protein unfolding no increase in conf energy

From: Odysseas Axillews (
Date: Wed May 12 2010 - 05:25:24 CDT

Dear Sir,

My name is Pentas Stefanos I am a phd student at the Aristoteles University of Thessaloniki and I am working on a project on a mixed urea and heat induced deneturation of a protein (a1 domain of von willebrand) i have achieved  a full deneturation of the protein in 30 ns in 600 K. I mean the helical and beta sheet content is minimal and the total structured is complete disrupted. I am measuring the configuration energy and the nonbonded energy of the protein (van der Waals and electrostatic). I expected to see a considerable increase in the configurational energy when the protein is denatured (as the a helix and the beta sheet a structures of minimal energy). I also expected to see  a decrease in nonbonded energy when the protein energy is denatured because the different parts of the protein are at a great distance from each other in comparison to the crystal structure. However, the configurational energy and the nonbonded energy remain the same during
 the whole time of the denaturation. There is only a little fluctuation of the values (5%) . Is this a little bit strange? I have measured the energies with the namd energy module. The same energies (only a very little fluctuation of the values) appear in the log file of the denaturation which the namd produces.How can this result be interpreted?  I would really be grateful if you could help me with this problem.

Yours sincerely

Stefanos Pentas

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