[gmx-users] on MD simulation of ATP hydrolysis driven protein conformational change

[Ana Sofia Fernandes Oliveira]

Dear Brett:

The answer to your questions is yes. In our lab, we use MD simulations to
study  and identify the ATP-hydrolysis induced conformational changes in
several ABC transporters (both exporters and importers). You can check our
papers if you are interested:


   - "Insights into the Molecular Mechanism of an ABC Transporter:
   Conformational Changes in the NBD Dimer of MJ0796" (
   http://pubs.acs.org/doi/full/10.1021/jp905735y)



   - "Structural consequences of ATP hydrolysis on the ABC transporter NBD
   dimer: Molecular dynamics studies of HlyB" (
   http://onlinelibrary.wiley.com/doi/10.1002/pro.650/abstract)



   - "Conformational changes induced by ATP-hydrolysis in an ABC
   transporter: A molecular dynamics study of the Sav1866 exporter" (
   http://onlinelibrary.wiley.com/doi/10.1002/prot.23023/abstract)



   - "Inter-domain Communication Mechanisms in an ABC Importer: A Molecular
   Dynamics Study of the MalFGK2E Complex" (
   http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002128
   )


Cheers,
Ana Oliveira

On Tue, Jul 28, 2015 at 1:46 PM, Brett <brettliu123 at 163.com> wrote:

> Dear All,
>
>
> There are some biological processes involving ATP hydrolysis driven
> protein conformational change. By MD, can we simulate the protein global
> conformational change driven by ATP hydrolysis? Or by MD can we investigate
> how the energy stored in ATP converts to protein conformational change?
>
>
> Brett
> --
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-- 
Ana Sofia Fernandes Oliveira
PhD Student
Protein Modeling Group
Instituto de Tecnologia Química e Biológica
Avenida da Republica
Estação Agronómica Nacional
2780-157 Oeiras
Portugal
Phone: (+351) 21 446 91 00
Fax: (+351) 21 441 12 77