Where and how can i find sizes of pituitary glands' proteins? When i use Entrez or other bioinformatic sites, it only has human proteins and not specifically human pituitary glands' proteins.
Hope for ideas.
You'll need to think about what makes up a the set of proteins which are expressed in the pituitary gland, these can be split into two sets, those which are expressed in all cells - "house keeping genes", and those expressed specifically in the pituitary.
There are a range of practical ways of determining which genes are expressed in a particular tissue. Looking at the abundance of mRNA using microarrays comprising expressed sequence tags is one such method.
mRNA analyis is used in this publication on pituitary specifc proteins:
Once you know what proteins you are interested in you can determine the sizes of the protein in a range of practical or computer assisted ways.
I know which proteins i am looking for, but i can not find any bioinformatic tools where i can get the information about their sizes.
I'll take as an example Pituitary gland specific factor 1
Has the protein sequence and a calculated mass, this calculated mass doesn't take into account any post-translational modifications - this mass might not be the one observed by a Western, or Mass Spec.
You can also use SwissProt/TrEMBL to search for Pituitary proteins:http://www.expasy.ch/cgi-bin/get-entries?Tissue=Pituitary
If you find a sequence - there are many on and off line applications which will translate it for you if required - and calculate a mass from an amino acid sequence.
The NCBI Sequence viewer is a good place to go for sequence data:NCBI - Sequence Viewer
The ENSEMBL human protview has data on variations
For this protein I didn't find an experimentally determined mass.
I really appreciate your great help. I wonder if the proteins in The Swiss-Prot database are only in precursor form? I am going to do the western blot and for that I really need their active forms.
Do you know how I can find the sizes of their active form based on the information I have from Swiss-Prot?
For example I will find the active form of Pituitary gland Secretogranin V
Thank you alot!
Hope for your kind answer.
The molecular weight of the protein that you observe in a western blot will depend on many things including dimerisation and how much post translational processing including glycosylation has occured. These things will depend on where you get your sample from and how you prepare it.
In terms of Neuroendocrine protein 7B2 - the protein you linked to, see:
That review contains information about the various post-translational modifications you can expect.
Thanks again, Taylor.
I have another question regarding proteins.
As you know i am looking for the sizes of human pituitary glands' proteins. i asked my supervisor about the size of pituitary gland's glucocorticoid receptor. To my surprise what he did was using the Pubmed to search for "human glucocorticoid receptor" to get the size of this pituitary gland's receptor. it did not say anything of the size of this receptor is also for the pituitary gland.
MY question: why did he take it for granted that this receptor has identical size for all human tissues including pituitary gland? I can ask him, but i did not, since i should know about it.
The question is if there is alternative splicing, or alternative post translational modifications for this protein in different tissues which would lead to varients of this protein with different masses depending on both tissue, subcellular location, and other factors.
In the case of glucocorticoid receptor there are alternative splicing pathways resulting in final proteins of different mass.
The range of isoforms of this protein are reviewed:http://www.annalsnyas.org/cgi/content/full/1024/1/102
And information on the isoforms are available:http://us.expasy.org/cgi-bin/niceprot.pl?P04150
I'm moving this conversation to the Bioinformatics category to share with the rest of the scientist solutions community.