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Functional analysis of Ms cyt bd -II from MD simulations. ( A ) MD simulations of putative menaquinone binding sites. MQ N interacts with E268 C and H250 C , and surrounding nonspecific residues (M254 C , H257 C , I303 C , A304 C ). MQ C interacts with the propionates of heme b 595 and E382 C , and with surrounding nonspecific residues (Q24 C , A27 C , F28 C , Y417 C ). ( B ) Dynamics of modeled menaquinol (MQ) within the Q-loop. Both MQ C and MQ N remain close ( ca. 4 to 6 Å) to heme b 595 , but MQ N forms a more stable binding pose relative to MQ C . Bottom : calculated binding energies and oxidation potentials for MQ N and MQ C from MD simulations ( SI Appendix , Extended Methods ). ( C ) MD sampling of the inward (+60°, blue) and outward (−60°, red) conformation of F117 C , with histograms of the dihedral angle (N-Ca-Cb-Cg) based on 500 ns MD simulations of each state. ( D ) Putative <t>O</t> <t>2</t> pathway along the conserved residues W62 B , F21 B , and F180 B . Another putative pathway forms along W70 B , W71 B , and W275 B . The O 2 tunnels are depicted in blue and red, and correspond to the inward and outward orientations of F117 C , respectively.
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Functional analysis of Ms cyt bd -II from MD simulations. ( A ) MD simulations of putative menaquinone binding sites. MQ N interacts with E268 C and H250 C , and surrounding nonspecific residues (M254 C , H257 C , I303 C , A304 C ). MQ C interacts with the propionates of heme b 595 and E382 C , and with surrounding nonspecific residues (Q24 C , A27 C , F28 C , Y417 C ). ( B ) Dynamics of modeled menaquinol (MQ) within the Q-loop. Both MQ C and MQ N remain close ( ca. 4 to 6 Å) to heme b 595 , but MQ N forms a more stable binding pose relative to MQ C . Bottom : calculated binding energies and oxidation potentials for MQ N and MQ C from MD simulations ( SI Appendix , Extended Methods ). ( C ) MD sampling of the inward (+60°, blue) and outward (−60°, red) conformation of F117 C , with histograms of the dihedral angle (N-Ca-Cb-Cg) based on 500 ns MD simulations of each state. ( D ) Putative <t>O</t> <t>2</t> pathway along the conserved residues W62 B , F21 B , and F180 B . Another putative pathway forms along W70 B , W71 B , and W275 B . The O 2 tunnels are depicted in blue and red, and correspond to the inward and outward orientations of F117 C , respectively.
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Functional analysis of Ms cyt bd -II from MD simulations. ( A ) MD simulations of putative menaquinone binding sites. MQ N interacts with E268 C and H250 C , and surrounding nonspecific residues (M254 C , H257 C , I303 C , A304 C ). MQ C interacts with the propionates of heme b 595 and E382 C , and with surrounding nonspecific residues (Q24 C , A27 C , F28 C , Y417 C ). ( B ) Dynamics of modeled menaquinol (MQ) within the Q-loop. Both MQ C and MQ N remain close ( ca. 4 to 6 Å) to heme b 595 , but MQ N forms a more stable binding pose relative to MQ C . Bottom : calculated binding energies and oxidation potentials for MQ N and MQ C from MD simulations ( SI Appendix , Extended Methods ). ( C ) MD sampling of the inward (+60°, blue) and outward (−60°, red) conformation of F117 C , with histograms of the dihedral angle (N-Ca-Cb-Cg) based on 500 ns MD simulations of each state. ( D ) Putative <t>O</t> <t>2</t> pathway along the conserved residues W62 B , F21 B , and F180 B . Another putative pathway forms along W70 B , W71 B , and W275 B . The O 2 tunnels are depicted in blue and red, and correspond to the inward and outward orientations of F117 C , respectively.
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Functional analysis of Ms cyt bd -II from MD simulations. ( A ) MD simulations of putative menaquinone binding sites. MQ N interacts with E268 C and H250 C , and surrounding nonspecific residues (M254 C , H257 C , I303 C , A304 C ). MQ C interacts with the propionates of heme b 595 and E382 C , and with surrounding nonspecific residues (Q24 C , A27 C , F28 C , Y417 C ). ( B ) Dynamics of modeled menaquinol (MQ) within the Q-loop. Both MQ C and MQ N remain close ( ca. 4 to 6 Å) to heme b 595 , but MQ N forms a more stable binding pose relative to MQ C . Bottom : calculated binding energies and oxidation potentials for MQ N and MQ C from MD simulations ( SI Appendix , Extended Methods ). ( C ) MD sampling of the inward (+60°, blue) and outward (−60°, red) conformation of F117 C , with histograms of the dihedral angle (N-Ca-Cb-Cg) based on 500 ns MD simulations of each state. ( D ) Putative <t>O</t> <t>2</t> pathway along the conserved residues W62 B , F21 B , and F180 B . Another putative pathway forms along W70 B , W71 B , and W275 B . The O 2 tunnels are depicted in blue and red, and correspond to the inward and outward orientations of F117 C , respectively.
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Functional analysis of Ms cyt bd -II from MD simulations. ( A ) MD simulations of putative menaquinone binding sites. MQ N interacts with E268 C and H250 C , and surrounding nonspecific residues (M254 C , H257 C , I303 C , A304 C ). MQ C interacts with the propionates of heme b 595 and E382 C , and with surrounding nonspecific residues (Q24 C , A27 C , F28 C , Y417 C ). ( B ) Dynamics of modeled menaquinol (MQ) within the Q-loop. Both MQ C and MQ N remain close ( ca. 4 to 6 Å) to heme b 595 , but MQ N forms a more stable binding pose relative to MQ C . Bottom : calculated binding energies and oxidation potentials for MQ N and MQ C from MD simulations ( SI Appendix , Extended Methods ). ( C ) MD sampling of the inward (+60°, blue) and outward (−60°, red) conformation of F117 C , with histograms of the dihedral angle (N-Ca-Cb-Cg) based on 500 ns MD simulations of each state. ( D ) Putative O 2 pathway along the conserved residues W62 B , F21 B , and F180 B . Another putative pathway forms along W70 B , W71 B , and W275 B . The O 2 tunnels are depicted in blue and red, and correspond to the inward and outward orientations of F117 C , respectively.

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: The Mycobacterium smegmatis bd -II terminal oxidase employs a carboxylate shift mechanism

doi: 10.1073/pnas.2515348123

Figure Lengend Snippet: Functional analysis of Ms cyt bd -II from MD simulations. ( A ) MD simulations of putative menaquinone binding sites. MQ N interacts with E268 C and H250 C , and surrounding nonspecific residues (M254 C , H257 C , I303 C , A304 C ). MQ C interacts with the propionates of heme b 595 and E382 C , and with surrounding nonspecific residues (Q24 C , A27 C , F28 C , Y417 C ). ( B ) Dynamics of modeled menaquinol (MQ) within the Q-loop. Both MQ C and MQ N remain close ( ca. 4 to 6 Å) to heme b 595 , but MQ N forms a more stable binding pose relative to MQ C . Bottom : calculated binding energies and oxidation potentials for MQ N and MQ C from MD simulations ( SI Appendix , Extended Methods ). ( C ) MD sampling of the inward (+60°, blue) and outward (−60°, red) conformation of F117 C , with histograms of the dihedral angle (N-Ca-Cb-Cg) based on 500 ns MD simulations of each state. ( D ) Putative O 2 pathway along the conserved residues W62 B , F21 B , and F180 B . Another putative pathway forms along W70 B , W71 B , and W275 B . The O 2 tunnels are depicted in blue and red, and correspond to the inward and outward orientations of F117 C , respectively.

Article Snippet: The catalytic activity of cyt bd -II was assessed using an O 2 electrode (Hansatech instruments) with reduced 2,3-dimethyl-[1,4]-naphthoquinone (DMNQ) as the substrate.

Techniques: Functional Assay, Binding Assay, Sampling