Jul 2026· Biochemistry and Biophysics Reports· Vol 47, pp. 102706· 0 citations· 248 references
Medicine
TL;DR
A cross-kingdom synthesis of disorder-based chromatin regulation is developed, demonstrating that bacterial nucleoid-associated proteins, plant transcription factors, and mammalian chromatin regulators share a conserved charge-regulatory logic, mediated by PTM-dependent mechanisms that dynamically couple environmental signals with genome organization.
Abstract
Intrinsically disordered proteins (IDPs) and regions (IDRs) challenge the classical structure–function paradigm by fulfilling essential biological roles in the absence of a stable three-dimensional fold. Rather than occupying fixed conformations, IDPs exist as dynamic ensembles that enable high-specificity, low-affinity interactions, multivalent regulatory functions, and context-dependent binding across diverse cellular environments. This conformational plasticity underlies their central roles in signaling, transcriptional regulation, chromatin organization, and the assembly of membrane-less organelles through liquid–liquid phase separation (LLPS). The present review offers several conceptual contributions. First, we develop a cross-kingdom synthesis of disorder-based chromatin regulation, demonstrating that bacterial nucleoid-associated proteins, plant transcription factors, and mammalian chromatin regulators share a conserved charge-regulatory logic, mediated by PTM-dependent mechanisms that dynamically couple environmental signals with genome organization. Second, we integrate mechanistically related but frequently siloed disease pathways, including mitophagy dysfunction, oxidative stress signaling, neuroinflammation, and aberrant phase separation, into a unified framework linking IDP conformational dysregulation to neurodegeneration and cancer. Third, we highlight underexplored regulatory dimensions of IDP biology, including proline isomerization and ubiquitylation-driven condensate formation, that influence conformational ensembles and signaling outputs in ways not captured by conventional structural approaches. Finally, we critically evaluate recent advances in AI-assisted disorder prediction and hybrid experimental-computational ensemble characterization, emphasizing both their transformative potential and current limitations. Dysregulation of IDPs underlies a broad spectrum of human pathologies, and we discuss the emerging opportunities and persistent challenges in targeting these conformationally dynamic proteins therapeutically, including through PROTAC-based degraders, condensate modulators, and ensemble-based drug screening strategies.
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack stable tertiary structures yet perform essential roles in cellular signaling, molecular recognition, transcriptional regulation, and biomolecular assembly. Their conformational flexibility enables functional adaptability but also increases susceptibility to aberrant intermolecular interactions and protein aggregation. Unlike folded proteins, aggregation in IDPs arises from transient conformational ensembles that expose cryptic aggregation-prone regions (APRs), facilitating oligomerization and fibril formation under specific cellular and environmental conditions. Several studies have further established a mechanistic relationship between intrinsic disorder, liquid–liquid phase separation (LLPS), and pathological aggregation, where dynamic condensates can undergo maturation into irreversible amyloid-like assemblies. These transitions are strongly influenced by sequence grammar, charge distribution, aromatic residue patterning, post-translational modifications, molecular crowding, and proteostasis regulation. This mini-review summarizes the molecular principles governing aggregation in disordered systems, with emphasis on conformational ensemble dynamics, disorder-to-order transitions, and the interplay between LLPS and fibrillization. The review further discusses computational approaches used to predict aggregation propensity in IDRs, including classical physicochemical predictors, ensemble-aware simulations, molecular dynamics frameworks, and emerging protein language model-based methods. Further, integration of artificial intelligence, structural biophysics, and multiscale modeling have substantially improved understanding of disorder-driven aggregation pathways. Collectively, these findings support a unified framework in which sequence composition, conformational heterogeneity, and cellular environment cooperatively regulate functional assembly and pathological aggregation in intrinsically disordered proteins.
Rahul Kaushik, Suyong Re· Frontiers in Biophysics· 1 citation
Protein self-interaction to form homodimers and higher-order homo-oligomers is a ubiquitous phenomenon fundamental to living organisms. Recent structural, system-level, and computational insights reveal that self-interacting proteins dictate the specificity, rewiring, and topological complexity of cellular signaling networks and macromolecular assemblies. Beyond their physiological roles, aberrant or dysregulated homotypic interactions disrupt cellular proteostasis, driving the formation of toxic non-native oligomers, pathological amyloid fibrillization, or aberrant liquid–liquid phase separation transitions linked to neurodegenerative and systemic diseases. This review provides a comprehensive overview of the state-of-the-art experimental methodologies, including proximity labeling, as well as the advanced computational frameworks, such as deep learning architectures and protein language models, used to map the structural dynamics of SIPs. Furthermore, we dissect the evolutionary trajectories of SIPs within protein–protein interaction networks, which are underpinned by dosage-balance constraints, and highlight their diverse functional advantages, ranging from allosteric modulation to biomolecular condensation. Finally, we summarize the molecular mechanisms linking pathological self-associations to human disorders, underscoring the emerging paradigm of targeting homotypic interfaces as a promising frontier for precision therapeutics.
Yuanxiao Gao, Wenyu Zhang, Guang Hu· International Journal of Mol...· 0 citations
Protein-RNA complexes underlie essential cellular processes and understanding their functional mechanisms requires structural analysis. Yet, their inherent flexibility, multi-valency, and dynamics make them challenging targets for structural biology. Integrative approaches, combining nuclear magnetic resonance (NMR), small-angle scattering, cryo-electron microscopy (cryo-EM), cryo-electron tomography (cryo-ET), crosslinking mass spectrometry, single-molecule techniques, and artificial intelligence (AI)-based predictions, have enabled the characterization of increasingly complex ribonucleoprotein (RNP) assemblies, in vitro and in their cellular contexts. These strategies have begun to capture molecular architecture and dynamic behaviors across time and space, paving the way for 4D structural biology. Here, we review recent developments in integrative modeling of protein-RNA complexes, highlighting advances in in-cell, 4D and condensate structural biology, and discuss how these approaches shape our understanding of RNP assembly, regulation, and function in physiologically relevant environments.
Simone Heber, Janosch Hennig· Current Opinion in Structura...· 1 citation
Physical remodeling of chromatin by non-histone architectural proteins of the High Mobility Group B (HMGB) family is central to eukaryotic transcriptional regulation. Nhp6A, the prototypical single-HMG-box protein from yeast, harbors both ordered and disordered regions enabling it to bind and bend DNA without sequence specificity. Here, we integrate ensemble experiments, single-molecule FRET, statistical mechanical modeling and atomistic simulations to dissect the structural and functional consequences of context-dependent phosphorylation in the ordered domain and its interplay with the intrinsically disordered region in Nhp6A. We find that Nhp6A occupies a narrow thermodynamic window, with a melting temperature close to the growth temperature of its host organism and high unfolding cooperativity, a feature conserved across the HMG-box family. Phosphorylation extents – mimicked by multisite phosphomimetic substitutions at residue positions conserved across fungal taxa – smoothly tuning the conformational equilibria between at least two different substates in the native ensemble, apart from the unfolded state. This intrinsic plasticity enables close packing of Nhp6A on DNA through two degenerate binding modes, accompanied by two distinct DNA bending geometries. DNA rescues a strongly destabilized mutant, T63D, through favorable intermolecular interactions, thus effectively acting as a chaperone driving folding. Our findings thus reveal a conserved sequence-ensemble-dynamics code in Nhp6A wherein not just stability, but also phosphorylation-induced conformational switching, disordered tail dynamics, and DNA binding-bending closely coordinate chromatin accessibility. The combination of marginal stability, large cooperativity and electrostatic frustration emerges as a design principle to encode charge sensitivity into proteins, and may represent a general strategy for multisite post-translational regulation.
Shilpi Laha, H. Madhan, Yuji Itoh et al.· bioRxiv· 0 citations
Among non‐classical nucleic acid secondary structures, G‐quadruplexes (G4s) play diverse roles in cellular functions and disease pathogenesis. However, the molecular mechanisms underlying the assembly of endogenous G4s into punctate condensates in cells remain unclear. Biomolecular condensates can arise from weak multivalent intermolecular interactions involving proteins and/or nucleic acids; this phenomenon is frequently linked to liquid–liquid phase separation. Recent research has provided compelling evidence for G4s driving biomolecular condensation. In this review, we first summarize the latest breakthroughs in the structural classification of G4s. In addition to frequently reported intramolecular G4s, intermolecular G4s have also been observed in cellular environments. Next, we discuss the regulatory role of G4s in condensation. Although G4s can independently form condensates, they primarily serve as structural platforms that facilitate condensate formation and regulate their phase transitions. Ultimately, this review reveals the multifaceted physiological and pathological functions of G4‐driven condensates, including chromatin organization, assembly of stress granules and paraspeckles, abnormal transcriptional activation, telomere maintenance, neurodegenerative disease‐associated protein aggregation, and viral inclusion body formation.
Wenmeng Wang, Qingqing Xu, Yuxin Zhang et al.· Advancement of science· 0 citations
Intragenomic homologs are widespread, but their physiological roles are often masked by redundancy. Histone-like nucleoid structuring protein (H-NS), a nucleoid-associated protein in Gram-negative bacteria, typically coexists with homologs like StpA, whose functions are obscured by a lack of strong phenotypes. We demonstrate here that the interaction between H-NS and StpA fine-tunes the physico-chemical properties of nucleoid-associated compartments. Although H-NS forms dynamic condensates in vitro, StpA assembles into stable insoluble fibrils. However, together the two proteins form liquid-like droplets, whose fluidity and stability are tunable by their relative stoichiometry. By increasing the levels of StpA over H-NS, bacteria stabilize heterochromatin-associated compartments, thereby preserving gene repression and optimizing bacterial growth under stress. Structural differences at these proteins' dimerization sites help explain their distinct phase behaviors. Our findings reveal a paradigm in which intragenomic homologs that are positioned at the opposite ends of the phase spectrum can fine-tune subcellular organization to promote survival in fluctuating environments.
Jian Guan, Bikash R. Sahoo, Tyler S. Brant et al.· Molecules and Cells· 0 citations