Protein folding and stability of human CDK inhibitor p19INK4d

Zeeb, Markus; Rösner, Heike I.; Zeslawski, Wojciech; Canet, Denis; Holak, Tad A.; Balbach, Jochen

doi:10.1006/jmbi.2001.5242

Cited by 56 publications

(69 citation statements)

References 44 publications

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“…It is clear that at least one additional species is involved in the kinetics of p16 INK4A folding, although the number of intermediates and the kinetic mechanism of interconversion is unclear. Like p16 INK4A , the refolding of the five ankyrin repeat p19 INK4D shows three kinetic phases, the slowest of which is accelerated by prolyl isomerase [57]. A similar result is seen for the β-helix protein pelC, which shows four kinetic refolding phases, and appears to fold through a partly folded intermediate with substantial secondary and tertiary structure [84,87].…”

Section: Nih-pa Author Manuscriptmentioning

confidence: 61%

“…p19 INK4D , another cyclin-dependent kinase inhibitor that contains five ankyrin repeats, shows a third species that forms in the transition region, as monitored by heteronuclear NMR [57]. Although unfolding transitions monitored by CD in the α-helical region match those monitored by phenylalanine fluorescence, the latter signal is likely to be distributed over four of the five repeats, and is thus likely to show a similar response to unfolding as CD, even if partly folded conformations are populated.…”

Section: Multistate Equilibrium Folding Of Repeat Proteinsmentioning

confidence: 99%

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Repeat-protein folding: New insights into origins of cooperativity, stability, and topology

Kloss

Courtemanche

Barrick

2008

Archives of Biochemistry and Biophysics

101

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Although our understanding of globular protein folding continues to advance, the irregular tertiary structures and high cooperativity of globular proteins complicates energetic dissection. Recently, proteins with regular, repetitive tertiary structures have been identified that sidestep limitations imposed by globular protein architecture. Here we review recent studies of repeat-protein folding. These studies uniquely advance our understanding of both the energetics and kinetics of protein folding. Equilibrium studies provide detailed maps of local stabilities, access to energy landscapes, insights into cooperativity, determination of nearest-neighbor interaction parameters using statistical thermodynamics, relationships between consensus sequences and repeat-protein stability. Kinetic studies provide insight into the influence of short-range topology on folding rates, the degree to which folding proceeds by parallel (versus localized) pathways, and the factors that select among multiple potential pathways. The recent application of force spectroscopy to repeat-protein unfolding is providing a unique route to test and extend many of these findings. KeywordsRepeat-protein; Ankyrin repeat; protein folding; energy landscape; atomic force microscopy In the last twenty-five years, advances in experimental studies and in computation and theory have greatly improved our understanding of protein folding. On the experimental side, advances have come from new and improved techniques, including site-directed mutagenesis, hydrogen exchange (HX) methods, improvements to rapid mixing devices, and development of single-molecule fluorescence and force spectroscopy. Experimental advances have also come in the form of generalizations and insights from expanding databases of thermodynamic and kinetic constants for protein folding [1][2][3][4][5].On the computational side, advances in our understanding of protein folding have come from huge increases in computer speed and storage capacity, in innovative methods to study energetics of folding such as ensemble-based approaches and replica exchange methods [6,7], and distributed computing methods [8]. As with experiment, computational studies of folding, and in particular, fold prediction, have greatly benefited from expanding databases of protein structure [9,10]. On the theoretical side, the application of ideas from condensed-matter *Correspondence: barrick@jhu.edu, (410) 516-0409. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access Author ManuscriptArch Biochem Biophys. Author manuscript; available in PMC 2009 January ...

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Section: Nih-pa Author Manuscriptmentioning

confidence: 61%

Section: Multistate Equilibrium Folding Of Repeat Proteinsmentioning

confidence: 99%

Repeat-protein folding: New insights into origins of cooperativity, stability, and topology

Kloss

Courtemanche

Barrick

2008

Archives of Biochemistry and Biophysics

101

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“…To date, the equilibrium unfolding data of four natural AR proteins have been reported. These are myotrophin (N2C), with ⌬G ϭ 5.1 kcal͞mol (38); the INK4 family members p16 (N2C), with ⌬G ϭ 3.1 kcal͞mol (39) and p19 (N3C), where no two-state unfolding was observed (40) and notch (N5C), with ⌬G ϭ 8 kcal͞mol (41). The thermodynamic stability of our consensus repeat proteins is thus clearly higher than that of the reported natural AR proteins.…”

Section: Resultsmentioning

confidence: 99%

Designed to be stable: Crystal structure of a consensus ankyrin repeat protein

Kohl

Binz

Forrer

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

264

283

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Ankyrin repeat (AR) proteins mediate innumerable protein-protein interactions in virtually all phyla. This finding suggested the use of AR proteins as designed binding molecules. Based on sequence and structural analyses, we designed a consensus AR with fixed framework and randomized interacting residues. We generated several combinatorial libraries of AR proteins consisting of defined numbers of this repeat. Randomly chosen library members are expressed in soluble form in the cytoplasm of Escherichia coli constituting up to 30% of total cellular protein and show high thermodynamic stability. We determined the crystal structure of one of those library members to 2.0-Å resolution, providing insight into the consensus AR fold. Besides the highly complementary hydrophobic repeat-repeat interfaces and the absence of structural irregularities in the consensus AR protein, the regular and extended hydrogen bond networks in the ␤-turn and loop regions are noteworthy. Furthermore, all residues found in the turn region of the Ramachandran plot are glycines. Many of these features also occur in natural AR proteins, but not in this rigorous and standardized fashion. We conclude that the AR domain fold is an intrinsically very stable and well-expressed scaffold, able to display randomized interacting residues. This scaffold represents an excellent basis for the design of novel binding molecules.

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“…Furthermore, ARs 3, 4, and 5 of Notch are structured in this intermediate, while ARs 2, 6, and 7 remain largely unstructured, which become structured in the subsequent conversion to the native ensemble (42). As for AR 1 of Notch, it is not well structured until it binds to its targets (32,43,44). Taken together, these studies suggested that couplings between neighboring ARs contribute to the folding cooperativity of AR proteins.…”

Section: Folding and Stabilitymentioning

confidence: 93%

Ankyrin Repeat: A Unique Motif Mediating Protein−Protein Interactions

2006

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Ankyrin repeat, one of the most widely existing protein motifs in nature, consists of 30−34 amino acid residues and exclusively functions to mediate protein−protein interactions, some of which are directly involved in the development of human cancer and other diseases. Each ankyrin repeat exhibits a helix−turn−helix conformation, and strings of such tandem repeats are packed in a nearly linear array to form helix−turn−helix bundles with relatively flexible loops. The global structure of an ankyrin repeat protein is mainly stabilized by intra- and inter-repeat hydrophobic and hydrogen bonding interactions. The repetitive and elongated nature of ankyrin repeat proteins provides the molecular bases of the unique characteristics of ankyrin repeat proteins in protein stability, folding and unfolding, and binding specificity. Recent studies have demonstrated that ankyrin repeat proteins do not recognize specific sequences, and interacting residues are discontinuously dispersed into the whole molecules of both the ankyrin repeat protein and its partner. In addition, the availability of thousands of ankyrin repeat sequences has made it feasible to use rational design to modify the specificity and stability of physiologically important ankyrin repeat proteins and even to generate ankyrin repeat proteins with novel functions through combinatorial chemistry approaches.

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Protein folding and stability of human CDK inhibitor p19INK4d

Cited by 56 publications

References 44 publications

Repeat-protein folding: New insights into origins of cooperativity, stability, and topology

Repeat-protein folding: New insights into origins of cooperativity, stability, and topology

Designed to be stable: Crystal structure of a consensus ankyrin repeat protein

Ankyrin Repeat: A Unique Motif Mediating Protein−Protein Interactions

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