# adding NCAA to the N-terminal of RCSB pdb

5 posts / 0 new
adding NCAA to the N-terminal of RCSB pdb
#1

Hello,

I usually use my NCAAs by mutation in the sequences.

Now, I am looking for a way or application in Rosetta to add, not mutation, NCAAs to the N- terminal and C- terminal of the sequences.

The RCSB pdb starts with leu at N- terminal in attached picture that we need to add pyroglutamate before that

I wonder if anyone could let me know how I can add pyroglutamate using params file and rotlib file to the sequence.

AttachmentSize
9.56 KB
Post Situation:
Tue, 2021-06-08 08:24
ate

A terminal residue in a params file is straightforward and is just a regular polymer residue with three differences.

• For a cap at the N-terminal of your peptide, you simply need in addition to your UPPER C a LOWER_CONNECT NONE
• the variant LOWER_TERMINUS_VARIANT and TERMINUS
• MAINCHAIN_ATOMS C CA N

However, just like proline, you don't need to make it a N-terminal cap and it can be a regular residue with a regular hydrogen as a cap.

rotlib file --> surely you want solely the cis or the trans rotamer, so you have a single rotamer, so all is good.

Something like this (assuming I got L and trans right)

NAME GLP
# *C(=O)[C@@]1([H])N(*)C(=O)C([H])([H])C1([H])[H]
IO_STRING GLP X
TYPE POLYMER
AA UNK
ATOM  N   Npro  X   -0.3191635
ATOM  CA  CAbb  X   0.0924442
ATOM  C   CObb  X   0.1642444
ATOM  O   OCbb  X   -0.2966219
ATOM  CG2 CNH2  X   0.2234999
ATOM  OD  ONH2  X   -0.2748662
ATOM  C4   CH2  X   0.0291256
ATOM  CB   CH2  X   -0.0165311
ATOM  HA  Hapo  X   0.0614358
ATOM  H2  Hapo  X   0.0367724
ATOM  H3  Hapo  X   0.0367724
ATOM  H4  Hapo  X   0.0297496
ATOM  H5  Hapo  X   0.0297496
ATOM  H6  Hpol  X   0.1637134
BOND_TYPE  O    C   2
BOND  C    CA
BOND  CA   N
BOND  N    CG2
BOND_TYPE  CG2  OD  2
BOND  CG2  C4
BOND  C4   CB
BOND  CB   CA
BOND  CA   HA
BOND  C4   H2
BOND  C4   H3
BOND  CB   H4
BOND  CB   H5
BOND  N    H6
CUT_BOND  CA   CB
PROPERTIES PROTEIN ALPHA_AA L_AA TERMINUS LOWER_TERMINUS_VARIANT
FIRST_SIDECHAIN_ATOM CB
BACKBONE_AA ALA
UPPER_CONNECT  C
LOWER_CONNECT  NONE
MAINCHAIN_ATOMS C CA N
NBR_ATOM  CA
ICOOR_INTERNAL   N       0.000000    0.000000    0.000000  N     CA    C
ICOOR_INTERNAL   CA      0.000000  179.999999    1.447078  N     CA    C
ICOOR_INTERNAL   C      -0.000000   64.649829    1.513661  CA    N     C
ICOOR_INTERNAL  UPPER  -33.014224   56.297984    1.546869  C     CA    N
ICOOR_INTERNAL   O    -165.732734   54.741215    1.222596  C     CA   UPPER
ICOOR_INTERNAL   H6    -59.664243   62.085696    1.485798  N     CA    C
ICOOR_INTERNAL   CG2  -163.501542   68.887970    1.405668  N     CA    H6
ICOOR_INTERNAL   OD    175.186746   51.825532    1.222447  CG2   N     CA
ICOOR_INTERNAL   C4   -175.863181   71.620578    1.506041  CG2   N     OD
ICOOR_INTERNAL   CB    -16.423738   76.149073    1.514332  C4    CG2   N
ICOOR_INTERNAL   HA   -122.036063   70.765589    1.097590  CA    C     N
ICOOR_INTERNAL   H2   -120.197236   69.070629    1.092834  C4    CG2   CB
ICOOR_INTERNAL   H3    118.690248   71.317031    1.094440  C4    CG2   CB
ICOOR_INTERNAL   H4    121.846624   67.735679    1.094995  CB    C4    CA
ICOOR_INTERNAL   H5   -119.724197   70.713668    1.097572  CB    C4    CA  

Wed, 2021-06-09 02:59
matteoferla

Thank you for your explanation and example file Could you please let me know how I can add the ncaa to n-terminal of pdb file

I mean, What script or application should be used

Fri, 2021-06-11 11:31
ate

I normally use Pyrosetta for everything and do not know how one could do it with Rosetta Scripts.

One crude option is to add a proline in PyMOL by selecting the pre-cap residue's N atom (editor mode), then menu -> builder -> add proline, and the making that wretched amino acid GLP or whatever you want to call it (has to match the topology file) by typing alter chain X and resi xx, "resn='GLP'" and sort, where xx and X are residue index and chain. Rosetta when reading this file will have a fit and the wrong atom names —but the first three atoms match so will fix it as it does for missing sidechains (but not for C-alpha traces). As I said, this is really nasty. An alternative is loading a file with GLP and an amino acid and aligning it to say a temporary residue build at the N-terminal or aligned via a second residue on GLP (see below).

The topology file is fine, except for me I had to delete LOWER_TERMINUS_VARIANT from the params file, so TERMINUS is all that is required, property-wise, sorry for the incorrect info!

But doing the following gives me the attached figure. I am not suggesting switching to PyRosetta as I think regular Rosetta may be able to do what you hope.

import pyrosetta
pyrosetta.init()
pose = pyrosetta.Pose()
params_filenames = pyrosetta.rosetta.utility.vector1_string(1)
params_filenames[1] = 'GLP.params'
rts = pyrosetta.generate_nonstandard_residue_set(pose, params_filenames)
pyrosetta.rosetta.core.pose.make_pose_from_sequence(pose=pose,
sequence='X[GLP]TRASPICYCHILLI',
residue_set=rts,
auto_termini=True)
print(pose.sequence())
# relax or you get the "eye of Sauron conformer"
scorefxn = pyrosetta.get_fa_scorefxn()
cycles = 1
relax = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn, cycles)
relax.apply(pose)
# check
view = nv.show_rosetta(pose)
view.clear_representations()
view.center('1')
view # Jupyter notebook end of cell => IPython.display.display(view)

Which makes me realise that the cys/trans business does not apply to N-terminal residues —ops again.

The PDB block of the first two residues looks like:

HETATM    1  N   GLP A   1       0.000   0.000   0.000  1.00  0.00           N
HETATM    2  CA  GLP A   1       1.447   0.000   0.000  1.00  0.00           C
HETATM    3  C   GLP A   1       2.095   1.368   0.000  1.00  0.00           C
HETATM    4  O   GLP A   1       3.252   1.601   0.321  1.00  0.00           O
HETATM    5  CG2 GLP A   1      -0.506  -0.956  -0.897  1.00  0.00           C
HETATM    6  OD  GLP A   1      -1.672  -1.274  -1.084  1.00  0.00           O
HETATM    7  C4  GLP A   1       0.656  -1.643  -1.565  1.00  0.00           C
HETATM    8  CB  GLP A   1       1.828  -0.726  -1.287  1.00  0.00           C
HETATM    9  H6  GLP A   1      -0.696   0.663   1.133  1.00  0.00           H
HETATM   10  HA  GLP A   1       1.789  -0.562   0.879  1.00  0.00           H
HETATM   11  H2  GLP A   1       0.478  -1.759  -2.637  1.00  0.00           H
HETATM   12  H3  GLP A   1       0.797  -2.624  -1.100  1.00  0.00           H
HETATM   13  H4  GLP A   1       2.770  -1.274  -1.189  1.00  0.00           H
HETATM   14  H5  GLP A   1       1.950  -0.029  -2.126  1.00  0.00           H
ATOM     15  N   THR A   2       1.487   2.606  -0.701  1.00  0.00           N
ATOM     16  CA  THR A   2       0.223   2.533  -1.423  1.00  0.00           C
ATOM     17  C   THR A   2       0.222   3.467  -2.627  1.00  0.00           C
ATOM     18  O   THR A   2       0.765   3.136  -3.644  1.00  0.00           O
ATOM     19  OXT THR A   2      -0.323   4.534  -2.558  1.00  0.00           O
ATOM     20  CB  THR A   2      -0.962   2.875  -0.502  1.00  0.00           C
ATOM     21  OG1 THR A   2      -2.192   2.719  -1.222  1.00  0.00           O
ATOM     22  CG2 THR A   2      -0.852   4.307   0.001  1.00  0.00           C
ATOM     23  H   THR A   2       1.979   3.487  -0.657  1.00  0.00           H
ATOM     24  HA  THR A   2       0.091   1.514  -1.788  1.00  0.00           H
ATOM     25  HB  THR A   2      -0.968   2.196   0.351  1.00  0.00           H
ATOM     26  HG1 THR A   2      -2.732   2.052  -0.792  1.00  0.00           H
ATOM     27 1HG2 THR A   2      -1.697   4.530   0.650  1.00  0.00           H
ATOM     28 2HG2 THR A   2       0.077   4.425   0.559  1.00  0.00           H
ATOM     29 3HG2 THR A   2      -0.855   4.991  -0.847  1.00  0.00           H 

This can be used for alignments. Actually, even with PyRosetta you'd make a dipeptide with GLP and align that to the pose before removing the second residue, removing the terminal cap on the proper protein pose and appending the latter to the former —with some code to copy along the PDBInfo.

File attachments:
Sat, 2021-06-12 13:34
matteoferla

I am sorry. I do not have any help, advice or solutions to offer as I am very new to Rosetta.

Could you share with me any material or literature that goes into detail and could guide me in mutating canonical amino acids in peptides to NCAA (such as D amino acids, AIB etc.) ?

Thank you.

Email ID - subhrodeeps@iisc.ac.in

Sat, 2021-06-19 07:17
Subhrodeep Saha