Native-state conformational dynamics of GART: A regulatory pH-dependent coil–helix transition examined by electrostatic calculations

摘要

Glycinamide ribonucleotide transformylase (GART) undergoes a pH-dependent coil–helix transition with pKa ∼ 7. An α-helix is formed at high pH spanning 8 residues of a 21-residue-long loop, comprising the segment Thr120–His121–Arg122–Gln123–Ala124–Leu125–Glu126–Asn127. To understand the electrostatic nature of this loop–helix, called the activation loop–helix, which leads to the formation and stability of the α-helix, pKa values of all ionizable residues of GART have been calculated, using Poisson–Boltzmann electrostatic calculations and crystallographic data. Crystallographic structures of high and low pH E70A GART have been used in our analysis. Low pKa values of 5.3, 5.3, 3.9, 1.7, and 4.7 have been calculated for five functionally important histidines, His108, His119, His121, His132, and His137, respectively, using the high pH E70A GART structure. Ten theoretical single and double mutants of the high pH E70A structure have been constructed to idey pairwise interactions of ionizable residues, which have aided in elucidating the multiplicity of electrostatic interactions of the activation loop–helix, and the impact of the activation helix on the catalytic site. Based on our pKa calculations and structural data, we propose that: (1) His121 forms a molecular switch for the coil–helix transition of the activation helix, depending on its protonation state; (2) a strong electrostatic interaction between His132 and His121 is observed, which can be of stabilizing or destabilizing nature for the activation helix, depending on the relative orientation and protonation states of the rings of His121 and His132; (3) electrostatic interactions involving His119 and Arg122 play a role in the stability of the activation helix; and (4) the activation helix contains the helix-promoting sequence Arg122–Gln123–Ala124–Leu125–Glu126, but its alignment relative to the N and C termini of the helix is not optimal, and is possibly of a destabilizing nature. Finally, we provide electrostatic evidence that the formation and closure of the activation helix create a hydrophobic environment for catalytic-site residue His108, to facilitate catalysis.