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Structural Determinants of Misfolding in Multidomain Proteins.

Tian P, Best RB - PLoS Comput. Biol. (2016)

Bottom Line: Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data.Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients.Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.

ABSTRACT
Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins.

No MeSH data available.


Native states of the single domains.The experimentally determined structure of a single domain of each of the protein domains studied here: (a) SH3, (b) SH2, (c) TNfn3, (d) PDZ, (e) Titin I27, (f) Ubiquitin and (g) Protein G. The PDB accession code are 1SHG, 1TZE, 1TEN, 2VWR, 1TIT, 1UBQ and 1GB1, respectively.
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pcbi.1004933.g002: Native states of the single domains.The experimentally determined structure of a single domain of each of the protein domains studied here: (a) SH3, (b) SH2, (c) TNfn3, (d) PDZ, (e) Titin I27, (f) Ubiquitin and (g) Protein G. The PDB accession code are 1SHG, 1TZE, 1TEN, 2VWR, 1TIT, 1UBQ and 1GB1, respectively.

Mentions: In order to investigate the misfolding propensity of different types of domains, we have chosen seven domains, based on (i) the superfamilies with the largest abundance of repeats in the human genome [24], (ii) proteins for which some experimental evidence for misfolding (or lack thereof) is available and (iii) proteins for which data on folding kinetics and stability is available for their circular permutants (only some of the proteins meet criterion (iii)). The circular permutant data are relevant because the misfolding intermediates suggested by simulations and experiment [7, 12] can be viewed as circular permutants of the original structure (Fig 1d). Each of the chosen proteins is illustrated in Fig 2 and described briefly in Materials and Methods. We study the folding and misfolding of the seven protein domains, using the same structure-based model as that successfully employed to treat Titin I27 [7, 12]. Molecular simulations are carried out to characterize the possible structural topologies of the misfolded intermediates and the mechanism of their formation. Our model is consistent with available experimental information for the systems studied, in terms of which proteins misfold and what misfolded structures they tend to form. We then investigated what factors influence the propensity of multidomain proteins to misfold. The simplest rationalization of the propensity of a multidomain protein for domain-swapped misfolding would seem to be offered by parameterizing a kinetic model based on the scheme shown in Fig 1, particularly for the steps Fig 1a–1b versus 1a–1d. We hypothesized that the propensity to misfold might be characterized in terms of the folding kinetics of the isolated circular permutants representing the domain-swapped intermediates in Fig 1d. However, contrary to this expectation, we found that the stability of such isolated domains, rather than their folding rate, is the main determinant of misfolding propensity. Although superficially this appears to differ from previously suggested kinetic models [12], it is completely consistent, with a specific interpretation of the rates. Building on this understanding, we developed a very simplified model which can be used to predict which domains are likely to be susceptible to domain-swapped misfolding. Finally, we have investigated the effect of the composition and length of the linker between the tandem repeats on the misfolding propensity.


Structural Determinants of Misfolding in Multidomain Proteins.

Tian P, Best RB - PLoS Comput. Biol. (2016)

Native states of the single domains.The experimentally determined structure of a single domain of each of the protein domains studied here: (a) SH3, (b) SH2, (c) TNfn3, (d) PDZ, (e) Titin I27, (f) Ubiquitin and (g) Protein G. The PDB accession code are 1SHG, 1TZE, 1TEN, 2VWR, 1TIT, 1UBQ and 1GB1, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4862688&req=5

pcbi.1004933.g002: Native states of the single domains.The experimentally determined structure of a single domain of each of the protein domains studied here: (a) SH3, (b) SH2, (c) TNfn3, (d) PDZ, (e) Titin I27, (f) Ubiquitin and (g) Protein G. The PDB accession code are 1SHG, 1TZE, 1TEN, 2VWR, 1TIT, 1UBQ and 1GB1, respectively.
Mentions: In order to investigate the misfolding propensity of different types of domains, we have chosen seven domains, based on (i) the superfamilies with the largest abundance of repeats in the human genome [24], (ii) proteins for which some experimental evidence for misfolding (or lack thereof) is available and (iii) proteins for which data on folding kinetics and stability is available for their circular permutants (only some of the proteins meet criterion (iii)). The circular permutant data are relevant because the misfolding intermediates suggested by simulations and experiment [7, 12] can be viewed as circular permutants of the original structure (Fig 1d). Each of the chosen proteins is illustrated in Fig 2 and described briefly in Materials and Methods. We study the folding and misfolding of the seven protein domains, using the same structure-based model as that successfully employed to treat Titin I27 [7, 12]. Molecular simulations are carried out to characterize the possible structural topologies of the misfolded intermediates and the mechanism of their formation. Our model is consistent with available experimental information for the systems studied, in terms of which proteins misfold and what misfolded structures they tend to form. We then investigated what factors influence the propensity of multidomain proteins to misfold. The simplest rationalization of the propensity of a multidomain protein for domain-swapped misfolding would seem to be offered by parameterizing a kinetic model based on the scheme shown in Fig 1, particularly for the steps Fig 1a–1b versus 1a–1d. We hypothesized that the propensity to misfold might be characterized in terms of the folding kinetics of the isolated circular permutants representing the domain-swapped intermediates in Fig 1d. However, contrary to this expectation, we found that the stability of such isolated domains, rather than their folding rate, is the main determinant of misfolding propensity. Although superficially this appears to differ from previously suggested kinetic models [12], it is completely consistent, with a specific interpretation of the rates. Building on this understanding, we developed a very simplified model which can be used to predict which domains are likely to be susceptible to domain-swapped misfolding. Finally, we have investigated the effect of the composition and length of the linker between the tandem repeats on the misfolding propensity.

Bottom Line: Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data.Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients.Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.

ABSTRACT
Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins.

No MeSH data available.