaptation.
Notes on 2008 Biophysical Journal paper analyzing the thermodynamics of membrane insertion for an H-ras lipopeptide anchor (ANCH), highlighting the role of enthalpy-driven hydrophobic effects and conformational selection.
Notes on 2000 Proteins paper introducing the concept of ’natively unfolded’ proteins and how charge and hydrophobicity dictate their intrinsic disorder under physiological conditions.
Notes on 2004 JMB paper exploring how preformed structural elements in intrinsically disordered proteins (IDPs) facilitate efficient binding and partner recognition.
Notes on a 2001 JBIC review comparing structural features of Ca2+ and lanthanide-binding sites in proteins. Discusses coordination geometries, ligand types, and structural classes of metal-binding motifs, including under-representation of EF-hand in structural databases.
Notes on 2013 PNAS paper introducing the role of charge distribution pattern (κ) in shaping IDP conformations. Highlights how linear charge segregation influences whether IDPs adopt random coil or compact, hairpin-like structures.
Notes on a 1999 Proteins review analyzing the conformational diversity of EF-hand motifs in calcium-binding proteins. Introduces Vector Geometry Mapping (VGM) to dissect helix movements beyond simple interhelical angles, and discusses functional implications of EF-hand plasticity.
Notes on 2010 PNAS paper exploring how net charge per residue (NCPR) governs the balance between collapsed and extended conformations in intrinsically disordered proteins (IDPs), with implications for understanding IDP behavior and function.
Notes on 2006 JMB review detailing EF-hand protein diversity, mechanisms of Ca2+ binding, and conformational change. Highlights the EFbeta-scaffold model and structural determinants of domain opening in calcium-binding proteins.
Notes on 2007 Biochemical Journal review discussing EF-hand structural diversity, Ca²⁺/Mg²⁺ binding properties, cooperativity, and conformational changes. Focus on EF-hand pairing, metal selectivity, and functional adaptation for signaling.
Notes on a 2002 Trends in Cell Biology review introducing phosphorylation-specific prolyl isomerization as a novel signaling mechanism. Pin1-mediated cis-trans switching of pSer/Thr-Pro motifs acts as a conformational timer for cellular signaling, impacting activity, interactions, and localization of key regulatory proteins.
