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
✍ Scribed by Minoru Saito; Isao Okazaki
- Publisher
- John Wiley and Sons
- Year
- 2007
- Tongue
- English
- Weight
- 550 KB
- Volume
- 28
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
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 deviations from the initial X‐ray structure (an oxy T‐state hemoglobin with PDB code: 1GZX) and root‐mean‐square fluctuations around the average structure from the simulation trajectories. The four subunits (α~1~, α~2~, β~1~, and β~2~) 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 α~1~β~1~ and α~2~β~2~ 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 dimers (α~1~β~1~ and α~2~β~2~) 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 a few tens of nanoseconds. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007