Biophysical Journal
Volume 100, Issue 9, 4 May 2011, Pages 2243-2252
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Article
Compaction Properties of an Intrinsically Disordered Protein: Sic1 and Its Kinase-Inhibitor Domain

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Abstract

IDPs in their unbound state can transiently acquire secondary and tertiary structure. Describing such intrinsic structure is important to understand the transition between free and bound state, leading to supramolecular complexes with physiological interactors. IDP structure is highly dynamic and, therefore, difficult to study by conventional techniques. This work focuses on conformational analysis of the KID fragment of the Sic1 protein, an IDP with a key regulatory role in the cell-cycle of Saccharomyces cerevisiae. FT-IR spectroscopy, ESI-MS, and IM measurements are used to capture dynamic and short-lived conformational states, probing both secondary and tertiary protein structure. The results indicate that the isolated Sic1 KID retains dynamic helical structure and populates collapsed states of different compactness. A metastable, highly compact species is detected. Comparison between the fragment and the full-length protein suggests that chain length is crucial to the stabilization of compact states of this IDP. The two proteins are compared by a length-independent compaction index.

Abbreviations used

CKI
cyclin-dependent kinase inhibitor
KID
kinase inhibitory domain
IDP
intrinsically disordered protein
IFSU
intrinsically folded structural unit
NMR
nuclear magnetic resonance
FT-IR
Fourier-transform infrared
ESI
electrospray ionization
MS
mass spectrometry
IM
ion mobility
CSD
charge-state distribution
FSD
Fourier-self-deconvoluted
Rh
hydrodynamic radius
CI
compaction index

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Stefania Brocca and Lorenzo Testa contributed equally to this work.