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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

Head-to-tail arrangement of NP7 in the crystal lattice.(a) Arrangement of molecules in the crystal lattice of NP7. (b) Crystal contact between two neighboring molecules in the NP7 crystal. (c) The electrostatic potential of NP7. The red and blue colors show the negative and positive potentials, respectively.
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f2: Head-to-tail arrangement of NP7 in the crystal lattice.(a) Arrangement of molecules in the crystal lattice of NP7. (b) Crystal contact between two neighboring molecules in the NP7 crystal. (c) The electrostatic potential of NP7. The red and blue colors show the negative and positive potentials, respectively.

Mentions: One of the most interesting features of NP7 is its ability to bind to negatively charged membranes. The crystal structures demonstrate the extensive clustering of Lys side-chains at the protein surface opposite the heme pocket that accomplishes the strong protein-membrane interaction. On the other hand, the side of the heme mouth has a negative charge potential leading to a total bipolar charge distribution. It was previously noticed that NP7 tends to aggregate at elevated concentrations8,35, which can be explained by a charge stabilized aggregation process. X-ray crystallography indeed supports such a head-to-tail interaction, which involves a variety of salt bridges (Figure S1), leading to chain-like arrangement in the crystal lattice (Figure 2a).


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)

Head-to-tail arrangement of NP7 in the crystal lattice.(a) Arrangement of molecules in the crystal lattice of NP7. (b) Crystal contact between two neighboring molecules in the NP7 crystal. (c) The electrostatic potential of NP7. The red and blue colors show the negative and positive potentials, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Head-to-tail arrangement of NP7 in the crystal lattice.(a) Arrangement of molecules in the crystal lattice of NP7. (b) Crystal contact between two neighboring molecules in the NP7 crystal. (c) The electrostatic potential of NP7. The red and blue colors show the negative and positive potentials, respectively.
Mentions: One of the most interesting features of NP7 is its ability to bind to negatively charged membranes. The crystal structures demonstrate the extensive clustering of Lys side-chains at the protein surface opposite the heme pocket that accomplishes the strong protein-membrane interaction. On the other hand, the side of the heme mouth has a negative charge potential leading to a total bipolar charge distribution. It was previously noticed that NP7 tends to aggregate at elevated concentrations8,35, which can be explained by a charge stabilized aggregation process. X-ray crystallography indeed supports such a head-to-tail interaction, which involves a variety of salt bridges (Figure S1), leading to chain-like arrangement in the crystal lattice (Figure 2a).

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