Thanks Jason,
The "lid" is kept in position NOT by the terminal carboxylate but by adjacent residues forming Hbonds. The terminal carboxylate does not form Hbonds.
George
On Jan 31, 2012, at 2:00 PM, Jason Swails wrote:
> Sander cannot currently titrate termini, although that's on the list of things to do (at some point).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Jan 31, 2012, at 7:26 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Hi everybody,
>>
>> I'm dealing with a protein in which the C-terminal end forms a lid over the binding site. I has been proposed that this lid is acid labile and that at low pH it "uncovers" the binding pocket thus releasing the bound ligand.
>>
>> My question is whether the constant pH in method in combination with conventional MD as implemented in Sander is appropriate to study whether this hypothesis is right?
>>
>> I'm asking this before going into a wild goose chase. Any suggestions will be most welcome.
>>
>> Many thanks in advance for any advice.
>>
>> George
>>
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Received on Tue Jan 31 2012 - 05:30:04 PST
