Yes. The migration of the protein on the gel depends not only on the size but also its charge. And also, it depends on posttranslational modifications such as glycosylation, methylation, acetylation etc. which increase its molecular weight and charge. Sometimes even secondary structure by improper denaturation of a protein also causes differences in migration on the gel.

Yes. The migration of the protein on the gel depends not only on the size but also its charge. And also, it depends on posttranslational modifications such as glycosylation, methylation, acetylation etc. which increase its molecular weight and charge. Sometimes even secondary structure by improper denaturation of a protein also causes differences in migration on the gel.

Some denatured proteins don't even move if their Isoelectric points are equal to the resolving gel's pH

Determination of molecular weight of a protein at SDS PAGE is a function of the nature of protein. Some protein, based on the amino acids they are composed of, tend to bind more or less SDS than they are suppose to and thus appear to be larger or smaller than the expected.

Another factor which is suppose to be influencing the protein size at SDS PAGE,as described by Budida, is post-translational modification of protein which may increase the protein MW.

Its may belong to posttranslation midification and if its contain more than one peptide chain in wuaternsry structure may give it larger size on gel

Thank you everyone for your kind replies. They have been really helpful. One more thing which I needed  to ask was that if the size of proteins appear different on gel than their theoretical size, then how can we know whether the correct protein has been expressed or not?

@Afruza,

You first need to follow the existing literature. It will help you find out how the protein behaves in the gel. Additionally, the antibody vendor provides a SDS-PAGE picture for the protein detection, which gives you a first glans of where you can see the protein in the gel. If it is a previously unknown protein, other proteomics techniques such as mass spec, a 2-D gel will help you to find out more.

If antibodies are available, western blot will tell for sure if it's your recombinant protein.