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Design of protein assembly structure

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 Understanding structural determinants of protein oligomerization

The atomic interactions between subunits in protein assemblies are finely tuned to control affinity as well as quaternary structure. Large protein assemblies are typically held together by weak interactions between individual components but the multiplicity of interactions among the large number of subunits can lead to exquisite specificity. Revealing how molecular interactions are optimized to control both oligomerization state and assembly pathway in protein assemblies is of vital importance for our understanding of biomedically important biological assemblies, as well as for efforts to manipulate them. The coiled coil is one of most recurring structural motifs in eucarytotic proteins, found in for example transcription factors, motor and skeletal proteins. Coiled coils have been at the focus of much attention over the last 20 years due to their biological significance as well as their suitability as simple model system for studies of oligomerization and binding specificity. Although simple on a sequence level, there is a large amount of structural variation in coiled-coils. They can form homo- or heterocomplexes, align in parallel or antiparallel orientation and form dimeric, trimeric, tetrameric and pentameric assemblies. Our investigations are aimed at understanding how molecular interactions are tuned in coiled coils to encode specific oligomerization states and how at the same time others are selected against. We use computational protein design methods to change protein sequence in order to modify the oligomerization properties of coiled coils. The redesigned proteins are then characterized experimentally.

Design of novel self-assembling proteins and peptides

Nature has a remarkable ability to create self-assembling materials and machines with amazing properties. The ability to custom-make novel protein containers, fibrils, and channels will have major impact on nanobiotechnology. We are interested in using the principle of self-assembly to design novel protein based biomolecules with functions not observed in nature. Our goal is to achieve molecular level control of protein self-assembly. We use structure based modeling and computational protein design methods to optimize the protein sequence of proteins and peptides in order to control their assembly. The biophysical properties of the designed proteins are then experimentally tested in the lab.

King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, André I, Gonen T, Yeates TO, Baker D. "Computational design of self-assembling protein nanomaterials with atomic level accuracy". (2012) Science. Jun 1;336(6085):1171-4.  

I. Using Leucine Rich Repeats for the rational design of protein function

Repeat proteins feature prominently in biology and serves as a diverse scaffold for protein-protein interactions. One class of repeat proteins, Leucine Rich Repeats (LRRs), is widely used in nature. For example, the innate immune system relies mainly on LRRs for target recognition. LRRs are composed of consecutively arranged structural units (repeats) that form elongated structure. Each repeat contains a beta strand connected to a helix by a short loop. A classic example of a LRR is the Ribonuclease inhibitor, which adopts a horseshoe shape with the beta-strands forming a beta barrel on the inside where its protein-protein binding site is found. Due to the wide range of binding targets, their large interaction surfaces and biophysical properties, LRR proteins have been suggested as alternatives to antibodies as scaffolds for protein binding.

We are interested in how LRR proteins evolved, the self-assembly properties of individual repeats and the rational design of protein binders using this versatile scaffold. 

Rämisch S, Weiniger U, Martinsson J, Akke M and Andre I "Computational design of Leucine-Rich Repeat proteins with a defined geometry" Proc Natl Acad Sci, 2014, pii: 201413638.

II. Rational design of amyloid-like fibrils

Misfolding of proteins sometimes leads to the formation of certain type of aggregates, amyloids, which can cause diseases such as Alzheimer's, ParkinsonÕs, type II diabetes and Creutzfeldt-Jakob. Due to their central role in disease, significant research efforts are targeted towards interfering with the process of amyloid formation. But amyloids have also sparked an interest in nanotechnology because of their unique biophysical properties. The same reasons that make amyloids lethal in biology make them useful as biomaterials (such as their superior stability). However, their use as biomaterials is limited by our lack of rational control of their structural and biophysical properties. Today, we have to work with the variety provided by naturally occurring amyloid fibrils. Our approach is to develop novel biomaterials based on the structure-based redesign of amyloid-like fibrils with the ultimate goal being the creation of a conducting protein nanowires.

Kaltofen S, Li C, Huang PS, Serpell LC, Barth A and André I. Computational de novo design of a self-assembling Peptide with predefined structure. Journal of molecular biology. 2015;427:550-62.

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