RESEARCH @ PATRICIA L. CLARK LAB
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overview | folding in the cell | co-translational | autotransporters | bio-materials

A major difference between "good" bacteria (such as the ones that reside in your gut and assist with food digestion) and "bad" bacteria (pathogenic strains that cause serious and/or fatal infectious diseases) is that "bad" bacteria express a wide variety of virulence proteins, and secrete these out to the outer surface of the bacteria, where these proteins assist the bacteria in the adhesion to, invasion of, and recruitment of nutrients from, host cells. In fact, protein secretion is so important to virulence that Gram-negative bacterial pathogens (think contaminated spinach, and Jack-in-the-Box hamburgers) have evolved no less than seven discrete mechanisms to secrete proteins across their double-walled envelope.

We are studying the autotransporter (AT; also called Type Va) secretion mechanism in Gram-negative pathogens. AT proteins represent the largest family of outer membrane secreted proteins in Gram-negative bacteria, and nearly all are associated with virulence. The name "autotransporter" refers to the apparent ability of these proteins to transport themselves across the outer membrane in the absence of ATP, a proton gradient, or any obvious source of energy. AT proteins vary widely in size, sequence, and function, but we have shown that >97% contain a specific structural domain, a monomeric right-handed beta-helix. Moreover, we have shown that a portion of this beta-helix is more stable than the remainder of the protein, and this portion is the first part of the protein to cross the bacterial membrane. We have hypothesized that the folding properties of this portion of the beta-helix contribute to efficient outer membrane secretion. Intriguingly, AT beta-helices fold very slowly in vitro, which might mimic the environment encountered in the intra-membrane space (periplasm), where premature folding of the beta-helix could block transport across the outer membrane.

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]

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]