On Tue, Apr 05, 2016, YanhuaOuyang wrote:
> In fact, I just have a fasta file of the protein sequence, I just don’t
> know how to convert the peptide sequence to a pdb file of a protein
> which is phosphorylated at Serine and Threonine. Can you tell me the
> detailed steps.
Converting a sequence to a (folded) structure is commonly called the "protein
folding problem", and Google or Wikipedia can help you find lots of approaches
to this. A *lot* depends on whether there is a known structure with a similar
sequence (and how similar the sequences are). Amber is not generally the type
of program one would use for homology modeling, nor for protein folding
simulations, although the following paper shows some promising results:
%A H. Nguyen
%A J. Maier
%A H. Huang
%A V. Perrone
%A C. Simmerling
%T Folding Simulations for Proteins with Diverse Topologies Are Accessible in
Days with a Physics-Based Force Field and Implicit Solvent
%J J. Am. Chem. Soc.
%V 136
%P 13959-13962
%D 2014
If/when you get a three-dimensional structure that you have enough confidence
in to continue, getting an initial structure with their phosphorylated
analogues can be straightforward if the residues are surface exposed, as they
are likely to be: remove the H atom connected to O on the side chain in the
PDB file, rename the residues to their phosphorylated counterparts (you have
to decide whether you want the mono-anion or di-anion forms), and let LEaP
build in the phosphate groups. Then you have to hope that molecular dynamics
can convert that rough starting structure into something that will be useful
to you. Again, a *lot* depends on what you are trying to learn.
This is a long-winded answer, but I hope it helps (both you and others
interested in similar modeling exercises). You have to expect to spend time
gaining experience, and understanding how simulation programs work. There are
no "detailed steps" that will lead to success. The fact that you are
asking how to convert a sequence to a PDB file suggests that you are new to
our field; in that case, expect to spend a considerable amount of time and
effort.
....regards...dac
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Received on Mon Apr 04 2016 - 19:00:04 PDT
