[RASMB] Vbar for a peptide

Wed May 9 08:08:49 PDT 2018

Be sure you are not comparing *residue* values with *full amino acid* values...

________________________________
Da: prasun kumar <prasun30 at gmail.com>
Inviato: mercoledì 9 maggio 2018 17:05:58
A: Rocco Mattia
Cc: Laue, Thomas; rasmb at list.rasmb.org
Oggetto: Re: [RASMB] Vbar for a peptide

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<mailto: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<mailto:rasmb-bounces at list.rasmb.org>> per conto di Laue, Thomas <Tom.Laue at unh.edu<mailto:Tom.Laue at unh.edu>>
Inviato: mercoledì 9 maggio 2018 16:46:55
A: prasun kumar; rasmb at list.rasmb.org<mailto: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<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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