© Animation Research Labs, University of Washington. With permission.
rendered an initial misdiagnosis of multiple sclerosis) with which I have been afflicted
for almost 2 decades, substantial nutritional protein intake is a major determinant
in my physiological functioning.
multiplayer online) gamers, released through its 3D molecular modelling software known as Foldit.
As a former student of architecture, I translated Foldit's fundamental premise: that form follows
function. A protein's optimal, intended functioning is predicated upon primary
structuring of its inherent amino acid sequencing; a stabilized environment buttressed
by strong hydrogen bonds in which the folding process occurs; all of which predetermines
the eventual native 3D structure. Playing the game, I became acquainted with concepts
of hydrophobic collapse, steep walls, and energy landscapes, partially-folded proteins
trapped within poorly-defined structures. Flawed protein formation follows malevolent
intent inherent within faulty engineering of its amino acids. Pathology –understood
within context of the game- is a matter of molecular design failure. Foldit's
proteomic tool meets the challenge of death by design by utilizing human visualization to discover and disrupt pathways of misfolded malfunction in proteins.
which dysfunctional protein links along the autoimmune chain will first be broken, thereby directing biomedicine's way forward in drug-discovery and leading biotech in the freeing of disease-burdened
bodies from currently-incurable anomalies?
©Animation Research Labs, University of Washington. With permission. Image: Protein conformation in progress.
Quite possibly. Foldit gamers have garnered top-winning places for their solutions in the CASP8
(Critical Assessment of Techniques for Protein Structure Prediction) competition. Cybervolunteers
first practice on known human protein structures and advance to more difficult
conformations for which optimal folding is not yet understood.
Foldit regularly receives requests for creation of protein puzzles as supplementary homework assignments for college students. Having recently read a grant proposal abstract
submitted by the research team to the MacArthur Foundation for the underwriting of a STEM gaming initiative for middle and high school students,
I had occasion to query Dr. Zoran Popović (Associate Professor in University of Washington's Department of project) about the game vis-à-vis NanoScience/NanoTechnology and its particular implications for NanoMedicine.
Thus spoke Zoran: "With recent introduction of
design puzzles, and future direct connections with researchers working on drug
and vaccine design, we intend to pioneer a new research cycle, where lab
experiments are driven by the results of Foldit design challenge puzzles.
We are also looking to design new games specifically towards creation of
nano-machines. We think that people will be particularly good at
designing new nano-structures. All that is missing is a way for them to
directly experiment in the nano-physics world." (quoted with permission)
"We are developing new genre of science-centric serious games, including games that lead to scientific
discoveries in biochemistry with implications towards curing diseases,
discovering vaccines, and developing novel biofuels." (quoted from Popović 's UW bio webpage)
Among the other game development project members working in collaboration with Dr. Popović is Dr. David Baker (Professor of Biology, Adjunct Professor of Genome Sciences and Bioengineering at
University of Washington). Baker was a winner in the 2008 Sackler International Prize in Biophysics in the field of the physics of structure formation and self-assembly of proteins and nucleic acids.
Baker was awarded the Foresight Nanotech Institute Feynman Prize for Theory in 2004.
© Animation Research Labs, University of Washington. With permission. Image: Puzzle 48. Folded protein.
From the macro to the micro to the nano, from the known to the unknown, TINC members are encouraged to participate and compete in the CASP9 experiment
and to sign on in the name of science.