Why is the observed Western Blot band size different from predicted size?
The predicted M.W. is based on protein sequence analysis; however, some factors might lead to an observed band size that is different from the predicted size. The reasons might include:
1.Post-translational modification (PTM):
a. Some post-translational modifications might lead to increased protein size, including
phosphorylation, acetylation, methylation, glycosylation, sumoylation, ubiquitination,
etc.
b. Some post-translational modifications might lead to decreased protein size including
phosphatidylethanolamine conjunction (e.g. LC3-II)
c. Some proteins may be cleaved to form an active or mature form; this process will
lead to a decreased protein size (e.g. Notch activation, Caspase activation, etc.)
d. Some websites provide useful PTM information
i.HPRD http://www.hprd.org/
ii.ProSite http://www.expasy.org/prosite/
iii.ELM http://elm.eu.org/
iv.CBS data sets http://www.cbs.dtu.dk/databases/
v.CBS prediction Servers http://www.cbs.dtu.dk/services/
2.mRNA splice variants (Isoforms):
Through alternative splicing, one gene can generate different proteins with different M.W. Regulation of alternative splicing depends upon cell type, conditions, etc.
3.Multimerization:
Some proteins could form dimers or multimers, increasing the M.W. This phenomenon usually can be found in reducing gel condition; however, strong interactions may still be seen with higher molecular weight proteins even in denaturing gel.
4.Protein charge:
The observed size could also potentially be influenced by the protein charge
5.Different species:
Different species likely have different protein sequence and PTM, which can lead to a different protein M.W.