Which bonds an amino acid can make ?

[Meglab]

Hi,

 

In many articles describing a protein-protein interactrion we notice the explanation of the bonds (hydrogen, hydrophobic...) that a group of AA can make with their counterparts in the interacting protein. However, I found no review or book describing amino acid interactions in general (in protein-protein interactions and not in tertiary structure of a protein), at each time it is description of specefic case in a research article.

 

Ant suggestion ?

Thanks

[CaptainPanic]

If you want to read more: check out "Amino Acids" in an organic chemistry book. I'm sure those will be more general.

 

Covalent bonds: obviously all atoms in the protein are bonded with covalent bonds. But amino acids can form peptide bonds too, linking them together.

 

Ionic attraction: dependent on the pH, protons move around. -NH2 groups and -COOH groups get or lose a proton depending on the pH. Also, other functional groups present may affect at what pH this happens.

 

Hydrogen bonds: interactions between the many functional groups. These forces, together with the ionic attraction are one of the reasons why large proteins can form such complex helix.

 

I'm sure there's a lot more, and please note this is an oversimplification of the real complex nature of proteins... but those three are probably your main interactions.

[Meglab]

thanks for the answer,

 

What I am exactly looking for is the kind of interaction each specefic amino acid can make in protein-protein interaction. In other words, I want to know for instance that: - valine can make a hydrophobic interaction with another hydrophobic AA.

- serine can make a hydrogen bond through the presence of OH group.

....

This kind of info can be guessed or found in some specefic examples, but I didn't find data describing all kinds of interactions each AA (one by one) can have. This may simplify answering some questions like: can a negatively charged AA intercat with asparagine ?

 

Maybe I should look as u said in orgnic chemistry books rather than biochemistry ones.

Regards,

[mississippichem]

thanks for the answer,

 

What I am exactly looking for is the kind of interaction each specefic amino acid can make in protein-protein interaction. In other words, I want to know for instance that: - valine can make a hydrophobic interaction with another hydrophobic AA.

- serine can make a hydrogen bond through the presence of OH group.

....

This kind of info can be guessed or found in some specefic examples, but I didn't find data describing all kinds of interactions each AA (one by one) can have. This may simplify answering some questions like: can a negatively charged AA intercat with asparagine ?

 

Maybe I should look as u said in orgnic chemistry books rather than biochemistry ones.

Regards,

 

Short and probably unsatisfying answer:

 

-all amino acids will have some (though sometimes very little) hydrophobic interaction with other amino acids.

 

-all amino acids with a an -OH, or -NH will display some varying degree hydrogen bonding activity with water and other similar amino acids

 

-any amino acid with an ionizable proton has the ability to have ionic interactions with other species at some pH (though in some cases it may be an extreme pH).

 

The best advice:

 

Draw out the two amino acids in question. See for yourself if there could be any of the above mentioned intermolecular forces between the two. It is surprisingly easy.

 

At the more advanced level (shameless plug for computational chemistry here ) you can use the UFF (universal [Newtonian] force field) to do molecular dynamics simulations and can quantify these interactions with a surprising degree of accuracy.

[WorldOfBiochemistry]

Hi,

 

before you start to analyse a pecific bond, there are some general rules that can easier your work.

1 - All aminoacids have at least a carboxylic and an amine group. Since they are polar groups, that can establish polar bonds with other aminoacids. That is, dipole-dipole bonds. Moreover, once they have very electronegative atoms and hydrogens bonded to them, they can establish hydrogen bonds. Also, they are ionizable, which means that they also might establish ionic bridges.

2 - Each aminoacid have a specific lateral group that may be hydrophobic, polar (uncharged) and polar (charged). Hydrophobic groups establish hydrophobic interactions with other hydrophobic groups. Polar (uncharged) establish dipole-dipole bonds (in some cases hydrogen bonds, that is a specific type of dipole-dipole bonds). Polar (charged) establish the same as the polar (uncharged) plus salt bridges.

 

Thus, what I recommend you is to divide the aminoacids in groups accordingly the chemical properties of the lateral groups. Then is just necessary to apply the rules that I have mentioned before.

 

In respect to covalent bonds between aminoacids, the most common are peptide bonds and disulphide bonds.

 

Hi,

 

In many articles describing a protein-protein interactrion we notice the explanation of the bonds (hydrogen, hydrophobic...) that a group of AA can make with their counterparts in the interacting protein. However, I found no review or book describing amino acid interactions in general (in protein-protein interactions and not in tertiary structure of a protein), at each time it is description of specefic case in a research article.

 

Ant suggestion ?

Thanks