AMBER Archive (2005)

Subject: Re: Re: AMBER: Protein with structural ions

From: Yong Xu (yxu_at_mail.sioc.ac.cn)
Date: Tue Apr 05 2005 - 23:34:55 CDT

Dear Oliver and amber-users

I encounter almost the same problem on metalloproteinase simulation.
In my simulational system, there are three HIS coordinated with Zn2+. several MD simulation were performed with different ligands (the initial conformation of Ligands is from the result of autodock).
I found that in one simulation three HIS residues keep a distance ~ 2A with Zn during 500 ps. But in some other trajectory, only two HIS keep this optimal coordinated distance, ~2A.

some articles have reported "no-bonded model" successfully both with MM-PBSA and with MM-GBSA method. (1) Robert C. Rizzo, Samuel Toba, and Irwin D. Kuntz, J. Med. Chem. 2004, 47, 3065-3074 (2) Tingjun Hou, Senli guo, Xiaojie Xu, J. phys. chem. B 2002, 106, 5527-5535. ....

are there some tips for modeling metalloproteinase?

is it feasible to restaint the distance of Zn and N of HIS? further more, how to restaint the distance of ZN and N of HIS? I use makeDIST to produce restaint file, it seems that Zn can not be recoganized.

 
        

======= 2005-04-05 14:42:00 ÄúÔÚÀ´ÐÅÖÐдµÀ£º=======

>Kara,
>
>a straightforward method is the "bonded model" developed in the group of
>K. Merz. If this is interesting for you, please have a look e.g. at:
>
>@Article{70838,
> author = {S. C. Hoops and K. W. Anderson and K. M. Merz},
> title = {Force field design for metalloproteins},
> journal = {J. Am. Chem. Soc.},
> year = {1991},
> key = {metalloproteins ; force field development},
> volume = {113},
> pages = {8262-8270},
>}
>
>@Article{70863,
> author = {D. Suarez and E. N. Brothers and K. M. Merz},
> title = {Insights inton the structure and dynamics of the dinuclear
>zinc $\beta$ lactamase site from {\sl bacteroides fragilis}},
> journal = {Biochemistry},
> year = {2002},
> key = {AMBER ; zinc enzyme ; bonded model ; method ; force field ;
>QM/MM},
> volume = {41},
> pages = {6615-6630},
>}
>
>You basically would have to introduce covalent bonds between the
>ligating side chains and the metal ion. For that purpose you need to
>recalculate the partial charges of the metal plus the side chains bound
>to it in order to model the charge transfer.
>
>OLiver
>
>________________________________________________________________
>
>Oliver Hucke, Dr.
>Biomolecular Structure Center Health Sciences Building - K418C
>Dept. of Biochemistry 1959 NE Pacific St.
>University of Washington phone: (206) 685 7046
>Box 357742 fax : (206) 685 7002
>Seattle, WA 98195-7742 email: ohucke_at_u.washington.edu
>________________________________________________________________
>
>Kara Wald wrote:
>> I'm beginning to run a protein/inhibitor and noticed that after an
>> initial minimization with implicint solvent, the structural zinc and
>> calcium atoms seemed to "float" away from the protein. Is there a way
>> to stop this in an uncomplicated way?
>>
>> Thanks,
>>
>> Kara Di Giorgio
>>
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>
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= = = = = = = = = = = = = = = = = = = =
                        

Best regards!
                                 
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Yong Xu
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡yxu_at_mail.sioc.ac.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-04-06
===========================================================
* Yong Xu
* State Key Lab of Bioorganic & Natural Product Chemistry
* Shanghai Institute of Organic Chemistry
* Chinese Academy of Science
           
* 354 Feng Lin Road, Xu Hui District
* Shanghai, 200032, China
        
* Email: yxu_at_mail.sioc.ac.cn
* yxuemail_at_sina.com
===========================================================
¡¡¡¡¡¡¡¡¡¡¡¡

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