Paper Citing NAMD - Abstract
Yuan, Ye; Knaggs, Michael H.; Poole, Leslie B.; Fetrow, Jacquelyn S.; Salsbury, Freddie R., Jr.
Conformational and Oligomeric Effects on the Cysteine pK(a) of Tryparedoxin Peroxidase
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:51-70, AUG 2010
Typical 2-Cys peroxiredoxins (Prxs) are peroxidases which regulate cell signaling pathways, apoptosis, and differentiation. These enzymes are obligate homodimers. and can form decamers in solution. During catalysis. Prxs exhibit cysteine-dependent reactivity which requires the deprotonation of the peroxidatic cysteine (C-p) supported by a lowered pK(a) in the initial step. We present the results of molecular dynamics simulations combined with pK(a) calculations on the monomeric, dimeric and decameric forms of one typical 2-Cys Prx, the tryparedoxin peroxidase from Trypanosoma cruzi (PDB id. luul). The calculations indicate that C-p(C52) pK(a) values are highly affected by oligomeric state; an unshifted C-p pK(a) (similar to 8.3, comparable to the pK(a) of isolated cysteine) is calculated for the monomer. In the dimers, starting with essentially identical structures, the C(p)s evolve dynamically asymmetric pK(a)s during the simulations; one subunit's C-p pK(a) is shifted downward at a time. while the other is unshifted However, when averaged over time, or multiple simulations, the two subunits within a dimer exhibit the same C-p, showing no preference for a lowered pK(a) in either subunit. Two conserved pathways that communicate the asymmetric pK(a)s between C(p)s of different subunits can he identified. In the decamer, all the C-p pK(a)s are shifted downward, with slight asymmetry in the chillers which form the decamers. Structural analyses implicate oligomerization effects as responsible for these oligomeric state-dependent C-p pK(a) shifts. The intra-dimer and the inter-chimer subunit contacts in the decamer restrict the conformations of the side chains of several residues (T49, T54 and E55) calculated to be key in shifting the C-p pK(a). In addition, the backbone fluctuations of a few residues (M46, D47 and F48) result in a different electrostatic environment for the C-p in dimers relative to the monomers. These side chain and backbone interactions which contribute to pK(a) modulation indicate the importance of oligomerization to the function of the typical 2-Cys Prxs.
