Proteomusic
Twisted music inspired by genomes and proteomes

ACGT <-> ACDEFGHIKLMNPQRSTVWY <-> ABCDEFG

History

Twisted Music Player

This is not pop music. It is a full integration of science and music ("scimusic" or "muscience", take your pick). It is beautiful biological atonality created by considering interactions of all the atoms in a system, i.e., more than just taking strings representing protein sequences and assigning them to notes. Later compositions will highlight how the songs are built up but the initial ones are presented in their full lush complexity, which may makes it hard to figure out what's going on beyond the wall of sound. To do this, one can wait for the compositions that showcase the song buildup or, for now, load the MIDI files into a (computer or other) sequencer and create and listen to your own (minimalist and varied) mixes.

The beauty of what we're doing isn't just making and playing programmatic music but that we're giving people the opportunity who cannot visually see protein structures hear it in exquisite detail (which may be further improved by the manipulation of the MIDI files provided, or by playing with the structure_to_music program in the RAMP software suite under "Music related programs" (without necessarily needing to recompile). The rough version of the patterns (codes) I've used is available and visually depicted below.

The songs are listed below with a brief comment regarding the composition. Clicking on, or selecting, the name of a song will take you to the song with the coordinates (the "lyrics"), and the opportunity to hear the sound in stereo MPEG1 Layer 3 (mp3) format (approximately one MB/minute). You can also download the song in MIDI and play around with tracks and mixes as you wish, change patches, soundfonts, effects, and so on, with a software or hardware sequencer (like a digital piano or keyboard). This means that the MIDI sounds are likely to come out of your computer which typically aere worse sounding than sophisticated synthesisers and drum modules. But if you find an arrangemnt that you would like, I'd be happy to process the MIDI file through our sounds.

translation (1ctf - 68 residues - 1:07)
Translation is the process describing how proteins are made, where messenger RNA transcribed from DNA are translated by the ribosome using the genetic code to make chains of amino acids. Musically, this track represents the C terminal domain of the L7/L12 ribosomal protein from E. coli solved by M. Leijonmarck and M. Liljas (PDB identifier 1ctf). In my early structure prediction research, this was one of the first proteins I used to debug my software. It's a small 68 residue protein with both helix and strand secondary structure (listen to the beat variation -- helices are the fastest, strands are the slowest, and coil is in between). This is presented "as is" using the default chromatic scale note assignment.
design (1qys-A - 92 residues - 1:30)
Design is a process where scientists are able to design novel folds with properties not observed in nature. This particular design track pays homage to the top7 protein designed by David Baker's group at the University of Washington. David and his group have generated a completely novel fold (not osberved in nature) and that is extremely stable lika rock. This is the first time a design of this calibre has been accomplished which is why I selected it for this track. I processed top7 (PDB identifier 1qys-A) through my structure_to_midi program for my proteomusic album, then ran the MIDI signal from my iMac to new Yahama DTX 900 drum module. It contains some amazing drum sounds and a GM set made up from the Yamaha Motif samples which are considered state of the art. It's an all digital recording (transferring data from USB back and forth, amazing how that technology works). Musically, this track represents the top7 synthetic protein designed by David Baker's group and solved by Kuhlman B, Dantas G. Ireton GC, Varani G, Stoddard BL, Baker D (PDB identifier 1qys-A). This is presented "as is" using the default chromatic scale note assignment. The only change betewen the translation track and this design track is the use of different electronic modules to generate the sounds. I have a bunch of observations about how this novel designed protein is different sounding from naturally occuring proteins, and also provide additional music that compare and contrast the two sound modules I'm using, for further exploration.
twisted helices (th - 20 residues - 0:15)
Twisted helices is a name for any weird looking helix-turn-helix protein structural motif. Musically, this track represents the short protein sequence and structure used to generate the TWISTED HELICES logo. It essentially contains the amino acids from the name plus some glycine spacers to display the side chains aesthetically. It was derived from a helix-turn-helix (ergo, twisted helices) motif in leghaemoglobin protein (PDB identifier 2lh4). This is presented "as is" using the default chromatic scale note assignment.

This work is released in accordance with the Free Music Philosophy; there is no abridgement on your freedom to copy, modify, distribute, and use this work, for any purpose (commercial or noncommercial).

All programming by Ram. All songs were recorded, mixed, and produced by Ram. Graphics and design on this page and on the album also by Ram. Read the history for more information on the software as well as ways to listen to any protein structure in the Protein Data Bank. Thanks to Jeremy and CompBio.

This album is dedicated to my family: Mali, Aphiwat, Uma (who particularly was helpful with her honest criticism), and Maya (who was simply honest).

TWISTED HELICES || Ram Samudrala || [email protected]