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The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures.

Ferreiro DU, Walczak AM, Komives EA, Wolynes PG - PLoS Comput. Biol. (2008)

Bottom Line: The one-dimensional nature of the model implies there are simple relations for the experimental observables: folding free-energy (DeltaG(water)) and the cooperativity of denaturation (m-value), which do not ordinarily apply for globular proteins.To illustrate the ideas, we present a case-study of a family of tetratricopeptide (TPR) repeat proteins and quantitatively relate the results to the experimentally observed folding transitions.Based on the dramatic effect that single point mutations exert on the experimentally observed folding behavior, we speculate that natural repeat proteins are "poised" at particular ratios of inter- and intra-element interaction energetics that allow them to readily undergo structural transitions in physiologically relevant conditions, which may be intrinsically related to their biological functions.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America.

ABSTRACT
Repeat-proteins are made up of near repetitions of 20- to 40-amino acid stretches. These polypeptides usually fold up into non-globular, elongated architectures that are stabilized by the interactions within each repeat and those between adjacent repeats, but that lack contacts between residues distant in sequence. The inherent symmetries both in primary sequence and three-dimensional structure are reflected in a folding landscape that may be analyzed as a quasi-one-dimensional problem. We present a general description of repeat-protein energy landscapes based on a formal Ising-like treatment of the elementary interaction energetics in and between foldons, whose collective ensemble are treated as spin variables. The overall folding properties of a complete "domain" (the stability and cooperativity of the repeating array) can be derived from this microscopic description. The one-dimensional nature of the model implies there are simple relations for the experimental observables: folding free-energy (DeltaG(water)) and the cooperativity of denaturation (m-value), which do not ordinarily apply for globular proteins. We show how the parameters for the "coarse-grained" description in terms of foldon spin variables can be extracted from more detailed folding simulations on perfectly funneled landscapes. To illustrate the ideas, we present a case-study of a family of tetratricopeptide (TPR) repeat proteins and quantitatively relate the results to the experimentally observed folding transitions. Based on the dramatic effect that single point mutations exert on the experimentally observed folding behavior, we speculate that natural repeat proteins are "poised" at particular ratios of inter- and intra-element interaction energetics that allow them to readily undergo structural transitions in physiologically relevant conditions, which may be intrinsically related to their biological functions.

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Experimental observations of the effect of single point mutants on the overall folding behavior.(A) Folding parameters determined by urea denaturation of various mutants of ankyrin repeat proteins, upon fitting to two-state models [8], [18], [38]–[40]. (B) Folding parameters determined by urea (closed circles) or guanidinum hydrochloride (open circles) denaturation of various mutants of IκB-α, upon fitting to two-state model [18].
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pcbi-1000070-g009: Experimental observations of the effect of single point mutants on the overall folding behavior.(A) Folding parameters determined by urea denaturation of various mutants of ankyrin repeat proteins, upon fitting to two-state models [8], [18], [38]–[40]. (B) Folding parameters determined by urea (closed circles) or guanidinum hydrochloride (open circles) denaturation of various mutants of IκB-α, upon fitting to two-state model [18].

Mentions: Both the one-dimensional model and the native topology-based perfect funnel simulations presented above show a fundamental relationship between the stability and the cooperativity of the folding of repeat-containing proteins. The model predicts that single site mutations will affect both of these global folding descriptors simultaneously. In order to test this prediction, we collected data from the literature for several independent folding experiments performed on distinct repeating proteins [8], [18], [38]–[40]. As mentioned earlier, the folding profiles for these relatively short proteins (between 4 and 7 repeats) can usually be approximated by a two-state folding model, so a single m-value and the free energy in water is usually reported. Figure 9A shows the experimental folding parameters for single amino acid mutations performed on several ankyrin-repeat proteins. Indeed, a steep relation is found between the two global folding descriptors, even when the proteins analyzed have different numbers of repeats, the mutations are not necessarily analogous, and are distributed along different units. The slope of the m vs. ΔG plot is constant for each set of mutants, and we attribute the offset between them to the fact that the proteins themselves and the experimental conditions under which they were measured are not identical, and are expected to change the definition of ‘native’ stability. This indicates that the (de)stabilizing effect of a single mutation can be explained only in terms of the alteration it causes to the interactions of the repeat with its immediate neighbors, modifying the cooperative behavior of the whole system, as predicted from the analytical model (Figure 3C).


The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures.

Ferreiro DU, Walczak AM, Komives EA, Wolynes PG - PLoS Comput. Biol. (2008)

Experimental observations of the effect of single point mutants on the overall folding behavior.(A) Folding parameters determined by urea denaturation of various mutants of ankyrin repeat proteins, upon fitting to two-state models [8], [18], [38]–[40]. (B) Folding parameters determined by urea (closed circles) or guanidinum hydrochloride (open circles) denaturation of various mutants of IκB-α, upon fitting to two-state model [18].
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2366061&req=5

pcbi-1000070-g009: Experimental observations of the effect of single point mutants on the overall folding behavior.(A) Folding parameters determined by urea denaturation of various mutants of ankyrin repeat proteins, upon fitting to two-state models [8], [18], [38]–[40]. (B) Folding parameters determined by urea (closed circles) or guanidinum hydrochloride (open circles) denaturation of various mutants of IκB-α, upon fitting to two-state model [18].
Mentions: Both the one-dimensional model and the native topology-based perfect funnel simulations presented above show a fundamental relationship between the stability and the cooperativity of the folding of repeat-containing proteins. The model predicts that single site mutations will affect both of these global folding descriptors simultaneously. In order to test this prediction, we collected data from the literature for several independent folding experiments performed on distinct repeating proteins [8], [18], [38]–[40]. As mentioned earlier, the folding profiles for these relatively short proteins (between 4 and 7 repeats) can usually be approximated by a two-state folding model, so a single m-value and the free energy in water is usually reported. Figure 9A shows the experimental folding parameters for single amino acid mutations performed on several ankyrin-repeat proteins. Indeed, a steep relation is found between the two global folding descriptors, even when the proteins analyzed have different numbers of repeats, the mutations are not necessarily analogous, and are distributed along different units. The slope of the m vs. ΔG plot is constant for each set of mutants, and we attribute the offset between them to the fact that the proteins themselves and the experimental conditions under which they were measured are not identical, and are expected to change the definition of ‘native’ stability. This indicates that the (de)stabilizing effect of a single mutation can be explained only in terms of the alteration it causes to the interactions of the repeat with its immediate neighbors, modifying the cooperative behavior of the whole system, as predicted from the analytical model (Figure 3C).

Bottom Line: The one-dimensional nature of the model implies there are simple relations for the experimental observables: folding free-energy (DeltaG(water)) and the cooperativity of denaturation (m-value), which do not ordinarily apply for globular proteins.To illustrate the ideas, we present a case-study of a family of tetratricopeptide (TPR) repeat proteins and quantitatively relate the results to the experimentally observed folding transitions.Based on the dramatic effect that single point mutations exert on the experimentally observed folding behavior, we speculate that natural repeat proteins are "poised" at particular ratios of inter- and intra-element interaction energetics that allow them to readily undergo structural transitions in physiologically relevant conditions, which may be intrinsically related to their biological functions.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America.

ABSTRACT
Repeat-proteins are made up of near repetitions of 20- to 40-amino acid stretches. These polypeptides usually fold up into non-globular, elongated architectures that are stabilized by the interactions within each repeat and those between adjacent repeats, but that lack contacts between residues distant in sequence. The inherent symmetries both in primary sequence and three-dimensional structure are reflected in a folding landscape that may be analyzed as a quasi-one-dimensional problem. We present a general description of repeat-protein energy landscapes based on a formal Ising-like treatment of the elementary interaction energetics in and between foldons, whose collective ensemble are treated as spin variables. The overall folding properties of a complete "domain" (the stability and cooperativity of the repeating array) can be derived from this microscopic description. The one-dimensional nature of the model implies there are simple relations for the experimental observables: folding free-energy (DeltaG(water)) and the cooperativity of denaturation (m-value), which do not ordinarily apply for globular proteins. We show how the parameters for the "coarse-grained" description in terms of foldon spin variables can be extracted from more detailed folding simulations on perfectly funneled landscapes. To illustrate the ideas, we present a case-study of a family of tetratricopeptide (TPR) repeat proteins and quantitatively relate the results to the experimentally observed folding transitions. Based on the dramatic effect that single point mutations exert on the experimentally observed folding behavior, we speculate that natural repeat proteins are "poised" at particular ratios of inter- and intra-element interaction energetics that allow them to readily undergo structural transitions in physiologically relevant conditions, which may be intrinsically related to their biological functions.

Show MeSH
Related in: MedlinePlus