[RASMB] Regarding V-bar calculation of peptide containing non-natural amino acid

[Rocco Mattia]

Hi Prasun,
 
good work. To answer your question, it depends on the level of accuracy you need for the computed vbar... and bearing in mind that even the best computed vbar could be different from a real, measured one.
 
If you're going to try and calculate a vbar using the Durchschlag/Zipper rules, my suggestion is that you first try to reproduce already calculated vbars for a couple of AA residues. You can find their values in the US-SOMO somo.residue table, accessible from the pull-down menu on the top left side of the main program. Please feel free to come back to me for any further assistance.
 
All the best - Mattia

________________________________

From: prasun kumar [mailto:prasun30 at gmail.com]
Sent: Fri 9/29/2017 9:46 AM
To: Rocco Mattia
Cc: rasmb at list.rasmb.org
Subject: Re: [RASMB] Regarding V-bar calculation of peptide containing non-natural amino acid


Hi Mattia and the group: 

Thank You for the response. I installed US-SOMO and just to check whether it is working for peptides with non-natural amino acids, I used one PDB ID (1GOE). It contains DPN and AIB. 

Program says it has got unrecognised residues and asked me to take the average value or stop processing......
I chose the first option and got the V-bar value. 

Now the question is whether considering the average values for the non-natural amino acids is a good idea or not.... If no then do you think I should also go back and refer to the "bible". 

I am doing my experiments in PBS+Water solvent (pH 7.4)

Regards
Prasun 

PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success

On Thu, Sep 28, 2017 at 10:49 AM, Rocco Mattia <mattia.rocco at hsanmartino.it> wrote:


	Hello Prasun,
	
	if you have a PDB file for your peptide, you can try uploading it in US-SOMO and see if the non-standard AA are recognized and a vbar calculated.
	
	Otherwise, the computations are a bit complicated... we usually do them, when facing non-standard residues, using an Excel worksheet based on the "bible" for vbar calculations:  Durchschlag and Zipper, Prog. Colloid Polym. Sci. 94:20-39, 1994
	
	Hope this helps!
	
	Mattia
	
	________________________________
	
	From: RASMB on behalf of prasun kumar
	Sent: Thu 9/28/2017 11:34 AM
	To: rasmb at list.rasmb.org
	Subject: [RASMB] Regarding V-bar calculation of peptide containing non-natural amino acid
	


	Hi All:
	
	I have a peptide that contain non-natural amino acids. My query: how to calculate the V-bar of this peptide?
	Any suggestions will be really helpful to me.
	
	Regards
	Prasun
	
	PRASUN (ASHOKA)
	Desire + stability = Resolution
	Resolution + Hard work = Success