Comparative molecular dynamics simulation study of aquaporin Z.
The structural and functional divergence between two 30 ns simulations of aquaporin Z in a solvated membrane, one using the General AMBER force field and the other a modified GROMOS-87 force field, ffgmx, was determined. The protein in the AMBER run displayed water transport activity and typical...
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| Format: | Final Year Project |
| Language: | English |
| Published: |
2009
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| Subjects: | |
| Online Access: | http://hdl.handle.net/10356/16349 |
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| Institution: | Nanyang Technological University |
| Language: | English |
| Summary: | The structural and functional divergence between two 30 ns simulations of aquaporin Z
in a solvated membrane, one using the General AMBER force field and the other a
modified GROMOS-87 force field, ffgmx, was determined. The protein in the AMBER
run displayed water transport activity and typical water-protein interaction. The
simulation using ffgmx, despite an outwardly normal structure, did not have any water
transport activity as a result of channel occlusion. The channel was blocked essentially
permanently at the cytoplasmic end by a deformed loop B, due to a loss of constraining
hydrogen bonds. Reversible and transient constrictions also arise at the selectivity filter
as a result of artificially elevated side chain motion of its constituent residues and loss of
important stabilising Van der Waals contacts – most significant is the aromatic side
chain of Phe-43 whose face becomes perpendicular to the channel axis. These
observations highlighted the deficiencies of the ffgmx/Berger force field combination in
preserving critical hydrophobic contacts and hydrogen bonds in flexible moieties. |
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