RE: NAMDenergy plugin_van der Waal interactions

From: Bruno Luís Pinto de Oliveira (boliveira_at_itn.pt)
Date: Mon Feb 20 2012 - 07:01:14 CST

Hi everyone,

I realized that my webpage was down. Perhaps this was the reason no one answered me (I was thinking the question didn't make a lot of sense).

I will try again ;)

I am simulating two organometallic compounds, which are very similar, complexed with the same protein (iNOS).

The differences between the compounds is on the type of atoms that are coordenating the Metal(CO)3 core. The rest of the molecules is the same. Please find an image here for clarification:

http://www.boliveira.net/NAMD4.html

In one case the Rhenium(CO)3 is well accomodated inside the active pocket (better inhibitor), while in the ohter case after 3ns the Rhenium(CO)3 is oriented toward the peripheral pocket situated at the surface of the enzyme (worst inhibitor).

I would like to know if I can use the NAMDenergy plugin to analyse the vdwaals interactions between the Rhenium(CO)3 part and the residues of the active pocket to identify which residues contribute for the repulsion or stability of the Re(CO)3? (considering that less positive vdwaals energy = more stable = less repulsion; more positive vdwaals = less stable = more repulsion).

Can I also use the electrostatic energies to identify which residues contribute for stabilization of the Rhenium(CO)3 part inside the active pocket (in the case of the better inhibitor)?

If not can someone suggest me please another approach to trying to get an understanding why in one case the Re(CO)3 core is accomodated inside the active pocket and in the other case is repulsed.

Thank you in advance

Regards

Bruno
....................................................................................................................................................
Bruno L. Oliveira
Radiopharmaceutical Sciences Group
Chemistry Department , ITN
http://www.itn.pt/sec/qui/qir/uk_qir_index.htm
http://www.boliveira.net

________________________________________
De: Chris Harrison [charris5_at_gmail.com]
Enviado: quarta-feira, 15 de Fevereiro de 2012 21:27
Para: Bruno Luís Pinto de Oliveira
Cc: namd-l_at_ks.uiuc.edu
Assunto: Re: namd-l: NAMDenergy plugin_van der Waal interactions

Dear Bruno,

1) Your site, www.boliveira.com, appears to be dead, so I couldn't see
the image.

2) Yes you can measure the VDW with NAMDEnergy, however you don't
mention electrostatics in your message. You may want to also
investigate the electrostatic interactions which predominate over VDW
at longer ranges.

Best,
Chris

On Thu, Feb 2, 2012 at 11:06 AM, Bruno Luís Pinto de Oliveira
<boliveira_at_itn.pt> wrote:
> Hi everyone,
>
> I am simulating two organometallic coumpounds, which are very similar, complexed with the same protein (iNOS).
>
> The differences between the compounds is on the type of atoms that are coordenating the Rhenium(CO)3 core. The rest of the molecules is the same. Please find an image here for clarification:
>
> http://www.boliveira.com/NAMD4.html
>
> In one case the Rhenium(CO)3 is well accomodated inside the active pocket (better inhibitor), while in the ohter case after 3ns the Rhenium(CO)3 is oriented toward the peripheral pocket situated at the surface of the active site (worst inhibitor).
>
> I would like to know if I can use the NAMDenergy plugin to analyse the vdwaal interactions between the Rhenium(CO)3 part and the residues of the active pocket to indentify which residues contribute for the repulsion or stability of the Re(CO)3? (considering that less positive vdwaal energy = more stable = less repulsion and more positive vdwaal = less stable = more repulsion).
>
> If not can someone suggest me another aproach to trying to get an understanding of the contributions to protein-ligand stabilities.
>
> Thank you
>
> Regards
>
> ....................................................................................................................................................
> Bruno L. Oliveira
> Radiopharmaceutical Sciences Group
> Chemistry Department , ITN
> http://www.itn.pt/sec/qui/qir/uk_qir_index.htm
> http://www.boliveira.com
>
>
>
>

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 773-570-6078
http://www.ks.uiuc.edu/~char                Fax: 217-244-6078

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