Archive for December, 2008

Another R parallel package: SPRINT

Tuesday, December 30th, 2008

Just notice another group published a R parallel package (link).

An interesting biocompute group at Italy

Tuesday, December 16th, 2008

There is a biocompute group at Italy has many interesting gadgets. The url is here.

One unrelated paper I found of interests is here.

A program to predict mutation is called Auto-Mute, a similar paper.

A paper on membrane insertion from influenza a virus

Thursday, December 11th, 2008

One recent paper published on Biophysics Journal is focused on the M2 transmembrane insertion. The authors did MD and consider the lipid as a continuum and then profiled the free energy of the insertion. I’d like to quote their conclusion here:

The minimum in the calculated free-energy surface of peptide insertion
corresponds to a fully inserted, helical peptide spanning the membrane. The free-energy profile also shows that there is a
significant barrier for the peptide to enter into this minimum in a nonhelical conformation. The sequence of the peptide is such that
hydrophilic amino acid residues at the ends of the otherwise primarily hydrophobic peptide create a trapped, U-shaped conformation
with the hydrophilic residues associated with the aqueous phase and the hydrophobic residues embedded in themembrane. Analysis
of the free energy shows that the barrier to insertion is largely enthalpic in nature, whereas themembrane-spanning globalminimumis
favored by entropy.

The authors are In-Chul Yeh, Mark A. Olson, Michael S. Lee, and Anders Wallqvist.

Their results, in particular, the transmembrane-spanning is favored by entropy is same as (to some extent) other findings regarding the insertion of helices in membrane. For example, I heard that helices prefer tilted position to the position is perpendicular to the lipids planes. And it is due to entropy.