Biology subjects

Dijkgraaf, I.

Publications and source records attributed to Dijkgraaf, I..

4 recordsLinked to original sources

bioRxiv2025

Condensate-based shells and scaffolds via interfacial liquid-to-solid transition of disordered peptides

Living organisms use biomolecular condensates to respond to dynamic environments and create functional materials with complex architectures. Exploring such phase-separated systems beyond the naturally occurring scenarios may offer valuable insights for emergent synthetic biosystems. Here, we report the self-assembly behavior of a short, disordered peptide sequence (termed CT45) derived from a protein present in the bioad-hesive system of tick ectoparasites. We show that CT45 spontaneously accumulates at polar-nonpolar interfaces, and further undergoes liquid-liquid and liquid-to-solid phase transitions to create mechanically stable structures. When encapsulated within vesicles and presented with a stable oil-water interface, CT45 rapidly forms solid shells, which can be reinforced by up-concentrating the material through osmotic imbalance. Unex-pectedly, when presented with a transient acetone-water interface, CT45 condenses at the evaporating interface and forms interconnected, porous mesoscopic scaffolds. The underlying mechanism is found to be the amphiphilic nature of CT45 leading to in-terfacial accumulation, enhancing intermolecular{pi} -based interactions to trigger phase transitions. The micron-sized shells exhibit appreciable mechanical strength and the porous scaffolds present a highly stable platform capable of retaining molecules. In conclusion, the presented condensate-based microscopic and mesoscopic scaffolds hold significance in customizable condensate architectures, with potential applications in biomedical engineering and synthetic biology.

bioengineering↗

bioRxiv2025

Chemokine-binding all-D-CLIPS™ peptides identified using mirror-image phage display

Chemokines are secreted blood proteins, which steer leukocyte migration in the inflammatory response. Neutralization of chemokines is believed to be a beneficial therapeutic strategy for the treatment of inflammation-associated diseases. Proteolytically stable chemokine-binding peptides could be suitable candidates for the development of chemokine-neutralizing agents. Here, we report mirror-image phage display selection of cyclic all-D-peptides against the C-X-C motif chemokine ligand 8 (CXCL8). Selection yielded structurally diverse all-D-peptides with sub-micromolar affinity to the target CXCL8 chemokine and different selectivity to related chemokines. Binding of these all-D-peptides caused dissociation of the native CXCL8 dimer and disruption of its binding to GAGs, without effect on in vitro cell migration. This work demonstrates the example of mirror-image phage display selection of cyclized all-D-peptides and its utility for the development of chemokine-binding agents.

biochemistry↗

bioRxiv2025

pH-Responsive Phase Separation Dynamics of Intrinsically Disordered Peptides

Liquid-liquid phase separation of biomolecules is crucial for maintaining the functional organization in biological systems. Intrinsically disordered proteins are particularly prone to form phase-separated condensates in response to various physicochemical triggers. While the effect of ionic strength and temperature on phase separation dynamics have been studied extensively, the influence of pH is less explored. Here, we study a model glycine-rich protein present in the tick bioadhesive, given its capability to undergo phase separation. After confirming its disordered nature through spectroscopy, we investigated its pH dependence and underlying molecular mechanisms. Our findings reveal that pH significantly influences the protein hydrophobicity via ionic residues, driving notable variations in the coacervation behavior (propensity, progression) and in shaping the material properties (viscosity, interfacial activity) of the formed condensates. Given the ubiquitous presence of disordered proteins in biology, this study provides valuable insights about the broad implications of the pH-dependent behavior of intrinsically disordered proteins.

biochemistry↗

bioRxiv2023

Phase Separation and Ageing of Glycine-Rich Protein from Tick Adhesive

Hard ticks feed on their host for multiple days. To ensure firm attachment, they secrete a protein-rich saliva that eventually forms a solid cement cone. The underlying mechanism of this liquid-to-solid transition is not yet understood. This study focuses on the phase transitions of a disordered glycine-rich protein (GRP) that is prominent in tick saliva. We show that GRP undergoes liquid-liquid phase separation via simple coacervation to form biomolecular condensates in salty environments. Cation-pi and pi-pi interactions near the C-terminus promote coacervation while a negatively charged N-terminus prolongs its onset through electrostatic repulsion. Interestingly, GRP condensates exhibit ageing and undergo liquid-to-gel transition to form viscoelastic networks as well as solid-like condensates. Lastly, we provide evidence for protein-rich condensates in natural tick saliva. Our findings provide a starting point to gain insights into the bioadhesion of ticks, develop novel tick control strategies, and towards biomedical applications such as tissue sealants.

biochemistry↗