[gmx-users] Long distance effects of mutation and stability
fanc232 at nenu.edu.cn
Fri Apr 22 15:32:07 CEST 2016
Hi, I hope this paper could help you. The title is "Drug Resistance Conferred by Mutations Outside the Active Site through Alterations in the Dynamic and Structural Ensemble of HIV‑1 Protease" <br/>dx.doi.org/10.1021/ja504096m| J. Am. Chem. Soc.2014, 136, 11956−11963
在 2016-04-21 04:34:26，"Jorge Fernández de Cossío Díaz" <j.cossio.diaz at gmail.com> 写道：
>I forgot to mention, I may also do simulations with the complex, mutated
>protein + partner, again addressing the same questions. Will 100 ns be
>enough, even for the larger complex?
>In general, how can I know if the simulation time is enough, that I am not
>missing modes of motion?
>On Wed, Apr 20, 2016 at 4:32 PM, Jorge Fernández de Cossío Díaz <
>j.cossio.diaz at gmail.com> wrote:
>> I want to analyse the effects of a point mutation in a protein. The
>> protein is 150 amino acids long.
>> I have experimental evidence that a mutation has a distant effect in the
>> protein. More precisely, the mutation affects the binding of the protein to
>> another partner, even though the mutation occurs far from the binding site
>> (almost on the opposite side).
>> I don't know if the mutation is affecting the overall folded state, or if
>> it has a long-range effect locally on the binding site.
>> I have two broad questions:
>> 1) Can GROMACS help me to answer this question? More precisely, are there
>> papers published that use GROMACS to study stability effects of mutation,
>> or long-range effects?
>> 2) How long should I run the simulation to see long-range effects?
>> Currently I have a 100ns simulation. In your experience, is this enough?
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