[RASMB] Vbar for a peptide

[Laue, Thomas]

Hi Prasun-
The vbar for an uncharged grouping (I’m not sure what AiB is, but assume it is uncharged) may be calculated from the atomic composition and bonds using the method of Traube (which adds together the atomic volumes, then subtracts a ‘co-volume’ that accounts for the volume reduction due to the bonding). This is similar to what you are describing. There is a description of how to do this calculation in Cohn & Edsall. The method is inaccurate for charged species in water due to the water collapse around the charged groups, which reduces the vbar. The measured values given by Cohn & Edsall are for blocked amino acids (or their side chains) in water. By using water, they reduced the error that accompanies H-bond formation with the solvent (a problem that reduces the accuracy of merely inverting the density of a substance to get its vbar).
Best wishes,
Tom

From: RASMB [mailto:rasmb-bounces at list.rasmb.org] On Behalf Of prasun kumar
Sent: Wednesday, May 9, 2018 10:25 AM
To: rasmb at list.rasmb.org
Subject: [RASMB] Vbar for a peptide

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Hi Group:

I have gone through most of the discussions on Vbar and related stuff here. However, I thought to put my procedure for discussion...

I have a peptide that consist of 2 AiB residues alongwith other natural residues.
Since, the Vbar for AiB is not available, I was considering AiB as Ala and calculating the Vbar of the peptide. However, if Vbar goes down, it overestimates the Mol. Weight of the assembly. I was bit worried about this fact. Then I came across the paper by Durchschlag and Zipper in Jl of Appl. Cryst. (1997). In this paper authors have tried to calculate the partial specific volumes of small molecules and polymers based on volume increment method.

After going through the above article, I decided to randomize my sequence such that the constituent residues and their numbers remain same. I calculated the Vbar of both sequences and found no difference in Vbar at 20 C.

I also realized that 2 AiB residues can be replaced by one Ala and one Val. for example:
......AiB AiB........ can be ......AV.....

after replacing AiB AiB by AV, I calculated the Vbar of my peptide.

Here, it is important to note that I am not changing the charged or aromatic residues.
Any suggestion on the appropriateness of my procedure is welcome.

Regards
Prasun


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