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Literature DB >> 19256528

Development and evaluation of a structural model for SF1B helicase Dda.

Lauren P Blair¹, Alan J Tackett, Kevin D Raney.

Abstract

Helicases are proteins that unwind double-stranded nucleic acids. Dda helicase from bacteriophage T4 has served as an excellent model for understanding the molecular mechanism of this class of enzymes. Study of the structure of Dda may reveal why some helicases translocate in a 5' to 3' direction on DNA, while others translocate in a 3' to 5' direction. Attaining a structure of Dda has proven difficult because the protein fails to readily form crystals and is too large for current NMR technologies. We have developed a homology model of the enzyme which will serve to guide studies that examine the structural and functional significance of the interaction between Dda and DNA and how this interaction affects translocation and unwinding of DNA. We have tested the structural model by using methods for mapping protein domains and for examining protein surfaces that interact with DNA.

Entities: Chemical Disease Gene Species

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Year: 2009 PMID： 19256528 PMCID： PMC2664552 DOI： 10.1021/bi801919s

Source DB: PubMed Journal: Biochemistry ISSN： 0006-2960 Impact factor: 3.162

44 in total

1. Non-Watson-Crick interactions between PNA and DNA inhibit the ATPase activity of bacteriophage T4 Dda helicase.

Authors: Alan J Tackett; David R Corey; Kevin D Raney
Journal: Nucleic Acids Res Date: 2002-02-15 Impact factor: 16.971

2. Pre-steady-state DNA unwinding by bacteriophage T4 Dda helicase reveals a monomeric molecular motor.

Authors: Bindu Nanduri; Alicia K Byrd; Robert L Eoff; Alan J Tackett; Kevin D Raney
Journal: Proc Natl Acad Sci U S A Date: 2002-10-31 Impact factor: 11.205

3. Identification of specific HIV-1 reverse transcriptase contacts to the viral RNA:tRNA complex by mass spectrometry and a primary amine selective reagent.

Authors: Mamuka Kvaratskhelia; Jennifer T Miller; Scott R Budihas; Lewis K Pannell; Stuart F J Le Grice
Journal: Proc Natl Acad Sci U S A Date: 2002-12-02 Impact factor: 11.205

4. Evidence for a functional monomeric form of the bacteriophage T4 DdA helicase. Dda does not form stable oligomeric structures.

Authors: P D Morris; A J Tackett; K Babb; B Nanduri; C Chick; J Scott; K D Raney
Journal: J Biol Chem Date: 2001-02-27 Impact factor: 5.157

5. Measurement of steady-state kinetic parameters for DNA unwinding by the bacteriophage T4 Dda helicase: use of peptide nucleic acids to trap single-stranded DNA products of helicase reactions.

Authors: B Nanduri; R L Eoff; A J Tackett; K D Raney
Journal: Nucleic Acids Res Date: 2001-07-01 Impact factor: 16.971

6. The PredictProtein server.

Authors: Burkhard Rost; Guy Yachdav; Jinfeng Liu
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

7. Dual functions of single-stranded DNA-binding protein in helicase loading at the bacteriophage T4 DNA replication fork.

Authors: Yujie Ma; Tongsheng Wang; Jana L Villemain; David P Giedroc; Scott W Morrical
Journal: J Biol Chem Date: 2004-02-09 Impact factor: 5.157

Review 8. Helicase mechanisms and the coupling of helicases within macromolecular machines. Part I: Structures and properties of isolated helicases.

Authors: Emmanuelle Delagoutte; Peter H von Hippel
Journal: Q Rev Biophys Date: 2002-11 Impact factor: 5.318

Review 9. Helicase mechanisms and the coupling of helicases within macromolecular machines. Part II: Integration of helicases into cellular processes.

Authors: Emmanuelle Delagoutte; Peter H von Hippel
Journal: Q Rev Biophys Date: 2003-02 Impact factor: 5.318

6. Cross-talk between the catalytic core and the regulatory domain in cystathionine β-synthase: study by differential covalent labeling and computational modeling.

Authors: Ales Hnízda; Vojtech Spiwok; Vojtech Jurga; Viktor Kozich; Milan Kodícek; Jan P Kraus
Journal: Biochemistry Date: 2010-11-17 Impact factor: 3.162

6 in total

Development and evaluation of a structural model for SF1B helicase Dda.

1. Non-Watson-Crick interactions between PNA and DNA inhibit the ATPase activity of bacteriophage T4 Dda helicase.

2. Pre-steady-state DNA unwinding by bacteriophage T4 Dda helicase reveals a monomeric molecular motor.

3. Identification of specific HIV-1 reverse transcriptase contacts to the viral RNA:tRNA complex by mass spectrometry and a primary amine selective reagent.

4. Evidence for a functional monomeric form of the bacteriophage T4 DdA helicase. Dda does not form stable oligomeric structures.

5. Measurement of steady-state kinetic parameters for DNA unwinding by the bacteriophage T4 Dda helicase: use of peptide nucleic acids to trap single-stranded DNA products of helicase reactions.

6. The PredictProtein server.

7. Dual functions of single-stranded DNA-binding protein in helicase loading at the bacteriophage T4 DNA replication fork.

Review 8. Helicase mechanisms and the coupling of helicases within macromolecular machines. Part I: Structures and properties of isolated helicases.

Review 9. Helicase mechanisms and the coupling of helicases within macromolecular machines. Part II: Integration of helicases into cellular processes.

10. Protein displacement by an assembly of helicase molecules aligned along single-stranded DNA.

1. Physical analysis of recombinant forms of the human mitochondrial DNA helicase.

2. Viral Satellites Exploit Phage Proteins to Escape Degradation of the Bacterial Host Chromosome.

3. The T4 phage SF1B helicase Dda is structurally optimized to perform DNA strand separation.

4. A selectivity study on mTOR/PI3Kα inhibitors by homology modeling and 3D-QSAR.

5. A maternal high-fat diet modulates fetal SIRT1 histone and protein deacetylase activity in nonhuman primates.

6. Cross-talk between the catalytic core and the regulatory domain in cystathionine β-synthase: study by differential covalent labeling and computational modeling.