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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.

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

Pol β/DNA/8-oxoG complexes Transition states Order parametersa τb (ps) ΔEAB vs ΔEBAc Rate constantsd
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
  1. a. Order parameters for transition states on the conformational closing pathways of the two complexes. The transition regions are shown in parentheses.
  2. 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).
  3. c. Free energy barriers ΔEAB and ΔEBAcomputed 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).
  4. d. Rate constants for each transition estimated from equation
  5. k T S T A B = 1 τ m o l e − β Δ F A B b a r r i e r MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemivaqLaem4uamLaemivaqfabaGaemyqaeKaemOqaieaaOGaeyypa0ZaaSaaaeaacqaIXaqmaeaaiiGacqWFepaDdaWgaaWcbaGaemyBa0Maem4Ba8MaemiBaWgabeaaaaGccqWGLbqzdaahaaWcbeqaaiabgkHiTiab=j7aIjabfs5aejabdAeagnaaDaaameaacqWGbbqqcqWGcbGqaeaacqWGIbGycqWGHbqycqWGYbGCcqWGYbGCcqWGPbqAcqWGLbqzcqWGYbGCaaaaaaaa@4E75@
  6. where τ is the time to transverse the energy barrier, and ΔF is the free energy barrier value.
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