Speaker: Wei-Feng Xue
Department: School of Biosciences, University of Kent
Subject: Nano-scale Properties of the Amyloid Life-cycle
Location: TU Delft, Bionanoscience, Kavli Institute of Nanoscience
Author: Mirte Golverdingen
Xue started his talk by introducing amyloid and prions. Amyloid and prions are important biological structures. Amyloids are fibrillar structures that are formed from proteins or peptides. They are only around 10 nm width, up top micrometers long. Amyloids are associated with diseases such as type II diabetes, Alzheimer’s disease and Parkinson’s disease. Prions are transmissible amyloid associated with diseases such as mad-cow disease, scrapie and Variant Creutzfeldt-Jakob disease.
However, Amyloids are also potential candidate as high-performance nano-material. The fibers have interesting mechanical and elastic properties. Xue and his group try to understand these properties.
The Amyloid fiber structure involves multiple β-sheets that run parallel to the fiber axis, with individual β-strands perpendicular to the fiber axis. However, this is only concluded from models, the actual structure is not precisely known yet. Amyloid fibers are very tightly controlled and their functions are more and more discovered.
The biophysics of the amyloid fibers is a very slow and complex process. All the amyloid has the same free energy; this makes them very hard to distinguish. The free energy barrier is very high, so it is very hart to cross the border and to form filaments. The kinetics of amyloid forming is very slow.
Xue sees the aggregation pathway of amyloid forming as a life cycle. His research focusses on this life cycle of amyloid assembly. To start this cycle prima
ry nucleation occurs, this is de novo formation of amyloid fibers. After that, secondary nucleation and fragmentation occurs. So this pathway results in fragments that on their turn can form assemblies again. This life cycle, therefore, is also a positive feedback loop. See figure 1.
Schematic illustration of the lifecycle of amyloid. (Circles) Soluble monomeric protein. (Parallelograms) Monomeric units in the amyloid cross-β conformation. (Colored arrows) Main processes in amyloid assembly. (Red arrows) Primary nucleation, which may occur as homogeneous nucleation in solution or heterogeneous nucleation at interfaces. (Purple arrow) Secondary nucleation, which may occur as heterogeneous nucleation at surfaces presented by preformed aggregates. (Blue and orange arrows) Key nonnucleation based processes elongation growth, and breakage division, respectively. (Single arrowsmay represent multiple consecutive steps; arrow thickness symbolizes relative rates involved in the processes.) Wei-Feng Xue, Nucleation: The Birth of a New Protein Phase, Biophysical Journal, Volume 109, Issue 10, 17 November 2015, Pages 1999-2000, ISSN 0006-3495, http://dx.doi.org/10.1016/j.bpj.2015.10.011.
Xue and his lab are also interested in the structure of the fibers, however, not in the atomic level structure. The mesoscopic level is more interesting because the amyloid fibril size and shape defines their biological activities. Amyloid can form a lot of different fibers, from curly to clumps, networks and combinations of them. However, amyloid fibers are never branched. The amyloid structure is a stable structure. However, in the lab, you sometimes give a kickstart to the reaction. This results in a condition that changes the binding. So then the amyloid structure can become less stable. Moreover, if you remove chaperones and other control molecules of the amyloid fiber polymerization, the amyloid fibers also will become less stable.
The properties of amyloid fibers, like size distribution, persistence length and force resistance are important in the interaction of the fibers. However, it is not yet known how they interact with each other and surfaces. Xue uses the AFM technique to scan the surface of the fibers. Using this method makes that individual amyloid particles can be studied in great detail. He uses a program called Trace-Y in Matlab to trace the polymers. In this way he can use the raw data to make models of the folding of the fibers.
This models are, however, not enough to answer questions like: ‘how does de novo amyloid formation involves stochastic nucleation?’ and ‘Can we prevent amyloid to form de novo in the first place?’. Xue and his group use theoretical models to show how they think amyloid nucleation works. These models are then tested on the data. They for example showed, when looking at the concentration of the monomer, that decreasing the monomer concentration results in a longer forming time of the amyloid fibers.
The fibril fragmentation of the amyloid growth and the activity of the fibrils are also very interesting. Fragmentation controls the number and length of amyloid particles; it therefore also controls the fibrils’ environment. Fibril fragmentation accelerates amyloid growth. Moreover, Xue showed that the length of the fibrils interacts different with the cell than longer fibers. Short particles make the membrane bend and destroyed while long fibers do not have this effect. This shows that structures with the same atomic structure can have a different effect when they have different length scales.
This talk highlighted the complexity of one small compartment of the cell. Moreover, it showed the importance of the mesoscopic level. Even if molecules have the same atomic structure, their behavior can be different because of their behavior on the mesoscopic level. During Xue’s talk it became clear that there is still a lot of research needed to fully understand the behavior of small structures.