Hi Fred, I would say that the helix stability will generally be affected by its context within the protein, unless it is (unlikely?) separated from the core of the protein and it has intrinsic stability (some peptide sequences do). Also, in a particular context, you may have mutations that unfold or distort the helix, without seriously affecting the stability of the protein as a whole, for this can be compensated by new interactions. Therefore, unless you have good reasons to consider the helix separated from the rest, I would always consider the whole protein.
Now, for stability calculations, you can use a range of methods to estimate their free energy change; from "simple" approaches available on-line such as that of the CUPSAT server (http://cupsat.tu-bs.de/) to more complicated ones involving molecular dynamics and MM-PBSA or MM-GBSA calculations. Concerning the dipole moment (whether of the helix or of the whole protein), if you have the pdb2pqr program available, or if you generate a pqr file online (for example at: http://pdb2pqr-1.wustl.edu/pdb2pqr/) from your coordinates, you can use a simple python script (dipole.py) that you can download from: http://www.ysbl.york.ac.uk/~mol/scripts.html<http://www.ysbl.york.ac.uk/%7Emol/scripts.html> The script will tell you the magnitude and orientation of the dipole. It will also produce a bild file that can be read by programs such as Chimera ( http://www.cgl.ucsf.edu/chimera/) to represent the dipole moment vector. Miguel 2008/6/26 Frederico Moraes Ferreira <[EMAIL PROTECTED]>: > Hi everyone, > Has anybody know some program to calculate the dipole moment of helices? > Which relevant parameters should I have to calculate to compare stability of > helices? I would like to compare the stability of different mutations on > helices, but don't know if it makes sense when you take the helix out of the > protein. > Thanks in advance, > Fred > > -- > University of Sao Paulo > School of Medicine > Sao Paulo Brazil > -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens
