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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

Hemeb nomenclature and heme orientation inside the pocket of NP7.The heme pocket of NP7 is indicated by the three green circles corresponding to the position of the three aliphatic side-chains pointing from the top of the distal pocket onto the heme plane. The two possible heme orientations are indicated asA andB.
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f3: Hemeb nomenclature and heme orientation inside the pocket of NP7.The heme pocket of NP7 is indicated by the three green circles corresponding to the position of the three aliphatic side-chains pointing from the top of the distal pocket onto the heme plane. The two possible heme orientations are indicated asA andB.

Mentions: The presence of Glu27 residue in the heme pocket of NP7 is unique among NPs36,37. Upon homology modeling it was noticed that the Glu27 carboxylate must somewhat interfere with the hydrophobic site of the cofactor, i.e., its vinyl and methyl substituents. OnlyA orientation is observed in NP78,30, whereasB orientation is favored in NP238,39 (Figure 3). Interestingly, the mutant that converts Glu27 to Val, i.e. the residue found in all the other NPs (NP7(E27V)), demonstrated that the heme orientation was reversed fromA toB, whereas the replacement of Glu27 by Gln, NP7(E27Q), did not change the heme orientation compared to the wild type, and replacement of Val24 by Glu in NP2, NP2(V24E), resulted in theB →A reorientation of the cofactor30.


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)

Hemeb nomenclature and heme orientation inside the pocket of NP7.The heme pocket of NP7 is indicated by the three green circles corresponding to the position of the three aliphatic side-chains pointing from the top of the distal pocket onto the heme plane. The two possible heme orientations are indicated asA andB.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Hemeb nomenclature and heme orientation inside the pocket of NP7.The heme pocket of NP7 is indicated by the three green circles corresponding to the position of the three aliphatic side-chains pointing from the top of the distal pocket onto the heme plane. The two possible heme orientations are indicated asA andB.
Mentions: The presence of Glu27 residue in the heme pocket of NP7 is unique among NPs36,37. Upon homology modeling it was noticed that the Glu27 carboxylate must somewhat interfere with the hydrophobic site of the cofactor, i.e., its vinyl and methyl substituents. OnlyA orientation is observed in NP78,30, whereasB orientation is favored in NP238,39 (Figure 3). Interestingly, the mutant that converts Glu27 to Val, i.e. the residue found in all the other NPs (NP7(E27V)), demonstrated that the heme orientation was reversed fromA toB, whereas the replacement of Glu27 by Gln, NP7(E27Q), did not change the heme orientation compared to the wild type, and replacement of Val24 by Glu in NP2, NP2(V24E), resulted in theB →A reorientation of the cofactor30.

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