Helicase: Mystery of Progression

Overview

Journal Mol Biol Rep

Specialty Molecular Biology

Date 2006 Nov 23

PMID 17120115

Authors

Rajneesh Kumar Gaur

Affiliations

Soon will be listed here.

Abstract

Helicases mode of unwinding the nucleic acids and translocation along single stranded nucleic acids is still a subject of great curiosity. Based on the energy transduction and electrophilic interactions, we present a model to explain the mode of action of active helicases. This model considers that both strand separation as well as translocation is active processes fueled by NTP hydrolysis. The model proposes that the translocation appears to involve creeping of helicase over the ssNA lattice rather than inchworm movement.

References

Yarranton G, Gefter M . Enzyme-catalyzed DNA unwinding: studies on Escherichia coli rep protein. Proc Natl Acad Sci U S A. 1979; 76(4):1658-62. PMC: 383449. DOI: 10.1073/pnas.76.4.1658. View

Soultanas P, Dillingham M, Wiley P, Webb M, Wigley D . Uncoupling DNA translocation and helicase activity in PcrA: direct evidence for an active mechanism. EMBO J. 2000; 19(14):3799-810. PMC: 313991. DOI: 10.1093/emboj/19.14.3799. View

Taylor A, Smith G . RecBCD enzyme is a DNA helicase with fast and slow motors of opposite polarity. Nature. 2003; 423(6942):889-93. DOI: 10.1038/nature01674. View

Betterton M, Julicher F . Opening of nucleic-acid double strands by helicases: active versus passive opening. Phys Rev E Stat Nonlin Soft Matter Phys. 2005; 71(1 Pt 1):011904. DOI: 10.1103/PhysRevE.71.011904. View

Singleton M, Dillingham M, Gaudier M, Kowalczykowski S, Wigley D . Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Nature. 2004; 432(7014):187-93. DOI: 10.1038/nature02988. View

Yao N, Hesson T, Cable M, Hong Z, Kwong A, Le H . Structure of the hepatitis C virus RNA helicase domain. Nat Struct Biol. 1997; 4(6):463-7. DOI: 10.1038/nsb0697-463. View

Levin M, Gurjar M, Patel S . ATP binding modulates the nucleic acid affinity of hepatitis C virus helicase. J Biol Chem. 2003; 278(26):23311-6. DOI: 10.1074/jbc.M301283200. View

Dillingham M, Wigley D, Webb M . Demonstration of unidirectional single-stranded DNA translocation by PcrA helicase: measurement of step size and translocation speed. Biochemistry. 2000; 39(1):205-12. DOI: 10.1021/bi992105o. View

Soultanas P, Wigley D . DNA helicases: 'inching forward'. Curr Opin Struct Biol. 2000; 10(1):124-8. DOI: 10.1016/s0959-440x(99)00059-7. View

10.

von Hippel P, Kowalczykowski S, Lonberg N, Newport J, Paul L, Stormo G . Autoregulation of gene expression. Quantitative evaluation of the expression and function of the bacteriophage T4 gene 32 (single-stranded DNA binding) protein system. J Mol Biol. 1982; 162(4):795-818. DOI: 10.1016/0022-2836(82)90548-4. View

11.

Ma Y, Wang T, Villemain J, Giedroc D, Morrical S . Dual functions of single-stranded DNA-binding protein in helicase loading at the bacteriophage T4 DNA replication fork. J Biol Chem. 2004; 279(18):19035-45. DOI: 10.1074/jbc.M311738200. View

12.

Jankowsky E, Gross C, Shuman S, Pyle A . Active disruption of an RNA-protein interaction by a DExH/D RNA helicase. Science. 2001; 291(5501):121-5. DOI: 10.1126/science.291.5501.121. View

13.

Fairman M, Stillman B . Cellular factors required for multiple stages of SV40 DNA replication in vitro. EMBO J. 1988; 7(4):1211-8. PMC: 454458. DOI: 10.1002/j.1460-2075.1988.tb02933.x. View

14.

Liao J, Jeong Y, Kim D, Patel S, Oster G . Mechanochemistry of t7 DNA helicase. J Mol Biol. 2005; 350(3):452-75. DOI: 10.1016/j.jmb.2005.04.051. View

15.

Enemark E, Joshua-Tor L . Mechanism of DNA translocation in a replicative hexameric helicase. Nature. 2006; 442(7100):270-5. DOI: 10.1038/nature04943. View

16.

Wortman M, Johnson E, Bergemann A . Mechanism of DNA binding and localized strand separation by Pur alpha and comparison with Pur family member, Pur beta. Biochim Biophys Acta. 2005; 1743(1-2):64-78. DOI: 10.1016/j.bbamcr.2004.08.010. View

17.

Singleton M, Sawaya M, Ellenberger T, Wigley D . Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides. Cell. 2000; 101(6):589-600. DOI: 10.1016/s0092-8674(00)80871-5. View

18.

Chen Y, Zhuang W, Prohofsky E . Energy flow considerations and thermal fluctuational opening of DNA base pairs at a replicating fork: unwinding consistent with observed replication rates. J Biomol Struct Dyn. 1992; 10(2):415-27. DOI: 10.1080/07391102.1992.10508656. View

19.

Dekker J, Kanellopoulos P, van Oosterhout J, Stier G, TUCKER P, van der Vliet P . ATP-independent DNA unwinding by the adenovirus single-stranded DNA binding protein requires a flexible DNA binding loop. J Mol Biol. 1998; 277(4):825-38. DOI: 10.1006/jmbi.1998.1652. View

20.

Bianco P, Brewer L, Corzett M, Balhorn R, Yeh Y, Kowalczykowski S . Processive translocation and DNA unwinding by individual RecBCD enzyme molecules. Nature. 2001; 409(6818):374-8. DOI: 10.1038/35053131. View