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Ligand uptake in Mycobacterium tuberculosis truncated hemoglobins is controlled by both internal tunnels and active site water molecules.

Boron I, Bustamante JP, Davidge KS, Singh S, Bowman LA, Tinajero-Trejo M, Carballal S, Radi R, Poole RK, Dikshit K, Estrin DA, Marti MA, Boechi L - F1000Res (2015)

Bottom Line: In order to investigate the differences between these proteins, we performed experimental kinetic measurements, (•)NO decomposition, as well as molecular dynamics simulations of the wild type Mt-trHbN and two mutants, VG8F and VG8W.These mutations introduce modifications in both tunnel topologies and affect the incoming ligand capacity to displace retained water molecules at the active site.We found that a single mutation allows Mt-trHbN to acquire ligand migration rates comparable to those observed for Mt-trHbO, confirming that ligand migration is regulated by the internal tunnel architecture as well as by water molecules stabilized in the active site.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina.

ABSTRACT
Mycobacterium tuberculosis, the causative agent of human tuberculosis, has two proteins belonging to the truncated hemoglobin (trHb) family. Mt-trHbN presents well-defined internal hydrophobic tunnels that allow O 2 and (•)NO to migrate easily from the solvent to the active site, whereas Mt-trHbO possesses tunnels that are partially blocked by a few bulky residues, particularly a tryptophan at position G8. Differential ligand migration rates allow Mt-trHbN to detoxify (•)NO, a crucial step for pathogen survival once under attack by the immune system, much more efficiently than Mt-trHbO. In order to investigate the differences between these proteins, we performed experimental kinetic measurements, (•)NO decomposition, as well as molecular dynamics simulations of the wild type Mt-trHbN and two mutants, VG8F and VG8W. These mutations introduce modifications in both tunnel topologies and affect the incoming ligand capacity to displace retained water molecules at the active site. We found that a single mutation allows Mt-trHbN to acquire ligand migration rates comparable to those observed for Mt-trHbO, confirming that ligand migration is regulated by the internal tunnel architecture as well as by water molecules stabilized in the active site.

No MeSH data available.


Related in: MedlinePlus

Root Mean Square Deviation during MD simulations for all the Mt-trHbN studied: wild type (green), VG8F (orange) and VG8W (violet).
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SF1: Root Mean Square Deviation during MD simulations for all the Mt-trHbN studied: wild type (green), VG8F (orange) and VG8W (violet).

Mentions: In silico mutant proteins were built by using tLEaP module of AMBER12 package21, and underwent the same protocol used for wild type protein. Root Mean Square Deviation (RMSD) was used as structure stability controls. All structures were observed to be stables during the time scale of the simulation (Figure S1).


Ligand uptake in Mycobacterium tuberculosis truncated hemoglobins is controlled by both internal tunnels and active site water molecules.

Boron I, Bustamante JP, Davidge KS, Singh S, Bowman LA, Tinajero-Trejo M, Carballal S, Radi R, Poole RK, Dikshit K, Estrin DA, Marti MA, Boechi L - F1000Res (2015)

Root Mean Square Deviation during MD simulations for all the Mt-trHbN studied: wild type (green), VG8F (orange) and VG8W (violet).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591903&req=5

SF1: Root Mean Square Deviation during MD simulations for all the Mt-trHbN studied: wild type (green), VG8F (orange) and VG8W (violet).
Mentions: In silico mutant proteins were built by using tLEaP module of AMBER12 package21, and underwent the same protocol used for wild type protein. Root Mean Square Deviation (RMSD) was used as structure stability controls. All structures were observed to be stables during the time scale of the simulation (Figure S1).

Bottom Line: In order to investigate the differences between these proteins, we performed experimental kinetic measurements, (•)NO decomposition, as well as molecular dynamics simulations of the wild type Mt-trHbN and two mutants, VG8F and VG8W.These mutations introduce modifications in both tunnel topologies and affect the incoming ligand capacity to displace retained water molecules at the active site.We found that a single mutation allows Mt-trHbN to acquire ligand migration rates comparable to those observed for Mt-trHbO, confirming that ligand migration is regulated by the internal tunnel architecture as well as by water molecules stabilized in the active site.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina.

ABSTRACT
Mycobacterium tuberculosis, the causative agent of human tuberculosis, has two proteins belonging to the truncated hemoglobin (trHb) family. Mt-trHbN presents well-defined internal hydrophobic tunnels that allow O 2 and (•)NO to migrate easily from the solvent to the active site, whereas Mt-trHbO possesses tunnels that are partially blocked by a few bulky residues, particularly a tryptophan at position G8. Differential ligand migration rates allow Mt-trHbN to detoxify (•)NO, a crucial step for pathogen survival once under attack by the immune system, much more efficiently than Mt-trHbO. In order to investigate the differences between these proteins, we performed experimental kinetic measurements, (•)NO decomposition, as well as molecular dynamics simulations of the wild type Mt-trHbN and two mutants, VG8F and VG8W. These mutations introduce modifications in both tunnel topologies and affect the incoming ligand capacity to displace retained water molecules at the active site. We found that a single mutation allows Mt-trHbN to acquire ligand migration rates comparable to those observed for Mt-trHbO, confirming that ligand migration is regulated by the internal tunnel architecture as well as by water molecules stabilized in the active site.

No MeSH data available.


Related in: MedlinePlus