ArticleEuropean biophysics journal : EBJ2004
Homology modelling and molecular dynamics simulations: comparative studies of human aquaporin-1.
Article in European biophysics journal : EBJ, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Modeling of Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Molecular Dynamics Simulations of Mite Aquaporin DerfAQP1 from the Dust MiteBioMed research international · 2020Article
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- Single-channel permeability and glycerol affinity of human aquaglyceroporin AQP3.Biochimica et biophysica acta. Biomembranes · 2019Article
- Molecular dynamics of water in the neighborhood of aquaporins.European biophysics journal : EBJ · 2013Review
- Construction and validation of a homology model of the human voltage-gated proton channel hHV1.The Journal of general physiology · 2013Article
- Mercury inhibits the L170C mutant of aquaporin Z by making waters clog the water channel.Biophysical chemistry · 2012Article
- Plant aquaporin selectivity: where transport assays, computer simulations and physiology meet.Cellular and molecular life sciences : CMLS · 2009Review
- An ion gating mechanism of gastric H,K-ATPase based on molecular dynamics simulations.Biophysical journal · 2008Article
- Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF.Biophysical journal · 2008Article
- Article
- Homology modeling of major intrinsic proteins in rice, maize and Arabidopsis: comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters.BMC structural biology · 2007Article
- Molecular dynamics simulations of proteins in lipid bilayers.Current opinion in structural biology · 2005Review
- The fast gating mechanism in ClC-0 channels.Biophysical journal · 2005Article
- A gating mechanism proposed from a simulation of a human alpha7 nicotinic acetylcholine receptor.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: toward an understanding of Kir channel gating.Biophysical journal · 2005Article
- Homology modeling and molecular dynamics simulations of transmembrane domain structure of human neuronal nicotinic acetylcholine receptor.Biophysical journal · 2005Article
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2 authors.
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Abstract
The structures of the mammalian water transport protein Aqp1 and of its bacterial homologue GlpF enables us to test whether homology models can be used to explore relationships between structure, dynamics and function in mammalian transport proteins. Molecular dynamics simulations (totalling almost 40 ns) were performed starting from: the X-ray structure of Aqp1; a homology model of Aqp1 based on the GlpF structure; and intermediate resolution structures of Aqp1 derived from electron microscopy. Comparisons of protein RMSDs vs. time suggest that the homology models are of comparable conformational stability to the X-ray structure, whereas the intermediate resolution structures exhibit significant conformation drift. For simulations based on the X-ray structure and on homology models, the flexibility profile vs. residue number correlates well with the crystallographic B-values for each residue. In the simulations based on intermediate resolution structures, mobility of the highly conserved NPA loops is substantially higher than in the simulations based on the X-ray structure or the homology models. Pore radius profiles remained relatively constant in the X-ray and homology model simulations but showed substantial fluctuations (reflecting the higher NPA loop mobility) in the intermediate resolution simulations. The orientation of the dipoles of water molecules within the pore is of key importance in maintaining low proton permeability through Aqp1. This property seems to be quite robust to the starting model used in the simulation. These simulations suggest that homology models based on bacterial homologues may be used to derive functionally relevant information on the structural dynamics of mammalian transport proteins.
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