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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

Topological analysis of inner cavities and pathways.(a) Representation of the cavities that form the inner tunnel in NP7 (blue) as well as two additional pockets found around the heme (orange and magenta) identified by the MDpocket analysis. (b) Pathways connecting the heme cavity and the bulk solvent in the closed form of NP7.
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f10: Topological analysis of inner cavities and pathways.(a) Representation of the cavities that form the inner tunnel in NP7 (blue) as well as two additional pockets found around the heme (orange and magenta) identified by the MDpocket analysis. (b) Pathways connecting the heme cavity and the bulk solvent in the closed form of NP7.

Mentions: Recently we proposed that the reaction progress for NP7 can be described by a microscopic model which takes into account rebinding of photodissociated ligands from internal cavities that are accessible at room temperature57. The current data indicate that in addition to more remote internal cavities, capable of hosting the ligand for a relatively long time, at least one additional temporary docking site exists in the vicinity of the reaction site at the heme, which modulates sub-nanosecond geminate rebinding. From a structural point of view, this assumption is supported by the topological analysis of the inner cavities present in the snapshots sampled along the MD simulation of the closed form of NP7. Thus,Figure 10a shows the three major cavities that shape the tunnel leading from the heme pocket to the back of the protein59 (shown as magenta isocontour) determined by using the MDpocket tool60, and also confirmed by Implicit Ligand Sampling calculations61. Besides the inner tunnel,Figure 10a shows the presence of two additional pockets around the heme. Residues Ile121, Ile123, Leu135 and Ser137 shape the first pocket (orange isocontour), and the side chains of Glu27, Phe43, Phe45 and Leu139 contribute to the second pocket (blue isocontour). Hence, it can be expected that rebinding of photolyzed CO would occur from a variety of transient docking sites, reflecting the topological distribution of pockets located close to the heme (at around ~9 Å from the heme iron) as well as from inner cavities present at the rear of the protein (at around ~22 Å from the heme iron), which can be visited via the inner tunnel present as a distinctive feature in NP7 compared to other NPs.


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)

Topological analysis of inner cavities and pathways.(a) Representation of the cavities that form the inner tunnel in NP7 (blue) as well as two additional pockets found around the heme (orange and magenta) identified by the MDpocket analysis. (b) Pathways connecting the heme cavity and the bulk solvent in the closed form of NP7.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f10: Topological analysis of inner cavities and pathways.(a) Representation of the cavities that form the inner tunnel in NP7 (blue) as well as two additional pockets found around the heme (orange and magenta) identified by the MDpocket analysis. (b) Pathways connecting the heme cavity and the bulk solvent in the closed form of NP7.
Mentions: Recently we proposed that the reaction progress for NP7 can be described by a microscopic model which takes into account rebinding of photodissociated ligands from internal cavities that are accessible at room temperature57. The current data indicate that in addition to more remote internal cavities, capable of hosting the ligand for a relatively long time, at least one additional temporary docking site exists in the vicinity of the reaction site at the heme, which modulates sub-nanosecond geminate rebinding. From a structural point of view, this assumption is supported by the topological analysis of the inner cavities present in the snapshots sampled along the MD simulation of the closed form of NP7. Thus,Figure 10a shows the three major cavities that shape the tunnel leading from the heme pocket to the back of the protein59 (shown as magenta isocontour) determined by using the MDpocket tool60, and also confirmed by Implicit Ligand Sampling calculations61. Besides the inner tunnel,Figure 10a shows the presence of two additional pockets around the heme. Residues Ile121, Ile123, Leu135 and Ser137 shape the first pocket (orange isocontour), and the side chains of Glu27, Phe43, Phe45 and Leu139 contribute to the second pocket (blue isocontour). Hence, it can be expected that rebinding of photolyzed CO would occur from a variety of transient docking sites, reflecting the topological distribution of pockets located close to the heme (at around ~9 Å from the heme iron) as well as from inner cavities present at the rear of the protein (at around ~22 Å from the heme iron), which can be visited via the inner tunnel present as a distinctive feature in NP7 compared to other NPs.

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