This article is part of the supplement: Proceedings of the 6th International Conference of the Brazilian Association for Bioinformatics and Computational Biology (X-meeting 2010)

Open Access Proceedings

Molecular dynamics study of the archaeal aquaporin AqpM

Raul Araya-Secchi12*, JA Garate13, David S Holmes24 and Tomas Perez-Acle14

Author Affiliations

1 Computational Biology Laboratory, Centro de Modelamiento Matematico, Facultad de Ciencias Fisicas y Matematicas, Universidad de Chile, Santiago, Chile

2 Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile

3 School of Chemical and Bioprocess Engineering, University College Dublin, Dublin 4, Ireland

4 Fundacion Ciencia para la Vida, Santiago, Chile

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BMC Genomics 2011, 12(Suppl 4):S8  doi:10.1186/1471-2164-12-S4-S8

Published: 22 December 2011

Additional files

Additional file 1:

Cα-RMSD and Cα-RMSF of the simulated AqpM tetramer. This figure contains two panels: (a) Time evolution of Cα-RMSD for each AqpM monomer obtained from the 20ns production run. The last conformation obtained from the minimization-relaxation procedure (see methods) was used as reference structure for the measurement. (b) Cα-RMSF for each AqpM monomer obtained from the 20ns production run. Each colored solid line represents a monomer. The dashed black line represents the average RMSF. The solid lines below the curves indicate secondary structure elements of AqpM ( blue = TM-helix; orange = loops; green = loops B and E; red = NPA motifs; black = helix B and E). Light blue arrows indicate residues that comprise the selectivity filter (S.F) of AqpM; red arrows indicate hydrophobic residues that line the AqpM pore.

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