Integrative Biology Graduate Program
Molecular Biophysics Graduate Program
Studies in our laboratory focus on the folding, structure, and function of integral membrane proteins and their misfolding as the basis of human disease. The cystic fibrosis conductance regulator (CFTR) and microbial homologues have served as our favored models for the bulk of these biophysical, molecular biological, and cell biological studies. These proteins are members of the ABC transporter supergene family of ATP-dependent active transporters and channels. This supergene family is the largest in many of the completely sequenced microbial genomes and includes many medically relevant members, including ATP-driven drug efflux pumps and bacterial toxin transporters, in addition to CFTR. Mutations in CTFR (>900 to date) cause the fatal recessive disorder cystic fibrosis (CF). Many of these mutations alter the ability of the membrane protein to efficiently fold into a functional structure. Others alter the mechano-chemistry of the transport gating cycle. Understanding these defects at a molecular level is providing insight into how primary sequence encodes the folding pattern of integral membrane proteins, how cellular systems cope with the aberrant protein, and how the energy of ATP hydrolysis is utilized to effect movement of a solute across a membrane barrier.
Liu CW, Corboy MJ, DeMartino GN, Thomas PJ. (2003) Endoproteolytic Activity of the Proteasome. Science 299:408-11
Stidham RD, Wigley WC, Hunt JF, Thomas PJ. (2003) Assessment of protein folding/solubility in live cells. Methods Mol Biol 205:155-69.
Ko SB, Shcheynikov N, Choi JY, Luo X, Ishibashi K, Thomas PJ, Kim JY, Kim KH, Lee MG, Naruse S, Muallem S. (2002) A molecular mechanism for aberrant CFTR dependent HCO(3)(-) transport in cystic fibrosis. EMBO J 21:5662-72
Park M, Ko SB, Choi JY, Muallem G, Thomas PJ, Pushkin A, Lee MS, Kim JY, Lee MG, Muallem S, Kurtz I. (2002) The Cystic Fibrosis Transmembrane Conductance Regulator Interacts with and Regulates the Activity of the HCO3- Salvage Transporter Human Na+-HCO3-Cotransport Isoform 3. J Biol Chem 277:50503-50509
Smith PC, Karpowich N, Millen L, Moody JE, Rosen J, Thomas PJ, Hunt JF. (2002) ATP binding to the motor domain from an ABC transporter drives formation of a nucleotide sandwich dimer. Mol Cell 10:139-49
Liu CW, Millen L, Roman TB, Xiong H, Gilbert HF, Noiva R, DeMartino GN, Thomas PJ. (2002) Conformational remodeling of proteasomal substrates by PA700, the 19 S regulatory complex of the 26 S proteasome. J Biol Chem 277:26815-20
Moody JE, Millen L, Binns D, Hunt JF, Thomas PJ. (2002) Cooperative, ATP-dependent association of the nucleotide binding cassettes during the catalytic cycle of ATP-binding cassette transporters. J Biol Chem 277:21111-4
Wigley WC, Corboy MJ, Cutler TD, Thibodeau PH, Oldan J, Lee MG, Rizo J, Hunt JF, Thomas PJ. (2002) A protein sequence that can encode native structure by disfavoring alternate conformations. Nat Struct Biol 9:381-8
Stidham RD, Wigley WC, Thomas PJ. In vitro CFTR folding assays. Methods Mol Med 2002;70:311-22
Corboy MJ, Thomas PJ, Wigley WC. (2002) CFTR degradation and aggregation. Methods Mol Med 70:277-94
Berger AL, Ikuma M, Hunt JF, Thomas PJ, Welsh MJ. (2002) Mutations that change the position of the putative gamma-phosphate linker in the nucleotide binding domains of CFTR alter channel gating. J Biol Chem 277:2125-31
Thomas PJ, Hunt JF. (2001) A snapshot of Nature's favorite pump. Nat Struct Biol. 8:920-3
Karpowich, N., O. Martsinkevich, L. Millen, Y. Yuan, P.L. Dai, K. MacVey, P.J. Thomas, and J.F. Hunt. (2001). Crystal Structures of the MJ1267 ATP Binding Cassette Reveal an Induced-Fit Effect at the ATPase Active Site of an ABC Transporter. Structure (Camb) 9:571-86
Yuan, Y.R., S. Blecker, O. Martsinkevich, L. Millen, P.J. Thomas, and J. F. Hunt. (2001). The crystal structure of the MJ0796 ATP-binding cassette: Implications for the structural consequences of ATP hydrolysis in the active site of an ABC-transporter. J. Biol. Chem. 276:32313-21
Choi, J.Y., D. Muallem, K. Kiselyov, M.G. Lee, P.J. Thomas, and S. Muallem. (2001). Aberrant CFTR-dependent HCO3- transport in mutations associated with cystic fibrosis. Nature. 410:94-7.
Fabunmi, R.P., W.C. Wigley, P.J. Thomas, and G.N. DeMartino. (2001). Interferon gamma regulates accumulation of the proteasome activator PA28 and immunoproteasomes at nuclear PML bodies. J. Cell Sci 114:29-36.
Wigley, W.C., R.D. Stidham, N.M. Smith, J.F. Hunt, and P.J. Thomas. (2001). Protein solubility and folding monitored in vivo by structural complementation of a genetic marker protein. Nat Biotechnol 19:131-6
Strickland, E, K. Hakala, P.J. Thomas, and G.N. DeMartino. (2000). Recognition of misfolding proteins by PA700, the regulatory subcomplex of the 26 S proteasome. J Biol Chem 275:5565-72
Fabunmi, R.P., W.C. Wigley, P.J. Thomas, and G.N. DeMartino. (2000). Activity and regulation of the centrosome-associated proteasome. J Biol Chem 275:409-13.
Lee, M.G., J.Y. Choi, X. Luo, E. Strickland, P.J. Thomas, and S. Muallem. (1999). Cystic fibrosis transmembrane conductance regulator regulates luminal Cl-/HCO3- exchange in mouse submandibular and pancreatic ducts. J Biol Chem 274:14670-7
Wigley, W.C., R.P. Fabunmi, M.G. Lee, C.R. Marino, S. Muallem, G.N. DeMartino, and P.J. Thomas. (1999). Dynamic association of proteasomal machinery with the centrosome. J Cell Biol 145(3):481-90
Lee, M.G., W.C. Wigley, W. Zeng, L.E. Noel, C.R. Marino, P.J. Thomas, and S. Muallem. (1999). Regulation of Cl-/ HCO3- exchange by cystic fibrosis transmembrane conductance regulator expressed in NIH 3T3 and HEK 293 cells. J Biol Chem 274:3414-21
Wigley, W.C., S. Vijayakumar, J.D. Jones, C. Slaughter, and P.J. Thomas. (1998). Transmembrane domain of cystic fibrosis transmembrane conductance regulator: design, characterization, and secondary structure of synthetic peptides m1-m6. Biochemistry 37:844-53
Qu, B.H., E. Strickland, and P.J. Thomas. (1997). Cystic fibrosis: a disease of altered protein folding. J Bioenerg Biomembr 29:483-90
Strickland, E., B.H. Qu, L. Millen, and P.J. Thomas. (1997). The molecular chaperone Hsc70 assists the in vitro folding of the N-terminal nucleotide-binding domain of the cystic fibrosis transmembrane conductance regulator. J Biol Chem 272:25421-4
Qu, B.H., E.H. Strickland, and P.J. Thomas. (1997). Localization and suppression of a kinetic defect in cystic fibrosis transmembrane conductance regulator folding. J Biol Chem 272:15739-44
Qu, B.H., and P.J. Thomas. (1996). Alteration of the cystic fibrosis transmembrane conductance regulator folding pathway. J Biol Chem 271:7261-4
Thomas, P.J., B.H. Qu, and P.L. Pedersen. (1995). Defective protein folding as a basis of human disease. Trends Biochem Sci 20:456-9