DNA Variant Mining and In silico Analysis of Milk Proteins

Abstract

Milk is a resource of lipids, proteins, amino acids, vitamins, and minerals. Proteins in milk vary in biological activities which include among others antimicrobial, nutrients absorption facilitator, growth factors, hormones, enzymes, and antibodies. Milk proteins also exist in various isoforms which may differ in their activity. However, we still do not know much about the variation of milk proteins other than the major ones (the caseins, β- lactoglobulin and α-lactalbumin). The traditional methods of protein analysis (e.g. 2D PAGE) do not suffice to study minor milk proteins which comprise a very little fraction of milk protein. This project aims to find new milk protein variants in Dutch milk using genomic approach. DNA from 54 Dutch Holstein bulls are sequenced and called for variants. Variants effects on protein are predicted and protein variants from approximately 400 milk proteins are determined. Variants found in 209 proteins including the known variants of major milk proteins. Based on in silico protein analysis, ten variants are listed as the most interesting variants, including milk protein 4. LC-MS analysis confirms the presence of a milk protein 4 variant.