2006
DOI: 10.1002/prot.21004
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Ligand‐induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin‐N

Abstract: Mycobacterium tuberculosis, the causative agent of human tuberculosis, is forced into latency by nitric oxide produced by macrophages during infection. In response to nitrosative stress M. tuberculosis has evolved a defense mechanism that relies on the oxygenated form of "truncated hemoglobin" N (trHbN), formally acting as NO-dioxygenase, yielding the harmless nitrate ion. X-ray crystal structures have shown that trHbN hosts a two-branched protein matrix tunnel system, proposed to control diatomic ligand migra… Show more

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Cited by 97 publications
(171 citation statements)
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References 28 publications
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“…A total of 40 independent perturbations were performed. This approach was used in a variety of studies such as ligand entry, escape, dynamic control of tunnel opening, and various mutagenesis studies, yielding results that are in excellent agreement with the experimentally determined rates (42)(43)(44)(45)50). Because the reaction coordinate involves the formation of the O 2 -iron bond, a process not allowed in the standard MD force field, we introduced a Morse potential to describe this coordination (51),…”
Section: Methodsmentioning
confidence: 79%
“…A total of 40 independent perturbations were performed. This approach was used in a variety of studies such as ligand entry, escape, dynamic control of tunnel opening, and various mutagenesis studies, yielding results that are in excellent agreement with the experimentally determined rates (42)(43)(44)(45)50). Because the reaction coordinate involves the formation of the O 2 -iron bond, a process not allowed in the standard MD force field, we introduced a Morse potential to describe this coordination (51),…”
Section: Methodsmentioning
confidence: 79%
“…These peptides are the expected products of the T␤4 hydrolysis at the predicted meprin-␣ cleavage sites at E 21 -T 22 and E 24 -K 25 (41). In addition, data from mass spectrometry revealed two new putative cleavage sites at D 13 [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19] ; mass: 2,279.20 Da). This is consistent with the specificity of the active site of meprin-␣, which prefers acidic amino acids at positions near and adjacent to its cleavage site (20,21).…”
Section: Kh From Meprin-␣ Ko Mice Did Not Release Ac-sdkp From T␤4 Inmentioning
confidence: 99%
“…All simulations were performed at 300 K and pressures of 1 bar using Berendsen thermostat and barostat. The Amber99 force field (22) was used for all residues but not for the heme, whose parameters had been developed and thoroughly tested by our team in previous work (23)(24)(25)(26). All simulations were performed with the PMEMD module of the AMBER9 package (27).…”
Section: Classical Molecular Dynamicsmentioning
confidence: 99%