@article{15001,
  abstract     = {Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer’s A
 amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A
 fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor.},
  author       = {Curk, Samo and Krausser, Johannes and Meisl, Georg and Frenkel, Daan and Linse, Sara and Michaels, Thomas C.T. and Knowles, Tuomas P.J. and Šarić, Anđela},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences of the United States of America},
  number       = {7},
  publisher    = {Proceedings of the National Academy of Sciences},
  title        = {{Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites}},
  doi          = {10.1073/pnas.2220075121},
  volume       = {121},
  year         = {2024},
}

@article{14844,
  abstract     = {Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that these proteins induce. While the pairwise interaction potential of two membrane-deforming spheres has recently been measured, membrane-deformation-induced interactions have been predicted to be nonadditive, and hence their collective behavior cannot be deduced from this measurement. We here employ a colloidal model system consisting of adhesive spheres and giant unilamellar vesicles to test these predictions by measuring the interaction potential of the simplest case of three membrane-deforming, spherical particles. We quantify their interactions and arrangements and, for the first time, experimentally confirm and quantify the nonadditive nature of membrane-deformation-induced interactions. We furthermore conclude that there exist two favorable configurations on the membrane: (1) a linear and (2) a triangular arrangement of the three spheres. Using Monte Carlo simulations, we corroborate the experimentally observed energy minima and identify a lowering of the membrane deformation as the cause for the observed configurations. The high symmetry of the preferred arrangements for three particles suggests that arrangements of many membrane-deforming objects might follow simple rules.},
  author       = {Azadbakht, Ali and Meadowcroft, Billie and Majek, Juraj and Šarić, Anđela and Kraft, Daniela J.},
  issn         = {1542-0086},
  journal      = {Biophysical Journal},
  publisher    = {Elsevier},
  title        = {{Nonadditivity in interactions between three membrane-wrapped colloidal spheres}},
  doi          = {10.1016/j.bpj.2023.12.020},
  year         = {2023},
}

@article{13094,
  abstract     = {Endocytosis is a key cellular process involved in the uptake of nutrients, pathogens, or the therapy of diseases. Most studies have focused on spherical objects, whereas biologically relevant shapes can be highly anisotropic. In this letter, we use an experimental model system based on Giant Unilamellar Vesicles (GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first stage of the passive endocytic process: engulfment of an anisotropic object by the membrane. Our model has specific ligand–receptor interactions realized by mobile receptors on the vesicles and immobile ligands on the particles. Through a series of experiments, theory, and molecular dynamics simulations, we quantify the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages of the wrapping pathway. We find that the strong curvature variation in the neck of the dumbbell as well as membrane tension are crucial in determining both the speed of wrapping and the final states.},
  author       = {Azadbakht, Ali and Meadowcroft, Billie and Varkevisser, Thijs and Šarić, Anđela and Kraft, Daniela J.},
  issn         = {1530-6992},
  journal      = {Nano Letters},
  number       = {10},
  pages        = {4267–4273},
  publisher    = {American Chemical Society},
  title        = {{Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles}},
  doi          = {10.1021/acs.nanolett.3c00375},
  volume       = {23},
  year         = {2023},
}

@article{13971,
  abstract     = {When in equilibrium, thermal forces agitate molecules, which then diffuse, collide and bind to form materials. However, the space of accessible structures in which micron-scale particles can be organized by thermal forces is limited, owing to the slow dynamics and metastable states. Active agents in a passive fluid generate forces and flows, forming a bath with active fluctuations. Two unanswered questions are whether those active agents can drive the assembly of passive components into unconventional states and which material properties they will exhibit. Here we show that passive, sticky beads immersed in a bath of swimming Escherichia coli bacteria aggregate into unconventional clusters and gels that are controlled by the activity of the bath. We observe a slow but persistent rotation of the aggregates that originates in the chirality of the E. coli flagella and directs aggregation into structures that are not accessible thermally. We elucidate the aggregation mechanism with a numerical model of spinning, sticky beads and reproduce quantitatively the experimental results. We show that internal activity controls the phase diagram and the structure of the aggregates. Overall, our results highlight the promising role of active baths in designing the structural and mechanical properties of materials with unconventional phases.},
  author       = {Grober, Daniel and Palaia, Ivan and Ucar, Mehmet C and Hannezo, Edouard B and Šarić, Anđela and Palacci, Jérémie A},
  issn         = {1745-2481},
  journal      = {Nature Physics},
  pages        = {1680--1688},
  publisher    = {Springer Nature},
  title        = {{Unconventional colloidal aggregation in chiral bacterial baths}},
  doi          = {10.1038/s41567-023-02136-x},
  volume       = {19},
  year         = {2023},
}

@article{12708,
  abstract     = {Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter.},
  author       = {Araújo, Nuno A.M. and Janssen, Liesbeth M.C. and Barois, Thomas and Boffetta, Guido and Cohen, Itai and Corbetta, Alessandro and Dauchot, Olivier and Dijkstra, Marjolein and Durham, William M. and Dussutour, Audrey and Garnier, Simon and Gelderblom, Hanneke and Golestanian, Ramin and Isa, Lucio and Koenderink, Gijsje H. and Löwen, Hartmut and Metzler, Ralf and Polin, Marco and Royall, C. Patrick and Šarić, Anđela and Sengupta, Anupam and Sykes, Cécile and Trianni, Vito and Tuval, Idan and Vogel, Nicolas and Yeomans, Julia M. and Zuriguel, Iker and Marin, Alvaro and Volpe, Giorgio},
  issn         = {1744-6848},
  journal      = {Soft Matter},
  pages        = {1695--1704},
  publisher    = {Royal Society of Chemistry},
  title        = {{Steering self-organisation through confinement}},
  doi          = {10.1039/d2sm01562e},
  volume       = {19},
  year         = {2023},
}

@article{12756,
  abstract     = {ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling.},
  author       = {Hurtig, Fredrik and Burgers, Thomas C.Q. and Cezanne, Alice and Jiang, Xiuyun and Mol, Frank N. and Traparić, Jovan and Pulschen, Andre Arashiro and Nierhaus, Tim and Tarrason-Risa, Gabriel and Harker-Kirschneck, Lena and Löwe, Jan and Šarić, Anđela and Vlijm, Rifka and Baum, Buzz},
  issn         = {2375-2548},
  journal      = {Science Advances},
  number       = {11},
  publisher    = {American Association for the Advancement of Science},
  title        = {{The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division}},
  doi          = {10.1126/sciadv.ade5224},
  volume       = {9},
  year         = {2023},
}

@article{11400,
  abstract     = {By varying the concentration of molecules in the cytoplasm or on the membrane, cells can induce the formation of condensates and liquid droplets, similar to phase separation. Their thermodynamics, much studied, depends on the mutual interactions between microscopic constituents. Here, we focus on the kinetics and size control of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids, we model a system of two species of proteins, giving origin to specific heterotypic bonds. We find that concentrations, together with valence and bond strength, control both the size and the growth time rate of the clusters. In particular, if one species is in large excess, it gradually saturates the binding sites of the other species; the system then becomes kinetically arrested and cluster coarsening slows down or stops, thus yielding effective size selection. This phenomenology is observed both in solid and fluid clusters, which feature additional generic homotypic interactions and are reminiscent of the ones observed on biological membranes.},
  author       = {Palaia, Ivan and Šarić, Anđela},
  issn         = {1089-7690},
  journal      = {The Journal of Chemical Physics},
  keywords     = {Physical and Theoretical Chemistry, General Physics and Astronomy},
  number       = {19},
  publisher    = {AIP Publishing},
  title        = {{Controlling cluster size in 2D phase-separating binary mixtures with specific interactions}},
  doi          = {10.1063/5.0087769},
  volume       = {156},
  year         = {2022},
}

@article{11841,
  abstract     = {Primary nucleation is the fundamental event that initiates the conversion of proteins from their normal physiological forms into pathological amyloid aggregates associated with the onset and development of disorders including systemic amyloidosis, as well as the neurodegenerative conditions Alzheimer’s and Parkinson’s diseases. It has become apparent that the presence of surfaces can dramatically modulate nucleation. However, the underlying physicochemical parameters governing this process have been challenging to elucidate, with interfaces in some cases having been found to accelerate aggregation, while in others they can inhibit the kinetics of this process. Here we show through kinetic analysis that for three different fibril-forming proteins, interfaces affect the aggregation reaction mainly through modulating the primary nucleation step. Moreover, we show through direct measurements of the Gibbs free energy of adsorption, combined with theory and coarse-grained computer simulations, that overall nucleation rates are suppressed at high and at low surface interaction strengths but significantly enhanced at intermediate strengths, and we verify these regimes experimentally. Taken together, these results provide a quantitative description of the fundamental process which triggers amyloid formation and shed light on the key factors that control this process.},
  author       = {Toprakcioglu, Zenon and Kamada, Ayaka and Michaels, Thomas C.T. and Xie, Mengqi and Krausser, Johannes and Wei, Jiapeng and Šarić, Anđela and Vendruscolo, Michele and Knowles, Tuomas P.J.},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences of the United States of America},
  number       = {31},
  publisher    = {Proceedings of the National Academy of Sciences},
  title        = {{Adsorption free energy predicts amyloid protein nucleation rates}},
  doi          = {10.1073/pnas.2109718119},
  volume       = {119},
  year         = {2022},
}

@article{12108,
  abstract     = {The sequential exchange of filament composition to increase filament curvature was proposed as a mechanism for how some biological polymers deform and cut membranes. The relationship between the filament composition and its mechanical effect is lacking. We develop a kinetic model for the assembly of composite filaments that includes protein–membrane adhesion, filament mechanics and membrane mechanics. We identify the physical conditions for such a membrane remodeling and show this mechanism of sequential polymer assembly lowers the energetic barrier for membrane deformation.},
  author       = {Meadowcroft, Billie and Palaia, Ivan and Pfitzner, Anna Katharina and Roux, Aurélien and Baum, Buzz and Šarić, Anđela},
  issn         = {1079-7114},
  journal      = {Physical Review Letters},
  number       = {26},
  publisher    = {American Physical Society},
  title        = {{Mechanochemical rules for shape-shifting filaments that remodel membranes}},
  doi          = {10.1103/PhysRevLett.129.268101},
  volume       = {129},
  year         = {2022},
}

@article{12152,
  abstract     = {ESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks.},
  author       = {Jiang, Xiuyun and Harker-Kirschneck, Lena and Vanhille-Campos, Christian Eduardo and Pfitzner, Anna-Katharina and Lominadze, Elene and Roux, Aurélien and Baum, Buzz and Šarić, Anđela},
  issn         = {1553-7358},
  journal      = {PLOS Computational Biology},
  keywords     = {Computational Theory and Mathematics, Cellular and Molecular Neuroscience, Genetics, Molecular Biology, Ecology, Modeling and Simulation, Ecology, Evolution, Behavior and Systematics},
  number       = {10},
  publisher    = {Public Library of Science},
  title        = {{Modelling membrane reshaping by staged polymerization of ESCRT-III filaments}},
  doi          = {10.1371/journal.pcbi.1010586},
  volume       = {18},
  year         = {2022},
}