I think the rule is that the protein should be capitalized, but in the case of MAPK, people use the non-capitalized form (p38 and p42 for instance). Is that because it is a subunit?
Related to that, when specifying the phosphorylation state, how should we write it: Phospho-p38, P-p38, p-p38, pp38? Is there a specific rule? Any reference for that?
Actually any of the terms you propose should suffice provided that you designate which one refers to the phosphorylated form on first encounter. Personally I am not very fond of too many abbreviations and I prefer to write phospho-p38
http://en.wikipedia.org/wiki/HUGO_Gene_Nomenclature_Committee
The HGNC symbols are used for genes and are italic types. However, there are no uniform names for proteins. The phosphorylation sites are usually represented by the position and amino acid, e. g. MeCP2 S421..
Dear Nicholas,
This may be of help: Nomenclature of Phosphorus-Containing Compounds of Biochemical Importance from the INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY
and INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY- IUPAC-IUB Commission on Biochemical Nomenclature (CBN) http://www.chem.qmul.ac.uk/iupac/misc/phospho.html
-The J Craig Venter Institute have developed this rules database to "address the need to generate high quality protein names, and capture our significant experience correcting protein names manually, we have developed the Protein Naming Utility (PNU). The PNU is a web based database for storing and applying naming rules to identify and correct syntactically incorrect protein names or to replace synonyms with their preferred name. The PNU allows users to generate and manage collections of naming rules" http://www.jcvi.org/pn-utility/web/smarty_wrapper/about.php
-Mouse nomenclature http://www.informatics.jax.org/mgihome/nomen/index.shtml
-In addition, the INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY- Recommendations on Biochemical & Organic Nomenclature, Symbols & Terminology etc. has this web site the offer rules organized by the type of proteins: isomerases, transferferases, lyases, steroids, etc.
http://www.chem.qmul.ac.uk/iubmb/
Good luck!
I have come across several papers, where they mention phospho proteins in several ways..I prefer to mention initially as full name and then abbreviate in Parentheses e.g. Phosphorylated ERK1/2 (pERK1/2). After that I used pERK1/2 throughout the paper. As George Komis mentioned, once you define during first encounter, it will be easy to follow by other people. I don't think there is any specific rule to write phosphoproteins in definite pattern.
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