How to delete an amino acid residue in order to reduce the loop size of a protein?

When deleting an amino acid residue from a protein structure to reduce the loop size, it's important to consider the impact on the overall structure and stability of the protein. Deleting a residue can disrupt the local folding and interactions within the loop, potentially affecting the structural integrity of the protein. However, if you still want to proceed with deleting the residue and connect the loose ends without inserting another residue, one approach you can try is loop modeling. Here's a suggested procedure using PyMOL and MODELLER:

Open the protein structure in PyMOL.

Identify the residue you want to delete and note down its position or residue number.

Select the residues surrounding the loop you want to modify. You can use the PyMOL selection syntax (e.g., sele) or the graphical interface to select the residues.

Delete the residue: In PyMOL, you can delete the residue by using the command remove sele or by using the graphical interface (Edit > Delete).

Save the modified structure in PDB format.

Use MODELLER or a similar software package to rebuild the loop and connect the loose ends. MODELLER is a popular software for comparative protein modeling and can be used to generate loop conformations.a. Install and set up MODELLER according to the software instructions.b. Prepare the input files: You'll need the modified PDB file (from step 5) and a script file (in Python or MODELLER script format) that specifies the modeling procedure.c. Write the MODELLER script: The script should include instructions to model the loop region by connecting the loose ends and generating a suitable conformation. You can specify the restraint energy or other parameters to guide the modeling process.d. Run the MODELLER script: Execute the script using MODELLER, which will generate a new PDB file with the modeled loop.

Visualize and analyze the new structure: Load the new PDB file in PyMOL or any other molecular visualization software to examine the modeled loop and assess the quality of the structure.

Keep in mind that loop modeling is a computationally intensive process, and the results may vary depending on the complexity of the loop and the accuracy of the modeling algorithm. It's always a good idea to validate the modeled loop using structural analysis tools, such as energy minimization, molecular dynamics simulations, or validation software (e.g., PROCHECK, MolProbity).

Additionally, consider that reducing the loop size may affect the protein's function and stability. It's important to carefully evaluate the potential consequences and consult with experts in the field before making significant modifications to a protein structure.

error in running a model in Abaqus

error in modelling model in Abaqus

MGL tools

what is the simplest definition of ion exchange capacity

what is the simplest definition of ion exchange capacity

i have some problem with chtMultiRegionSimpleFoam

Can we classify HV and LV lines based on line length?

What is the production process of CaFe ferroalloys?

Chlorinated organic formation in odor control scrubbers using hypochlorite?

Resistor definition in Piezoelectric bimorph with ANSYS workbench