Helicase mechanisms and the coupling of helicases within macromolecular machines. Part I: Structures and properties of isolated helicases

Quarterly Reviews of Biophysics

Volumn 35, Issue 4, 2002, Pages 431-478

  Delagoutte, Emmanuelle ^a   Von Hippel, Peter H ^a  

^a UNIVERSITY OF OREGON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APOENZYME; APOPROTEIN; HELICASE; OLIGOMER; RNA HELICASE; SULFATE;

AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; BASE PAIRING; BINDING SITE; BIOCHEMISTRY; BIOPHYSICS; CHEMICAL ANALYSIS; CHEMICAL REACTION KINETICS; CHEMISTRY; CORRELATION ANALYSIS; CRYSTAL STRUCTURE; DNA DENATURATION; DNA REPLICATION; HEPATITIS C VIRUS; HYDROLYSIS; MACHINE; MACROMOLECULE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN ISOLATION; PROTEIN STABILITY; PROTEIN STRUCTURE; REGULATORY MECHANISM; REVIEW; THERMODYNAMICS;

BASE PAIRING; DNA HELICASES; ENZYME STABILITY; MACROMOLECULAR SUBSTANCES; MOLECULAR MOTOR PROTEINS; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RNA HELICASES; RNA, DOUBLE-STRANDED; STRUCTURE-ACTIVITY RELATIONSHIP;

HEPATITIS C VIRUS;

EID: 0036880196     PISSN: 00335835     EISSN: None     Source Type: Journal    
DOI: 10.1017/S0033583502003852     Document Type: Review

References (172)

1. ADACHI, Y., USUKURA, J. & YANAGIDA, M. (1997). A globular complex formation by Nda1 and the other five members of the MCM protein family in fission yeast. Genes to Cells 2, 467-479.
2. ALI, J. A. & LOHMAN, T. M. (1997). Kinetic measurement of the step size of DNA unwinding by Escherichia coli UvrD helicase. Science 275, 377-380.
3. ALI, J. A., MALUF, N. K. & LOHMAN, T. M. (1999). An oligomeric form of E. coli UvrD is required for optimal helicase activity. J. molec. Biol. 293, 815-834.
4. AMARATUNGA, M. & LOHMAN, T. M. (1993). Escherichia coli Rep helicase unwinds DNA by an active mechanism. Biochemistry 32, 6815-6820.
5. ARAI, N. & KORNBERG, A. (1981). Rep protein as a helicase in an active, isolatable replication fork of duplex phi X174 DNA. J. biol. Chem. 256, 5294-5298.
6. ASTUMIAN, R. D. (1997). Thermodynamics and kinetics of a Brownian motor. Science 276, 917-922.
7. BEAR, D. G., HICKS, P. S., ESCUDERO, K. W., ANDREWS, C. L., McSWIGGEN, J. A. & VON HIPPEL, P. H. (1988). Interactions of Escherichia coli transcription termination factor Rho with RNA. II. Electron microscopy and nuclease protection experiments. J. molec. Biol. 199, 623-635.
8. BERTRAM, R. D., HAYES C. J. & SOULTANAS, P. (2002). Vinylphosphonate internucleotide linkages inhibit the activity of PcrA DNA helicase. Biochemistry 41, 7725-7731.
9. BIANCO, P. R., BREWER, L. R., CORZETT, M., BALHORN, R., YEH, Y., KOWALCZYKOWSKI, S. C. & BASKIN, R. J. (2001). Processive translocation and DNA unwinding by individual RecBCD enzyme molecules. Nature 409, 374-378.
10. BIANCO, P. R. & KOWALCZYKOWSKI, S. C. (2000). Translocation step size and mechanism of the RecBC DNA helicase. Nature 405, 368-372.
11. BJORNSON, K. P., AMARATUNGA, M., MOORE, K. J. & LOHMAN T. M. (1994). Single-turnover kinetics of helicase-catalyzed DNA unwinding monitored continuously by fluorescence energy transfer. Biochemistry 33, 14306-14316.
12. BJORNSON, K. P., MOORE, K. J. & LOHMAN, T. M. (1996a). Kinetic mechanism of DNA binding and DNA-induced dimerization of the Escherichia coli Rep helicase. Biochemistry 35, 2268-2282.
13. BJORNSON, K. P., WONG, I. & LOHMAN, T. M. (1996b). ATP hydrolysis stimulates binding and release of single stranded DNA from alternating subunits of the dimeric E. coli Rep helicase: implications for ATP-driven helicase translocation. J. molec. Biol. 263, 411-422.
14. BOGDEN, C. E., FASS, D., BERGMAN, N., NICHOLS, M. D. & BERGER, J. M. (1999). The structural basis for terminator recognition by the Rho transcription termination factor. Molec. Cell 3, 487-493.
15. BOYER, P. D. (1993). The binding change mechanism for ATP synthase - some probabilities and possibilities. Biochim. Biophys. Acta 1140, 215-250.
16. BRESLAUER, K. J., FRANK, R., BLOCKER, H. & MARKY, L. A. (1986). Predicting DNA duplex stability from the base sequence. Proc. natn. Acad. Sci. USA 83, 3746-3750.
17. BRIKI, F., RAMSTEIN, J., LAVERY, R. & GENEST, D. (1991). Evidence for the stochastic nature of base pair opening in DNA: a Brownian dynamics simulation. J. Am. chem. Soc. 113, 2490-2494.
18. BUJALOWSKI, W. & JEZEWSKA, M. J. (1995). Interactions of Escherichia coli primary replicative helicase DnaB protein with single-stranded DNA. The nucleic acid does not wrap around the protein hexamer. Biochemistry 34, 8513-8519.
19. BUJALOWSKI, W. & JEZEWSKA, M. J. (2000). Kinetic mechanism of nucleotide cofactor binding to Escherichia coli replicative helicase DnaB protein. Stopped-flow kinetic studies using fluorescent, ribose- and base-modified nucleotide analogues. Biochemistry 39, 2106-2122.
20. BUJALOWSKI, W. & KLONOWSKA, M. M. (1993). Negative cooperativity in the binding of nucleotides to Escherichia coli replicative helicase DnaB protein. Interactions with fluorescent nucleotide analogs. Biochemistry 32, 5888-5900.
21. BUJALOWSKI, W. & KLONOWSKA, M. M. (1994a). Close proximity of tryptophan residues and ATP-binding site in Escherichia coli primary replicative helicase DnaB protein. Molecular topography of the enzyme. J. biol. Chem. 269, 31359-31371.
22. BUJALOWSKI, W. & KLONOWSKA, M. M. (1994b). Structural characteristics of the nucleotide-binding site of Escherichia coli primary replicative helicase DnaB protein. Studies with ribose and base-modified fluorescent nucleotide analogs. Biochemisty 33, 4682-4694.
23. BURGESS, B. R. & RICHARDSON, J. P. (2001a). RNA passes through the hole of the protein hexamer in the complex with the Escherichia coli Rho factor. J. biol. Chem. 276, 4182-4189.
24. BURGESS, B. R. & RICHARDSON, J. P. (2001b). Transcription factor Rho does not require a free end to act as an RNA-DNA helicase on an RNA. J. biol. Chem. 276, 17106-17110.
25. CANTOR, C. R. & SCHIMMEL, P. R. (1980a). Part I: The conformation of biological macromolecules. In Biophysical Chemistry. San Francisco: W. H. Freeman & Co.
26. CANTOR, C. R. & SCHIMMEL, P. R. (1980b). Part II: Techniques for the study of biological structure and function. In Biophysical Chemistry, pp. 591-642. San Francisco: W. H. Freeman & Co.
27. CHAO, K. & LOHMAN, T. M. (1990). DNA and nucleotide-induced conformational changes in the Escherichia coli Rep and helicase II (UvrD) proteins. J. biol. Chem. 265, 1067-1076.
28. CHAO, K. L. & LOHMAN, T. M. (1991). DNA-induced dimerization of the Escherichia coli Rep helicase. J. molec. Biol. 221, 1165-1181.
29. CHEN, J. Y., STANDS, L., STALEY, J. P., JACKUPS, JR., R. R., LATUS, L. J. & CHANG, T. H. (2001). Specific alterations of U1-C protein or U1 small nuclear RNA can eliminate the requirement of Prp28p, an essential DEAD box splicing factor. Molec. Cell 7, 227-232.
30. CHEN, Y. Z., ZHUANG, W. & PROHOFSKY, E. W. (1992). Energy flow considerations and thermal fluctuational opening of DNA base pairs at a replicating fork: unwinding consistent with observed replication rates. J. biomolec. struct. Dyn. 10, 415-427.
31. CHENG, W., BRENDZA, K. M., GAUSS, G. H., KOROLEV, S., WAKSMAN, G. & LOHMAN, T. M. (In Press). The 2B domain of the E. coli Rep protein is not required for the DNA helicase activity. Proc. natn. Acad. Sci. USA.
32. CHENC, W., HSIEH, J., BRENDZA, K. M. & LOHMAN, T. M. (2001). E. coli Rep oligomers are required to initiate DNA unwinding in vitro. J. molec. Biol. 310, 327-350.
33. CHENG, Y. K. & PETTITT, B. M. (1992). Stabilities of double- and triple-strand helical nucleic acids. Progr. Biophys. molec. Biol. 58, 225-257.
34. Cox, M. M., GOODMAN, M. F., KREUZER, K. N., SHERRATT, D. J., SANDLER, S. J. & MARIANS, K. J. (2000). The importance of repairing stalled replication forks. Nature 404, 37-41.
35. DAUNE, M. (1999). Molecular Biophysics: Structure in Motion. New York: Oxford University Press.
36. DILLINGHAM, M. S., SOULTANAS, P. WILEY, P., WEBB, M. R. & WIGLEY, D. B. (2001). Defining the roles of individual residues in the single-stranded DNA binding site of PcrA helicase. Proc. natn. Acad. Sci. USA 98, 8381-8387.
37. DILLINGHAM, M. S., WIGLEY, D. B. & WEBB, M. R. (2000). Demonstration of unidirectional single-stranded DNA translocation by PcrA helicase: measurement of step size and translocation speed. Biochemistry 39, 205-212.
38. DILLINGHAM, M. S., WIGLEY, D. B. & WEBB, M. R. (2002). Direct measurement of single-stranded DNA translocadon by PcrA helicase using the fluorescent base analogue 2-aminopurine. Biochemistry 41, 643-651.
39. DONG, F., GOGOL, E. P. & VON HIPPEL, P. H. (1995). The phage T4-coded DNA replication helicase (gp41) forms a hexamer upon activation by nucleoside triphosphate. J. biol. Chem. 270, 7462-7473.
40. DORNBERGER, U., LEIJON, M. & FRITZSCHE, H. (1999). High base pair opening rates in tracts of GC base pairs. J. biol. Chem. 274, 6957-6962.
41. EGELMAN, H. H., Yu, X., WILD, R., HINGORANI, M. M. & PATEL, S. S. (1995). Bacteriophage T7 helicase/primase proteins form rings around single-stranded DNA that suggest a general structure for hexameric helicases. Proc. natn. Acad. Sci. USA 92, 3869-3873.
42. ENGLANDER, S. W. (1963). A hydrogen exchange method using tritium and sephadex: its application to ribonuclease. Biochemistry 2, 798-807.
43. ENGLANDER, S. W. & KRISHNA, M. M. (2001). Hydrogen exchange. Nat. struct. Biol. 8, 741-742.
44. ENGLANDER, S. W., SOSNICK, T. R., ENGLANDER, J. J. & MAYNE, L. (1996). Mechanisms and uses of hydrogen exchange. Curr. Opin. struct. Biol. 6, 18-23.
45. FOLTA-STOGNIEW, E. & RUSSU, I. M. (1994). Sequence dependence of base-pair opening in a DNA dodecamer containing the CACA/GTGT sequence motif. Biochemistry, 33, 11016-11024.
46. FOSTER, J. E., HOLMES, S. F. & ERIE, D. A. (2001). Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation. Cell 106, 243-252.
47. GEISELMANN, J. & VON HIPPEL, P. H. (1992). Functional interactions of ligand cofactors with Escherichia coli transcription termination factor Rho. I. Binding of ATP. Protein Sci. 1, 850-860.
48. GEISELMANN, J., WANG, Y., SEIFRIED, S. E. VON HIPPEL, P. H. (1993). A physical model for the translocation and helicase activities of Escherichia coli transcription termination protein Rho. Proc. natn. Acad. Sci. USA 90, 7754-7758.
49. GORBALENYA, A. E. & KOONIN, E. V. (1993). Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Opin. struct. Biol. 3, 419-429.
50. GREGG, A. V., McGLYNN, P., JAKTAJI, R. P. & LLOYD, R. G. (2002). Direct rescue of stalled DNA replication forks via the combined action of PriA and RecG helicase activities. Molec. Cell 9, 241-251.
51. GUERON, M. & LEROY, J. L. (1992). Base-pair opening in double-stranded nucleic acids. Nucleic Acids and molec. Biol. 6, 1-22.
52. GUERON, M. & LEROY, J. L. (1995). Studies of base pair kinetics by NMR measurement of proton exchange. Meth. Enzymol. 261, 383-413.
53. GWACK, Y., KIM, D. W., HAN, J. H. & CHOE, J. (1996). Characterization of RNA binding activity and RNA helicase activity of the hepatitis C virus NS3 protein. Biochem. biophys. Res. Commun. 225, 654-659.
54. HACKER, K. J. & JOHNSON, K. A. (1997). A hexameric helicase encircles one DNA strand and excludes the other during DNA unwinding. Biochemistry 36, 14080-14087.
55. HALL, M. C. & MATSON, S. W. (1999). Helicase motifs: the engine that powers DNA unwinding. Molec. Microbiol. 34, 867-877.
56. HESSON, T., MANNARINO, A. & CABLE, M. (2000). Probing the relationship between RNA-stimulated ATPase and helicase activities of HCV NS3 using 2′-O-methyl RNA substrates. Biochemistry 39, 2619-2625.
57. HINGORANI, M. M. & PATEL, S. S. (1993). Interactions of bacteriophage T7 DNA primase/helicase protein with single-stranded and double-stranded DNAs. Biochemistry 32, 12478-12487.
58. HINGORANI, M. M. & PATEL, S. S. (1996). Cooperative in teractions of nucleotide ligands are linked to oligomerization and DNA binding in bacteriophage T7 gene 4 helicases. Biochemistry 35, 2218-2228.
59. HINGORANI, M. M., WASHINGTON, M. T., MOORE, K. C. & PATEL, S. S. (1997). The dTTPase mechanism of T7 DNA helicase resembles the binding change mechanism of the F1-ATPase. Proc. natn. Acad. Sci. USA 94, 5012-5017.
60. HSIEH, J., MOORE, K. J. & LOHMAN, T. M. (1999). A two-site kinetic mechanism for ATP binding and hydrolysis by E. coli Rep helicase dimer bound to a single-stranded oligodeoxynucleotide. J. molec. Biol. 288, 255-274.
61. INMAN, R. B. (1966). A denaturation map of the lambda phage DNA molecule determined by electron microscopy. J. molec. Biol. 18, 464-476.
62. IORDANESCU, S. (1993). Characterization of the Staphylococcus aureus chromosomal gene pcrA, identified by mutations affecting plasmid pT181 replication. Molec. Gen. Genet. 241, 185-192.
63. ISHIMI, Y. (1997). A DNA helicase activity is associated with an MCM4, -6 and -7 protein complex. J. biol. Chem. 272, 24508-24513.
64. JEONG, Y. J., KIM, D. E. & PATEL, S. S. (2002). Kinetic pathway of dTTP hydrolysis by hexameric T7 helicase-primase in the absence of DNA. J. biol. Chem. 277, 43778-43784.
65. JEZEWSKA, M. J. & BUJALOWSKI, W. (1996). Global conformational transitions in Escherichia coli primary replicative helicase DnaB protein induced by ATP, ADP, and single-stranded DNA binding. Multiple conformational states of the helicase hexamer. J. biol. Chem. 271, 4261-4265.
66. JEZEWSKA, M. J., KIM, U. S. & BUJALOWSKI, W. (1996a). Binding of Escherichia coli primary replicative helicase DnaB protein to single-stranded DNA. Long-range allosteric conformational changes within the protein hexamer. Biochemistry 35, 2129-2145.
67. JEZEWSKA, M. J., KIM, U. S. & BUJALOWSKI, W. (1996b). Interactions of Escherichia coli primary replicative helicase DnaB protein with nucleotide cofactors. Biophys. J. 71, 2075-2086.
68. JEZEWSKA, M. J., RAJENDRAN, S., BUJALOWSKA, D. & BUJALOWSKI, W. (1998a). Does single-stranded DNA pass through the inner channel of the protein hexamer in the complex with the Escherichia coli DnaB helicase? Fluorescence energy transfer studies. J. biol. Chem. 273, 10515-10529.
69. JEZEWSKA, M. J., RAJENDRAN, S. & BUJALOWSKI, W. (1998b). Complex of Escherichia coli primary replicative helicase DnaB protein with a replication fork: recognition and structure. Biochemistry 37, 3116-3136.
70. KADARE, G. & HAENNI, A.-L. (1997). Virus-encoded RNA helicases. J. Virol. 71, 2583-2590.
71. KANAI, A., TANABE, K. & KOHARA, M. (1995). Poly(U) binding activity of hepatitis C virus NS3 protein, a putative helicase. FEBS Lett. 376, 221-224.
72. KAPLAN, D. L. (2000). The 3′-tail of a forked-duplex sterically determines whether one or two DNA strands pass through the central channel of a replication-fork helicase. J. molec. Biol. 301, 285-299.
73. KHU, Y. L., KOH, E., LIM, S. P., TAN, Y. H., BRENNER, S., LIM, S. G., HONG, W. J. & GOH, P. Y. (2001). Mutations that affect dimer formation and helicase activity of the hepatitis C virus helicase. J. Virol 75, 205-214.
74. KIM, D. E., NARAYAN, M. & PATEL, S. S. (2002). A molecular motor that processively and unidirectionally translocates along single-stranded DNA. J. molec. Biol. 321, 807-819.
75. KIM, D. E. & PATEL, S. S. (1999). The mechanism of ATP hydrolysis at the noncatalytic sites of the transcription termination factor Rho. J. biol. Chem. 274, 32667-32671.
76. KIM, D. E., SHIGESADA, K. & PATEL, S. S. (1999). Transcription termination factor Rho contains three noncatalytic nucleotide binding sites. J. biol. Chem. 274, 11623-11628.
77. KIM, D. W., GWACK, Y., HAN, J. H. & CHOE, J. (1995). C-terminal domain of the hepatitis C virus NS3 protein contains an RNA helicase activity. Biochem. biophys. Res. Commun. 215, 160-166.
78. KIM, D. W., KIM, J., GWACK, Y., HAN, J. H. & CHOE, J. (1997). Mutational analysis of the hepatitis C virus RNA helicase. J. Virol. 71, 9400-9409.
79. KIM, J. L., MORGENSTERN, K. A., GRIFFITH, J. P., DWYER, M. D., THOMSON, J. A., MURCKO, M. A., LIN, C. & CARON, P. R. (1998). Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding. Structure 6, 89-100.
80. KOCHOYAN, M., LEROY, J. L. & GUERON, M. (1990). Processes of base-pair opening and proton exchange in Z-DNA. Biochemistry 29, 4799-4805.
81. KORNBERG, A., SCOTT, J. F. & BERTSCH, L. L. (1978). ATP utilization by Rep protein in the catalytic separation of DNA strands at a replicating fork. J. biol. Chem. 253, 3298-3304.
82. KOROLEV, S., HSIEH, J., GAUSS, G. H., LOHMAN, T. M. & WAKSMAN, G. (1997). Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP. Cell 90, 635-647.
83. LANE, H. E. & DENHARDT, D. T. (1975). The rep mutation. IV. Slower movement of replication forks in Escherichia coli rep strains. J. molec. Biol. 97, 99-112.
84. LEE, C., SCHWARTZ, M. P., PRAKASH, S., IWAKURA, M. & MATOUSCHEK, A. (2001). ATP-dependent proteases degrade their substrates by processively unraveling them from the degradation signal. Molec. Cell. 7, 627-637.
85. LEE, J. K. & HURWITZ, J. (2001). Processive DNA helicase activity of the minichromosome maintenance proteins 4, 6, and 7 complex requires forked DNA structures. Proc. natn. Acad. Sci. USA 98, 54-59.
86. LEFEVRE, J. F., LANE, A. N. & JARDETZKY, O. (1985). Nuclear magnetic resonance study of the proton exchange rate in the operator-promoter DNA sequence of the trp operon of Escherichia coli. J. molec. Biol. 185, 689-699.
87. LEIJON, M., SEHLSTEDT, U., NIELSEN, P. E. & GRASLUND, A. (1997). Unique base-pair breathing dynamics in PNA-DNA hybrids. J. molec. Biol. 271, 438-455.
88. LEROY, J. L., CHARRETIER, E., KOCHOYAN, M. & GUERON, M. (1988). Evidence from base-pair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature. Biochemistry 27, 8894-8898.
89. LEVIN, M. K. & PATEL, S. S. (1999). The helicase from hepatitis C virus is active as an oligomer. J. biol. Chem. 274, 31839-31846.
90. LEVIN, M. K. & PATEL, S. S. (2002). Helicase from hepatitis C virus: energetics of DNA binding, J. biol. Chem. 277, 37292-37300.
91. LILLEY, D. M. (1988). DNA opens up - supercoiling and heavy breathing. Trends Genet. 4, 111-114.
92. LIN, C. & KIM, J. L. (1999). Structure-based mutagenesis study of hepatitis C virus NS3 helicase. J. Virol. 73, 8798-807.
93. LINDAHL, T. (1996). The Croonian Lecture, 1996: Endogenous damage to DNA. Phil. Trans. R. Soc. Lond. (B: Biol. Sci.) 351, 1529-1538.
94. LOCATELLI, G. A., SPARADI, S. & MAGA, G. (2002). Hepatitis C virus NS3 ATPase/helicase: an ATP switch regulates the cooperativity among the different substrate binding sites. Biochemisty 41, 10332-10343.
95. LOHMAN, T. M. & BJORNSON, K. P. (1996). Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 65, 169-214.
96. LOHMAN, T. M., CHAO, K., GREEN, J. M., SAGE, S. & RUNYON, G. T. (1989). Large-scale purification and characterization of the Escherichia coli rep gene product. J. biol. Chem. 264, 10139-10147.
97. LUCIUS, A. L., VINDIGNI, A., GREGORIAN, R., ALI, J. A., TAYLOR, A. F., SMITH G. R. & LOHMAN, T. M. (In Press). DNA, unwinding step size of E. coli RecBCD helicase determined from single turnover chemical quenched-flow kinetic studies. J. molec. Biol.
98. 2+ counterions. Biopolymers 11, 951-955.
99. MARIANS, K. J. (1992). Prokaryotic DNA replication. Annu. Rev. Biochem. 61, 673-719.
100. MARIANS, K. J. (2000). PriA-directed replication fork restart in Escherichia coli. Trends biochem. Sci. 25, 185-189.
101. McCONNELL, B. & VON HIPPEL, P. H. (1970a). Hydrogen exchange as a probe of the dynamic structure of DNA. I. General acid-base catalysis. J. molec. Biol. 50, 297-316.
102. McCONNELL, B. & VON HIPPEL, P. H. (1970b). Hydrogen exchange as a probe of the dynamic structure of DNA. II. Effects of base composition and destabilizing salts. J. molec. Biol. 50, 317-332.
103. McGHEE, J. D. & VON HIPPEL, P. H. (1975a). Formaldehyde as a probe of DNA structure. I. Reaction with exocyclic amino groups of DNA bases. Biochemistry 14, 1281-1296.
104. McGHEE, J. D. & VON HIPPEL, P. H. (1975b). Formaldehyde as a probe of DNA structure. II. Reaction with endocyclic imino groups of DNA bases. Biochemistry 14, 1297-1303.
105. McGLYNN, P. & LLOYD, R. G. (2001). Rescue of stalled replication forks by RecG: simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation. Proc. natn. Acad. Sci. USA 98, 8227-8234.
106. McGLYNN, P., LLOYD, R. G. & MARIANS, K. J. (2001). Formation of Holliday junctions by regression of nascent DNA in intermediates containing stalled replication forks: RecG stimulates regression even when the DNA is negatively supercoiled. Proc. natn. Acad. Sci. USA 98, 8235-8240.
107. McGLYNN, P., MAHDI, A. A. & LLOYD, R. G. (2000). Characterisation of the catalytically active form of RecG helicase. Nucleic Acids Res. 28, 2324-2332.
108. MOORE, K. J. & LOHMAN, T. M. (1994a). Kinetic mechanism of adenine nucleotide binding to and hydrolysis by the Escherichia coli Rep monomer. 1. Use of fluorescent nucleotide analogues. Biochemistry 33, 14550-14564.
109. MOORIS, K. J. & LOHMAN, T. M. (1994b). Kinetic mechanism of adenine nucleotide binding to and hydrolysis by the Escherichia coli Rep monomer. 2. Application of a kinetic competition approach. Biochemistry 33, 14565-14578.
110. MORRIS, P. D., BYRD, A. K., TACKETT, A. J., CAMERON, C. E., TANEGA, P., OTT, R., FANNING, E. & RANEY, K. D. (2002). Hepatitis C virus NS3 and simian virus 40 T antigen helicases displace streptavidin from 5′-biotinylated oligonucleotides but not from 3′-biotinylated oligonucleotides: evidence for directional bias in translocation on single-stranded DNA. Biochemistry 41, 2372-2378.
111. NELSON, H. C., FINCH, J. T., LUISI, B. F. & KLUG, A. (1987). The structure of an oligo(dA).oligo(dT) tract and its biological implications, Nature 330, 221-226.
112. NOEL, J. P., HAMM, H. E. & SIGLER, P. B. (1993). The 2.2 A crystal structure of transducin-alpha complexed with GTP gamma S. Nature 366, 654-663.
113. NOIROT-GROS, M. F., SOULTANAS, P., WIGLEY, D. B., EHRLICH, S. D., NOIROT, P. & PETIT, M. A. (2002). The beta-propeller protein YxaL increases the processivity of the PcrA helicase. Molec. Genet. Genomics 267, 391-400.
114. NONIN, S., LEROY, J. L. & GUERON, M. (1995). Terminal base pairs of oligodeoxynucleotides imino proton exchange and fraying. Biochemistry 34, 10652-10659.
115. OHMS, J. & ACKERMANN, T. (1990). Thermodynamics of double- and triple-helical aggregates formed by selfcomplementary oligoribonucleotides of the type rAx-Uy. Biochemistry 29, 5237-5244.
116. PANG, P. S., JANKOWSKY, E., PLANET, P. J. & PYLE, A. M. (2002). The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding. EMBO J. 21, 1168-1176.
117. PAOLINI, C., DE FRANCESCO, R. & GALLINARI, P. (2000a). Enzymatic properties of hepatitis C virus NS3-associated helicase. J. Gen. Virol. 81, 1335-1345.
118. PAOLINI, C., LAHM, A., DE FRANCESCO, R. & GALLINARI, P. (2000b). Mutational analysis of hepatitis C virus NS3-associated helicase. J. Gen. Virol. 81, 1649-1658.
119. PATEL, S. S. & HINGORANI, M. M. (1995). Nucleotide binding studies of bacteriophage T7 DNA helicase-primase protein. Biophys. J. 68, 186S-189S; discussion 189S-190S.
120. PATEL, S. S., HINGORANI, M. M. & NG, W. M. (1994). The K318A mutant of bacteriophage T7 DNA primase-helicase protein is deficient in helicase but not primase activity and inhibits primase-helicase protein wild-type activities by heterooligomer formation. Biochemistsy 33, 7857-7868.
121. PATEL, S. S. & PICHA, K. M. (2000). Structure and function of hexameric helicases. Annu. Rev. Biochem. 69, 651-697.
122. PETIT, M. A., DERVYN, E., ROSE, M., ENTIAN, K. D., McGOVERN, S., EHRLICH, S. D. & BRUAND, C. (1998). PcrA is an essential DNA helicase of Bacillus subtilis fulfilling functions both in repair and rolling-circle replication. Molec. Microbiol. 29, 261-273.
123. POHORILLE, A., ROSS, W. S. & TINOCO, JR., I. (1990). DNA dynamics in aqueous solution: opening the double helix. Int. J. Supercomput. Appl. 4, 81-96.
124. 2, and poly(rU). Two ADP binding sites on the enzyme-nucleic acid complex. J. biol. Chem. 273, 7390-7396.
125. PORTER, D. J. (1998b). A kinetic analysis of the oligonucleodde-modulated ATPase activity of the helicase domain of the NS3 protein from hepatitis C virus. The first cycle of interaction of ATP with the enzyme is unique. J. biol. Chem. 273, 14247-14253.
126. cat for the hepatitis C virus helicase-catalyzed strand separation of short duplex DNA. J. biol. Chem. 273, 18906-18914.
127. PREUGSCHAT, F., AVERETT, D. R., CLARKE, B. E. & PORTER, D. J. T. (1996). A steady-state and pre-steady-state kinetic analysis of the NTPase activity associated with the hepatitis C virus NS3 helicase domain. J. biol Chem. 271, 24449-24457.
128. PRINTZ, M. P. & VON HIPPEL, P. H. (1965). Hydrogen exchange studies of DNA structure. Proc. natn. Acad. Sci. USA 53, 363-370.
129. RAMSTEIN, J. & LAVERY, R. (1988). Energetic coupling between DNA bending and base pair opening. Proc. natn. Acad. Sci. USA 85, 7231-7235.
130. RAMSTEIN, J. & LAVERY, R. (1990). Base pair opening pathways in B-DNA. J. biomolec. struct. Dyn. 7, 915-933.
131. + effects on transition of DNA and polynucleoddes of variable linear charge density. Biopolymers 15, 893-915.
132. ROMAN, L. J. & KOWALCZYKOWSKI, S. C. (1989). Characterization of the hehcase activity of the Escherichia coli RecBCD enzyme using a novel helicase assay. Biochemistry 28, 2863-2873.
133. 31P-NMR spectra. Biochemistry 29, 5245-5258.
134. SAWAYA, M. R., Guo, S., TABOR, S., RICHARDSON, C. C. & ELLENBERGER, T. (1999). Crystal structure of the helicase domain from the replicative helicase primase of bacteriophage T7. Cell 99, 167-177.
135. SCHEFFZEK, K., AHMADIAN, M. R., KABSCH, W., WIESMULLER, L., LAUTWEIN, A., SCHMITZ, F. & WITTINGHOFER, A. (1997). The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. Science 277, 333-338.
136. SCHMITZ, U., SETHSON, I., EGAN, W. M. & JAMES, T. L. (1992). Solution structure of a DNA octamer containing the Pribnow box via restrained molecular dynamics simulation with distance and torsion angle constraints derived from two-dimensional nuclear magnetic resonance spectral fitting. J. molec. Biol. 227, 510-531.
137. SCHWACHA, A. & BELL, S. P. (2001). Interactions between two catalytically distinct MCM subgroups are essential for coordinated ATP hydrolysis and DNA replication. Molec. Cell 8, 1093-1104.
138. SINGH, S., PATEL, P. K. & HOSUR, R. V. (1997). Structural polymorphism and dynamism in the DNA segment GATCTTCCCCCCGGAA: NMR investigations of hairpin, dumbbell, nicked duplex, parallel strands, and i-motif. Biochemistry 36, 13214-13222.
139. SINGLETON, M. R., SAWAYA, M. R., ELLENBERGER, T. & WIGLEY, D. B. (2000). Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides. Cell 101, 589-600.
140. SINGLETON, M. R., SCAIFE, S. & WIOLEY, D. B. (2001). Structural analysis of DNA replication fork reversal by recg. Cell 107, 79-89.
141. SMITH, K. R., YANCEY, J. E. & MATSON, S. W. (1989). Identification and purification of a protein that stimulates the helicase activity of the Escherichia coli Rep protein. J. biol. Chem. 264, 6119-126.
142. SOULTANAS, P., DILLINGHAM, M. S., VELANKAR, S. S. & WIGLEY, D.B. (1999). DNA binding mediates conformational changes and metal ion coordination in the active site of PcrA helicase. J. molec. Biol. 290, 137-148.
143. SOULTANAS, P., DILLINGHAM, M. S., WILEY, P., WEBB, M. R. & WIGLEY, D. B. (2000). Uncoupling DNA translocation and helicase activity in PcrA: direct evidence for an active mechanism. EMBO J. 19, 3799-3810.
144. SPRANG, S. R. (1997). G protein mechanisms: insights from structural analysis. Annu. Rev. Biochem. 66, 639-78.
145. STITT, B. L. (2001). Escherichia coli transcription termination factor Rho binds and hydrolyzes ATP using a single class of three sites. Biochemistry 40, 2276-2281.
146. STITT, B. L. & Xu, Y. (1998). Sequential hydrolysis of ATP molecules bound in interacting catalytic sites of Escherichia coli transcription termination protein Rho. J. biol. Chem. 273, 26477-26486.
147. STORY, R. M. & STEITZ, T. A. (1992). Structure of the RecA protein-ADP complex. Nature 355, 374-376.
148. SUBRAMANYA, H. S., BIRD, L. E., BRANNIGAN, J. A. & WIGLEY, D. B. (1996). Crystal structure of a DExx box DNA helicase. Nature 384, 379-383.
149. SUZICH, J. A., TAMURA, J. K., PALMER-HILL, F., WARRENER, P., GRAKOUI, A., RICE, C. M., FEINSTONE, S. M. & COLLETT, M. S. (1993). Hepatitis C virus NS3 protein polynucleotide-stimulated nucleoside triphosphatase and comparison with the related pestivirus and flavivirus enzymes. J. Virol. 67, 6152-6158.
150. TACKETT, A. J., MORRIS, P. D., DENNIS, R., GOODWIN, T. E. & RANEY, K. D. (2001). Unwinding of unnatural substrates by a DNA helicase. Biochemistry 40, 543-548.
151. TAI, C. L., CHI, W. K., CHEN, D. S. & HWANG, L. H. (1996). The helicase activity associated with hepatitis C virus nonstructural protein 3 (NS3). J. Virol. 70, 8477-8484.
152. TYE, B. K. & SAWYER, S. (2000). The hexameric eukaryotic MCM helicase: building symmetry from nonidentical patrs. J. biol. Chem. 275, 34833-34836.
153. VELANKAR, S. S., SOULTANAS, P., DILLINGHAM, M. S., SUBRAMANYA, H. S. & WIGLEY, D. B. (1999). Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97, 75-84.
154. VON HIPPEL, P. H. & DELAGOUTTE, E. (2001). A general model for nucleic acid helicases and their 'coupling' within macromolecular machines. Cell 104, 177-190.
155. VON HIPPEL, P. H. & PASMAN, Z. (In Press). Reaction pathways in transcription elongation. Biophys. Chem.
156. VON HIPPEL, P. H. & PRINTZ, M. P. (1965). Dynamic aspects of DNA structure as studies by hydrogen exchange. Fedn Proc. 24, 1458-1465.
157. WALSTROM, K. M., DOZONO, J. M. & VON HIPPEL, P. H. (1997). Kinetics of the RNA-DNA helicase activity of Escherichia coli transcription termination factor Rho. 2. Processivity, ATP consumption and RNA binding. Biochemistry 36, 7993-8004.
158. WANG, Y. & VON HIPPEL, P. H. (1993a). Escherichia coli transcription termination factor Rho. I. ATPase activation by oligonucleotide cofactors. J. biol. Chem. 268, 13940-13946.
159. WANG, Y. & VON HIPPEL, P. H. (1993b). Escherichia coli transcription termination factor Rho. II. Binding of oligonucleotide cofactors. J. biol. Chem. 268, 13947-13955.
160. WARDELL, A. D., ERRINGTON, W., CIARAMELLA, G., MERSON, J. & McGARVEY, M. J. (1999). Characterization and mutational analysis of the helicase and NTPase activities of hepatitis C virus full-length NS3 protein. J. Gen. Virol. 80, 701-709.
161. WASHINGTON, M. T. & PATEL, S. S. (1998). Increased DNA unwinding efficiency of bacteriophage T7 DNA helicase mutant protein 4A'/E348K. J. biol. Chem. 273, 7880-7887.
162. WITTINGHOPER, A. (1998). Signal transduction via Ras. Biol. Chem. 379, 933-937.
163. WONG, I., AMARATUNGA, M. & LOHMAN, T. M. (1993). Heterodimer formation between Escherichia coli Rep and UvrD proteins. J. biol. Chem. 268, 20386-20391.
164. WONG, I., CHAO, K. L., BUJALOWSKI, W. & LOHMAN, T. M. (1992). DNA-induced dimerization of the Escherichia coli rep helicase. Allosteric effects of single-stranded and duplex DNA. J. biol. Chem. 267, 7596-7610.
165. WONG, I. & LOHMAN, T. M. (1992). Allosteric effects of nucleotide cofactors on Escherichia coli Rep helicase-DNA binding. Science 256, 350-355.
166. WONG, I. & LOHMAN, T. M. (1996). ATPase activity of Escherichia coli Rep helicase crosslinked to single-stranded DNA: implications for ATP driven helicase translocation. Proc. natn. Acad. Sci. USA 93, 10051-10056.
167. WONG, I. & LOHMAN, T. M. (1997). A two-site mechanism for ATP hydrolysis by the asymmetric Rep dimer P2S as revealed by site-specific inhibition with ADP-A1F4. Biochemistry 36, 3115-125.
168. WONG, I., MOORE, K. J., BJORNSON, K. P., HSIEH, J. & LOHMAN, T. M. (1996). ATPase activity of Escherichia coli Rep helicase is dramatically dependent on DNA ligation and protein oligomeric states. Biochemistry 35, 5726-5734.
169. YAO, N., HESSON, T., CABLE, M., HONG, Z., KWONG, A. D., LE, H. V. & WEBER, P. C. (1997). Structure of the hepatitis C virus RNA helicase domain. Nat. struct. Biol. 4, 463-467.
170. YARRANTON, G. T. & GEFTER, M. L. (1979). Enzyme-catalyzed DNA unwinding: studies on Escherichia coli rep protein. Proc. natn. Acad. Sci. USA 76, 1658-1662.
171. YU, X., HINGORANI, M. M., PATEL, S. S. & EGELMAN, E. H. (1996). DNA is bound within the central hole to one or two of the six subunits of the T7 DNA helicase. Nat. struct. Biol. 3, 740-743.
172. ZIMM, B. H. (1960). Theory of 'melting' of the 'helical' form in double chains of DNA type. J. Chem. Res. 1960, 1349-1356.