After purifying my GPCR, I found that the protein, which is expected to be around 44 kDa, appears to be less than 40 kDa on SDS-PAGE. What could be the possible reasons for this unexpected lower molecular weight?
One of the common reasons is incomplete glycosylation or post-translational modifications. Also, improper or incomplete binding of SDS to the protein can lead to different migration of the membrane proteins, like your GPCR, which may not denature fully. Additionally, Adam B Shapiro mentioned about proteolytic cleavage during purification is another possibility, where a portion of the protein is degraded, leading to a truncated form.
While the previous posts could explain your observation, in my experience many integral membrane proteins show anomalous migration behaviour in SDS-PAGE, leading to smaller apparent MW and frequently also additional oligomeric bands of aggregated molecules with a regular size pattern of their monomeric size. One extreme example is bacteriorhodpsin (also 7 TM domains like GPCRs) with ~16-18 kDa on the gel instead of the correct ~26 kDa. The reason seems to be that the transmembrane helices are not bound to the average ~2 SDS per amino acid like "normal" proteins because of the highly hydrophobic properties which makes it difficult to fully unfold these regions. So you have an unfolded SDS-protein complex that appears more compact, i.e. smaller and migrates like a smaller protein.