research | reviews

RESEARCH ARTICLES

Braselmann E. & Clark P.L. (2012) Autotransporters: The cellular environment reshapes a folding mechanism to promote protein transport. Journal of Physical Chemistry Letters 3:1063-1071. [PDF] [cover]

Renn J.P., Junker M., Besingi R.N., Braselmann E. & Clark P.L. (2012) ATP-independent control of autotransporter virulence protein transport via the folding properties of the secreted protein.Chemistry & Biology 19:287-296. [PDF] [cover]

Bryan A.W., Starner-Kreinbrink J., Hosur R., Clark P.L. & Berger B. (2011) Structure-based prediction reveals capping motifs inhibit β-helix aggregation. Proceedings of the National Academy of Sciences USA 108:11099-11104. [PDF]

Ugrinov K.G. & Clark P.L. (2010) Co-translational folding increases GFP folding yield. Biophysical Journal 98, 1312-1320. [PDF]

Clarke T.F. IV & Clark P.L. (2010) Increased incidence of rare codon clusters at gene termini: Implications for function. BMC Genomics 11, 118. [PDF]

Junker M. & Clark P.L. (2010) Slow formation of aggregation-resistant beta-sheet folding intermediates. Proteins: Structure, Function & Bioinformatics 78, 812-824. [PDF]

Junker M., Besingi R.N. & Clark P.L. (2009) Vectorial transport and folding of an autotransporter virulence protein during outer membrane secretion. Molecular Microbiology 71, 1323-1332. [PDF]

Clarke T.F. IV & Clark P.L. (2008) Rare codons cluster. PLoS ONE 3, e3412 doi:10.1371/journal.pone.0003412 . [PDF] [online rare codon calculator]

Evans M.S., Sander I.M & Clark P.L. (2008) Co-translational folding promotes beta-helix formation and prevents aggregation in vivo. Journal of Molecular Biology 383, 683-692. [PDF]

Renn J.P. & Clark P.L. (2008) A conserved stable core structure in the passenger domain beta-helix of autotransporter virulence proteins. Biopolymers 89, 420-427. [PDF]

Junker M., Schuster C., McDonnell, A.V., Sorg K.E., Finn M.C., Berger, B. & Clark P.L. (2006) The pertactin beta-helix folding mechanism suggests common themes for secretion and folding of autotransporter proteins. Proceedings of the National Academy of Sciences USA 103, 4918-4923. [PDF]

Evans M.S., Ugrinov, K.G., Frese, M. & Clark P.L. (2005) Homogeneous stalled ribosome nascent chain complexes produced in vivo or in vitro. Nature Methods 2, 757-762. [PDF]

Jain M., Evans M.S., King J. & Clark P.L. (2005) Monocolonal antibody epitope mapping describes tailspike beta-helix folding and aggregation intermediates. Journal of Biological Chemistry 280, 23032-23040. [PDF]

Clark P.L. (2004) Protein folding in the cell: Reshaping the folding funnel. Trends in Biochemical Sciences 29: 527-534. [PDF: article] [PDF: cover]

Benton C.B., King, J. & Clark P.L. (2002) Characterization of a trimeric intermediate on the folding pathway of an interdigitated beta-helix structure. Biochemistry 41, 5093-5103. [PDF]

Clark P.L. & King J. (2001) A newly synthesized, ribosome-bound polypeptide chain adopts conformations dissimilar from early in vitro refolding intermediates. Journal of Biological Chemistry 276, 25411-25420. [PDF]

Raso S.W., Clark P.L., Haase-Pettingell C., King J. & Thomas G.J. (2001) Distinct cysteine sulfhydryl environments detected by analysis of Raman S-H markers of Cys->Ser mutant proteins. Journal of Molecular Biology 307, 899-911. [PDF]

Clark P.L., Weston B.F. & Gierasch L.M. (1998) Probing the folding of a b-clam protein using single-tryptophan constructs. Folding & Design 3, 401-412. [PDF]

Clark P.L., Liu Z.P., Rizo J. & Gierasch L.M. (1997) Cavity formation before stable hydrogen bonding in the folding of a beta-clam protein. Nature Structural Biology 4, 883-886. [PDF]

Clark P.L., Liu Z.P., Zhang J. & Gierasch L.M. (1996) Intrinsic tryptophans of CRABPI as probes of structure and folding. Protein Science 5, 1108-1117. [PDF]

REVIEW ARTICLES

Renn J. & Clark P.L. (2011) The contribution of protein folding to autotransporter outer membrane secretion: kinetics and thermodynamics. Methods in Enzymology 492, 233-251. [PDF]

Clark P.L. (2011) Adding protease digestion to the membrane protein toolbox. Journal of Molecular Biology 406, 543-544. [PDF]

Clark P.L. & Ugrinov K.G (2009) Measuring co-translational conformations of nascent polypeptide chains. Methods in Enzymology 466, 565-588. [PDF]

Evans M.S., Clarke T.F. & Clark P.L. (2005) Conformations of co-translational folding intermediates. Protein & Peptide Letters 12, 189-195. [PDF]