[RASMB] Vbar for a peptide

[Rocco Mattia]

You can easily correct for the vbar temperature dependence. The equation is :


vbar(T °C) = vbar(20 °C) + [4.25 x 10-4 (T - T(20 °C))]

Mattia


________________________________
Da: RASMB <rasmb-bounces at list.rasmb.org> per conto di prasun kumar <prasun30 at gmail.com>
Inviato: mercoledì 9 maggio 2018 16:54:10
A: Laue, Thomas
Cc: rasmb at list.rasmb.org
Oggetto: Re: [RASMB] Vbar for a peptide

Sorry for not mentioning about AiB. It is 2-aminoisobutyric acid, an analogue of Alanine (https://en.wikipedia.org/wiki/2-Aminoisobutyric_acid).

I have run the sedimentation equillibration at 20 C. However in the 1997 paper by Durchschlag and Zipper, data are given at 25 C. Hence, I was bit hesitant to use the given data as Vbar varries with temperature.

Regards
Prasun

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

On Wed, May 9, 2018 at 3:46 PM, Laue, Thomas <Tom.Laue at unh.edu<mailto:Tom.Laue at unh.edu>> wrote:

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<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<mailto:rasmb at list.rasmb.org>
Subject: [RASMB] Vbar for a peptide



Caution - External Email

________________________________

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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