**************** The 7th., Lab Seminar ****************************

Date: Mon, June 18, 2007  PM 1:30-

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

Speaker: Iwahashi Chiharu

Title: A 45-ns Molecular Dynamics Simulation of Hemoglobin in Water by 
Vectorizing and Parallelizing COSMOS90 on the Earth Simulator: 
Dynamics of Tertiary and Quaternary Structures

Abstract:
 Molecular dynamics (MD) simulations of human adult hemoglobin (HbA) were 
carried out for 45 ns in water with all degrees of freedom including bond 
stretching and without any artificial constraints. To perform such 
large-scale simulations, one of the authors (M.S.) accelerated his own 
software COSMOS90 on the Earth Simulator by vectorization and parallelization. 
The dynamical features of HbA were investigated by evaluating root-mean-square 
fluctuations around the average structure from the simulation trajectories. 
The four subunits (α1, α2, β1, and β2) of HbA maintained structures close
 to their respective X-ray structures during the simulations even though no 
constraints were applied to HbA in the simulations. Dimers α1β1 and α2β2 
also maintained structures close to their respective X-ray structures while 
they moved relative to each other like two stacks of dumbbells. 
The distance between the two dimmers (α1β1 and α2β2) increased by 2 Å 
(7.4％) in the initial 15 ns and stably fluctuated at the distance with the 
standard deviation 0.2 Å. The relative orientation of the two dimers 
fluctuated between the initial X-ray angle -100° and about -105° with 
intervals of few tens of nanoseconds.

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