Mechanism of Assembly of the Non-Covalent Spectrin Tetramerization Domain from Intrinsically Disordered Partners

Hill, Stéphanie; Kwa, Lee Gyan; Shammas, Sarah L.; Lee, Jennifer C.; Clarke, Jane

doi:10.1016/j.jmb.2013.08.027

Cited by 32 publications

(44 citation statements)

References 62 publications

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“…The alanine mutant could then be used as an appropriate pseudo wild-type during analysis. These alanine-glycine (Ala-Gly) scanning mutations have been shown to specifically destabilize helical secondary structure (43,44) and have been used to probe helix formation in protein folding (45) and coupled folding and binding reactions (15,18,20). Eight positions along the solvent-exposed side of PUMA were subjected to Ala-Gly scanning (SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein

Rogers

Oleinikovas

Shammas

et al. 2014

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

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154

181

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Protein-protein interactions are at the heart of regulatory and signaling processes in the cell. In many interactions, one or both proteins are disordered before association. However, this disorder in the unbound state does not prevent many of these proteins folding to a well-defined, ordered structure in the bound state. Here we examine a typical system, where a small disordered protein (PUMA, p53 upregulated modulator of apoptosis) folds to an α-helix when bound to a groove on the surface of a folded protein (MCL-1, induced myeloid leukemia cell differentiation protein). We follow the association of these proteins using rapid-mixing stopped flow, and examine how the kinetic behavior is perturbed by denaturant and carefully chosen mutations. We demonstrate the utility of methods developed for the study of monomeric protein folding, including β-Tanford values, Leffler α, Φ-value analysis, and coarse-grained simulations, and propose a self-consistent mechanism for binding. Folding of the disordered protein before binding does not appear to be required and few, if any, specific interactions are required to commit to association. The majority of PUMA folding occurs after the transition state, in the presence of MCL-1. We also examine the role of the side chains of folded MCL-1 that make up the binding groove and find that many favor equilibrium binding but, surprisingly, inhibit the association process.Protein folding | stopped flow | coarse-grained simulation | protein-protein interactions | BCL-2

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Section: Resultsmentioning

confidence: 99%

“…Biophysical techniques (12), NMR in particular (13), can characterize isolated IDPs in detail. Despite this progress, the number of studies examining kinetics and the mechanisms of binding remains relatively small (14)(15)(16)(17)(18)(19)(20)(21) given that the most commonly observed function of IDPs is in coupled folding and binding reactions (22).…”

mentioning

confidence: 99%

Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein

Rogers

Oleinikovas

Shammas

et al. 2014

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

Self Cite

154

181

View full text Add to dashboard Cite

show abstract

“…Interestingly it is seen that CD spectra reveals subtle differences in the folding and conformation of these spectrin domains which are consistent with previous literature on these domains. CD spectroscopy reveals that the lowest MRE values at 222 nm are those of the EF domain, SH3 domain and β‐tetramerization domain, which can be explained by the fact that β‐dimerization domain has a nonstructured tail (Hill, Kwa, Shammas, Lee, & Clarke, ) which decreases its α‐helical nature; similarly SH3 domain has a globular fold (Viguera et al, ) and EF domain while α‐helical is made up sequences nonhomologous to the spectrin repeat domain (Trave, Pastore, et al, ).…”

Section: Discussionmentioning

confidence: 99%

Localizing the chaperone activity of erythroid spectrin

Bose

Chakrabarti

2019

Cytoskeleton

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Spectrin, the major protein of the erythrocyte membrane skeleton has canonically been thought to only serve a structural function. We have previously described a novel chaperone‐like property of spectrin and also hypothesized that the chaperone activity and binding of a hydrophobic ligand, Prodan are localized in the self‐association domain. Here we probe the location and molecular origin of the chaperone activity of multi‐domain spectrin using a selection of individual recombinant spectrin domains, which we have characterized using intrinsic tryptophan fluorescence and CD spectroscopy to show their identity to native spectrin. Aggregation assays using insulin, ADH, α‐ and β‐globin as well as enzyme refolding assays using alkaline phosphatase and α‐glucosidase show that the chaperone activity is not only localized in the self‐association domain but is a generalized property of spectrin domains. This is to our understanding, a unique feature in the case of modular multi‐repeat proteins, possibly implicating that the large family of “spectrin‐repeat” domain containing proteins may also have chaperone like property. Substrate selectivity of chaperone activity as evidenced by the preferential protection of α‐ over β‐globin chains is seen; which has implications in hemoglobin diseases. Moreover, enzyme‐refolding assays also indicate alternate modes of chaperone action. We propose that the molecular origin of chaperone activity resides in the surface exposed hydrophobic patches of the spectrin domains as shown by ANS (1‐anilinonaphthalene‐8‐sulfonic acid) and Prodan (6‐propionyl‐2[dimethylamino]‐naphthalene) binding. We also show that Prodan does indeed have a unique binding site on spectrin located at the self‐association domain.

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“…Hill et al found that this tetramerization domain is highly stable, and used protein engineering to describe the assembly mechanism of this domain. 24 The authors ultimately found that this mechanism is distinct from other known folding mechanisms of spectrin domains.…”

Section: Studies On Structural Properties Of Idps and Idprsmentioning

confidence: 95%

Quarterly intrinsic disorder digest (January-February-March, 2014)

DeForte

Reddy

Uversky

2016

Intrinsically Disordered Proteins

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This is the 5 th issue of the Digested Disorder series that represents a reader's digest of the scientific literature on intrinsically disordered proteins. We continue to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the first quarter of 2014; i.e., during the period of January, February, and March of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings. The goal of this series is to provide an unbiased and condensed survey of the literature on intrinsically disordered proteins on a quarterly basis. As in the previous issues, no special filtering was used except to verify the print date, and exclude those papers not related to the topic. The digest article is structured hierarchically and papers are grouped in several sections: (1) structures of intrinsically disordered proteins (IDPs); (2) functions of IDPs; (3) methods for the IDP analysis; (4) proteomics of IDPs; (5) IDPs and diseases; and (6) IDPs/IDPRs as drugs or drug targets. One should keep in mind that the unambiguous classification of many papers is challenged by the intertwining of the topics they cover.In the 5 th digest of this series, we cover papers published in January, February, and March of 2014. We used the following search term in PubMed: (intrinsically OR natively OR naturally OR inherently) AND (disordered OR unfolded OR unstructured OR denatured) AND (protein OR region OR peptide OR domain) AND ("2014/01" [PPDAT]: "2014/ 03"[PPDAT]), which returned 103 hits. After filtering hits not relevant to the topic, we have covered 94 articles here. Figure 1 represents a word cloud, which shows the most represented words from all the abstracts of papers included in this issue.We also introduce below a new rubric "Spotlight" that specifically emphasize some of the most interesting and important developments in the field of intrinsically disordered proteins during the covered quarter. Spotlight: IDP databases and the rise of the ensemble viewDatabases of experimentally verified IDPs are critical for the development of tools that predict intrinsic disorder, and provide an important data set for the study of IDP functions, motifs and structural behavior. One of the first databases to provide experimental evidence of intrinsic disorder was oddly enough, the Protein Data Bank, where regions of missing electron density in x-ray crystal structures provide an indication of possible disorder. The major databases for IDPs are Disprot 5 and the recently updated IDEAL 6 and the mostly predictor based databases d2p2 7 and MobiDB.8 CONTACT Vladimir N. Uversky

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Mechanism of Assembly of the Non-Covalent Spectrin Tetramerization Domain from Intrinsically Disordered Partners

Cited by 32 publications

References 62 publications

Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein

Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein

Localizing the chaperone activity of erythroid spectrin

Quarterly intrinsic disorder digest (January-February-March, 2014)

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