I am wanting to take a 10-12 residue loop from an E.coli enzyme polypeptide which confers a particular allosteric mechanism(substrate specificity) and apply it to a non-homologous mouse catalytic enzyme in order to generate a novel enzyme whose hybrid loop I can then refine and adjust to see if we can make it produce a similar allosteric selectivity depending on the loop orientation in response to different substrates binding at the active site.
Now, my question is this; what freely available computational resources exist that can do this?
I'm vaguely familiar with a number of various programs and servers, but Rosetta match/design/dock is too non-user friendly and overly complex with no clear indication it can accomplish what I want specfifically ( I'm aware it offers loopbuilding, or matching or modelling, but I cannot find evidence of any others doing this with loops in the literature, and theres no clear answer as to whether or not it is able to select specific location/orientation to place loop, the existing literature seems to only ever use comparative modelling which is no use here as there's no homology, we are trying to create a novel function. (and no clear GUI so I can observe/experiment with placement.)
pymols build function, Chimeras loop builder and Peptidebuilder all seem to suggest their builders and minimizers can do what I need them to, but there's never a clear 'add this loop to this protein in this specific location' function, it's always too indirect.
I'm fairly new to computational biochemistry, can someone please point me in the right direction, how can I simply and clearly cut a loop from one protein, stick it on another myself computationally and then assess whether it modulates enzyme specificity?
Is there a service or program that does this? Or is my best bet using the likes of I-TASSER, zdock or Rosetta?
Thanks in advance, I'm probably missing something alarmingly obvious, but I've been going round in circles and it's giving me such a headache!
If you feel fairly familiar with Rosetta codes (https://www.rosettacommons.org/), they prove very helpful on how to do these manipulations in your proteins .
@StannersYour problem can be solved by writing some code,provided the loop you cut fits into the location where it is inserted (is it possibly another loop ?).If this is possible you can use canned software to optimize it.If you send me
pdb files of the two proteins and the segments involved,I could try to solve the problem and send you a pdb file of the new structure.
Dikeos Mario
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Enzymology
- Enzymes