The impact of translational delay on co-translational folding. Left: Amino acid sequence (from 958 to stop codon) of MDR1. Domain sequences are in bold. Putative amino acids (ranging from 30 to 72) occluded by the ribosome complex when the A-site interacts with the isoleucine codon (Ile1145) are underlined. Underlined domains include the Q-loop and Walker-A domains. Right: Translation pause caused by synonymous mutation leads to a change in co-translation folding. When the ribosome complex runs along the mRNA, it decodes the information on the transcript by recruiting aminoacyl tRNA to the A-site, where the tRNA anticodon base pairs with its complementary sequence on the mRNA. The amino acid that the aminoacyl tRNA carries is covalently bound to the growing polypeptide. The nascent chain passes through a tunnel in the ribosome complex. Interaction with chaperone proteins that aid the folding process starts from the tunnel exit. This process is believed to be precise and highly organized, determining the fate of the protein. Properly folded protein will be transferred to its correct destination. Unfolded proteins detected by “surveillance” proteins are targeted for degradation. A synonymous mutation may create a translation pause, which slows down the ribosome. A significant delay could interrupt the timing of chaperone-protein interaction and produce a protein with a slight conformation change. The change could be subtle, and the resulting molecule would not be considered as an unfolded or improperly folded protein. The translation pause may also affect the folding pathway of adjacent motifs.

Schematic diagram of MDR1 showing the amino acids affected by SNPs. This is a hypothetical two-dimensional model of human MDR1. Each circle represents one amino acid residue. Red circles represent the amino acids affected by SNPs. Amino acid residues affected by synonymous SNPs are marked with triangles. The SNPs of the MDR1 haplotype (G412, A893 and I1145) are circled. The regions that encode A-loops, D-loops, H-loops, Q-loops, signature motifs, Walker-A and Walker-B motifs are colored in green, and the amino acid positions of these motifs are summarized in the table. Phosphorylation sites and glycosylation are also shown. (Modified from Ambudkar, SV, et al., Biochemical, cellular, and pharmacological aspects of the multidrug transporter, Annu. Rev. Pharmacol. Toxicol. (1999):39:361-98)