[RASMB] vbar of glycosylated proteins

[Rocco Mattia]

If I may add a further bit of advice, if you know the composition (%-wise) of the different carbohydrate units present in you protein, you can further fine tune your mw estimation by using the individual vbar values. There are some differences in that value for, say, mannose, N-acetyl glucosammine, and sialic acid...


Best - Mattia

________________________________
Da: RASMB <rasmb-bounces at list.rasmb.org> per conto di John Philo <jphilo at mailway.com>
Inviato: lunedì 21 maggio 2018 19:48:02
A: 'RASMB List'
Oggetto: Re: [RASMB] vbar of glycosylated proteins

Borries, FYI I use and recommend the carbohydrate vbar values from the Lewis
2000 paper. Those have given total average molar mass values from AUC
consistent with independent methods (e.g. MALDI mass spec) even for heavily
glycosylated proteins such as erythropoietin (~30% carbohydrate).
John
-----Original Message-----
From: RASMB <rasmb-bounces at list.rasmb.org> On Behalf Of Borries Demeler
Sent: Friday, May 18, 2018 1:48 PM
To: RASMB List <rasmb at list.rasmb.org>
Subject: Re: [RASMB] vbar of glycosylated proteins

Thanks to all who have responded! To summarize for the RASMB archives, here
is a list of responses:

Luitgard pointed me to:

Perkins SJ.  Protein volumes and hydration effects. The calculations of
partial specific volumes, neutron scattering matchpoints and 280-nm
absorption coefficients for proteins and glycoproteins from amino acid
sequences.  Eur J Biochem. 1986 May 15;157(1):169-80.
(https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1432-1033.1986.tb09653.x)

Allen Minton suggested:

> Borries -
>
> If you know the mass percentage of sugar, a very good estimate of the
> vbar of the glycoprotein would be a mass-average of the "standard"
> vbar for peptides (~.73) and the "standard" vbar for saccharides (~.61 I
think).
>
> Allen

Thanks, Allen, that works just fine for my purposes! And it even comes very
close to the mass spec molar mass for my protein of interest :)

Tom (Laue) thought there was some work done by Steve Shire and John Philo.

My own literature search turned up this paper:

Lewis MS, Junghans RP. Ultracentrifugal analysis of molecular mass of
glycoproteins of unknown or ill-defined carbohydrate composition. Methods
Enzymol. 2000;321:136-49. (https://www.ncbi.nlm.nih.gov/pubmed/10909055)

A great weekend to all!

-Borries
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