A silent mutation affects pain perception?

Earlier this week you probably read the whole saga of how researchers tracked down some individuals who could not sense pain. They then identified the gene responsible as SCN9A, a voltage-gated sodium channel and that was published in Nature. But in Science there was another report of a gene, Catechol-O-Methyltransferase (S-COMT), that is critical for pain perception ...

Well it turns out that the data in the Science paper is much more interesting than the flashy (yet uninsightful) observations of individuals walking on hot coal and receiving knife stabs into their arms without even flinching. Here are the mutations in the S-COMT gene:

one located in the S-COMT promoter region (A/G; rs6269) and three in the S- and MB-COMT coding region at codons his62his (C/T; rs4633), leu136leu (C/G; rs4818), and val158met (A/G; rs4680)

Yes 3 of the mutants are SILENT mutations (and the fourth is in the promoter). In other words the translation product is not altered at the amino acid level. So what is the problem? Expression level perhaps? Here's what the researchers have to say about the most interesting mutation:

[tissue culture neurons expressing the APS mutant form of S-COMT] displayed a moderate 2.5- and 3-fold reduction in enzymatic activity for S- and MB-COMT constructs, respectively, while protein expression levels did not differ.

Silent mutation => no change in protein LEVEL??? => change in protein activity??????

The authors hypothesize that the major defect is ... mRNA secondary structure. The mRNA secondary structure affects either mRNA stability or translation efficiency as in the HPS mutant (see pic), but in the APS mutant form? Protein thermostability.

The moderate reduction in enzymatic activity produced by the APS haplotype is most likely due to the previously reported decrease in protein thermostability coded by the met158 allele.

In other words, the silent mutation (and thus mRNA structure) is affecting protein folding. Very interesting hypothesis. mRNA secondary structure could slow down the ribosome at certain points along the transcript and thus affects the kinetics of co-translational folding. In other words, perhaps a substable protein-fold is formed during synthesis, but for it form you need to stall the ribosome. This same fold could be inhibited by parts of the protein that are made subsequently - thus if you allow folding befor making the rest of the protein, you're OK. Make the protein too fast and the substable-fold can't form properly.

Unfortunately they don't have great proof for this idea. I guess you could perform NMR or get an X-ray structure of the two forms. But for all those researchers who model protein folding, take notice! And for the rest ... again from the paper:

Our data have very broad evolutionary and medical implications for the analysis of variants common in the human population. The fact that alterations in mRNA secondary structure resulting from synonymous changes have such a pronounced effect on the level of protein expression emphasizes the critical role of synonymous nucleotide positions in maintaining mRNA secondary structure and suggests that the mRNA secondary structure, rather than independent nucleotides in the synonymous positions, should undergo substantial selective pressure (22).

Ref:
A. G. Nackley, S. A. Shabalina, I. E. Tchivileva, K. Satterfield, O. Korchynskyi, S. S. Makarov, W. Maixner, L. Diatchenko
Human Catechol-O-Methyltransferase Haplotypes Modulate Protein Expression by Altering mRNA Secondary Structure
Science (2006) 314:1930 - 1933