How do you biologists draw a protein when you write a paper?

Question

The following is one example of protein structure diagram that I want to put in my research paper. I took this from

Koniev, O. & Wagner, A. “Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation.” Chem. Soc. Rev. 44, 5495–5551 Jan. 2015, DOI: 10.1039/C5CS00048C

As a Chemist, the only drawing tool I have used so far is ChemDraw and it does not provide such protein structure; The only protein diagram it provides is a Y-shaped IgG. How do you biologists draw such convoluted proteins when writing a paper? Do you use a specialized software for this?

They're not drawn they are produced by software from crystal structure data. Look up PyMOL. — user40950, Jun 02 '20 at 11:11
Does this answer your question? Molecular graphics, if not, try this Mac-specific one or this one. Also look at the PDB link in my answer to this one. — David, Jun 02 '20 at 13:53

timeskull · Accepted Answer · 2020-06-02T15:26:31.693

As mentioned in the comments, diagrams like these are generated by software. The one I use is Chimera, it is free. The structure of the protein is recorded as a list of atoms and their 3D coordinates, as well as bonds, helices, sheets, etc. When a structure file is loaded, the software generates a 3D model based on the data. The user can rotate the model, move it, zoom in, change the color, an many other options, then export a 2D image when they are satisfied. If you want to use structure data files other researchers have generated, the Protein Data Bank is probably the best resource. Research articles that involve new structural data will list the PDB numbers of their structures near the end. In the article you link, the authors include pdb accession numbers for the structures they used for their figures. For the image you use as an example, here is the caption:

Fig. 56 PEGylation of four solvent-accessible Tyr residues of chymotrypsinogen (pdb: 1EX3) reported by Francis et al.

score 2 · Answer 2 · answered Jun 02 '20 at 15:05

There are various software programs available to design a protein structure based on your requirement.

These programs can be used to:

Design atomic model based on the amino acid sequence of particular protein.
Predicting protein's 3-Dimensional structure.
Determining secondary and tertiary structure of protein based on it's protein folding properties and statistical tendencies of conformational features.
For checking whether protein contains transmembrane domain or signal peptide.

I have used Rosetta to design specific antibody for my protein.

Reference: https://en.wikipedia.org/wiki/List_of_protein_structure_prediction_software

How do you biologists draw a protein when you write a paper?

2 Answers2