[RASMB] Vbar for a peptide

[prasun kumar]

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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