Notes on 2004 PNAS paper introducing the concept of anchor residues as key pre-configured side chains that drive protein–protein interactions. The study highlights a two-step binding mechanism, combining preformed ‘anchor’ interactions and induced-fit adjustments.
Notes on 2014 Cell paper that identifies the ‘DFG+1’ residue as a key determinant of Ser/Thr kinase phosphoacceptor specificity, with structural and biochemical validation.
An elegant dissection of how the C-terminal tail (C-tail) in AGC kinases serves as a cis-acting regulatory module, driving functional divergence from other kinase families. Through conserved interactions and structural specialization, the C-tail orchestrates key regulatory processes, acting as a unique hallmark of AGC kinases.
A groundbreaking exploration of how sequence patterning, especially proline and charge distributions, governs the conformational behavior of intrinsically disordered regions (IDRs) even under multisite phosphorylation, with compensatory conformational changes maintaining overall dimensions.
A conceptual leap in understanding protein folding, showing how water molecules and molecular chaperones act as weak, transient links that smooth energy landscapes and prevent conformational traps. This paper connects protein folding, dynamic networks, and game theory, offering a new way to see how folding and interaction landscapes are managed in crowded cellular environments.
A modern view of allostery as an intrinsic property of protein dynamics, where conformational shifts, weak interactions, and energy landscapes enable regulation of function. Bridging classical models with cutting-edge experimental and theoretical insights, this review explores how proteins use dynamic ensembles and independent dynamic segments to facilitate signaling, folding, and ligand binding — redefining allostery beyond static views.
A groundbreaking study connecting protein folding energy landscapes to functional conformational changes in signaling proteins, showing how transient, non-native hydrogen bonds lower transition barriers and facilitate activation without unfolding.
Notes on 2002 APS paper analyzing the topology of potential energy landscapes, showing how minima and transition states form a static scale-free and small-world network. Offers insights into energy landscape organization, optimization, and system dynamics.
Notes on 2023 ACS paper exploring structural differences between serine and threonine phosphorylation, focusing on phosphothreonine’s preference for ordered conformations.
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.
An in-depth study of EGFR activation focusing on transmembrane and juxtamembrane coupling, density-dependent activation, and the role of the plasma membrane in maintaining autoinhibition.
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.
A detailed analysis of Rhodopsin Kinase (RK) autophosphorylation sites and their functional implications, highlighting purification strategies and structural analysis using proteolysis and mass spectrometry.
Comprehensive 2016 Frontiers review on the diverse binding mechanisms of intrinsically disordered proteins (IDPs), covering theory, simulations, and experimental insights into how disorder facilitates interaction dynamics, specificity, and versatility in cellular signaling.
A 2010 Cell review expanding the classical models of protein-ligand binding to a dynamic landscape of conformational selection, induced fit, and independent dynamic segments. The paper highlights how ‘NOISE’—conformational fluctuations—can amplify signaling and regulate allosteric interactions, reshaping our understanding of binding and protein communication.
