Hi all,
I want to display a nanobody on the surface of a protein nanocage. My nanocage is an icosahedron porous (9 nm pores) homomeric protein (60-mer) which is constructed of 20 trimeric building blocks. I selected the N-terminal of the nanocage building block to link my nanobody with a flexible linker (GGS)4 to construct Nanobody-Linker-Nanocage. But when I modeled the trimeric building block with Modeller and Galaxy-homomer tools my nanobody appeared inside the protein nanocage. I found that a flexible region was in the C-terminal of the nanobody and with the addition of flexible linker this region become more and more flexible. I deleted the flexible linker and modeled Nanobody-Nanocage, but again the nanobody appeared inside the nanocage even without the flexible linker. I used a rigid linker and the problem was repeated again.
Can anyone help me to display my nanobody on the surface of my protein nanocage!
I attached the figure of my model. A GFP-Nanocage model was also provided for comparison.
Any help would be appreciated.
Thanks
When modeling multi-domain constructs connected by flexible linker, model each component individually, then use a visualization program to put the individual in a reasonable relative position, the use this assembly as starting structure to model in the connecting linkers.
Dear Dr. Annemarie Honegger
Thanks for your response.
My fusion protein is constructed of 2 domains which are connected by a Linker.
I modeled these domains individually with Modeller software, but the flexible linker was modeled automatically by the software.
My questions are:
How are the flexible regions such as flexible linkers in proteins? Are they completely flexible?
Can the domains connected with a flexible linker bend to reach distant points?
I know that the "GGSGGSGGSGGS" linker has a length of 3.6 nm, but what is meant really?
If I attach domain A to domain B with this linker each of these domains can bend around 3.6 nm in their space?
If it is true I can attach the nanobody to the protein nanocage with this linker because the nanobody can bend to reach its target ligand out of the nanocage.
My aim of modeling the nanobody-linker-nanocage structure is to find an appropriate linker and make sure that the nanobody can reach its ligand on target cells.
Gly-Ser linkers are very flexible. As a rule of thumb, I make the linker large enough to connect the distance between the two domains in a semi-circle to allow for some wriggle room.
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