An expanded view of the protein folding landscape of PDZ domains

Hultqvist, Greta; Pedersen, Søren W.; Celestine, N.; Strømgaard, Kristian; Gianni, Stefano; Jemth, Per

doi:10.1016/j.bbrc.2012.04.042

Cited by 13 publications

(20 citation statements)

References 14 publications

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“…The chevron plots for both the pseudo wild type and the amide-to-ester mutants displayed a curvature in the refolding arm in agreement with previous folding experiments on PDZ domains [13], [15]. This curvature was interpreted as a change in rate-limiting step between two transition states, which are separated by a high-energy intermediate.…”

Section: Resultssupporting

confidence: 87%

“…The arrows indicate the two transition states that were probed by the amide-to-ester mutations. See Hultqvist et al [15] for a detailed analysis of the folding kinetics and four-state model.…”

Section: Resultsmentioning

confidence: 99%

“…The PSD-95 PDZ2 construct was similar to the one used in earlier folding studies [13], [15], containing residues 155–249 of human PSD-95 including a mutation, Y190W in β3 to probe folding by fluorescence spectroscopy. To make amide-to-ester substitutions in the backbone, an additional mutation, (V178C) was introduced.…”

Section: Methodsmentioning

confidence: 99%

“…For example, in a system where we assume that the denatured state is always in fast equilibrium with the folded state, without accumulation of intermediates (two-state), m TOT is the sum of the slopes of log k F2 and log k U2 versus urea concentration. See Hultqvist et al [15] and Calosci et al [16] for details on the equation used in the kinetic analysis.…”

Section: Methodsmentioning

confidence: 99%

“…PDZ domains bind peptide segments of target proteins, often at the C-terminus [8]–[10]. This protein family has also served as a model system for detailed studies of protein folding [11]–[15]. These studies include detailed models of the transition states of folding characterized by conventional Φ-value analyses [16]–[18].…”

Section: Introductionmentioning

confidence: 99%

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The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain

et al. 2014

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Backbone hydrogen bonds are important for the structure and stability of proteins. However, since conventional site-directed mutagenesis cannot be applied to perturb the backbone, the contribution of these hydrogen bonds in protein folding and stability has been assessed only for a very limited set of small proteins. We have here investigated effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability. The amide-to-ester mutation removes NH-mediated hydrogen bonds and destabilizes hydrogen bonds formed by the carbonyl oxygen. The overall stability of the PDZ domain generally decreased for all amide-to-ester mutants due to an increase in the unfolding rate constant. For this particular region of the PDZ domain, it is therefore clear that native hydrogen bonds are formed after crossing of the rate-limiting barrier for folding. Moreover, three of the five amide-to-ester mutants displayed an increase in the folding rate constant suggesting that the hydrogen bonds are involved in non-native interactions in the transition state for folding.

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Section: Resultssupporting

confidence: 87%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain

et al. 2014

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Functional role of transient conformations: Rediscovering “chronosteric effects” thirty years later

Ascenzi

Gianni

2013

IUBMB Life

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Proteins are dynamic entities that exert, in some cases, their functions via complex pathways, involving active transient species. This phenomenon was highlighted for the first time in 1983 by Antonini et al. (J. Biol. Chem. 258,[4676][4677][4678], who demonstrated that at least one intermediate occurring in the formation of the bovine b-trypsin-Kunitz inhibitor complex displayed catalytic properties different from those of the active enzyme and of the inactive enzyme-inhibitor adduct. Since it was impossible to explain this phenomenon in terms of static three-dimensional structures, the term "chronosteric effects" was coined to capture the observation that transient species are relevant to protein function(s). Here, some recent results on the folding and function of proteins are reported on the light of chronosteric effects.

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Cryptic binding properties of a transient folding intermediate in a PDZ tandem repeat

et al. 2022

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PDZ domains are the most diffused protein–protein interaction modules of the human proteome and are often present in tandem repeats. An example is PDZD2, a protein characterized by the presence of six PDZ domains that undergoes a proteolytic cleavage producing sPDZD2, comprising a tandem of two PDZ domains, namely PDZ5 and PDZ6. Albeit the physiopathological importance of sPDZD2 is well‐established, the interaction with endogenous ligands has been poorly characterized. To understand the determinants of the stability and function of sPDZD2, we investigated its folding pathway. Our data highlights the presence of a complex scenario involving a transiently populated folding intermediate that may be accumulated from the concurrent denaturation of both PDZ5 and PDZ6 domains. Importantly, double jump kinetic experiments allowed us to pinpoint the ability of this transient intermediate to bind the physiological ligand of sPDZD2 with increased affinity compared to the native state. In summary, our results provide an interesting example of a functionally competent misfolded intermediate, which may exert a cryptic function that is not captured from the analysis of the native state only.

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An expanded view of the protein folding landscape of PDZ domains

Cited by 13 publications

References 14 publications

The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain

The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain

Functional role of transient conformations: Rediscovering “chronosteric effects” thirty years later

Cryptic binding properties of a transient folding intermediate in a PDZ tandem repeat

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