Bioinformatics and biochemical methods to study the structural and functional elements of DEAD-box RNA helicases

Methods in Molecular Biology

Volumn 1259, Issue , 2015, Pages 165-181

  Banroques, Josette ^a   Tanner, N Kyle ^a  

^a NONE

Author keywords

ATPase; DEAD box; DExD H box; EMSA; Malachite green; RecA like; RNA helicase; Structural domains; Superfamily 2; Unwinding

Indexed keywords

ADENOSINE TRIPHOSPHATASE; DEAD BOX PROTEIN; RNA BINDING PROTEIN;

ARTICLE; ATPASE ACTIVITY ASSAY; BIOCHEMISTRY; BIOINFORMATICS; ENZYME ACTIVITY; GEL MOBILITY SHIFT ASSAY; GENE AMPLIFICATION; IN VITRO STUDY; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SITE DIRECTED MUTAGENESIS; STRUCTURAL HOMOLOGY; BIOLOGY; ENZYME SPECIFICITY; METABOLISM; PROCEDURES;

ADENOSINE TRIPHOSPHATASES; COMPUTATIONAL BIOLOGY; DEAD-BOX RNA HELICASES; SUBSTRATE SPECIFICITY;

EID: 84952653339     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-2214-7_11     Document Type: Article

References (23)

1. Byrd AK, Raney KD (2012) Superfamily 2 helicases. Front Biosci (Landmark Ed) 17: 2070–2088
2. Fairman-Williams ME, Guenther UP, Jankowsky E (2010) SF1 and SF2 helicases: family matters. Curr Opin Struct Biol 20: 313–324
3. Pyle AM (2008) Translocation and unwinding mechanisms of RNA and DNA helicases. Annu Rev Biophys 37:317–336
4. Singleton MR, Dillingham MS, Wigley DB (2007) Structure and mechanism of helicases and nucleic acid translocases. Annu Rev Biochem 76:23–50
5. Jacob F (1977) Evolution and tinkering. Science 196:1161–1166
6. Cordin O, Banroques J, Tanner NK et al (2006) The DEAD-box protein family of RNA helicases. Gene 367:17–37
7. Linder P, Jankowsky E (2011) From unwinding to clamping – the DEAD box RNA helicase family. Nat Rev Mol Cell Biol 12:505–516
8. Banroques J, Cordin O, Doere M et al (2011) Analyses of the functional regions of DEADbox RNA “helicases” with deletion and chimera constructs tested in vivo and in vitro. J Mol Biol 413:451–472
9. Altschul SF, Madden TL, Schaffer AA et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
10. Apweiler R, Martin MJ, O’Donovan C et al (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 39:D214–D219
11. Rost B, Yachdav G, Liu J (2004) The PredictProtein server. Nucleic Acids Res 32:W321–W326
12. Guex N, Peitsch MC, Schwede T (2009) Automated comparative protein structure modeling with SWISS-MODEL and Swiss- PdbViewer: a historical perspective. Electrophoresis 30:S162–S173
13. Hirose S, Shimizu K, Kanai S et al (2007) POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions. Bioinformatics 23:2046–2053
14. Linding R, Russell RB, Neduva V et al (2003) GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res 31: 3701–3708
15. Obenauer JC, Cantley LC, Yaffe MB (2003) Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 31:3635–3641
16. Finn RD, Mistry J, Tate J et al (2010) The Pfam protein families database. Nucleic Acids Res 38:D211–D222
17. Chan KM, Delfert D, Junger KD (1986) A direct colorimetric assay for Ca2+ -stimulated ATPase activity. Anal Biochem 157:375–380
18. Pugh GE, Nicol SM, Fuller-Pace FV (1999) Interaction of the Escherichia coli DEAD box protein DbpA with 23S ribosomal RNA. J Mol Biol 292:771–778
19. Panuska JR, Goldthwait DA (1980) A DNAdependent ATPase from T4-infected Escherichia coli. Purifi cation and properties of a 63,000-dalton enzyme and its conversion to a 22,000-dalton form. J Biol Chem 255: 5208–5214
20. Kiianitsa K, Solinger JA, Heyer WD (2003) NADH-coupled microplate photometric assay for kinetic studies of ATP-hydrolyzing enzymes with low and high specifi c activities. Anal Biochem 321:266–271
21. Tanner NK, Cordin O, Banroques J et al (2003) The Q motif: a newly identifi ed motif in DEAD box helicases may regulate ATP binding and hydrolysis. Mol Cell 11:127–138
22. Turner DH, Mathews DH (2010) NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res 38:D280–D282
23. Sengoku T, Nureki O, Nakamura A et al (2006) Structural basis for RNA unwinding by the DEAD- box protein Drosophila Vasa. Cell 125:287–300