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Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7.

Knipp M, Ogata H, Soavi G, Cerullo G, Allegri A, Abbruzzetti S, Bruno S, Viappiani C, Bidon-Chanal A, Luque FJ - F1000Res (2015)

Bottom Line: However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7.Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route.Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.

View Article: PubMed Central - PubMed

Affiliation: Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, 45470, Germany.

ABSTRACT
Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.

No MeSH data available.


Related in: MedlinePlus

Time (ns) evolution of the estimated area (Å2) of the heme cavity mouth determined from the triangles defined by the Cα atoms of residues His60, Lys66, Phe88 and Ile132.Wild type NP7 in open and closed states is shown as red and black lines; Δ(1-3) variant in open and closed states is shown as blue and green lines.
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sf4: Time (ns) evolution of the estimated area (Å2) of the heme cavity mouth determined from the triangles defined by the Cα atoms of residues His60, Lys66, Phe88 and Ile132.Wild type NP7 in open and closed states is shown as red and black lines; Δ(1-3) variant in open and closed states is shown as blue and green lines.

Mentions: The behavior observed for the open forms of wild type NP7 and its Δ(1-3) variant is highly similar, mainly reflecting significant fluctuations of the A-B loop irrespective of the length of the N-terminus (Figure 7a), which for NP7 fills the region between A-B and G-H loops, thus resembling the arrangement found in the X-ray structures of NP7 (Figure S2). This structural resemblance is reduced in the closed state, because the A-B and G-H loops exhibit larger fluctuations in the wild type protein compared to the Δ(1-3) species (Figure 7b), and this effect is accompanied by the enhanced conformational flexibility of the Leu1-Pro2-Gly3 stretch in NP7, which is in contrast with the more rigid structure adopted by the N-terminus in the Δ(1-3) variant. Interestingly, superposition of the snapshots sampled for wild type and Δ(1-3) proteins reveals a widening of the heme cavity mouth in the wild type protein (Figure 7b), which would suggest a higher probability for the formation of transient pathways that connect the heme cavity with the bulk solvent. This is noted, for instance, in the larger area estimated for the heme cavity mouth for the closed states of the wild type NP7 and its Δ(1-3) variant (Figure S4).


Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7.

Knipp M, Ogata H, Soavi G, Cerullo G, Allegri A, Abbruzzetti S, Bruno S, Viappiani C, Bidon-Chanal A, Luque FJ - F1000Res (2015)

Time (ns) evolution of the estimated area (Å2) of the heme cavity mouth determined from the triangles defined by the Cα atoms of residues His60, Lys66, Phe88 and Ile132.Wild type NP7 in open and closed states is shown as red and black lines; Δ(1-3) variant in open and closed states is shown as blue and green lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4482215&req=5

sf4: Time (ns) evolution of the estimated area (Å2) of the heme cavity mouth determined from the triangles defined by the Cα atoms of residues His60, Lys66, Phe88 and Ile132.Wild type NP7 in open and closed states is shown as red and black lines; Δ(1-3) variant in open and closed states is shown as blue and green lines.
Mentions: The behavior observed for the open forms of wild type NP7 and its Δ(1-3) variant is highly similar, mainly reflecting significant fluctuations of the A-B loop irrespective of the length of the N-terminus (Figure 7a), which for NP7 fills the region between A-B and G-H loops, thus resembling the arrangement found in the X-ray structures of NP7 (Figure S2). This structural resemblance is reduced in the closed state, because the A-B and G-H loops exhibit larger fluctuations in the wild type protein compared to the Δ(1-3) species (Figure 7b), and this effect is accompanied by the enhanced conformational flexibility of the Leu1-Pro2-Gly3 stretch in NP7, which is in contrast with the more rigid structure adopted by the N-terminus in the Δ(1-3) variant. Interestingly, superposition of the snapshots sampled for wild type and Δ(1-3) proteins reveals a widening of the heme cavity mouth in the wild type protein (Figure 7b), which would suggest a higher probability for the formation of transient pathways that connect the heme cavity with the bulk solvent. This is noted, for instance, in the larger area estimated for the heme cavity mouth for the closed states of the wild type NP7 and its Δ(1-3) variant (Figure S4).

Bottom Line: However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7.Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route.Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.

View Article: PubMed Central - PubMed

Affiliation: Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, 45470, Germany.

ABSTRACT
Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.

No MeSH data available.


Related in: MedlinePlus