[Chimera-users] Electrostatics potential of amino acid residues

[George Tzotzos]

Hi,

Following this thread prompts me to ask the following question. Assume that one is dealing with highly homologous proteins, is there a way of telling the "fine" differences in the electrostatic potential of the residues encompassing the binding cavity (buried residues).

Thanks in advance for any suggestions.

George


On Jan 13, 2012, at 7:14 PM, Elaine Meng wrote:

> Hi Ankush,
> For calculating ESP of only certain atoms, you would delete the other atoms first... however, it may not be meaningful.  The simpler, more approximate Coulombic ESP is additive, but Poisson-Boltzmann ESP depends on the shape of the whole protein and locations of all of the charges (it is not simply adding contributions of each atom). 
> 
> Regardless of how you calculate the values, to do the 2D plotting you would need to use another program.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> 
> On Jan 13, 2012, at 9:50 AM, Ankush Sharma wrote:
> 
>> file attached for better understanding.
>> 
>> On Fri, Jan 13, 2012 at 6:48 PM, Ankush Sharma <ankush.sak at gmail.com> wrote:
>> Regards Elaine ,
>> 
>> Thank s Elaine for your reply  i'm aware of these facts . what I wanted to say if we considered the protein divided into grid boxes , i need to calculate electrostatic potential of one particular area( in attached  fig box e) . Plot can be plotted on X axis as the distance acquired by electrostatic potential surface from the centre of the protein (for whole protein). For One grid or one box, distance acquired by the electrostatic potential surface from the centre of that part of protein to the distance of the  one grid( off course protein will be divided into many grids while performing these kinds of analysis.) and Y axis Will the electrostatic potential.
>> 
>> Thanks 
>> Ankush Sharma
>> 
>> 
>> 
>> 
>> 
>> 
>> Hi Ankush,
>> If you want to show the electrostatic potential by coloring the molecular surface in Chimera, please see this recent post for two possible ways:
>> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-January/007058.html>
>> 
>> See also this tutorial:
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
>> 
>> For plotting, you would need to use some other program.  Also, it is unclear what would be on the X-axis and Y-axis of this plot, since the potential varies in 3D space.  There is not a single potential value per residue or anything like that.
>> 
>> For comparing electrostatics of proteins, you might be interested in this web server:
>> <http://pipsa.eml.org/pipsa/>
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> On Jan 13, 2012, at 9:05 AM, Ankush Sharma wrote:
>> 
>>> Regards all,
>>> i wanted to calculate the calculate the Electrostatics potential associated with a specific part of the protein and differentiate from the other part of protein. How can it Possible . is there any method apart from MD to plot a graph of both to diffrentiate Quantitatively the The Potential
>>> Thanks in advance
>>> Ankush Sharma
>> 
>> 
>> 
>> 
>> -- 
>> Regards
>> Ankush Sharma
>> Doctoral student in Computational Biology
>> Second University of Naples & Centro Ricerche Oncologiche
>> di Mercogliano
>> Email ID : ankush.sharma at unina2.it
>> Phone: +39 331 831 6370
>> 
>> 
>> 
>> P Please do not print this email unless it is absolutely necessary. Spread environmental awareness.
>> 
>> 
>> 
>> 
>> 
>> -- 
>> Regards
>> Ankush Sharma
>> Doctoral student in Computational Biology
>> Second University of Naples & Centro Ricerche Oncologiche
>> di Mercogliano
>> Email ID : ankush.sharma at unina2.it
>> Phone: +39 331 831 6370
>> 
>> 
>> 
>> P Please do not print this email unless it is absolutely necessary. Spread environmental awareness.
>> 
>> 
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