Rerouting the Folding Pathway of the Notch Ankyrin Domain by Reshaping the Energy Landscape

Tripp, Katherine W.; Barrick, Doug

doi:10.1021/ja0763201

Cited by 48 publications

(52 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…9(B), black histogram bars], indicating that folding has been rerouted through repeats 6 and 7. 36 Landscape-based U values (Fig. 9, red histogram bars) have the same profile across the seven repeats as the experimentally determined U values, in both the wild-type and consensusstabilized construct.…”

Section: Predicting Folding Pathwayssupporting

confidence: 56%

“…23 For substitutions in repeats C1 and C2, we use values measured in the Nank1-5C2 construct. 36 To model the effect of urea, we treated each repeat as contributing equally to the m value (0.4 kcal/mol/M for each repeat). This urea dependence was chosen to match the urea dependence for equilibrium unfolding of the Notch ankyrin domain (2.8 kcal/mol/M).…”

Section: The Landscape-based Modelmentioning

confidence: 99%

See 1 more Smart Citation

Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape

Street

Barrick

2008

Protein Science

Self Cite

View full text Add to dashboard Cite

The Notch ankyrin domain is a repeat protein whose folding has been characterized through equilibrium and kinetic measurements. In previous work, equilibrium folding free energies of truncated constructs were used to generate an experimentally determined folding energy landscape (Mello and Barrick, Proc Natl Acad Sci USA 2004;101:14102-14107). Here, this folding energy landscape is used to parameterize a kinetic model in which local transition probabilities between partly folded states are based on energy values from the landscape. The landscape-based model correctly predicts highly diverse experimentally determined folding kinetics of the Notch ankyrin domain and sequence variants. These predictions include monophasic folding and biphasic unfolding, curvature in the unfolding limb of the chevron plot, population of a transient unfolding intermediate, relative folding rates of 19 variants spanning three orders of magnitude, and a change in the folding pathway that results from C-terminal stabilization. These findings indicate that the folding pathway(s) of the Notch ankyrin domain are thermodynamically selected: the primary determinants of kinetic behavior can be simply deduced from the local stability of individual repeats.

show abstract

Section: Predicting Folding Pathwayssupporting

confidence: 56%

Section: The Landscape-based Modelmentioning

confidence: 99%

Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape

Street

Barrick

2008

Protein Science

Self Cite

View full text Add to dashboard Cite

show abstract

“…This C-terminal stabilization greatly accelerates folding, suggesting that the transition state and pathway of folding has shifted, tracking the most stable region of the molecule [45]. Φ-value analysis in these consensus-stabilized constructs support this interpretation [66]. A shift in the folding pathway away from a destabilized set of ankyrin repeats has also been proposed in myotrophin [67].…”

Section: Transition State Structures and Pathwaysmentioning

confidence: 62%

“…In addition, when consensus repeats (described in the next section) are inserted between the central and C-terminal repeats (rather than substituting for the latter), multistate equilibrium unfolding results even without destabilizing point substitutions in the C-terminus [45]. Although analogous substitutions in the N-terminal ankyrin repeats of Notch retain equilibrium two-state character [65], these same N-terminal substitutions result in clear multistate unfolding (in which the N-terminal repeats unfold at low denaturant) in a background in which the C-terminus is stabilized by substitution with consensus repeats [45,66].…”

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

Self Cite

101

View full text Add to dashboard Cite

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 ...

show abstract

“…The keen interest in repeat proteins has led to successful protein design of consensus TPR (4), ankyrin (5,6), and LRR proteins (7) and extensive stability and folding studies on natural ankyrin repeat proteins (a 33-residue repeat that forms a ␤-turn followed by 2 antiparallel ␣-helices) (8)(9)(10)(11)(12)(13)(14). These studies have begun to dissect the equilibrium cooperativity and kinetic folding pathways of repeat proteins.…”

Section: Biophysics and Computational Biologymentioning

confidence: 99%

Exploring the folding energy landscape of a series of designed consensus tetratricopeptide repeat proteins

Javadi

Main

2009

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

View full text Add to dashboard Cite

Repeat proteins contain short, tandem arrays of simple structural motifs (20−40 aa). These stack together to form nonglobular structures that are stabilized by short-range interactions from residues close in primary sequence. Unlike globular proteins, they have few, if any, long-range nonlocal stabilizing interactions. One ubiquitous repeat is the tetratricopeptide motif (TPR), a 34-aa helix-turn-helix motif. In this article we describe the folding kinetics of a series of 7 designed TPR proteins that are assembled from arraying identical designed consensus repeats (CTPRa n ). These range from the smallest 2-repeat protein to a large 10-repeat protein (≈350 aa). In particular, we describe how the energy landscape changes with the addition of repeat units. The data reveal that although the CTPRa proteins have low local frustration, their highly symmetric, modular native structure is reflected in their multistate kinetics of unfolding and folding. Moreover, although the initial folding of all CTPRa n proteins involves a nucleus with similar solvent accessibility, their subsequent folding to the native structure depends directly on repeat number. This corresponds to an increasingly complex landscape that culminates in CTPRa10 populating a misfolded, off-pathway intermediate. These results extend our current understanding of the malleable folding pathways of repeat proteins and highlight the consequences of adding identical repeats to the energy landscape.

show abstract

Rerouting the Folding Pathway of the Notch Ankyrin Domain by Reshaping the Energy Landscape

Cited by 48 publications

References 45 publications

Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape

Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape

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

Exploring the folding energy landscape of a series of designed consensus tetratricopeptide repeat proteins

Contact Info

Product

Resources

About