"If you just look at the physics of the problem, protein folding is like playing Pebble Beach blindfolded, except much harder. The golf course here is the "conformational phase space" corresponding to a given chain of amino acids, a vast if notional terrain across which are laid out all the possible shapes that a given chain of amino acids could."
"In order to make experimental or theoretical progress in understanding the dynamics of folding, we need a simpler description that uses a far smaller number of coordinates. The most optimistic model is one-dimensional: protein folding is like the diffusion of a particle along a one-dimensional path."
"In reality, protein folding is like evolution by natural selection. As a protein starts to fold, local structures form quickly, leading to a dramatic reduction of the available 'space' to be searched. These local structures then try out a more limited number of structures, with successive steps nailing down more and more of the correct structure. What seemed like a miracle is now quite well-understood, although it's still a challenge to actually predict the specific steps for a given protein."
"One could say that a protein folding is like a child growing up. If he grows up nice, clean and proper (folds), Great!. If he's a foul mouthed hoodlum (sp?) mis-fold. Hmmmm "
" The process of protein folding is like rolling a ball from the top of the
funnel to the bottom. The funnel-shaped free energy landscape predict that
the protein folding is a parallel event rather than a sequential event."
Eventually it finds its lowest energy state at the bottom of the funnel, but the process is not a direct path.
METAMIA is a free database of analogy and metaphor. Anyone can contribute or search. The subject matter can be anything. Science is popular, but poetry is encouraged. The goal is to integrate our fluid muses with the stark literalism of a relational database. Metamia is like a girdle for your muses, a cognitive girdle.