Confused about Protein Structure

[magic-qwerty]

Hi there Science Forum !

 

I was just reading about the levels of protein structure, but was a bit confused what was meant by quaternity structure of a protein,

 

in that if you have a protein sequence i understand that it will form a tertiary structure from that amino acid sequence for sure, but will that same amino acid sequence also make it form a quternity structure (if that protein structure is of that kind ) aswell.

 

I mean take Heamoglobin ive read it has a quaternity structure , did that structure form by the amino acid sequence ? or does every protein form a tertiary structure only and then some how they join with other proteins to form a quaternity structure.?

 

 

Thanks for reading, (im a bit if an amateur to all of this, !)

 

 

Magic - qwerty

[Paralith]

you basically have it. quaternary structure is when multiple amino acid chains come together to form a super-structure, so how they fit together is determined by each individual chain's tertiary structure. In the end, it's still ultimately caused by the amino acid sequence.

[magic-qwerty]

Hi There Paralith

 

Thanks for replying,

so its like one single amino acid sequence e.g Heemoglobin that forms everything

 

i was kind of getting confused, i thought it was like different proteins joining togther to form a large unit

 

thanks again

 

m-qwerty

[Paralith]

well...it is different proteins joining together to form a large unit. It can be multiple copies of one amino acid sequence, aka multiple identical proteins joining together, or it can be multiple but different proteins joining together. The point is that if and how they join together depends on each individual protein's shape; a shape that is determined by that individual protein's amino acid structure. Please let me know if you're still confused.

[magic-qwerty]

Hi

 

Thanks a lot for clearing this up for me, ive defintenly got it now!...lol wish the text books were as clear , im not from a molecular biology background, but fascinated by proteins,,,

 

so these amino acids form the tertriay structure .or proteins, and proteins can join with other proteins to form a quaterniary structure if its possible..

 

it so fascinating , i mean these proteins joining togther,,,like some biig jigsaw puzzle...to form this quaterniry thing..

 

Just one thing im curious (sorry to keep posting) . if a amino acid sequence has all the info needed to make that protein and hence we get that 3d structure of it, does the quaterinly structure have anthing similar... i mean if we have a protein do we know just from its shape or architecture that its likes to be "sociallable" (join with others as a quaterniry) or prefer to be on its own,,

 

Thanks again

 

M Qwerty

[Paralith]

Well, I'm not an expert in proteomics, but researchers have begun to identify certain amino acid sequences that form specific structures, or motifs, as they're usually called. One sequence might form a DNA binding site, for instance; and yes, some sequences are known to form structures that interact with other proteins. But there is still a LOT left to be learned.

[Mr Skeptic]

Just one thing im curious (sorry to keep posting) . if a amino acid sequence has all the info needed to make that protein and hence we get that 3d structure of it, does the quaterinly structure have anthing similar... i mean if we have a protein do we know just from its shape or architecture that its likes to be "sociallable" (join with others as a quaterniry) or prefer to be on its own,,

 

Thanks again

 

M Qwerty

 

At least some proteins are folded into different shapes than they normally would by means of chaperone proteins. So the amino acid sequence is not everything.

 

As far as I know, the protein's function is determined by its shape.

[Paralith]

At least some proteins are folded into different shapes than they normally would by means of chaperone proteins. So the amino acid sequence is not everything.

 

As far as I know, the protein's function is determined by its shape.

 

Well, in order to interact with that chaperone protein, both the interactee and the interacter have to have the right shape motifs in order to bind to each other - which is, again, determined by each individual protein's amino acid sequence. But you are right, many proteins don't reach their functional conformation without interaction with other helper molecules - anything from other proteins to inorganic ions. Hemoglobin, as mentioned by qwerty, is four subunit proteins surrounding an iron atom. These subunit proteins in turn have structures that bind to oxygen; and when one of the subunits binds to and O2 molecule, this changes it's conformation slightly, which then slightly changes the conformation of the other three subunits, making them even more likely top pick up O2 molecules themselves. It's definitely all about shape and structure.

[magic-qwerty]

Thanks again Paralith,

 

Theres something so cool about the fact of every thing being "in the sequence",,, i guess its what appeals to people from a non biochemistry background.. like all these hidden secrets in the sequence ...

 

Mr Skeptic, thanks for adding, yes i used to think that as well..but as Paralith mentioned that a different sequence causes a different shape to form when they react with chaperones,,, so its i think just some thing additional to the "system" that makes the overall proteins... with the input being the sequence

 

 

Thanks Again

qwerty

[CharonY]

Actually building tertiary structure out of the pure amino acid sequence is extremely tricky. The calculation of all the interactions within a protein require massive amounts of computational power and often the results are not the same as in nature. To date one usually has to have an experimentally resolved tertiary structure (e.g. by x-ray crystallography) before one can model a similar sequence over it.

[magic-qwerty]

Didnt they use the most powerful computer ever built to do something like this,, and it was still to slow ..

just a thought though if you do have a some kind of approximate simulation, surely you can test how it works with a known structure , just input in a amino acid sequence of it and see how closely it resembles the one in real life...?

 

Im personally in to looking at sequences and what clues they might have with regards to the structures that are under simlar classsifications ( CATH, or SCOP etc)

[CharonY]

just a thought though if you do have a some kind of approximate simulation, surely you can test how it works with a known structure

 

Sure, and it is often done. However the results tend to be disappointing unless the structures are comparatively simple or conserved (e.g. HTH or variation thereof).

[magic-qwerty]

ok, had no idea the current "state of the art" in this area was so lame..

was reading up on things that try to simulate energys of protein shapes..,

all this molecular mechanics and dymanics is way above my head but it seems a lot of people need to go back to the drawing board

[pioneer]

Picture a protein as a long string of beads, with each bead, the peptide linkage of the amino acid. Sticking out of top of each bead is a flag, which is the particular R-group of a particular animo acid.

 

Because of hydrogen bonding along the axis of the string of beads, the protein string gets a helical twist. Now all the flags are no longer on the same side, like the above simplification, but they became orientated in 3-D along the axis of the string of beads.

 

Because these are distributed in 3-D space along the helix, like flags will attract like flags, such that the entire string begins to distort into smaller groupings. This is due to secondary bonding forces such as van der Waals that bind the organic flags, ionic interaction for the polar flags and hydrogen bonding where ever this is able to occur. These smaller groupings combine to form larger groupings, etc., due to similar bonding forces.

 

To this grouping dynamics we also need to add the affect of water. The water creates surface tension affects, like oil in water, where the organic groups cluster while trying to avoid the water and the ionic groups cluster but like the water. The net affect is the water pushes the organics in the middle and causes the ionic groups to stay more near the surface. This simplified perfection is not always possible. For example, if we have three flags in a row with two big organics and one small ionic, the little ionic gets sort of man handled and can get buried in the middle. This stores potential. It creates surface tension stuck in the middle of the oil.

 

There is another consideration. If we take a long protein chain and let it form in water, it will reach a certain steady state shape. This is the scenario that was discussed above. If instead, we had a little hole in the side of the beaker of water and fed the end of the protein string out of the hole, a little at a time, the final structure will be different. The reason this is so, the little end sticking out, is temporarily the whole protein, so it will attempt to do the best it can, as far as lowering its potential in the water. As we feed out more protein, this little end knot, may not be able to rearrange itself so easly. Instead the protein may build on that knot. The full protein in water, may put that knot in any entirely different place.

 

If we feed out the protein string, instanteously, we get the linear protein in water, as discussed in the beginning. If we feed it out one animo acid per second, we will get another lowest energy configuration. The cell has it own metering rate so the final result is somewhere between these two.

 

There are also some hydrogen bonding considerations. The hydrogen bonding is the strongest of these secondary bonding forces. In the ideal world, all these strong hydrogen bonds would become optimized. But we also have large flag groups that can group at the expense of H-bonds. While conversely, H-bonds can form that prevent perfect flag groupings. The protein will end with minimum energy, but with energy potential.

 

Let me use an analogy, say we have two magnets, one is welded to a metal table and the other is welded to a screw in a frame. We can tighten the screw and cause the two magnetics to approach and then stop short. This is the minimal energy position under those conditions, since the magnets can not spontaneously cause the distance to get any smaller. Yet, we still have a magnetic potential set up due to the separation. There is potential energy there, that can cause the entire metal apparatus to begin to take on the properties of the magnetic separation. The energy within a protein is analogous in the sense the protein is integrated.

 

Beside the possible potentials stored within proteins, there can also be potentials within the water that can tweak the final protein state. This is sort of like having some exterior magnetics that are near our magnetic separation apparatus. When proteins leave the ribosomes, they go to the smooth ER to bake. There is water potential outside them causing some fine tuning. It sort of tweak the screw to improve the appartus profile. When the protein is transported to a new area, with different magnetics, so to speak, around it, this will create an odd profile, useful for work. The little enyzme beats its little heart out, but can't get rid of the potential. Not exactly, eventually the potential alters and its time for recycle.

[magic-qwerty]

Hi Pioneer

 

Thanks for your post,

 

Lots there to think about,,, so fascinating to picture this "tug of war" going on in side our bodys by all these forces acting on the protein, its remarkable with all the variables involved that proteins correclty form there shape.

its like as if the dna knows what sequence to use so that the forces acting on it will make that shape needed.

 

if the protein looses the tug of war and makes a wrong shape do we get ill..and die...?!

 

i guess the computer scientists / statisticians are working with the biophysicists to look for clues and patterns in existing known protein structures , and see how that data could help provide a better energy model for protein structures

 

Thanks

 

Qwerty

[pioneer]

Here is an interesting observaton, connected to making cell proteins. If we look at the DNA double helix, there are four bases that can only form two base pairs. Even if the bases are swapped between the sense strand and the anti-sense strand it is still the same base pair. The result is a binary coding along the DNA double helix. It is sort of a morse code of dots and dashes. The genes have a lot of dots at the beginning and a lot of dashes at the end, to show start-stop.

 

When we make the mRNA, for the protein template, the mRNA is single stranded. Instead of the binary base pair coding of the DNA double helix, the coding is closer to quaternary, where each base along its length is more distinct from the normal base pairing in the DNA. Some RNA forms regions of double helix, so these speak both binary and quaternary.

 

When proteins are made from the mRNA templates the coding is tertiary, where each animo acid, uses a particular combination of 3 of 4 bases. I am not sure if this cooincidental or whether the watchful eye of the DNA's binary code on the quaternary code of the mRNA, results in the tertiary compromise. Sort of the blending of two languages; DNA-RNAish. The protein translation does employ looped RNA who speak both languages.

 

Food for thought

 

What that could theoretically do, is create a rough translation connection between the DNA and the cytoplasm. The proteins can talk its own jive among other proteins, with the DNA picking up bits and pieces. When the proteins yell, "we neerd moe hunds her at the helm", the DNA sort of hears, "need at helm". So it gets ready for a chemical envoy to appear to make sure it heard correctly. I am sort of kidding. Cell speak is done using a single language the binary, tertiary and quaternary systems all have in common; hydrogen bonding. This is sort of like cell-latin from which cell French, Spanish and English stem. It helps to keeps the tasks distinct, yet integrated at the same time.

[magic-qwerty]

Hi Pioneer

 

Thanks again for your intersting post,

 

Theres so much complexity going on at the molecular level, everything seems so elegantly preprogrammed, its quite fascinating by the idea of how proteins and other components in the cell talk to each other.. and know what to do...like one massive piece of clockwork, with the proteins as the gears...

 

I guess this language cant properly be deciphered untill every protein structure in the cell is known ...

 

 

Thanks

 

Qwerty