[gmx-users] metal ligand bond

[Justin Lemkul]

On 7/28/12 1:43 PM, tarak karmakar wrote:
> Dear All,
>
>     The protein with which I'm working with, contains Zn metal and it
> has tetrahedral coordination site. There are HISTIDINE side chains
> within distance ~ 2.3 to 2.4 . So my questions are as follows
>
> (1) In that distance range there is no possibility to form a covalent
> bond between Zn and Nitrogen of the HISTIDINE side chain. So how can I
> model the interaction between the metal and the histidine nitrogen ?
> Should I keep the Zn(II) ion as isolated metal center ?
>

There are many ways to implement "bonds" of various sorts.  See Chapters 4 and 5 
of the manual.  Type 6 bonds may be useful, or distance restraints.

> (2) At pH 5.00 HISTIDINE side chain should be protonated. So when  a
> proton has been placed in between the metal center and the histidine
> nitrogen [Zn-H-N-his system ] then Zn-H distance is coming about ~1.0
> or below. After minimization HISTIDINE is moving far from the metal
> center. Then should I remove the protonated hydrogen of that
> particular HISTIDINE residue ?
>

Metal ions are strong Lewis acids and can dramatically shift pKa values.  So 
even at pH 5, nearby histidines may have their protonation state altered.

> (3) Should I fix the metal position during the equilibration run [short NVT] ?
>

That depends on how you treat point (1) above.  If the protein is restrained and 
the Zn ion is restrained to atoms within the protein, position restraints on the 
Zn ion are, in principle, unnecessary but probably can't hurt.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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