[lavache]

Hi can anyone explain why lysine and aspartate are particularly important in determining the shape into which a protein will fold - am assuming its based on their charge and hydro properties, but not sure if am missing something else.

thanks

[Yggdrasil]

I've never heard that aspartate and lysine are more important than other amino acids in determining the folding of a protein.  Aspartate and lysine are capable of forming a salt bridge (i.e. ionic bond) because of their opposite charge which will help to stabilize protein structure, but other amino acid residues are capable of contributing other stabilizing interactions.  The only thing special about these two amino acids right now that I can think of is that lysine is ubiquitinylated or SUMOylated in some proteins, but that doesn't have much of an effect on protein folding.

[lavache]

thanks, does the fact that aspartic acid has an extra cooh group and lysine an extra nh2 group have any bearing?

[sdekivit]

they casn form hydrogen bonds with aminoacids and are thus important for the tertiary structure of the protein.

[lavache]

thanks again, so would the ionic and/or hydrogen bonds therefore affect the overall shape?

[sdekivit]

thanks again, so would the ionic and/or hydrogen bonds therefore affect the overall shape?

yes indeed. It's also these interaction that cause enzymes to be inactive at a too low pH for example --> hydrogen bonds in the enzyme are disrupted that can lead to a wrong folding of the enzyme and hence its inactivity.

Another example is the disulfides formed by cysteine residues --> when ribonuclease is treated with mercaptoethanol, it will become inactive since de difulfide bridges are lost --> uncorrect folding and thus inactivity.

[lavache]

thanks sorry to be a pain but is the ph affected by the positive and negative charges? Basically I'm thinking that the extra cooh and nh2 along with the secondary and tertiary bonding (both ionic and hydrogen) can help form a stronger fold, therefore creating an amino acid which is more active.

I think I've got it if the above is true (I'm doing biology not chemistry so this although biologically makes sense to me sometimes the chemistry equations throw me off!!)

Thanks to all who have helped so far!

[Yggdrasil]

Secondary structure generally involves only hydrogen bonding between backbone attoms (i.e. the N-H and C=O groups in the backbone amide/peptide groups).  However, you are correct that lysine and aspartate will contribute to tertiary (and quaternary) structure through forming ionic and hydrogen bonds.  (NB: aspartate can also contribute to structure and function by coordinating metal ions).

Aspartates, lysines, and other acidic/basic groups can contribute to changes in the local pH in areas of the protein, but the generally won't change the pH of the aqueous environment in which they reside (since most biological systems are buffered).  For example, many DNA-binding proteins have basic regions (i.e. lots of lysines and arginines) which creates a positively-charged pocket to interact with the negatively-charged sugar-phosphate backbone of DNA.

[sdekivit]

Secondary structure generally involves only hydrogen bonding between backbone attoms (i.e. the N-H and C=O groups in the backbone amide/peptide groups). 

true, but when there is an incorrect secundary structure it may possibly lead to an incorrect tertiary structure and thus an impaired protein function. Only a single aminoacid has to be wrong to make the whole protein useless.