request for guidance on synthetic peptide design using pyrosetta

[rkgasn]

I am currently working on constructing a synthetic peptide using pyrosetta, specifically incorporating the unnatural amino acid 2-aminoisobutyric acid (AIB) into the sequence.

The sequence I am working with is: H (AIB) EGTFTSDVSSYLEGQAAKEFIAWLVRGRG.

However, I am encountering some difficulties. When visualizing the structure with ngl viewer and pymol, it appears to start with AIB instead of His. Additionally, the peptide should be an alpha helical peptide, but this is not the case in my current results.

I am relatively new to rosetta and pyrosetta and have found some useful tips on the Rosetta commons forum and the Github repositories extremely beneficial. I was wondering if you could provide some guidance on how to correct these issues with my code?

For your convenience, I have attached the AIB.params file and the sema-test pdb from pose and the python code below. Any suggestions you could provide would be greatly appreciated. Please note that this is just to get started, later on I will refine the parameters once I get the starting structure correct.

I can get a perfect alpha helical peptide from the sequence with Alanine inplace of AIB in rosetta.

Thank you in advance for your time and assistance.

import os
import nglview as nv
from rdkit_to_params import Params
import pyrosetta

Initialize PyRosetta

pyrosetta.init()

Step 1: Create Params for Unnatural Amino Acid

unnatural_smiles = 'O=C(O)C(N)(C)C'
unnatural_name = 'AIB' # Name of the unnatural amino acid
p = Params.from_smiles(unnatural_smiles, name=unnatural_name)
p.PROPERTIES.append('HYDROPHOBIC')

Save the .params file

params_filename = f"{unnatural_name}.params"
p.dump(params_filename)
print(f"Params file saved as: {params_filename}")

Step 2: Add the Residue Type to PyRosetta

pose = pyrosetta.Pose()
rst = p.add_residuetype(pose) # Add the custom residue type to the residue type set

Register the custom residue type with the pose's residue type set

residue_set = pose.residue_type_set_for_pose()
if not residue_set.has_name(unnatural_name):
raise RuntimeError(f"Residue type {unnatural_name} not registered correctly.")

Step 3: Build the Sequence

sequence = f'H[{unnatural_name}]EGTFTSDVSSYLEGQAAKEFIAWLVRGRG' # Full sequence starting with His and custom residue
pyrosetta.rosetta.core.pose.make_pose_from_sequence(pose, sequence, rst)

Step 4: Relax the Pose

scorefxn = pyrosetta.get_fa_scorefxn()
relax = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn, 15)
relax.apply(pose)

Step 5: Save the Pose as a .pdb File

pdb_filename = "sema_test.pdb"
pose.dump_pdb(pdb_filename)
print(f"PDB file saved as: {pdb_filename}")

Step 6: Visualize the Pose (optional)

nv.show_rosetta(pose)

AIB.params.txt
sema_test.pdb.txt

[vmullig]

AIB is already in the Rosetta database. You don't need to create a params file for it. Just add "X[AIB]" to your sequence where you want to insert AIB.

…

On Sat, Jan 4, 2025 at 6:55 PM Rittik Ghosh ***@***.***> wrote: I am currently working on constructing a synthetic peptide using pyrosetta, specifically incorporating the unnatural amino acid 2-aminoisobutyric acid (AIB) into the sequence. The sequence I am working with is: H (AIB) EGTFTSDVSSYLEGQAAKEFIAWLVRGRG. However, I am encountering some difficulties. When visualizing the structure with ngl viewer and pymol, it appears to start with AIB instead of His. Additionally, the peptide should be an alpha helical peptide, but this is not the case in my current results. I am relatively new to rosetta and pyrosetta and have found some useful tips on the Rosetta commons forum and the Github repositories extremely beneficial. I was wondering if you could provide some guidance on how to correct these issues with my code? For your convenience, I have attached the AIB.params file and the sema-test pdb from pose and the python code below. Any suggestions you could provide would be greatly appreciated. Please note that this is just to get started, later on I will refine the parameters once I get the starting structure correct. I can get a perfect alpha helical peptide from the sequence with Alanine inplace of AIB in rosetta. Thank you in advance for your time and assistance. import os import nglview as nv from rdkit_to_params import Params import pyrosetta Initialize PyRosetta pyrosetta.init() Step 1: Create Params for Unnatural Amino Acid unnatural_smiles = 'O=C(O)C(N)(C)C' unnatural_name = 'AIB' # Name of the unnatural amino acid p = Params.from_smiles(unnatural_smiles, name=unnatural_name) p.PROPERTIES.append('HYDROPHOBIC') Save the .params file params_filename = f"{unnatural_name}.params" p.dump(params_filename) print(f"Params file saved as: {params_filename}") Step 2: Add the Residue Type to PyRosetta pose = pyrosetta.Pose() rst = p.add_residuetype(pose) # Add the custom residue type to the residue type set Register the custom residue type with the pose's residue type set residue_set = pose.residue_type_set_for_pose() if not residue_set.has_name(unnatural_name): raise RuntimeError(f"Residue type {unnatural_name} not registered correctly.") Step 3: Build the Sequence sequence = f'H[{unnatural_name}]EGTFTSDVSSYLEGQAAKEFIAWLVRGRG' # Full sequence starting with His and custom residue pyrosetta.rosetta.core.pose.make_pose_from_sequence(pose, sequence, rst) Step 4: Relax the Pose scorefxn = pyrosetta.get_fa_scorefxn() relax = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn, 15) relax.apply(pose) Step 5: Save the Pose as a .pdb File pdb_filename = "sema_test.pdb" pose.dump_pdb(pdb_filename) print(f"PDB file saved as: {pdb_filename}") Step 6: Visualize the Pose (optional) nv.show_rosetta(pose) AIB.params.txt <https://github.com/user-attachments/files/18308626/AIB.params.txt> sema_test.pdb.txt <https://github.com/user-attachments/files/18308627/sema_test.pdb.txt> — Reply to this email directly, view it on GitHub <#287>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABACZUC2LA2VPHCUH4DN23T2JBYH3AVCNFSM6AAAAABUTRIRLGVHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZXG43TQMRQGU> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[rkgasn]

Thank you, that's great