PyMOL Tutorial: Modeling the SARS-CoV-2 RBD Interactions with ACE (COVID-19 Coronavirus Proteins)

A follow up PyMOL tutorial for my SARS-CoV-2 Structure. How I modeled the polar interactions between the spike protein RBD and ACE before the paper was published (and a follow up interaction now that the paper is published!)
PDB ID: 6VW1
Reference: Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., ... & Li, F. (2020). Structural basis of receptor recognition by SARS-CoV-2. Nature, 1-8.

[@stefanidno]

Love these videos thank you! A small time saving tip, instead of manually selecting all molecules within a chain you can just use the command: select chain A Alternatively you can use the command: split_chains this will split the chains into different objects while retaining contact information :)

[@MolecularMemory]

Nice! Thank you! This got most of the ligands too. I only had to grab the chlorine by hand.

[@nidafatimaali]

thank you so much, I LOVED this!! I really needed help finding interacting residues and this helped me out so much!!

[@rubenmontes_]

Best channel by far for modeling videos!

[@Clockworkbio]

Still getting used to Pymol--really happy I can get a tutorial mixed in with my current events! Thanks so much for this!

[@MolecularMemory]

Thanks for watching! Check out the other comments as well-there are some really helpful tips that others are posting.

[@dinhthuan-thien8048]

Love your video so much. Thank you.

[@diennguyen2627]

Thank you very much. You made my day

[@catalinagonzalez9456]

A million thanks! you saved me, you don't know how ahahaha A few days ago I started my research unit as a biochemist, but I had to work with bioinformatics, something that is seen very little or almost nothing in my career. My professor asked me to model the interaction of the Spike complex with ACE2, and I had only used PyMOL twice in my life to observe monomers.

[@chrisye8033]

Thank you for your video. Well done.

[@jaspreetkaur2459]

Excellent video

[@yhoff76]

Thanks for the amazing video. This was simply fascinating. Any chance of doing a video to compare and contrast the spike proteins of the different variants? It is my understanding that the lambda variant has demonstrated mutations on the spike protein itself. Would love to see that in PyMOL. In any event, thank you for all of your hard work.

[@federicosisti2608]

Awesome. Thanks a lot!

[@cklam123456789]

Very nice tutorial

[@karnpobkanhasut2084]

l like your videos very much. May gods bless you in every moment of life.

[@benkaa4915]

Thankyou Molecular Memory for your wonderful educational videos and encouraging words. This will help us in our understanding of disease and structure, so we can become part of the cure in future. Right now, regarding your video on " Sars - Cov - 2 Structure ( Covid - 19 Coronavirus ) I wish to enquire about the Hydrogen Bonding between the Receptor Binding Domain ( RBD ) on the virus and the host Angiotensin Converting Enzyme 2 ( ACE 2 ) receptor. Is there any way that this bonding can be disrupted? I was considering Hydrogen Fluoride ( HF ) through appropriate water Fluoridation

[@karthi6990]

For selecting chains, you can change the select mode to chains in bottom right corner, then you can revert back to residues. Time saver for me.

[@MolecularMemory]

Oh WOW! That is convenient! Thank you so much! I still have to select the ligands separately, but it saves me fumbling around trying to select the chain within the sequence. Thanks so much for watching and leaving me a comment :)

[@Waffe12]

@@MolecularMemory You can also type "sele chain A", this will select the chain AND the ligands - or directly rename and save the selection with "sele ACE1,chain A"

[@truenestpie]

I wish this had more than just 2k views!

[@LizRoyKi]

I use PDBePISA analysis for interface interaction list.

[@PJK_07]

Hi, can you give us a tutorial on how to compare Docked Structure with PDB structure for the same RNA-protein complex? Thank you.

[@lipingliao3421]

Thank you so much, it very helpful, but I still confused how to find non-polar contact in pymol? I do find- any contacts-between chains within5A ,then there get much dash lines within the same residues some are not OH or NH only C atom of Phenyl ? what does this mean? and then how to find that pi-pi interaction or other van der vals interaction?

[@no1reptilekeepeuk]

I've been having issues, when selecting the end protein sequences, as it does not have /DA/B/712 but shows NAG NAG BMA in pink, which doesn't link to any of the other structures colours on my Pymol. any help would be great!

[@gabrielemayr3517]

select interactionsiteAB, byres (chain B within 7 of chain A) or (chain A within 7 of chain B)

[@lilyzhang5700]

Like this one!

[@MolecularMemory]

It fixed itself btw! The resolution issue was a post-processing KZbin thing. Thanks for leaving me a comment so quickly so I could look into it.

[@jayapalreddy9]

Your videos are so helpful.. would you please so poseview in pymol to generate 2D protein-ligand interaction..Thanks in advance.​@@MolecularMemory

[@alanraetz]

To get contacts between chains (maybe?) you can do: action->find->polar contacts->between chains (bottom selection). I haven't tried this...

[@MolecularMemory]

This one didn't work for me when I was doing this. Not sure why-thanks for the comment!

[@user-lj7gk3sk8w]

@@MolecularMemory what worked for me was 'to other atoms in objects' instead of between chains

[@yyy6610]

Question：How to find salt bridges between protein-protein interface？

[@egs8545]

I have heard it is better to use APBS plug in rather than vacuum electrostatics can anyone tell me why?

[@flowermoon9595]

Can you tell me how to do the RBD interact with mutations on SARS-CoV-2??Thanks

[@xrpnewzealand1778]

Question - How many missing polar interactions does it take before the two proteins are unable to bind together to perform their operation.

[@MolecularMemory]

This is an interesting question, and I wish I had a good answer for you. Some of the interactions in the individual proteins are broken to create new interactions at the interface. I imagine it depends on both the number and strength of the interactions-interactions with ionic residues will be stronger than hydrogen bonds between things like OH groups. Again, wish I could answer you better, and thanks for watching!

[@xrpnewzealand1778]

@@MolecularMemory Thank you for taking the time to address my question. Absolutely love your channel by the way.

[@user-lj7gk3sk8w]

I got this from ur previous video but it did fade me here when we were manually selecting interchain residues that were interacting command: select NAME_SELECTION, byres SELECTION_NAME1 within 5 of SELECTION_NAME2

[@linkcloud2486]

Nice video, thanks so much! At ~10min, why not just show lines of interface area instead of the whole chain?

[@samofficial640]

What type of software is this?

[@ozgunteksoy4398]

Thank you for educational video but I want to warn you that ACE2 protein attaches to RBD1 subunit

[@valentinamonsalve4289]

Isn’t easier if you just put: “show sticks, byres all within 5 of RBD” and then for ACE2? Then you can click on polar contacts -> to other atoms in object. I did it for each one and I obteined good distances. If you think i did something Wrong please write me.

[@MolecularMemory]

I love the byres command and talk about it in another video! This looks like it should work. I'm having trouble executing it, though. For some reason, the byres command is showing the sticks for the whole protein, and not just at the interface in my model. I'll play around with this some more, and let me know if you did anything special that might help me out :) Thanks!

[@valentinamonsalve4289]

Molecular Memory YES! I saw your video so I thought about apply the idea and yes right, this command shows all the sticks for example for RBD1 y put it in the command but also you can get another sticks from the other molecule that you can select and do the same for the other molecule. You can save yourself a lot of work. Sorry maybe my english is not perfect but i hope these tricks work for you. Greetings from colombia!

[@MolecularMemory]

​@@valentinamonsalve4289 I was able to get this to work using the GUI buttons on the right! For the RBD object, I copied it. Then, I clicked A (action button) --> modify --> around --> residues within 5 A. Thank you for an excellent suggestion. Creo que su ingles es muy facil entender! Gracias por mirar mis videos, y muchas gracias por ayudarme! Voy a dar un workshop sobre PyMOL en una semana y utilizaré este estructura. Voy a demonstrar con este truco :) Saludos!

[@khairunafizzahismail4177]

Can PyMol generate pharmacophore model and validation?

[@helenageorge9223]

use "to other atoms in object" in place of " to any atoms "

[@MolecularMemory]

Thanks for leaving me a comment. It seems like this should work! When I apply it though, this only shows the contacts within each separate protein (like, within the alpha helix), and not across the interface. So odd!

[@alexvasile6182]

Plase i need spanish subtitles 😞😞

[@user-tm6lk3bo6l]

What is it?

[@nasserfaghih5345]

why you are not active now? we are worried about you. are you OK?

[@MolecularMemory]

Hi! I hope to get back to making Molecular Memory videos in August. I've been busy working on Crash Course Organic Chemistry this summer. You can keep up with my work there for now, if you like :) Thanks for the support and kind words! kzbin.info/aero/PL8dPuuaLjXtONguuhLdVmq0HTKS0jksS4

[@taresy6789pp]

Is this lady the next Einstein

[@elchippe]

360p?

[@MolecularMemory]

crazy! gonna retry!

[@MolecularMemory]

I think it corrected itself?

[@SvenKillig]

@@MolecularMemory The KZbin servers take their time to encode all the different resolutions and they begin with the lower ones. One way is to keep the video set to "not listed" until all resolutions are ready (might be an hour or so).

[@ZucchiZ]

Nature just said "69" lol

[@okaytoletgo]

please do ivermectin binding with ACE2. that will be useful. tHANK YOU/

[@pratwurschtgulasch6662]

i like pizza

[@za1981zee]

itni zyada detail pata hai fir b na vaccine na koi medicine..?

[@bangladesh6027]

Are you single?