Molecular dynamics study of the archaeal aquaporin AqpM

Raul Araya-Secchi, J. A. Garate, David S. Holmes, Tomas Perez-Acle

Resultado de la investigación: Article

8 Citas (Scopus)

Resumen

Background: Aquaporins are a large family of transmembrane channel proteins that are present throughout all domains of life and are implicated in human disorders. These channels, allow the passive but selective movement of water and other small neutral solutes across cell membranes. Aquaporins have been classified into two sub-families: i) strict aquaporins that only allow the passage of water and ii) the less selective aquaglyceroporins that transport water and other neutral solutes, such as glycerol, CO 2 or urea. Recently, the identification and characterization of a number of archaeal and bacterial aquaporins suggested the existence of a third sub-family; one that is neither a strict aquaporin nor an aquaglyceroporin. The function and phylogeny of this third family is still a matter of debate.Results: Twenty nanosecond molecular dynamics (MD) simulation of a fully hydrated tetramer of AqpM embedded in a lipid bilayer permitted predictions to be made of key biophysical parameters including: single channel osmotic permeability constant (p f), single channel diffusive permeability constant (p d), channel radius, potential water occupancy of the channel and water orientation inside the pore. These properties were compared with those of well characterized representatives of the two main aquaporin sub-families. Results show that changes in the amino acid composition of the aromatic/arginine region affect the size and polarity of the selectivity filter (SF) and could help explain the difference in water permeability between aquaporins. In addition, MD simulation results suggest that AqpM combines characteristics of strict aquaporins, such as the narrow SF and channel radius, with those of aquaglyceroporins, such as a more hydrophobic and less polar SF.Conclusions: MD simulations of AqpM extend previous evidence that this archaeal aquaporin exhibits hybrid features intermediate between the two known aquaporin sub-families, supporting the idea that it may constitute a member of a novel class of aquaporins.

Idioma originalEnglish
Número de artículoS8
PublicaciónBMC Genomics
Volumen12
N.ºSUPPL. 4
DOI
EstadoPublished - 22 dic 2011

Huella dactilar

Aquaporins
Molecular Dynamics Simulation
Aquaglyceroporins
Permeability
Water
Water Movements
Aromatic Amino Acids
Lipid Bilayers
Carbon Monoxide
Phylogeny
Glycerol
Arginine
Urea

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Citar esto

Araya-Secchi, R., Garate, J. A., Holmes, D. S., & Perez-Acle, T. (2011). Molecular dynamics study of the archaeal aquaporin AqpM. BMC Genomics, 12(SUPPL. 4), [S8]. https://doi.org/10.1186/1471-2164-12-S4-S8
Araya-Secchi, Raul ; Garate, J. A. ; Holmes, David S. ; Perez-Acle, Tomas. / Molecular dynamics study of the archaeal aquaporin AqpM. En: BMC Genomics. 2011 ; Vol. 12, N.º SUPPL. 4.
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abstract = "Background: Aquaporins are a large family of transmembrane channel proteins that are present throughout all domains of life and are implicated in human disorders. These channels, allow the passive but selective movement of water and other small neutral solutes across cell membranes. Aquaporins have been classified into two sub-families: i) strict aquaporins that only allow the passage of water and ii) the less selective aquaglyceroporins that transport water and other neutral solutes, such as glycerol, CO 2 or urea. Recently, the identification and characterization of a number of archaeal and bacterial aquaporins suggested the existence of a third sub-family; one that is neither a strict aquaporin nor an aquaglyceroporin. The function and phylogeny of this third family is still a matter of debate.Results: Twenty nanosecond molecular dynamics (MD) simulation of a fully hydrated tetramer of AqpM embedded in a lipid bilayer permitted predictions to be made of key biophysical parameters including: single channel osmotic permeability constant (p f), single channel diffusive permeability constant (p d), channel radius, potential water occupancy of the channel and water orientation inside the pore. These properties were compared with those of well characterized representatives of the two main aquaporin sub-families. Results show that changes in the amino acid composition of the aromatic/arginine region affect the size and polarity of the selectivity filter (SF) and could help explain the difference in water permeability between aquaporins. In addition, MD simulation results suggest that AqpM combines characteristics of strict aquaporins, such as the narrow SF and channel radius, with those of aquaglyceroporins, such as a more hydrophobic and less polar SF.Conclusions: MD simulations of AqpM extend previous evidence that this archaeal aquaporin exhibits hybrid features intermediate between the two known aquaporin sub-families, supporting the idea that it may constitute a member of a novel class of aquaporins.",
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Araya-Secchi, R, Garate, JA, Holmes, DS & Perez-Acle, T 2011, 'Molecular dynamics study of the archaeal aquaporin AqpM', BMC Genomics, vol. 12, n.º SUPPL. 4, S8. https://doi.org/10.1186/1471-2164-12-S4-S8

Molecular dynamics study of the archaeal aquaporin AqpM. / Araya-Secchi, Raul; Garate, J. A.; Holmes, David S.; Perez-Acle, Tomas.

En: BMC Genomics, Vol. 12, N.º SUPPL. 4, S8, 22.12.2011.

Resultado de la investigación: Article

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AB - Background: Aquaporins are a large family of transmembrane channel proteins that are present throughout all domains of life and are implicated in human disorders. These channels, allow the passive but selective movement of water and other small neutral solutes across cell membranes. Aquaporins have been classified into two sub-families: i) strict aquaporins that only allow the passage of water and ii) the less selective aquaglyceroporins that transport water and other neutral solutes, such as glycerol, CO 2 or urea. Recently, the identification and characterization of a number of archaeal and bacterial aquaporins suggested the existence of a third sub-family; one that is neither a strict aquaporin nor an aquaglyceroporin. The function and phylogeny of this third family is still a matter of debate.Results: Twenty nanosecond molecular dynamics (MD) simulation of a fully hydrated tetramer of AqpM embedded in a lipid bilayer permitted predictions to be made of key biophysical parameters including: single channel osmotic permeability constant (p f), single channel diffusive permeability constant (p d), channel radius, potential water occupancy of the channel and water orientation inside the pore. These properties were compared with those of well characterized representatives of the two main aquaporin sub-families. Results show that changes in the amino acid composition of the aromatic/arginine region affect the size and polarity of the selectivity filter (SF) and could help explain the difference in water permeability between aquaporins. In addition, MD simulation results suggest that AqpM combines characteristics of strict aquaporins, such as the narrow SF and channel radius, with those of aquaglyceroporins, such as a more hydrophobic and less polar SF.Conclusions: MD simulations of AqpM extend previous evidence that this archaeal aquaporin exhibits hybrid features intermediate between the two known aquaporin sub-families, supporting the idea that it may constitute a member of a novel class of aquaporins.

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Araya-Secchi R, Garate JA, Holmes DS, Perez-Acle T. Molecular dynamics study of the archaeal aquaporin AqpM. BMC Genomics. 2011 dic 22;12(SUPPL. 4). S8. https://doi.org/10.1186/1471-2164-12-S4-S8