Distinct energetics and closing pathways for DNA polymerase β with 8-oxoG template and different incoming nucleotides

Table 1 Transition states properties for the closing conformational profiles of the pol β 8-oxoG complexes with dC TP and dA TP incoming nucleotides.

Pol β/DNA/8-oxoG complexes	Transition states	Order parameters^a	τ^b (ps)	ΔE_AB vs ΔE_BA^c	Rate constants^d
Binding dA TP	Thumb closing	RMSD of α-helix N (4.5 Å to 2.5 Å)	60	13 4	32000 2.6 × 10⁸
	Asp192 flip	C-Cα-Cβ-Cγ (80° to 150°)	9.6	6 7	3.0 × 10⁸ 9.5 × 10⁷
	Arg258 rotation	Cβ-Cγ-Cδ-Nε (100° to 150°)	5.2	10 16	2.4 × 10⁷ 1.6 × 10⁵
	Phe272 flip	Cα-Cβ-Cγ-Cδ1 (-70° to 40°)	4.0	3 8	4.6 × 10⁴ 8 × 10⁸
	Nucleotidyl transfer		0.2		9.4
Binding dC TP	Thumb closing	RMSD of α-helix N (4.5 Å to 2.5 Å)	55	15 5	7200 9.6 × 10⁷
	Arg258 half-rotation	Cβ-Cγ-Cδ-Nε (-95° to -150°)	3	5 7	2.2 × 10⁹ 3.0 × 10⁸
	Arg258 full-rotation	Cγ-Cδ-Nε-Cζ (100° to 150°)	7.9	7 10	4.2 × 10⁷ 3.8 × 10⁶
	Phe272 flip	Cα-Cβ-Cγ-Cδ1 (-70° to -150°)	6.0	4 7	1.2 × 10¹⁰ 1.5 × 10⁸
	Nucleotidyl transfer		0.2		9.4

a. Order parameters for transition states on the conformational closing pathways of the two complexes. The transition regions are shown in parentheses.
b. Time required to transverse the transition region as obtained from the correlation function of each transition path sampling [see Additional file 1] (see additional figures 5 and 6).
c. Free energy barriers ΔE_AB and ΔE_BAcomputed by performing umbrella sampling using the "BOLAS" program [34]. Detailed free energy plots for each transition are shown in [Additional file 1] (see additional figures 7 and 8).
d. Rate constants for each transition estimated from equation
$k_{T S T}^{A B} = \frac{1}{τ_{m o l}} e^{- β Δ F_{A B}^{b a r r i e r}}$
where τ is the time to transverse the energy barrier, and ΔF is the free energy barrier value.

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