Dear Francois, Florent, Albert and all other CCLers:
I think I mentioned in my first email that the tyr is coordinating a
heme group. For the heme we plan to use standard parameters. Therefore,
the non integer charge of the Fe should be already considered in the
heme parameters. One big problem is that in the process we are looking
at, the coordination between heme and tyr will be broken. This will
probably also cause the tyr to get protonated. Nevertheless, I would
like to run the MD with the deprotonated tyr, since we first start with
the coordination intact. Probably some more sophisticated simulation
techniques (constant pH or QM/MM) are needed to describe the full
process. But I need to get an idea about the process with a classical MD
first. My hope is that we can separate the unbinding of the heme and the
protonation of the tyr.
If nobody else has parameters for tyr(-), I will try to build the
parameters with RED without including the metal ion. I hope that this
will give the best approximation for both the coordinated as well as the
free tyr(-) (even if this probably does not exists very long).
Any other suggestion is highly welcomed.
Thanks.
Thomas
FyD schrieb:
> Dear Florent, Albert and Thomas,
>
> Yes and if this Tyr(-) residue is connected to a metal ion, the charge
> derivation approach is different: the entire site (metal + all
> ligands/residues) has to be considered and involved in the QM job. In
> this case, the partial charge of the metal ion in the complex is far
> lower than the expected integer value...
>
> in this case, R.E.D. Server or R.E.D. Server Development can be used...
> http://q4md-forcefieldtools.org/REDS/
> http://q4md-forcefieldtools.org/REDS-Development/
>
> regards, Francois
>
>
>> Tyrosine can be deprotonated in the vicinity of a metallic cation.
>> Moreover, in electronic transfer of photosynthetic reactions a
>> specific tyrosine is deprotonated. See
>> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026808
>> for an example of such system.
>
>
>> On Sun, 05 Feb 2012 09:16:17 +0100
>> Albert<mailmd2011.gmail.com> wrote:
>>> I am just curious about in which condition the Tyr would be
>>> deprotanated? As far I know , from the aspect of pKa, it is very
>>> difficult for Tyr to be deprotanted.....
>>>
>>>
>>> On 02/05/2012 09:04 AM, FyD wrote:
>>>> Dear Thomas,
>>>>
>>>>> I would like to simulate a heme binding protein. In this protein,
>>>>> the
>>>>> heme is coordinated by a his and a tyr. From experimental
>>>>> investigations
>>>>> it is clear that the tyr is deprotonated. But unfortunately, I
>>>>> cannot
>>>>> find any parameters for the deprotonated tyr. Has anybody out there
>>>>> such
>>>>> parameters and is willing to share them.
>>>> You need a molecular fragment for this Tyr(-); three fragments can
>>>> be
>>>> built: N-terminal, C-terminal and central. This is likely you only
>>>> need the central one; See:
>>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10 using
>>>> R.E.D.
>>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15 using
>>>> R.E.D.Server
>>>>
>>>> Now R.E.D. Server can generate the three fragments in a single step;
>>>> See:
>>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
>>>> vs
>>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
>
>
>
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--
________________________________________________________________________________
Dr. Thomas E. Exner
Fachbereich Chemie und Zukunftskolleg
Universität Konstanz
78457 Konstanz
Tel.: +49-(0)7531-882015
Fax: +49-(0)7531-883587
Email: thomas.exner.uni-konstanz.de
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Received on Sun Feb 05 2012 - 03:30:02 PST
