Dear Yulia Ivanova ,

In the ‘perfect’ world you need to define ‘functional’ and come up with a bit more details about your protein. Matters that cross my mind are:

-Functional in what terms (enzymatic activity, binding capacity to some ligand, lipid binding ability and so on)?

-Is the 3D structure of your protein available?

-What is it you want to investigate (determination of binding and/or functional site, effect of mutation on overall behaviour of your protein)?

Anyway for now I suggest a number of things:

1. You can use I-Tasser in order to see whether you tertiary structure changes as a result of your mutation. Just use the so-called FASTA form for every mutation you want to check.

https://zhanglab.ccmb.med.umich.edu/I-TASSER/

2. You can use Heliquest to investigate the effect of the overall hydrophobicity of the region where you want to make a mutation.

http://heliquest.ipmc.cnrs.fr/

3. Check the effect of the mutation by using one of the many secondary structure prediction programs. Such like SOPMA (but there are many more!).

https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html

Apart from that it depends (too much) on what you really want. See for an example of how to use the above mentioned programs, for example:

Article The role and significance of potential lipid-binding regions...

Hope this helps you a bit further.

Best regards.

Hi Yulia,

You haven’t given specific details, so here are some basic suggestions:

1. Enter the amino acid sequence of the target protein into PSIPRED (http://bioinf.cs.ucl.ac.uk/psipred/) to predict the secondary structure and functional domain. If you do not want to change the function of the protein, it is best not to choose a mutation site in a secondary structure such as α-helix or β-sheet or other predicted functional domains.

2. If the three-dimensional structure of the wild-type protein of interest is known, then the effect of the mutation site on the protein structure can be analyzed using structural visualization software such as PyMOL.

3. As Adron Ung mentioned, if you need to maintain the structure and function of target protein, you will never mutate amino acid residues into some special amino acids, especially hydrophobic ones.

Hope it helps!