Because of neurologic maladies (lupus and Chiari Malformation; the combination of which
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.
http://fold.it/portal/info/science
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.
© Animation Research Labs, University of Washington. With permission.
Image:Puzzle 48. Unfolded protein.
Having suffered paralysis, stroke, ischemia, seizures, and migraines, I now perceive spatially the ravaging biochemical battle within, waged against the vulnerable, predisposed proteins of my cell nuclei; and can comprehend more acutely my experience with apoptosis - "programmed cell death". Interacting with the Foldit simulations, I wonder what antagonized those assassinating antibodies
into killing my neurons? What environmental provocation has engaged and conscripted
my proteins for almost 2 decades? Might a high-scoring Foldit gamerdiscover through play the means of blocking NR2 proteins from annihilating antibodies in a lupus case such as mine? Is it possible that the spinal fluid which may have built up as a result of my Chiari Malformation provide the anti-DNA sample test for my lupus? My challenge was to game while simultaneously grasping the inverse: in ailments such as Alzheimer's disease, the active, malformed proteins themselves are the agents provocateurs. Will Foldit's predictive gaming applications ultimately be the pattern-matching breakthrough mechanism by which and through
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.
(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 abstractsubmitted by the research team to the MacArthur Foundation for the underwriting of a STEM gaming initiative for middle and high school students,
http://www.dmlcompetition.net/pligg/story.php?title=849
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 ofdesign puzzles, and future direct connections with researchers working on drugand vaccine design, we intend to pioneer a new research cycle, where labexperiments are driven by the results of Foldit design challenge puzzles.We are also looking to design new games specifically towards creation ofnano-machines. We think that people will be particularly good atdesigning new nano-structures. All that is missing is a way for them todirectly experiment in the nano-physics world." (quoted with permission)
"We are developing new genre of science-centric serious games, including games that lead to scientificdiscoveries 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
http://predictioncenter.gc.ucdavis.edu/casp8/index.cgi
and to sign on in the name of science.
http://fold.it/portal/info/science
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