Hi,
I understand there are many protein structure prediction tools and what they produce are sometimes different from the actual x-ray crystallography results. Structure of one conserved domain of my protein of interest is available on NCBI's CDD and I'd like to see how a mutation can possibly alter the structure of this domain. So anyone to suggest a tool where we simply can change the amino acid to the mutated one and see the altered structure? Thanks.
Something similar to the link below?
Hi Harindra, you can easily do this with most structure modelling programmes such as COOT or O.
However, as you mention in your question, though the modified structure will have a different residue in the position you have mutated, the mutated protein might look very different in reality from the mutated model you just created. The reason for this is that mutating a residue in these modelling programmes does not change the position of any of the other amino acids in the structure and the overall shape of the protein will remain the same. Therefore doing this will only give you an indication of what other residues the mutated amino acid may interact with or if the change of amino acid requires the overall structure to change because the new amino acid clashes with other side chains and needs more room, or it has the wrong charge to interact with the neighbouring amino acids, etc.... What I mean is that doing this will only give you an idea of what a mutation might do to you protein, whereas the reality of how the mutation changes the structure might be very different from your prediction.
I hope this helped.
Pymol is free for academic users:
http://www.pymol.org/
Also CCP4MG
http://www.ccp4.ac.uk/MG/
Coot is nice but not simple, more for experts and those dealing with electronic density etc, in other words it will have loads of functions that you won't need/know about... the two programs above are cool and dedicated for visualization etc. If you need more tools let me know.
Antonio is right!! After the mutations, you can only see the change in the interactions but in reality, it will be very different. The tools that you can use are Pymol, Coot and also Accelrys Discovery Studio. But the discovery studio is commercial. You can also use UCSF Chimera. But I think you haven't asked about the simple tool, so Coot will be the best for these type of works. Swisspdb viewer is also a tool but sometimes it gives the problems due to the bugs.
The ones that I used a lot is UCSF Chimera. Embed a lot of functions, is simple and permits to create jaw dropping figures.
Pymol is definitely the best. You can try Rasmol too. Also, Jalview allows you to visualize the protein MSA, the phylogenetic tree and the protein structure at the same time, with interactions between the 3 windows.
The Upgraded version of RASMOL is RASTOP which is also best. SPDBV can also be one of the option to mutate a.a.
as Valerio Bianchi mentioned earlier , UCSF chimera images are way to good for publication or viewing.
Hi,
I would suggest pymol too, to visualize and to make small mutations...
But if what you are after is just to see how a mutated amino acid affects the stabiliy of a known structure, there are some specific tools for that, one of them that i used in the past and found it good is foldx:
http://foldx.crg.es/
Hi Harindra, I had a similar problem, and I wanted to see how the structure and the properties of a protein changed in case of a mutation. My protein was very big (a structural one).
Concerning the visualization, if you have a pdb file, you can use the classical protein viewer, or you can submit the modified FASTA of the mutated protein to a homology folding server to generate the pdb file and compare it with the original one of the not mutated protein. http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
Concerning the effect of a mutation, you can use the fasta file of the protein, change the sequence where the mutation occurs, then you can simply submit this FASTA to https://www.predictprotein.org and compare the results with the unmodified FASTA.
I found this web based tool very useful, because it predicted the secondary structure, and performed a lot of calculations, such as polarity, cellular localization, ecc.
Unfortunately this web based tool is not free, but it gives you the possibility to try it for free and submit three calculation once you subscribe.
Bye!!
You can download "Discovery Studio Visualizer" it has many features for protein structural editing and a very user friendly tool..
A few people have pointed out correctly that a mutation can affect the overall structure of your protein significantly. It's easy to swap out a residue with any of the tools mentioned, but you want to at least perform an energy minimization to see how the mutation affects your structure. You could use a molecular dynamics package for that or you can also use a tool like MODELLER. It's a package for homology modeling, which is what pretty much what you intend to do. You take a template structure and swap out residues - doesn't really matter if it's just one or 100 residues, it's the same basic concept. It will take a couple of tutorials to familiarize yourself with the input file syntax for running MODELLER, but it is a very powerful tool for building models/swapping residues and it implements various energy minimization methods.
http://salilab.org/modeller/
- Badges
- Science topic