Limits...
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.


Related in: MedlinePlus

Folding/misfolding funnel.Illustration of relation between folding funnels for native and domain-swapped domains. (A) Example native contact map, highly coarse-grained for simplicity. (B) Map of all possible native-like contacts for a two-domain protein, showing native contacts in black and domain-swapped contacts in blue. (C) In the context of the two-domain sequence, the folding funnels for a single native domain (green broken line) and domain-swapped domain (red broken line) are interconnected, forming part of a single global funnel (black line). States are considered part of the native funnel if all contacts formed belong to the native state, and to the domain-swap funnel if all contacts formed belong to the domain-swapped structure. Note that only a subset of possible states are shown, for clarity (e.g. other domain-swapped species are possible). Only states with a single native-like stretch of residues are considered, whose length does not exceed that of a single folded domain. Arrows connect states differing by a single coarse grained residue flipping between native and non-native.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4862688&req=5

pcbi.1004933.g006: Folding/misfolding funnel.Illustration of relation between folding funnels for native and domain-swapped domains. (A) Example native contact map, highly coarse-grained for simplicity. (B) Map of all possible native-like contacts for a two-domain protein, showing native contacts in black and domain-swapped contacts in blue. (C) In the context of the two-domain sequence, the folding funnels for a single native domain (green broken line) and domain-swapped domain (red broken line) are interconnected, forming part of a single global funnel (black line). States are considered part of the native funnel if all contacts formed belong to the native state, and to the domain-swap funnel if all contacts formed belong to the domain-swapped structure. Note that only a subset of possible states are shown, for clarity (e.g. other domain-swapped species are possible). Only states with a single native-like stretch of residues are considered, whose length does not exceed that of a single folded domain. Arrows connect states differing by a single coarse grained residue flipping between native and non-native.

Mentions: On the other hand, we did note that there was a significant, and unexpected, correlation between the population of the final folded or misfolded states and the stability ΔGs of the corresponding intermediate. Spearman rank correlation coefficients between the folded stability ΔGs of the intermediate structure and the frequency of folded/misfolded states were 0.63, 0.94, 0.74, 0.81, 0.86 for the SH3, PDZ, TNfn3, SH2 and Titin I27 domains respectively. We note that there is also a reasonable correspondence between the relative stabilities of circular permutants in simulation and experiment, where data are available [12, 26]. How can the correlation with stabilities rather than folding rates of the isolated domains be understood? The resolution lies in the difference between the folding to either type of intermediate represented in Fig 1, and folding of the single domain “models” for these species, namely that the intermediates fold in the context of the full sequence. This is important because a large fraction of native (or native-like) contacts are shared between the native fold and the various misfolded domains. As such, the native and misfolded states can be considered as belonging to the same folding funnel, with differentiation between the two occurring at a late stage of folding. This scenario is illustrated schematically in Fig 6, in which folding to either a state with one native domain folded (on left), or one possible domain-swapped misfolded intermediate (on right) are considered. The states of the proteins are represented by very coarse-grained contact maps (e.g. representing contacts between pairs of β-strands [73], rather than between residues). As can be seen, dividing this funnel into the separate funnels by considering only native contacts for the native or circularly permuted fold would be misleading (green and red funnels respectively), since the two funnels share several configurations, and many of their states can be converted to one in the other funnel by flipping a single coarse-grained “residue” between folded and unfolded states.


Structural Determinants of Misfolding in Multidomain Proteins.

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

Folding/misfolding funnel.Illustration of relation between folding funnels for native and domain-swapped domains. (A) Example native contact map, highly coarse-grained for simplicity. (B) Map of all possible native-like contacts for a two-domain protein, showing native contacts in black and domain-swapped contacts in blue. (C) In the context of the two-domain sequence, the folding funnels for a single native domain (green broken line) and domain-swapped domain (red broken line) are interconnected, forming part of a single global funnel (black line). States are considered part of the native funnel if all contacts formed belong to the native state, and to the domain-swap funnel if all contacts formed belong to the domain-swapped structure. Note that only a subset of possible states are shown, for clarity (e.g. other domain-swapped species are possible). Only states with a single native-like stretch of residues are considered, whose length does not exceed that of a single folded domain. Arrows connect states differing by a single coarse grained residue flipping between native and non-native.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi.1004933.g006: Folding/misfolding funnel.Illustration of relation between folding funnels for native and domain-swapped domains. (A) Example native contact map, highly coarse-grained for simplicity. (B) Map of all possible native-like contacts for a two-domain protein, showing native contacts in black and domain-swapped contacts in blue. (C) In the context of the two-domain sequence, the folding funnels for a single native domain (green broken line) and domain-swapped domain (red broken line) are interconnected, forming part of a single global funnel (black line). States are considered part of the native funnel if all contacts formed belong to the native state, and to the domain-swap funnel if all contacts formed belong to the domain-swapped structure. Note that only a subset of possible states are shown, for clarity (e.g. other domain-swapped species are possible). Only states with a single native-like stretch of residues are considered, whose length does not exceed that of a single folded domain. Arrows connect states differing by a single coarse grained residue flipping between native and non-native.
Mentions: On the other hand, we did note that there was a significant, and unexpected, correlation between the population of the final folded or misfolded states and the stability ΔGs of the corresponding intermediate. Spearman rank correlation coefficients between the folded stability ΔGs of the intermediate structure and the frequency of folded/misfolded states were 0.63, 0.94, 0.74, 0.81, 0.86 for the SH3, PDZ, TNfn3, SH2 and Titin I27 domains respectively. We note that there is also a reasonable correspondence between the relative stabilities of circular permutants in simulation and experiment, where data are available [12, 26]. How can the correlation with stabilities rather than folding rates of the isolated domains be understood? The resolution lies in the difference between the folding to either type of intermediate represented in Fig 1, and folding of the single domain “models” for these species, namely that the intermediates fold in the context of the full sequence. This is important because a large fraction of native (or native-like) contacts are shared between the native fold and the various misfolded domains. As such, the native and misfolded states can be considered as belonging to the same folding funnel, with differentiation between the two occurring at a late stage of folding. This scenario is illustrated schematically in Fig 6, in which folding to either a state with one native domain folded (on left), or one possible domain-swapped misfolded intermediate (on right) are considered. The states of the proteins are represented by very coarse-grained contact maps (e.g. representing contacts between pairs of β-strands [73], rather than between residues). As can be seen, dividing this funnel into the separate funnels by considering only native contacts for the native or circularly permuted fold would be misleading (green and red funnels respectively), since the two funnels share several configurations, and many of their states can be converted to one in the other funnel by flipping a single coarse-grained “residue” between folded and unfolded states.

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.


Related in: MedlinePlus