How do I delete an amino acid residue from a loop and then join the loose ends?

Question

I want to delete an amino acid residue from a loop and then join the loose ends. I intend to increase the thermal stability of the protein by reducing the size of the loop and its agitation. Pymol just deletes the residue and breaks the loop.

I intend to increase the optimal temperature of the protein, even if it costs some reduction in activity. The objective is to reduce protein agitation due to temperature increase. I will try point mutations that increase hydrogen interactions and eventually delete a loop located glycine to reduce its length and consequently its thermal agitation. All this work is aimed at preserving the catalytic site, but some loss of activity is acceptable.

As a complement to my question, I present an excerpt from the paper by Mahdie Rahban et al (2022) ; Thermal stability enhancement: Fundamental concepts of protein engineering strategies to manipulate the flexible structure.

Loop deletion or shortening by insertion of proline or deletion of Gly, coupled with loop anchoring by increasing the number of salt bridges, hydrogen bonds, or hydrophobicity, are good strategies to enhance the overall rigidity of a protein conformation leading to better compactness and a decreased number of internal cavities.

Answer 1

It depends on what software you have in hand and want to use. But basically, when you delete/add a residue, you can't just stick two parts together since it affects the whole conformation.

I suggest using AlphaFold2, and input it with different sequences (including deletion mutation) to see how it affects the structure.

Here is a link to AF2 colab: https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb