Biology Department Biology Department  



John M. Flanagan

Brookhaven National Laboratory
From: 4/26/93 -8/29/03

Currently at:  Penn State


Past BNL Research Interests

The protein folding problem is a fundamental question in molecular biology. We have initiated studies to examine the pathway of protein folding as it occurs in vitro and in vivo.

Protein folding, in vitro, can occur without the aid of additional factors, demonstrating that the amino-acid sequence contains the full information required to specify the native conformation. We have been examining models systems for studying the structure of possible folding intermediates using small-angle scattering, ultraviolet circular dichroism and nuclear magnetic resonance spectroscopy. These studies may aid in understanding the pathway of protein folding.

Recent evidence indicates that the in vivo folding process requires so-called molecular chaperones. These proteins interact with many unfolded or partially unfolded intermediates apparently without specific recognition of defined sequence motifs. We are interested in characterizing the interactions between molecular chaperones and their substrate proteins, as well as the functional complexes formed between individual chaperone proteins.

Three dimensional representations of two ClpP heptameric rings. Two of these rings stacked axially (B on top of A) yield the complete Clp protease. Sequence conservation in the Clp protease family is illustrated by the black colored residues in three subunits. (A) provides a view of the lower ring, the ring interface, and the large central cavity. (B) is a view of the outer surface along the sevenfold axis of the functional 14mer. From: J. Wang, J.A. Hartling and J.M. Flanagan, Cell, 91:447-456 (1997).


Past Selected Publications

  • Huang K., Ghose R., Flanagan J.M., Prestegard J.H.,
    Backbone dynamics of the N-terminal domain in E. coli DnaJ determined by (15)N- and (13)CO-relaxation measurements.
    Biochemistry, 38:10567-10577 (1999).  PDB files 1BQ0, 1BQZ  
  • Bewley M.C., Springer K., Zhang Y.-B., Freimuth P., and Flanagan J.M.
    Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, CAR.
    Science, 286:1579-1583 (1999).  Full Text (pdf)
    PDB files 1KAC, 1NOB 
  • Freimuth P., Springer K., Berard C., Hainfeld J., Bewley M., and Flanagan J.
    Coxsackievirus and adenovirus receptor amino-terminal immunoglobulin V-related domain binds adenovirus type 2 and fiber knob from adenovirus type 12.
    J. Virol., 73:1392-1398 (1999). 
  • Huang K., Flanagan J.M., and Prestegard J.H.
    The influence of C-terminal extension on the structure of the "J-domain" in E. coli DnaJ.
    Protein Sci., 8:203-214 (1999). 
  • Wang J., Hartling J.A., and Flanagan J.M.
    Crystal structure determination of Escherichia coli ClpP starting from an EM-derived mask.
    J. Struct. Biol., 124:151-163 (1998). 
  • Lupas A., Flanagan J.M., Tamura T., and Baumeister W.
    Self-compartmentalizing proteases.
    Trends Biochem. Sci., 22:399-404 (1997).
  • Wang J., Hartling J.A., and Flanagan J.M.
    The structure of ClpP at 2.3 Å resolution suggests a model for ATP-dependent proteolysis.
    Cell, 91:447-456 (1997).  PDB file 1TYF  
  • Tolman J.R., Flanagan J.M., Kennedy M.A., and Prestegard J.H.
    NMR evidence for slow collective motions in cyanometmyoglobin.
    Nat. Struct. Biol., 4:292-297 (1997).
  • Szabo A., Korszun Z.R., Hartl F.U., and Flanagan J.M.
    A Zinc Finger-Like Domain of the Molecular Chaperone DnaJ is Involved in Binding to Denatured Protein Substrates.
    EMBO J., 15:408-417 (1996).
  • Tolman J.R., Flanagan J.M., Kennedy M.A., and Prestegard J.H.
    Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution.
    Proc. Natl. Acad. Sci. USA, 92:9279-9283 (1995).  Full Text (pdf) 
  • Hill R.B., MacKenzie K.R., Flanagan J.M., Cronan J.E. Jr., and Prestegard J.H.
    Overexpression, purification, and characterization of Escherichia coli acyl carrier protein and two mutant proteins.
    Protein Expr. Purif., 6:394-400 (1995). 
  • Shanklin J., DeWitt N.D., and Flanagan J.M.
    The stroma of higher plant plastids contain ClpP and ClpC, functional homologs of Escherichia coli ClpP and ClpA: An archetypal two-component ATP-dependent protease.
    Plant Cell, 7:1713-1722 (1995). 
  • Flanagan J.M., Wall J.S., Capel M.S., Schneider D.K. and Shanklin, J.
    Scanning transmission electron microscopy and small-angle scattering provide evidence that native Escherichia coli ClpP is a tetradecamer with an axial pore.
    Biochemistry, 34:10910-10917 (1995). 
  • Hill R.B., Flanagan J.M., and Prestegard J.N.
    1H and 15N magnetic resonance assignments, secondary structure, and tertiary fold of Escherichia coli DnaJ(1-78).
    Biochemistry, 34:5587-5596 (1995). 
  • Kataoka M., Flanagan J.M., and Engelman D.M.
    Use of X-Ray Solution Scattering for Protein Folding Study.
    In: Synchrotron Radiation in Life Sciences, Oxford University Press (1994). 
  • Szabo A., Langer T., Schroder H., Flanagan J., Bukau B., and Hartl F.U.
    The ATP hydrolysis-dependent reaction cycle of the Escherichia coli Hsp7O System DnaK, DnaJ, and GrpE.
    Proc. Natl. Acad. Sci. USA, 91:10345-10349 (1994).  Full Text (pdf)
  • Kriwaki R.W. Hill R.B., Flanagan J.M., Caradonna J.P., and Prestegard J.H.
    New NMR methods for the characterization of bound waters in macromolecules.
    J. Am. Chem. Soc., 1155:8907-8911 (1993). 
  • Flanagan J.M., Kataoka M., Fujisawa T., and Engelman D.M.
    Mutations can cause large changes in the conformation of a denatured protein.
    Biochemistry, 32:10359-10370 (1993). 


Top of Page

Last Modified: April 10, 2009
Please forward all questions about this site to:
Kathy Folkers