Got an idea. You import your FASTA-file. you put your headers in one column, the corresponding sequence in the next column or something (anything that works for you).
Something like:
File = 'C:\Users\Documents\your_fastafile.fasta';
your_data = fastaread(File);
Note that both your header as the amino acid sequence are in quotations marks in the generated struct.
Now, remove those quotation marks with something similar to the following:
for i = 1:(length(your_data))
header{i,1} = {your_data(i).Header};
header_no_quotationmarks {i,1} = header{i,1}{:};
end
(this could be easier, but I had part of this still lying around from another project, I'm just copy-pasting here). Now you want to extract the part that describes your protein from the header; so let us take an example:
AMA1_PLACH P16445 plasmodium chabaudi. apical membrane antigen 1 precursor (merozoite surface antigen)
This can be seen as a string. And as you already noted yourself: there is some regularity in these strings. They all start with what you want: the AMA1_PLACH part. If you obtained the FASTA file from some other sources they tend to start with something like
sp|P0C2K0|A1KB_LOXBO etc. etc.
Where the sp|P0C2K0|-part will screw things up. Let me assume that ALL your headers start with the info you want. Anyway, we have a lot of strings containing the full header. Now take:
str = 'AMA1_PLACH P16445 plasmodium chabaudi. apical membrane antigen 1 precursor (merozoite surface antigen)'
Now use regexp (see help regexp / the online help documents of regexp for more info).
g = regexp(str, ' ', 'split');
What it does you generate 'g', which is your string 'str' which you split (hence 'split') in separate parts whenever it observes a space (the ' ' part in regexp).
if you now request
MATLAB looks at 'g' and takes the first.... your AMA1_PLACH!!!
So if you write your script/program/function to loop over all your data, take the header as string, split it whenever it sees a space, then take g{1} and stores that info in a cell/array (whatever works for you, probably you want it next to the amino acid sequence....).
Maybe you can have a look here, it is where I got the idea of the regexp. You can write this in many different ways, and maybe this is not the most elegant, but hey, it seems to work (at least for my own mini-fastafile). 
