|
|
SUMMARIES OF SELECTED SCIENTIFIC JOURNAL ARTICLESNature 2002 | JMB 2002 | Physical Review Letters 2001 Following is a simplified version of the article by Christopher D. Snow, Houbi Nguyen, Vijay S. Pande and Martin Gruebele titled ABSOLUTE COMPARASION OF SIMULATED AND EXPERIMENTAL PROTEIN-FOLDING DYNAMICS published on Nature, October 2002 Protein folding from extended state happens real fast. The complete folding process takes place in a few microseconds (microsecond = millionth of a second = 1 µs). This is indeed very fast to study the process in a lab situation experimentally. However, at the same time it is too slow to simulate protein folding using computers since any single computer is still too slow to do all the calculations in a reasonable amount of time. Currently computers can simulate only a few nanoseconds (nanosecond = billionth of a second = 1 nm). Even if the computers got faster in future, a single simulation of a single molecule may not give us all the details and we may miss some important steps proteins go through during folding. Here we are going to explain how these challenges were met by researchers of both worlds: computer simulations and experiments. EXPERIMENTAL | FOLDING@HOME SIMULATION First let us get into the experimental methods. We are all familiar with thing that glow (fluoresce) in the dark, children's toys that glow in the dark are primary examples. Here is a plant genetically engineered to glow in the dark:
In the picture above, black light is shining upon fluorescent paint: Some parts of a protein can be made to glow also when a UV light (LASER) shines upon it. As protein begin to fold the fluorescent part may begin to be buried inside, giving out less and less light. By measuring and analyzing the fluorescent light given out one can study the folding process and determine how long it takes for the protein to fold (or unfold) completely. The animation below will illustrate the lab process. Blue portions of protein represent areas that glow (for this illustration purpose only). The protein that is shown to unfold is actually a computer simulation of "Finger Zinc" by Pande group, however the rest of the animation is meant for illustration purposes only and do not represent scientific data. The UV LASER pulse cause parts of the protein to glow, in addition there is another LASER to heat up the sample protein to cause it to fold or unfold depending on the experiment. In actual experiments a large sample of proteins are used not a single one.
From this type of experiments relaxation (unfolding) rate detected was 1.5 ± 0.7 µs (1 µs = one millionth of a second) and the folding rate (the time it takes for this protein) was 7.5 ± 3.5 µs at a temperature of 298 K (77 degrees Fahrenheit) Web Author: Tug Sezen |
