**************** The 9th., Lab Seminar *****************

Date: Tue, September 5, 2006  PM 1:30-

Place: No.616 Seminar room
　　　　　　 Graduate School of Information Science

Speaker: Chiharu Iwahashi

Title: The barrier for heme-protein separation estimated by non-equilibrium 
molecular dynamics simulations
O.Edholm, P.I.Ohlsson, M.L.Smith, J.Paul
Chemical Physics Letters 291 (1998) 501-508.

Abstract:
 In heme-containing proteins the heme group is usually non-covalently bound
in a pocket. Molecular dynamics (MD) simulations have been performed to 
estimate the barrier height for heme-protein separation. In simulations of
myoglobin dissolved in water, a force has been applied to pull the heme out
of the binding pocket. With forces above 0.5 nN, the heme group is easily
pulled out of the pocket in times of the order of picoseconds. With weaker
forces, heme release becomes too slow to be monitored in an MD simulation
covering a couple of hundred picoseconds. These results are consistent with
a free energy barrier to heme release of about 100 kJ/mol. The results show
that the main energetic change that occurs during the release is a conversion
of these heme/protein Lennard-Jones energy into heme/water Lennard-Jones
energy. The release is essentially barrierless in energy indicationg that 
the main part of the barrier is entropic.

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