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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

Representation of the backbone structure of X-ray NP7 structures.(a) Overall fold of NP7. (b) Overall fold of NP7 (green) in comparison to NP2 (blue) (PDB code, 2A3F) and NP4 (orange) (PDB code, 1YWD).
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f1: Representation of the backbone structure of X-ray NP7 structures.(a) Overall fold of NP7. (b) Overall fold of NP7 (green) in comparison to NP2 (blue) (PDB code, 2A3F) and NP4 (orange) (PDB code, 1YWD).

Mentions: The overall fold of NP7 resembles that of other NPs. Eight anti-parallel β-strands (A to H) form a barrel that hosts the heme cofactor including the ligation by the proximal His60 residue. The structural identity reflected by the RMSD values obtained from the comparison of the backbone atoms of two of the isoforms correlates with the amino acid sequence identities (Table 2).Figure 1 displays the overall fold compared to those of NP2 and NP4. The core of the lipocalin fold is well superposed in all cases. The position of the two disulfide bridges, which is a common trait of the NPs, is very similar among all the NPs. The largest differences are found in the A-B, B-C and G-H loops. In detail, the bending of the β-strands (βB and βC) is significantly more similar in the case of NP7 and NP2 compared to NP4. This is also true for the AB-loop. On the other hand, significant differences are found in the spatial arrangement of the G-H loop, which is markedly bent in NP7 compared to NP2 and NP4 (Figure 1).


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)

Representation of the backbone structure of X-ray NP7 structures.(a) Overall fold of NP7. (b) Overall fold of NP7 (green) in comparison to NP2 (blue) (PDB code, 2A3F) and NP4 (orange) (PDB code, 1YWD).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Representation of the backbone structure of X-ray NP7 structures.(a) Overall fold of NP7. (b) Overall fold of NP7 (green) in comparison to NP2 (blue) (PDB code, 2A3F) and NP4 (orange) (PDB code, 1YWD).
Mentions: The overall fold of NP7 resembles that of other NPs. Eight anti-parallel β-strands (A to H) form a barrel that hosts the heme cofactor including the ligation by the proximal His60 residue. The structural identity reflected by the RMSD values obtained from the comparison of the backbone atoms of two of the isoforms correlates with the amino acid sequence identities (Table 2).Figure 1 displays the overall fold compared to those of NP2 and NP4. The core of the lipocalin fold is well superposed in all cases. The position of the two disulfide bridges, which is a common trait of the NPs, is very similar among all the NPs. The largest differences are found in the A-B, B-C and G-H loops. In detail, the bending of the β-strands (βB and βC) is significantly more similar in the case of NP7 and NP2 compared to NP4. This is also true for the AB-loop. On the other hand, significant differences are found in the spatial arrangement of the G-H loop, which is markedly bent in NP7 compared to NP2 and NP4 (Figure 1).

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