**************** The 6th., Lab Seminar ****************************

Date: Thu, July 30, 2009  PM 2:30-

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

Speaker: Susumu Otsuki

Title: "Nitric Oxide Dynamics in Truncated Hemoglobin: Docking Sites, Migration
Pathways, and Vibrational Spectroscopy from Molecular Dynamics
Simulations"
Sabyashachi Mishra and Markus Meuwly,"Nitric Oxide Dynamics in
Truncated Hemoglobin: Docking Sites, Migration Pathways, and Vibrational
Spectroscopy from Molecular Dynamics Simulations",Biophysical
Journal Volume 96 March 2009 2105.2118


Atomistic simulations of nitric oxide (NO) dynamics and migration in the
trHbN of Mycobacterium tuberculosis are reported. From extensive
molecular dynamics simulations (48 ns in total), the structural and
energeticproperties of the ligand docking sites in the protein have been
characterized and a connectivity network between the ligand docking sites 
has been built. Several novel migration and exit pathways are found and are 
analyzed in detail. The interplay between a hydrogen-bonding network involving 
residues Tyr33 and Gln58 and the bound O2 ligand is discussed and the role 
of Phe62 residue in ligand migration is examined. It is found that Phe62 
is directly involved in controlling ligand migration. This is reminiscent 
of His64 in myoglobin, which also plays a central role in CO migration pathways. 
Finally, infrared spectra of the NO molecule in different ligand docking 
sites of the protein are calculated. The pocket-specific spectra are typically 
blue-shifted by 5.10 cm＾-1, which should be detectable in future spectroscopic 
experiments.

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