A little surfactant song: SP-D

Science and art cover illustrations, surfactant proteins A and D, Ultimate order, the cell

MLLFLLSALVLLTQPLGYLE
AEMKTYSHRTMPSACTLVMCSSVES
GLPGRDGRDGREGPRGEKGDPGLPGAAGQAGMPGQAGPVGPKGDNGSVGEPGPKGDTGPSGPPGPPGVPGPAGREGPLGKQGNIGPQGKPGPKGEAGPKGEVGAPGMQGSAGARGLAGPKGERGVPGERGVPGNTGAAGSAGAMGPQGSPGARGPPGLKGDKGIPGDKGAKGESGLP
DVASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQ
SVGEKIFKTAGFVKPFTEAQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSK
TEGKFTYPTGESLVYSNWAPGEPNDDGGSEDCVEIFTNGKWNDRACGEKRLVVCEF

(MLLFLLSALVLLTQPLGYLEAEMKTYSHRTMPSACTLVMCSSVESGLPGRDGRDGREGPRGEKGDPGLPGAAGQAGMPGQAGPVGPKGDNGSVGEPGPKGDTGPSGPPGPPGVPGPAGREGPLGKQGNIGPQGKPGPKGEAGPKGEVGAPGMQGSAGARGLAGPKGERGVPGERGVPGNTGAAGSAGAMGPQGSPGARGPPGLKGDKGIPGDKGAKGESGLPDVASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTEAQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGEPNDDGGSEDCVEIFTNGKWNDRACGEKRLVVCEF)

This is a sequence which i believe I have correctly identified as human Surfactant Protein D from van Eijk’s publication (https://doi.org/10.1165/ajrcmb.26.6.4520). ( Green above is the signal peptide, the blue is the N terminal, the black is the collagen like sequence with proposed gycosylation site in light blue beginning the 70th aa) and the purple the coiled coil neck, and the red the carbohydrate recognition domain.

This is pretty relaxing music in my mind…..and it was interesting to be able to hear the music quality change in each of the domains.

The very first part is quite melodic (signal peptic sequence and the N terminal domain.  The coiled coil neck and the carbohydrate recognition domain are melodic as well….

The fun part is to try to identify the low “drone” of the “A” in the central part of this clip which represents the glycine amino acids and their recurring theme. This is in the collagen-like domain within the surfactant protein D molecule: on paper it is written usually as G x x  which are repeats:  a glycine, then another amino acid, and another, and then back to glycine…. )

It would be interesting to line up similar order of tones for a collagen molecule to reinforce the importance of the “drone” in identifying the collagen-like domain.

I didn’t not invent a really good way to assign the single letter codes for the amino acids that match notes on the 12 tone scale, so I just listed the amino acids sort of alphabetically. as is done in many text books and publications. There would be other ways to assign pitch, on charge and hydrophobicity or hydrophilicity, or some other property, that would be informative, and might work as a second or third track.  One could list those with letter assignments that match the piano scale using the duplicate first letters, e.g. alanine, argenine, asparagine, aspartic acid in different octaves but that is also just arbitrary… the more intelligent thing would for me to have arranged them according to physical properties rather than random.

And while it looks like a waste of time…. It helped me memorize the single letter nicknames for the 20 amino acids …as well as hearing the differences in the variation in amino acids incorporated into each of the four domains of surfactant protein D, and reminded me of how to use FLStudio.