The Four Levels of Protein Structure

This animation depicts the four levels of protein structure. The protein used in this animation is the HIV-1 Protease, a C2 symmetric homodimer aspartyl protease whose subunits each consist of 99 amino acids. I have outlined the course of the animation below.

The color code is as follows:
Blue = Nitrogen, N
Red = Oxygen, O
Yellow = Sulfur, S
Carbon varies

The animation begins showing the quaternary structure of the protein in a cartoon format. After one of the subunits is removed, the viewer is seeing subunit 1's tertiary structure. The animation then switches to stick representations and highlights a subsection of the subunit--this subsection, upon zooming, depicts the subunit's primary structure, or amino acid sequence.

The next portion shows an antiparallel beta sheet with a beta turn (secondary structure, the structure resulting from the backbone interactions of amino acids nearby one another in the polypeptide sequence)--note the backbone hydrogen bonding interactions. This is followed by a close-up view of a small alpha helix.

The animation then zooms out and depicts the polypeptide's tertiary structure via both cartoon and molecular surface representation. Side chain interactions are very important in establishing the long-range interactions which contribute to the polypeptide's 3D shape.

Finally, the animation shows the protein's quaternary structure upon incorporating the other subunit. The native, fully functional form of this protein is its quaternary structure.

Watch in 480p for better quality.

Category:

People & Blogs

Tags:

• 2BPZSStructure

[nj341]

Hi everyone--thank you all for your comments. I apologize for the "For Evaluation Only" -- at the time of rendering the images for this movie, I couldn't seem to find a free version of PyMOL that didn't brand each frame with "For Evaluation Only" (I ended up with the evaluation version of PyMOL). I will try to remake the video in the future if I have time--for now, I think that it might be best to read the description prior to viewing it (and keep it beside you as you view it). Thanks again

[cpz1019]

the For Evaluation Only i s going to give me a seizure

[Laghmanistan]

Quite brilliant. You have excellent software manipulation skills. I think you should add voice-over annotations to your video it'll be a big hit then.

[nicolaranno]

ok

[anaalst]

MA JOET JE, IK MAAK JE AF, JE BENT TE LAF OM ME TE BESTREIDEN, IK GA JE HOND BEREIDEN!

[nicolaranno]

GA NAAR DE MAAN

[nicolaranno]

DAAN IS EEN BANAAN

[anaalst]

WWWWWWWWWWWWWWWWWWWWWWWWWWWWWT­TTTTTTTTTTTTTTFFFFFFFFFFFFFFFF­FFFFFFFFFFFFFF ELLEN IS EEN HOND? JEFFREY GAAT MIJ MOLLEN ? FUUUUUUUUUUUUUUUUUUUUUUUUUUUCK

[agonizethis]

Next time use freeware video encoders like mediacoder. No bs for evaluation messages.

[mclaudtt]

@dkinuthia It's PyMol of course - great opensource software, main tool in molecular biology visualisation. Author should add it in tags. And instead of direct convertation of PyMol script to video, he uses some sh!tty piece of demoware.

[tensai420]

what is this????!!!!!!!!!!!!!!

[dkinuthia]

WHAT PROGRAM IS THIS YOU ARE USING?