42. Toseland CP, Martinez-Senac MM, Slatter AF,
Webb MR (2009) The ATPase cycle of PcrA
helicase and its coupling to translocation on
DNA. J Mol Biol 392(4):1020–1032
43. Kunzelmann S, Praefcke GJ, Herrmann C
(2006) Transient kinetic investigation of GTP
hydrolysis catalyzed by interferon-gammainduced hGBP1 (human guanylate binding
protein
1).
J
Biol
Chem
281
(39):28627–28635
44. Nixon AE, Brun ˜e M, Lowe PN, Webb MR
(1995) Kinetics of inorganic phosphate release
during the interaction of p21ras with the
GTPase-activating proteins, p 120-GAP and
Neurofibromin.
Biochemistry
34
(47):15592–15598
45. Goyal A, Belardinelli R, Maracci C, Milo ´ n P,
Rodnina MV (2015) Directional transition
from initiation to elongation in bacterial translation.
Nucleic
Acids
Res
43
(22):10700–10712
46. Savelsbergh A, Katunin VI, Mohr D, Peske F,
Rodnina MV, Wintermeyer W (2003) An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation.
Mol Cell 11(6):1517–1523
47. Toms ˇic J, Vitali LA, Daviter T, Savelsbergh A,
Spurio R, Striebeck P, Wintermeyer W, Rodnina MV, Gualerzi CO (2000) Late events of
translation initiation in bacteria: a kinetic analysis. EMBO J 19(9):2127–2136
48. Dillingham MS, Wigley DB, Webb MR (2000)
Demonstration of unidirectional singlestranded DNA translocation by PcrA helicase:
measurement of step size and translocation
speed. Biochemistry 39(1):205–212
49. Donmez I, Patel SS (2008) Coupling of DNA
unwinding to nucleotide hydrolysis in a ringshaped helicase. EMBO J 27(12):1718–1726
50. Sarlo ´ s K, Gyimesi M, Kova ´cs M (2012) RecQ
helicase translocates along single-stranded
DNA with a moderate processivity and tight
mechanochemical coupling. Proc Natl Acad
Sci U S A 109(25):9804–9809
51. Fersht A (1985) Enzyme structure and mechanism. Freeman, New York, p 144
52. Kuzmic P (1996) Program DYNAFIT for the
analysis of enzyme kinetic data: application to
HIV proteinase. Anal Biochem 237
(2):260–273
53. Takahashi Y, Tokumoto U (2002) A third bacterial system for the assembly of iron-sulfur
clusters with homologs in archaea and plastids.
J Biol Chem 277(32):28380–28383
54. Eccleston JF, Petrovic A, Davis CT,
Rangachari K, Wilson RJ (2006) The kinetic
mechanism of the SufC ATPase: the cleavage
step is accelerated by SufB. J Biol Chem 281
(13):8371–8378
55. Petrovic A, Davis CT, Rangachari K, Clough B,
Wilson RJ, Eccleston JF (2008) Hydrodynamic
characterization of the SufBC and SufCD complexes and their interaction with fluorescent
adenosine nucleotides. Protein Sci 17
(7):1264–1274
56. Arnold LH, Kunzelmann S, Webb MR, Taylor
IA (2015) A continuous enzyme-coupled assay
for triphosphohydrolase activity of HIV-1
restriction factor SAMHD1. Antimicrob
Agents Chemother 59(1):186–192
57. Pais JE, Bowers KE, Stoddard AK, Fierke CA
(2005) A continuous fluorescent assay for protein prenyltransferases measuring diphosphate
release. Anal Biochem 345(2):302–311
58. Hanes JW, Johnson KA (2007) A novel mechanism of selectivity against AZT by the human
mitochondrial DNA polymerase. Nucleic Acids
Res 35(20):6973–6983
59. Hanes JW, Johnson KA (2008) Real-time measurement of pyrophosphate release kinetics.
Anal Biochem 372(1):125–127
60. Li A, Gong S, Johnson KA (2016) Ratelimiting pyrophosphate release by HIV reverse
transcriptase improves Fidelity. J Biol Chem
291(51):26554–26565
61. Li J, Johnson KA (2016) Thumb site 2 inhibitors of hepatitis C viral RNA-dependent RNA
polymerase allosterically block the transition
from initiation to elongation. J Biol Chem
291(19):10067–10077
62. Eriksson J, Langel U (2016) Quantitative
microplate assay for real-time nuclease kinetics.
PLoS One 11(4):e0154099
63. Trentham DR, Eccleston JF, Bagshaw CR
(1976) Kinetic analysis of ATPase mechanisms.
Q Rev Biophys 9(2):217–281
64. Webb MR, McDonald GG, Trentham DR
(1978) Kinetics of oxygen-18 exchange
between inorganic phosphate and water catalyzed by myosin subfragment 1, using the 18O
shift in 31P NMR. J Biol Chem 253
(9):2908–2911
65. Yao N, Ledvina PS, Choudhary A, Quiocho FA
(1996) Modulation of a salt link does not affect
binding of phosphate to its specific active transport receptor. Biochemistry 35(7):2079–2085
318
Simone Kunzelmann
Webb MR (2009) The ATPase cycle of PcrA
helicase and its coupling to translocation on
DNA. J Mol Biol 392(4):1020–1032
43. Kunzelmann S, Praefcke GJ, Herrmann C
(2006) Transient kinetic investigation of GTP
hydrolysis catalyzed by interferon-gammainduced hGBP1 (human guanylate binding
protein
1).
J
Biol
Chem
281
(39):28627–28635
44. Nixon AE, Brun ˜e M, Lowe PN, Webb MR
(1995) Kinetics of inorganic phosphate release
during the interaction of p21ras with the
GTPase-activating proteins, p 120-GAP and
Neurofibromin.
Biochemistry
34
(47):15592–15598
45. Goyal A, Belardinelli R, Maracci C, Milo ´ n P,
Rodnina MV (2015) Directional transition
from initiation to elongation in bacterial translation.
Nucleic
Acids
Res
43
(22):10700–10712
46. Savelsbergh A, Katunin VI, Mohr D, Peske F,
Rodnina MV, Wintermeyer W (2003) An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation.
Mol Cell 11(6):1517–1523
47. Toms ˇic J, Vitali LA, Daviter T, Savelsbergh A,
Spurio R, Striebeck P, Wintermeyer W, Rodnina MV, Gualerzi CO (2000) Late events of
translation initiation in bacteria: a kinetic analysis. EMBO J 19(9):2127–2136
48. Dillingham MS, Wigley DB, Webb MR (2000)
Demonstration of unidirectional singlestranded DNA translocation by PcrA helicase:
measurement of step size and translocation
speed. Biochemistry 39(1):205–212
49. Donmez I, Patel SS (2008) Coupling of DNA
unwinding to nucleotide hydrolysis in a ringshaped helicase. EMBO J 27(12):1718–1726
50. Sarlo ´ s K, Gyimesi M, Kova ´cs M (2012) RecQ
helicase translocates along single-stranded
DNA with a moderate processivity and tight
mechanochemical coupling. Proc Natl Acad
Sci U S A 109(25):9804–9809
51. Fersht A (1985) Enzyme structure and mechanism. Freeman, New York, p 144
52. Kuzmic P (1996) Program DYNAFIT for the
analysis of enzyme kinetic data: application to
HIV proteinase. Anal Biochem 237
(2):260–273
53. Takahashi Y, Tokumoto U (2002) A third bacterial system for the assembly of iron-sulfur
clusters with homologs in archaea and plastids.
J Biol Chem 277(32):28380–28383
54. Eccleston JF, Petrovic A, Davis CT,
Rangachari K, Wilson RJ (2006) The kinetic
mechanism of the SufC ATPase: the cleavage
step is accelerated by SufB. J Biol Chem 281
(13):8371–8378
55. Petrovic A, Davis CT, Rangachari K, Clough B,
Wilson RJ, Eccleston JF (2008) Hydrodynamic
characterization of the SufBC and SufCD complexes and their interaction with fluorescent
adenosine nucleotides. Protein Sci 17
(7):1264–1274
56. Arnold LH, Kunzelmann S, Webb MR, Taylor
IA (2015) A continuous enzyme-coupled assay
for triphosphohydrolase activity of HIV-1
restriction factor SAMHD1. Antimicrob
Agents Chemother 59(1):186–192
57. Pais JE, Bowers KE, Stoddard AK, Fierke CA
(2005) A continuous fluorescent assay for protein prenyltransferases measuring diphosphate
release. Anal Biochem 345(2):302–311
58. Hanes JW, Johnson KA (2007) A novel mechanism of selectivity against AZT by the human
mitochondrial DNA polymerase. Nucleic Acids
Res 35(20):6973–6983
59. Hanes JW, Johnson KA (2008) Real-time measurement of pyrophosphate release kinetics.
Anal Biochem 372(1):125–127
60. Li A, Gong S, Johnson KA (2016) Ratelimiting pyrophosphate release by HIV reverse
transcriptase improves Fidelity. J Biol Chem
291(51):26554–26565
61. Li J, Johnson KA (2016) Thumb site 2 inhibitors of hepatitis C viral RNA-dependent RNA
polymerase allosterically block the transition
from initiation to elongation. J Biol Chem
291(19):10067–10077
62. Eriksson J, Langel U (2016) Quantitative
microplate assay for real-time nuclease kinetics.
PLoS One 11(4):e0154099
63. Trentham DR, Eccleston JF, Bagshaw CR
(1976) Kinetic analysis of ATPase mechanisms.
Q Rev Biophys 9(2):217–281
64. Webb MR, McDonald GG, Trentham DR
(1978) Kinetics of oxygen-18 exchange
between inorganic phosphate and water catalyzed by myosin subfragment 1, using the 18O
shift in 31P NMR. J Biol Chem 253
(9):2908–2911
65. Yao N, Ledvina PS, Choudhary A, Quiocho FA
(1996) Modulation of a salt link does not affect
binding of phosphate to its specific active transport receptor. Biochemistry 35(7):2079–2085
318
Simone Kunzelmann