Research Interests
Protein-RNA Interactions. The coat proteins of the RNA bacteriophages of E. coli interact with a stem-loop structure in viral RNA to repress replicase translation and to encapsidate the viral genome. Different RNA phage coat proteins possess similar tertiary structures but bind different RNA structures, providing a convenient model for understanding the basis of specificity in protein-RNA recognition. Making extensive use of genetics and biochemistry, we have characterized the RNA-binding sites of several coat proteins and have learned how to interchange their RNA-binding specificities. These studies are being extended to include investigation of coat protein folding and virus assembly.
For information about post-doc positions in the Peabody lab, see Job Opportunities.
Selected Publications
Link to PubMed
Ashley CE, Carnes EC, Phillips GK, Durfee PN, Buley MD, Lino
CA, Padilla DP, Phillips B, Carter MB, Willman CL, Brinker CJ, Caldeira
JD, Chackerian B, Wharton W, and Peabody, DS (2011) Cell-Specific
Delivery of Diverse Cargos by Bacteriophage MS2 Virus-like Particles.
ACS Nano 2011 Jun 7. [Epub ahead of print].
Caldeira JC and Peabody DS (2011) Thermal stability of RNA phage virus-like particles displaying foreign peptides. J Nanobiotechnology. 2011 May 24;9(1):22.
Chackerian B, Caldeira Jdo C, Peabody J, and Peabody, DS (2011) Peptide epitope identification by affinity selection on Bacteriophage MS2 Virus-Like Particles. J Mol Biol. 2011 Jun 3;409(2):225-37. Epub 2011 Apr 9.
Ashley CE, Carnes EC, Phillips GK, Padilla D, Durfee PN, Brown PA,
Hanna TN, Liu J, Phillips B, Carter MB, Carroll NJ, Jiang X, Dunphy DR,
Willman CL, Petsev DN, Evans DG, Parikh AN, Chackerian B, Wharton W,
Peabody DS, and Brinker CJ (2011) The targeted delivery of
multicomponent cargos to cancer cells by nanoporous particle-supported
lipid bilayers. Nat Mater. 2011 May;10(5):389-97. Epub 2011 Apr 17.
Ashley CE, Dunphy DR, Jiang Z, Carnes EC, Yuan Z, Petsev DN, Atanassov
PB, Velev OD, Sprung M, Wang J, Peabody DS, and Brinker CJ (2011)
Convective Assembly of 2D Lattices of Virus-like Particles Visualized
by In-Situ Grazing-Incidence Small-Angle X-Ray Scattering. Small. 2011
Apr 18;7(8):1043-50. Epub 2011 Mar 21.
Caldeira Jdo C, Medford A, Kines RC, Lino CA, Schiller JT, Chackerian
B, and Peabody DS (2010) Immunogenic display of diverse peptides,
including a broadly cross-type neutralizing human papillomavirus L2
epitope, on virus-like particles of the RNA bacteriophage PP7. Vaccine.
2010 Jun 17;28(27):4384-93. Epub 2010 Apr 29.
Peabody, DS, Jordan, SK, Caldeira, JC, Manifold-Wheeler, B, Medford, A
and Chackerian, B (2007) Immunogenic display of diverse peptides on
virus-like particles of RNA phage MS2. J. Mol. Biol. 380: 252-263.
Caldeira, JC and Peabody, DS (2007) Stability and assembly in vitro of
bacteriophage PP7 virus-like particles. J. Nanobiotech. 5: 10.
Chackerian, B, Rangel, M, Hunter, Z, and Peabody, DS. (2006) Virus-like
particle based immunogens for Alzheimer’s disease induce antibody
responses against amyloid-ß without concomitant T cell responses.
Vaccine, 24: 6321-6331.
Anderson, EA, Isaacman, S, Peabody, DS, Wang, EY, Canary, JW, and
Kershenbaum, K. (2006) Viral nanoparticles donning a paramagnetic coat:
conjugation of MRI contrast agents to the MS2 capsid. Nanoletters, 6:
1160-1164.
Lima, S.M.B., Vaz, ACQ, Souza, TLF, Peabody, DS, Silva JL, and
Oliveira, AC. (2006) Dissecting the role of protein–protein and
protein–nucleic acid interactions in MS2 bacteriophage stability. FEBS
J. 273: 1463-1475.
Horn, WT, Tars, K, Grahn, E, Helgstrand, C, Baron, AJ, Lago, H, Adams,
CJ, Peabody DS, Phillips, SEV, Stonehouse, NJ, Liljas, L, and Stockley,
PG (2006) Structural Basis of RNA Binding Discrimination between
Bacteriophages Qß and MS2. Structure 14: 487-495.
Lima, S. M. B., Peabody, D., Silva, J. L., Oliveira, A. C. (2004)
Mutations in the hydrophobic core and in the protein-RNA interface
affect the packing and pressure stability of MS2 virus capsids. Eur. J.
Biochem.271: 135-145.
Peabody, D.S. (2003) A viral platform for chemical modification and
multivalent display. J. Nanobiotech. 1: 5.
AnoBom, C.D., Albuquerque, S.C., Albernaz, F.P., Oliveira, A.C., Silva,
J.L., Peabody, D.S., Valente, A.P. and Almeida, F.C.L. (2003)
Structural Studies of MS2 Bacteriophage Virus Particle Disassembly by
Nucloear Magnetic Resonance Relaxation Measurements. Biophys. J. 84:
3894-3903.
Lim, F. and Peabody,D.S. (2002) RNA recognition site of PP7 coat
protein. Nucleic Acids Res. 30: 4138-4144.
Spingola, M., Lim, F., and Peabody, D.S. (2002) Binding of
Diverse RNAs by a Single Protein Structural Framework. Archives of
Biochemistry and Biophysics 405: 122-129
Peabody, D.S. and Al-Bitar, L. (2001) Isolation of Viral Coat Protein
Mutants With Altered Assembly and Aggregation Properties. Nucleic
Acids Research 29: e113.
Lim, F., Downey, T., Peabody D.S. (2001) Specific RNA Binding and
Translational Repression by PP7 Coat Protein. J. Biol. Chem. 276: 22507
Powell, A.J., Peabody, D.S. (2001) Asymmetric interactions in the
adenosine-binding pockets of the MS2 coat protein dimer. BMC Molecular
Biology 2: 6Peabody, D.S. and Chakerian, A. 1999.
Asymmetric Contributions to RNA Binding by the Thr45 Residues of the
MS2 Coat Protein Dimer. J. Biol. Chem. 274: 25403-25410.
Convery, M.A., Rowsell, S., Stonehouse, N.J., Ellington, A.D., Hirao,
I., Murray, J.B., Peabody, D.S., Phillips, S.E.V., and Stockley, P.G.
1998. Crystal structure of an RNA-aptamer-protein complex at 2.8
angstrom resolution. Nature Structural Biology 5: 133-139.
Rowsell, S., Stonehouse, M.J., Convery, M.A., Adams, C.J., Ellington,
A.D., Hirao, I., Peabody, D.S., Stockley, P.G., and Phillips, S.E.V.
1998. Crystal structures of a series of RNA aptamers complexed to the
same protein target. Nature Structural Biology 5: 970-975
Spingola, M. and Peabody, D.S. 1997. MS2 coat protein mutants which
bind Q-beta RNA. Nucleic Acids Res. 25: 2808-2815.
Peabody, D.S. 1997. Role of the coat protein-RNA interaction in the
life cycle of the bacteriophage MS2. Mol. Gen. Genet. 254: 358-364.
Lim, F., Spingola, M., and Peabody, D.S. 1996. The RNA-binding site of
Q-beta coat protein. J. Biol. Chem. 271: 31839-31845.
Peabody, D.S. and Lim, F. 1996. Complementation of RNA Binding Site
Mutations in Heterodimers of Bacteriophage MS2 Coat Protein. Nucleic
Acids Res. 24:2352-2359.
Ni,C.-Z., Syed, R., Kodandapani, R., Wickersham, J., Peabody, D.S.,
Ely, K.R. 1995. Crystal Structure of th Bacteriophage MS2 Coat Protein
Dimer: Implications for Virus Assembly and RNA Binding. Structure
3:255-263.
Lim, F. and Peabody, D.S. 1994. Mutations that Increase the Affinity of
a Transitional Repressor for RNA. Nucleic Acids Res. 22:3748-3752.
Lim, F., Spingola, M. and Peabody, D.S. 1994. Altering the RNA Binding
Specificity of a Translational Repressor. J. Biol. Chem. 269:9006-9010.
Peabody, D.S. 1993. The RNA-Binding Site of Bacteriophage MS2 Coat
Protein. EMBO J. 12:595-600.
Peabody, D.S. and Ely, K.R. 1992. Control of Translational Repression
by Protein-Protein Interactions. Nucleic Acids Res. 20:1649-1655.
