Archive for March, 2009

A paper on folding stability

Friday, March 20th, 2009

Sheena E Radford presented her work on protein folding stability design on Biophysics Society Meeting 2009. It is a nice presentation because she presented her computational design with the in vivo experimental verification. Some of her results have not been published yet, but the computational method was already published on Nature Structural & Molecular Biology. It is nice to look into it.

She started with a refolding measurement of the protein Im7, which is a colicin immunity binding protein. It has four helices and is a dimmer. The refolding measurement is measuring the fluorescence signal from the TYP residue on the last helice. This is a combination of stopped-flow and continues-flow because the time scale is seconds. The stopped-flow is good for shorter time range while the continuous is for relatively larger time range only. Based on the measurement and its interpretation, the folding process is a three fold, i.e., there is an intermediate state. Also, the interpretation of the 3 state folding dynamics lead to the folding rate parameters, i.e., the conversion rate between states. The phi values of the different states are then calculated from experiments.

Meanwhile, she setup a phi value from computational. Here the phi is defined as the ratio of the number of a native contacts in a conformation to in native fold. This calculated phi is used as the counterpart of the experimental phi, which I still don’t fully understand.

A target MD is used to make the simulation sampling “biased” toward the states defined by the experimental phi. The charmm force field is used with the additional constraints. A simple quadratic form constraint is used to penalize any move which cause the calculated phi far away from the experimental phi in MD.

Further analyze the trajectories generated from the target MD.

After read it, I don’t think it is that great, but still a very good one in terms of the way of thinking (phi) and solving (combination of experimental and computational tools).

test the hypothesis of normality in R

Wednesday, March 18th, 2009

library(nortest)
lillie.test(x)
#the null hypothesis is that x is a normal distribution.

Book review: Call me Ted

Sunday, March 8th, 2009

“Call me Ted” is an autobiography from Ted Turner who is famous of many things, among them one is the founder of CNN. He is an amazing figure and I found this book very much enjoyable. His father shaped him in many ways, some are good whilst some are very bad in my opinion. I’d like to quote some of the words from his father to him.

You can’t always be right. But you always can be on time.

Work hard and advertise.