Hi Jeff,
Thanks for your response.
I fully agree--ideally one needs an NMR or x-ray structure to compare
structural changes in wildtype versus mutant protein.
However, it is sometimes useful to mutate a residue on-the-fly to
demonstrate to novices how such a mutation might create a lethal cavity
that will likely affect protein structure and subsequently its catalytic
(if the mutation is located within or near active site) or binding capacity
(if the mutation is near a binding interface).
You understand what I mean. Of course, one could model the mutant protein
but that can be cumbersome if you are working with lots of mutations or
lots of proteins as I do in collaboration with genomicists.
There must be a way to mutate a residue in JMol. I know that PDBViewer can
do it but I would prefer to work with a browser-driven software such as
JMol that I can also share with my collaborators.
Thanks for your help!
*AMJAD FAROOQ PhD DIC | Associate Professor
Dept of Biochemistry & Molecular Biology | Miller School of Medicine |
University of Miami | Miami | FL 33136
Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami ,
FL 33136
am...@farooqlab.net | off 305-243-2429 | lab 305-243-9799 | fax
305-243-3955 | www.farooqlab.net*
On Thu, Aug 8, 2013 at 11:46 AM, Jeff Hansen <jhan...@depauw.edu> wrote:
> Compare how? Do you want to see how the mutation affects the structure?
> Really need and X-ray or NMR structure of each for that to have any real
> meaning.
>
>
> ***********************************************
> Jeff Hansen, Professor and Chair
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> jhan...@depauw.edu
> ***********************************************
>
> On Aug 8, 2013, at 11:32 AM, Amjad Farooq <amja...@gmail.com> wrote:
>
> Hi guys,
>
> Is it possible to mutate an amino acid in JMol.
>
> For example, how can I introduce the K63A mutation (mutate lysine 63 to
> alanine) into my protein to compare wildtype versus mutant?
>
> What is the JMol command?
>
> Thanks!
> Amjad
>
>
>
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