Question: Complete Protein Structure When Only Alpha Carbons Are Known
7
gravatar for Flow
8.7 years ago by
Flow1.5k
Flow1.5k wrote:

For some membrane protein (sequence known) I have found a pdb model that contains only coordinates for alpha carbons (and residue type). Which is the best method for adding/guessing the rest of the atoms pertaining to each residue supposing alpha carbon position is ok?

P.D. If I complete the structure using the sprout server or other, which program/method could I use later for performing energy minimization having already fixed alpha carbons?

P.D.2 Would a good post-approach be to do posterior energy minimization of the resulting structure fixing the alpha carbons? Restrained Molecular Dynamics? Restrained Protein Folding? Which would be the best software for this?

model prediction protein • 4.5k views
ADD COMMENTlink modified 8.7 years ago by Naga450 • written 8.7 years ago by Flow1.5k
9
gravatar for Naga
8.7 years ago by
Naga450
Germany
Naga450 wrote:

I am not sure about the best method, but here is a tool, MaxSprout, for generating protein backbone and side chain co-ordinates from a C(alpha) trace.

Update: Here is another tool REMO, which constructs protein atomic structures from C-alpha traces by optimizing the backbone hydrogen-bonding networks. You can check out the REMO paper here.

ADD COMMENTlink modified 8.7 years ago • written 8.7 years ago by Naga450
1

This looks like a great tool. One caveat though, is that I think the sidechains are handled a bit simplistically: "To construct full co-ordinates, side-chains are added from a library of frequently occurring rotamers using a simple and fast Monte Carlo procedure with simulated annealing." I think it would be really worthwhile to run the results from MaxSprout through SCWRL (http://dunbrack.fccc.edu/scwrl4/ or online webserver:http://www1.jcsg.org/scripts/prod/scwrl/serve.cgi). It is written by the lab that developed the rotamer libaries that MaxSprout uses (Dunbrack).

ADD REPLYlink written 8.7 years ago by Keith Callenberg900
1

I would recommend SCWRL itself for this task, but it requires the complete backbone (N,CA,C,O), not just C-alpha atoms.

ADD REPLYlink written 8.7 years ago by Keith Callenberg900

great, thanks !!

ADD REPLYlink written 8.7 years ago by Flow1.5k
3
gravatar for Jonasr
8.7 years ago by
Jonasr120
Jonasr120 wrote:

Take a look at Nir-Ben Tal's work in:

"Cα-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications" Proc Natl Acad Sci USA.; 2010; DOI: 10.1073/pnas.0914717107; PMID: 20534491

You can get the PDF here: http://ibis.tau.ac.il/wiki/nir_bental/index.php/Publications

ADD COMMENTlink written 8.7 years ago by Jonasr120
3
gravatar for Mndoci
8.7 years ago by
Mndoci1.2k
Issaquah, WA
Mndoci1.2k wrote:

This might be dated, but I did something like this back in grad school based on work published by and personal communications from Roman Osman's group.

This paper might be the one I am thinking about

http://www.ncbi.nlm.nih.gov/pubmed/8672466

If I recall, I created templates from alpha-Carbon traces, added side chains (in some models I didn't bother with loops, others I did), and did a bunch of refinements to try and come up with a stable structure. Where possible I applied constraints from experimental work being done in our lab.

More information to answer the updated question: IMO with just an Ca-trace to start with you have to use constraints. I liked using harmonic constraints plus any known interactions between residues across segments. Any reasonable MD package should work.

ADD COMMENTlink modified 8.7 years ago • written 8.7 years ago by Mndoci1.2k
1

upvote for mentioning my phd advisor!

ADD REPLYlink written 8.7 years ago by dimkal730

which MD package would you recommend for these constraints?

ADD REPLYlink written 8.7 years ago by Flow1.5k

I used CHARMM for all my work, but you have a lot more options these days.

ADD REPLYlink written 8.7 years ago by Mndoci1.2k
2
gravatar for Woa
8.7 years ago by
Woa2.8k
United States
Woa2.8k wrote:

Check papers From Harold Scheraga's group. So far I know they have extensively worked on this particular problem

ADD COMMENTlink written 8.7 years ago by Woa2.8k

which ones would you recommend?

ADD REPLYlink written 8.7 years ago by Flow1.5k
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