Research Topics
Genomes and GenesSpecies | Mark D SzczelkunSummaryAffiliation: University of Bristol Country: UK Publications
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Detail Information
Publications
The interrelationship of helicase and nuclease domains during DNA translocation by the molecular motor EcoR124IEva Sisáková
Institute of Microbiology, v v i, Academy of Sciences of the Czech Republic, Prague, Czech Republic
J Mol Biol 384:1273-86. 2008..The significance of these observations to our understanding of domain interactions in molecular machines is discussed...- Maintaining a sense of direction during long-range communication on DNAMark D Szczelkun
DNA Protein Interactions Unit, Department of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
Biochem Soc Trans 38:404-9. 2010..The generality of this mechanism to other ATP-dependent communication processes such as mismatch repair is also discussed... - Kinetic models of translocation, head-on collision, and DNA cleavage by type I restriction endonucleasesMark D Szczelkun
Department of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
Biochemistry 41:2067-74. 2002..Therefore, type I restriction enzymes can be described as having processive DNA translocation but, in some cases, nonprocessive DNA cleavage... - Translocation, switching and gating: potential roles for ATP in long-range communication on DNA by Type III restriction endonucleasesMark D Szczelkun
DNA Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
Biochem Soc Trans 39:589-94. 2011..Potential roles for ATP binding and hydrolysis by the helicase domains are discussed, with a focus on bipartite ATPases that act as molecular switches... - DNA cleavage and methylation specificity of the single polypeptide restriction-modification enzyme LlaGIRachel M Smith
DNA Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, BS8 1TD, UK
Nucleic Acids Res 37:7206-18. 2009.... - An Mrr-family nuclease motif in the single polypeptide restriction-modification enzyme LlaGIRachel M Smith
DNA Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, BS8 1TD, UK
Nucleic Acids Res 37:7231-8. 2009..Cleavage by LlaGI is not targeted to methylated DNA, suggesting that the conserved motifs in the Mrr domain are a conventional sub-family of the PD-(D/E)XK superfamily of DNA nucleases... - Subunit assembly modulates the activities of the Type III restriction-modification enzyme PstII in vitroAlice Sears
DNA Protein Interactions Unit, Department of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
Nucleic Acids Res 33:4788-96. 2005..A potential role for disassembly in control of restriction activity in vivo is discussed... - Enzyme-mediated DNA loopingStephen E Halford
Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
Annu Rev Biophys Biomol Struct 33:1-24. 2004..Both capture and translocation mechanisms are discussed here, with reference to the various types of restriction endonuclease that interact with two recognition sites before cleaving DNA... - Type III restriction enzymes cleave DNA by long-range interaction between sites in both head-to-head and tail-to-tail inverted repeatKara van Aelst
DNA Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, BS8 1TD, United Kingdom
Proc Natl Acad Sci U S A 107:9123-8. 2010..The ability to distinguish both inverted repeat substrates from direct repeat substrates in a manner independent of DNA topology or accessory proteins can only be reconciled with an alternative sliding mode of communication... - Evidence for DNA translocation by the ISWI chromatin-remodeling enzymeIestyn Whitehouse
Division of Gene Regulation and Expression, The Wellcome Trust Biocentre, Department of Biochemistry, University of Dundee, Dundee DD1 5EH, Scotland, UK
Mol Cell Biol 23:1935-45. 2003..In combination, these observations suggest that ISWI is a 3'-5'-strand-specific, ATP-dependent DNA translocase that may be capable of forcing DNA over the surface of nucleosomes... - Continuous assays for DNA translocation using fluorescent triplex dissociation: application to type I restriction endonucleasesSarah E McClelland
DNA-Protein Interactions Group, Department of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
J Mol Biol 348:895-915. 2005..Furthermore, we demonstrated that enzymes deficient in DNA cleavage but with maximal ATPase activity showed initiation and translocation rates identical to wild-type, confirming that DNA strand breaks are not a pre-requisite of motion... - DNA communications by Type III restriction endonucleases--confirmation of 1D translocation over 3D loopingLuke J Peakman
DNA Protein Interactions Group, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
Nucleic Acids Res 32:4166-74. 2004..No inhibition was observed, even under conditions where EcoPI translocation could also occur... - When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124ILouise K Stanley
DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, UK
EMBO J 25:2230-9. 2006..A model for dsDNA translocation is presented that could be applicable to a wide range of other enzyme complexes that are also labelled as helicases but which do not have actual unwinding activity... - The single polypeptide restriction-modification enzyme LlaGI is a self-contained molecular motor that translocates DNA loopsRachel M Smith
DNA Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, BS8 1TD, UK
Nucleic Acids Res 37:7219-30. 2009..LlaGI is therefore an example of a polypeptide that is a completely self-contained, multi-functional molecular machine... - S-adenosyl homocysteine and DNA ends stimulate promiscuous nuclease activities in the Type III restriction endonuclease EcoPILuke J Peakman
DNA Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
Nucleic Acids Res 37:3934-45. 2009..We suggest a model for how DNA communication events initiating from non-specific sites, and in particular free DNA ends, could produce the observed cleavage patterns... - Controlling the motor activity of a transcription-repair coupling factor: autoinhibition and the role of RNA polymeraseAbigail J Smith
DNA Protein Interactions Unit, Department of Biochemistry, University of Bristol, Bristol, UK
Nucleic Acids Res 35:1802-11. 2007.... - Direct and random routing of a molecular motor protein at a DNA junctionLouise K Stanley
DNA-Protein Interactions Unit, Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
Nucleic Acids Res 34:4387-94. 2006..Nonetheless, as the frequency of junction bypass events increases, the motor will occasionally jump tracks... - Characterization of the Type III restriction endonuclease PstII from Providencia stuartiiAlice Sears
DNA Protein Interactions Unit, Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
Nucleic Acids Res 33:4775-87. 2005..We also demonstrate that PstII and EcoP15I cannot interact and cleave a DNA substrate suggesting that Type III enzymes must make specific protein-protein contacts to activate endonuclease activity... - S-adenosyl methionine prevents promiscuous DNA cleavage by the EcoP1I type III restriction enzymeLuke J Peakman
DNA Protein Interactions Group, Department of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
J Mol Biol 333:321-35. 2003..However, given the right conditions, AdoMet is not strictly required for DNA cleavage by a type III enzyme... - How to get from A to B: strategies for analysing protein motion on DNAStephen E Halford
Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
Eur Biophys J 31:257-67. 2002.... - Recycling of protein subunits during DNA translocation and cleavage by Type I restriction-modification enzymesMichelle Simons
School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
Nucleic Acids Res 39:7656-66. 2011..Roles for Type I restriction endonuclease subunit dynamics in restriction alleviation in the cell are discussed... - A RecB-family nuclease motif in the Type I restriction endonuclease EcoR124IEva Sisáková
Institute of Microbiology v v i, Academy of Sciences of the Czech Republic, Prague, Czech Republic
Nucleic Acids Res 36:3939-49. 2008..Using mutagenesis, we examined the role of the Q and Y residues in DNA binding, translocation and cleavage. Roles for the QxxxY motif in coordinating the catalytic residues or in stabilizing the nuclease domain on the DNA are discussed... - Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124IRalf Seidel
Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
EMBO J 27:1388-98. 2008..Our observations form a framework for understanding energy coupling in a great many other motors that translocate along dsDNA rather than ssDNA... - Dynamics of initiation, termination and reinitiation of DNA translocation by the motor protein EcoR124IRalf Seidel
Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
EMBO J 24:4188-97. 2005..The dissociation/reassociation of motors during translocation allows dynamic control of the restriction process by the availability of motors. Direct evidence that this control mechanism is relevant in vivo is provided...