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Protein Science (2006), 15:395-409. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society
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Substitutions of prolines examine their role in kinetic trap formation of the caspase recruitment domain (CARD) of RICK

Yun-Ru Chen1 and A. Clay Clark

Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, USA

(RECEIVED November 1, 2005; FINAL REVISION December 14, 2005; ACCEPTED December 14, 2005)

Caspase recruitment domains (CARDs) are small helical protein domains that adopt the Greek key fold. For the two CARDs studied to date, RICK-CARD and caspase-1-CARD (CP1-CARD), the proteins unfold by an apparent two-state process at equilibrium. However, the folding kinetics are complex for both proteins and may contain kinetically trapped species on the folding pathway. In the case of RICK-CARD, the time constants of the slow refolding phases are consistent with proline isomerism. RICK-CARD contains three prolines, P47 in turn 3, and P85 and P87. The latter two prolines constitute a nonconserved PxP motif in helix 6. To examine the role of the prolines in the complex folding kinetics of RICK-CARD, we generated seven proline-to-alanine mutants, including three single mutants, three double mutants, and one triple mutant. We examined the spectroscopic properties, equilibrium folding, binding to CP1-CARD, and folding kinetics. The results show that P85 is critical for maintaining the function of the protein and that all mutations decrease the stability. Results from single mixing and sequential mixing stopped-flow studies strongly suggest the presence of parallel folding pathways consisting of at least two unfolded populations. The mutations affect the distribution of the two unfolded species, thereby affecting the population that folds through each channel. The two conformations also are present in the triple mutant, demonstrating that interconversion between them is not due to prolyl isomerism. Overall, the data show that the complex folding pathway, especially formation of kinetically trapped species, is not due to prolyl isomerism.

Keywords: caspase recruitment domain; RICK; Greek key; folding kinetics; equilibrium folding; folding intermediates; kinetic traps

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051943006.

Reprint requests to: A. Clay Clark, Department of Molecular and Structural Biochemistry, 128 Polk Hall, North Carolina State University, Raleigh, NC 27695-7622; e-mail: clay_clark{at}ncsu.edu; fax: (919) 515-2047.


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