[RASMB] Vbar for a peptide

prasun kumar prasun30 at gmail.com
Wed May 9 08:05:58 PDT 2018


Hi All:

I have tried calculating Vbar of the peptides (poly-tyr, poly alanine) from
the same article or even the single residues. I have got similar values by
UltraScan.
Here I must say that I am comparing the calculated value (using the formula
given in the paper) and Ultrascan.

I was not able to get the 0.653 vbar value for L-Alanine at 25 C using the
same calculation.
I am getting 0.73849 and Ultrascan gives 0.7400

Hope I am on right direction.

Regards
Prasun


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

On Wed, May 9, 2018 at 3:53 PM, Rocco Mattia <mattia.rocco at hsanmartino.it>
wrote:

> Hi!
>
> Tom, the Durchschlag and Zipper paper indeed describes their advancements
> over the old Traube method you mention, including how to properly deal with
> charged groups. So, if Prasum is using their scheme, he should be fine. To
> make sure he is implementing it correctly (it's tricky... ;-) ), I suggest
> that he should first see if he can correctly recalculate the vbar of some
> amino acids.
>
>
> Cheers - Mattia
> ------------------------------
> *Da:* RASMB <rasmb-bounces at list.rasmb.org> per conto di Laue, Thomas <
> Tom.Laue at unh.edu>
> *Inviato:* mercoledì 9 maggio 2018 16:46:55
> *A:* prasun kumar; rasmb at list.rasmb.org
> *Oggetto:* Re: [RASMB] Vbar for a peptide
>
>
> 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
>
>
>
> *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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