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PROJECT DEVELOPMENT

This section explains the evolution of our project. We have outlined how we arrived at the final amino acid-to-musical note assignment and rhythm using the human Thymidylate synthase A (ThyA) protein as a prototype. From the following explanations and examples, you can hear the different versions of the same ThyA protein based on the transitory assignment codes in addition to the final code that we implement in our GENE2MUSIC program. 

Amino acid to music assignment

Limitations of a one-to-one assignment: Initially, it may be most obvious to assign each amino acid to a single note starting on any given key, which results in a 20-note range since there are 20 amino acids. Previous groups have used such a method, and we show an example of the resulting music using the beginning of the human ThyA protein [AUDIO VISUAL] . However, we found that this one-to-one code has a 2.5 octave range and therefore results in a non-cohesive melody that is difficult to recognize or memorize. For musicality, we added another modification using three-note chords (triads) by building thirds off of the original single note, which creates a fuller sound and modulates the transition between consecutive notes. The triads also enabled us to incorporate different variations of a particular triad, such as G major root position and first inversion triads (Figure 1, left). The resulting ThyA protein using chords produces a fuller and more melodic sound.

Our reduced note assignment: In order to address the large range (2.5 octaves) that resulted from the one-to-one assignment, we reduced the initial number of notes to 13 by pairing similar amino acids such as Tyrosine (G major root position chord) and Phenylalanine (G major first inversion chord). We differentiated the amino acids among each pair by using a root position triad and first inversion triad to represent each amino acid that was included in a pair. An example of a G major root position and first inversion chord are shown below. Both forms of the same triad include the same individual notes, but the arrangement of these three notes differs from one form of the triad to another. Based on hydrophobicity, we were able to create a code (Figure 1, right). Based on the final coding assignment below, you can listen to the ThyA protein [AUDIO VISUAL 1 2] and compare it to what you heard initially from the one-to-one assignment.

Triad inversion example

 

 

Music Note
Root Position Chord
First Inversion Chord
C Trp
D Met
E Pro
F His
G Tyr Phe
A Leu Ile
B Val Ala
C Cys
D Gly
E Thr Ser
F Gln Asn
G Glu Asp
A Arg Lys

Figure 1: (LEFT) Example of root position chord (left) and first inversion chord (right) both in the key of G. (RIGHT) Final amino acid to music assignment.

Assigning Rhythm

Another key aspect of music is rhythm. We decided to use codon distribution (based on a frequency per thousand) to encode a rhythmic component to our conversions. Each amino acid is encoded by one to six codons (each codon is composed of 3 nucleotides). Every organism has a unique codon distribution that displays how frequently a given codon is used to specify a particular amino acid. For example, the codon GCG codes for the amino acid Alanine and occurs 7.5 times per thousand codons in the human. The range of the codon distribution for the human was sectioned into four parts, each of which was represented by either an eighth, quarter, half, or whole note (Figure 2). The final conversion of the ThyA protein with rhythm [AUDIO VISUAL 1 2 3] can be heard and compared to the previous musical conversions above.

Codon distribution (frequency per thousand)
Note Duration
0 up to 11
Eighth
11 up to 21
Quarter
21 up to 30
Half
30 and greater
Whole

Figure 2: Note duration assignment for each amino acid chord based on codon distribution.