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DNA and RNA Metabolism
My
lab is focused on protein-nucleic acid interactions. DNA and RNA must be
translocated (moved from place to place), unwound, unzipped, and hybridized in
order to serve their functions of information storage and transfer. The enzymes
that perform these critical tasks are called helicases. We study the biological
and biochemical mechanisms of helicases. For example, DNA replication, repair,
and recombination are processes that require the activity of at least one
helicase. If specific helicases are mutated, DNA metabolism can be disrupted
resulting in diseases such as cancer. The importance of RNA helicases is
increasingly becoming recognized. RNA transport, translation, and RNA
interference are some of the processes that require the activity of at least one
RNA helicase. Many viruses encode their own DNA or RNA helicase; therefore
these enzymes are potential targets for development of anti-viral drugs. We are
studying a DNA helicase from Bacteriophage T4 named Dda (for DNA-Dependent-ATPase).
Our goal in this project is to develop a detailed chemical and kinetic mechanism
for DNA unwinding by this DNA helicase. This work involves enzyme kinetics,
structural determination by x-ray crystallography, and structure-function
studies using mutagenesis. A second project involves the Hepatitis C viral
helicase NS3 (Non-Structural Protein 3). NS3 is an RNA helicase that is also
capable of unwinding DNA. We are studying the mechanism of NS3 as well as its
interactions with other HCV and cellular proteins with the goal being to
recapitulate RNA replication in vitro using biological relevant substrates and
proteins. This information is being used for development of chemical and
macromolecular approaches for inhibiting HCV replication in human cells. Our
research projects are currently expanding in two new directions: 1) development
of new tools for studying and disrupting protein-protein interactions using a
combination of chemical and macromolecular approaches coupled with protein mass
spectrometry, and 2) development of single-molecule enzymology using highly
fluorescent proteins and/or nanocrystals for studying individual proteins in
solution and in cells.
Selected Publications
Wang, X., Arnold, J.J., Uchida, A.,
Raney, K.D., and Cameron, C.E. (2009) "Phosphate release contributes to the
rate-limiting step for unwinding by an RNA helicase" Nucleic Acids Res.
epub ahead of press, doi: 10.1093/nar/gkp1118 [Abstract].
Blair, L. P., Tackett, A. J., and Raney, K. D. (2009) "Development and
evaluation of a structural model for SF1B Helicase Dda" Biochemistry, 48,
2321-2329 [Abstract].
Jennings, T.A., Mackintosh, S.G., Harrison, M.K., Sikora, D., Sikora, B.,
Tackett, A.J., Cameron, C.E., and Raney, K.D., (2009) "NS3 helicase from the
Hepatitis C Virus can function as a monomer or oligomer depending on enzyme and
substrate concentrations" J. Biol. Chem. 284, 4806-4814 [Abstract].
Sikora, B.T., Chen, Y., Lichti, C.F., Harrison, M.K., Jennings, T. A., Tang, Y.,
Tackett, A. J., Jordan, J. B., Sakon, J., Cameron, C. E., and Raney, K. D.
(2008) "Hepatitis C Virus NS3 helicase forms oligomeric structures that exhibit
optimal DNA unwinding in vitro" J. Biol. Chem. 283, 11516-11525 [Abstract].
Jennings, T. A., Chen, Y., Huang, L., Jankowsky, E.,
Tackett, A. J., Cameron, C. E., and Raney, K. D. (2008) "RNA unwinding activity
of the Hepatitis C virus NS3 helicase is modulated by the NS5B polymerase"
Biochemistry, 47, 1126-1135 [Abstract].
Sikora, B., Eoff, R. L., Matson, S. W., and
Raney, K. D.
(2006) "DNA Unwinding by Escherichia Coli DNA helicase I (TraI) Provides
Evidence for a Processive Monomeric Molecular Motor" J. Biol. Chem.,
281, 36110-36116 [Abstract].
Byrd, A. K., and
Raney, K. D. (2006)
"Displacement of a DNA Binding Protein by Dda Helicase" Nucleic Acids
Research, 34, 3020-3029.
[Abstract]
Eoff, R. L., and
Raney, K. D. (2006)
"Intermediates revealed in the kinetic mechanism for DNA unwinding by a
monomeric helicase" Nature. Structural and Mol. Biol. 13, 242-249. [Abstract]
Mackintosh, S. G., Lu, Z. L., Jordan, J. B., Harrison, M. K.,
Sikora, B., Sharma, S. D., Cameron, C. E., and
Raney, K. D.*
and Sakon, J.* (2006) "Structural and Biological Identification of residues on
the surface of NS3 helicase that are required for optimal replication of the
Hepatitis C Virus"
J. Biol. Chem.
281, 3528-3535. [Abstract]
*corresponding authors
Tang, Y., Chen, Y., Lichti, C. F., Hall,
R. A.,
Raney, K. D.
and Jennings, S. F. (2005) "CLPM: A Cross-Linked Peptide Mapping Algorithm for
Mass Spectrometric Analysis" BMC Bioinformatics, 6 (Suppl 2):S9, 1-14.
[Abstract]
Huang, L., Hwang, J., Sharma, S.D.,
Hargittai, M.R., Chen, Y., Arnold, J.J.,
Raney, K.D., and
Cameron, C.E. (2005) "Hepatitis C virus nonstructural protein 5A (NS5A) is an
RNA-binding protein." J. Biol. Chem., 280, 36417-36428. [Abstract]
Byrd, A. K. and
Raney, K. D.
(2004) "Protein displacement by an assembly of helicase molecules aligned along
single-stranded DNA" Nature Struct. Mol. Biol.,11, 531- 538. [Abstract]
Nanduri, B., Byrd, A. K., Eoff, R. L.,
Tackett, A. J., and
Raney, K. D.
(2002) "Pre-steady state DNA unwinding by bacteriophate T4 Dda helicase reveals
a monomeric molecular motor" Proc. Natl. Acad. Sci.
USA. 99, 14722-14727.[Abstract]
Morris, P. D. and
Raney, K. D. (1999)
"DNA Helicases Displace Streptavidin from Biotin-Labeled Oligonucleotides"
Biochemistry, 38, 5164-5171. [Abstract]
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E-mail:
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RaneyKevinD@uams.edu |
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Office:
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(501)
686-5244 Biomedical
Research Center 1 Room 405B |
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Labs: |
(501)
686-7254 Biomedical Research
Center 2 Rooms 421-2, 433-2, 419-2 and
417-2 |
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FAX: |
(501) 686-8169 |
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