[gmx-users] Re: Positive energy for Coulumb term. Does this mean Coulumb, interaction destabilizes protein? (Seungpyo Hong)

[Seungpyo Hong]

Dear Gerrit,

Thanks for your kind reply!
I just forget covalent bonds!

Best regards,
Seungpyo Hong

On Fri, Mar 6, 2009 at 8:05 PM, Gerrit Groenhof <ggroenh at gwdg.de> wrote:

> Coulomb 1-4 is only beteen the atoms that are 3 bonds away from each other.
> The bonds prevent these atoms to get apart too far, so 1-4 won't destabilize
> the overall structure. The SR part is negative, thus keeping your protein
> together.
>
> Gerrit
>
>
>
>> Message: 3
>> Date: Fri, 6 Mar 2009 19:43:19 +0900
>> From: Seungpyo Hong <sp1020 at gmail.com>
>> Subject: [gmx-users] Positive energy for Coulumb term. Does this mean
>>        Coulumb         interaction destabilizes protein?
>> To: gmx-users at gromacs.org
>> Message-ID:
>>        <bd5475eb0903060243q7a553766r70664758fa47f88c at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Dear GMX-Users,
>>
>> As I analyze energy terms of proteins, I found something looks weird.
>> I thought that fullly folded proteins are stabilized by Coulomb
>> interaction
>> (such as hydrogen bonds).
>> However, what I found embarasses me.
>>
>> The Coulomb interaction seems to destabilize the protein structure as its
>> energy is positive.
>>
>> Coul-SR + Coul-14 = 32 > 0
>> Coul-SR + Coul-14 + Coul-SR(Protein-Non-Protein) = 18 > 0
>>
>>
>> Energy                      Average       RMSD     Fluct.      Drift
>> Tot-Drift
>>
>> -------------------------------------------------------------------------------
>> Coul-SR:Protein-Protein    -11.6253    365.244    357.507  -0.735925
>> -259.047
>> LJ-SR:Protein-Protein      -6.51389    204.554    203.627   0.191426
>> 67.3824
>> Coul-14:Protein-Protein     38.5848    1212.26    1196.75    1.90253
>> 669.696
>> LJ-14:Protein-Protein       3.58465    112.688    112.645 -0.0303438
>> -10.6811
>> Coul-SR:Protein-Non-Protein   -14.1247    443.927    437.195   -0.75795
>> -266.8
>> LJ-SR:Protein-Non-Protein   -1.51471    47.6924    46.2568   -0.11429
>> -40.2302
>>
>>
>> I thought of the total charge of the protein; but it is only +2.
>> And, the structure is quite stable through the simulation. (RMSD: 0.17)
>>
>> I am quite confusing about the effect of Coulumb interaction on the
>> stability of the protein.
>> I feel like I am missing very important concept about the stability of
>> protein or the energy term used here.
>> Can anyone help me to understand the effect of Coulumb interaction in the
>> stability of the protein?
>>
>> Any opinion or comment would be great help for me.
>>
>> Thank you very much!
>>
>> Sincerely,
>> Seungpyo Hong
>>
>>
>>
>
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-- 
--------------------------------------------------
'God used beautiful mathematics in creating the world.'
-Paul Dirac
'At the same time, he allowed interaction among objects.'
-Seungpyo Hong

Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
sphong_ at kaist.ac.kr
sp1020 at gmail.com
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