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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.


Misfolding mechanism of tandem domains.The schematic shows the native-like stable intermediates populated en route to native folding (upper) or misfolding (lower), and used to explain single-molecule and ensemble folding kinetics [12]. The correctly folded dimer (c) is formed from the unfolded chain (a) via an intermediate (b) in which either of the domains folds natively. The misfolded dimers (e) form via initial formation of a domain-swapped “central domain” (d) formed by the central regions of the sequence, followed by a “terminal domain” formed by the terminal regions of the sequence. The blue and red dots indicate the N- and C- terminal respectively, in each case. The N- and C-terminal halves of the chain are also coloured in blue and red respectively.
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pcbi.1004933.g001: Misfolding mechanism of tandem domains.The schematic shows the native-like stable intermediates populated en route to native folding (upper) or misfolding (lower), and used to explain single-molecule and ensemble folding kinetics [12]. The correctly folded dimer (c) is formed from the unfolded chain (a) via an intermediate (b) in which either of the domains folds natively. The misfolded dimers (e) form via initial formation of a domain-swapped “central domain” (d) formed by the central regions of the sequence, followed by a “terminal domain” formed by the terminal regions of the sequence. The blue and red dots indicate the N- and C- terminal respectively, in each case. The N- and C-terminal halves of the chain are also coloured in blue and red respectively.

Mentions: Protein misfolding and aggregation are well-known for their association with amyloidosis and other diseases [1, 2]. Proteins with two or more domains are abundant in higher organisms, accounting for up to 70% of all eukaryotic proteins, and domain-repeat proteins in particular occupy a fraction up to 20% of the proteomes in multicellular organisms [3, 4], therefore their folding is of considerable relevance [5]. Since there is often some sequence similarity between domains with the same structure, it is easily possible to imagine that multidomain proteins containing repeats of domains with the same fold might be susceptible to misfolding. Indeed, misfolding of multidomain proteins has been observed in many protein families [6]. Single molecule techniques have been particularly powerful for studying folding/misfolding of such proteins, in particular Förster resonance energy transfer (FRET) and atomic force microscopy (AFM). For instance, recent studies using single-molecule FRET, in conjunction with coarse-grained simulations, have revealed the presence of domain-swapped misfolded states in tandem repeats of the immunoglobulin-like domain I27 from the muscle protein Titin [7] (an example is shown in Fig 1e). Domain-swapping [2] involves the exchange of secondary structure elements between two protein domains with the same structure. Remarkably, these misfolded states are stable for days, much longer than the unfolding time of a single Titin domain. The domain-swapped misfolds identified in the Titin I27 domains are also consistent with earlier observations of misfolding in the same protein by AFM, although not given a structural interpretation at the time [8]. In addition, AFM experiments have revealed what appears to be a similar type of misfolding in polyproteins consisting of eight tandem repeats of the same fibronectin type III domain from tenascin (TNfn3) [9], as well as in native constructs of tenascin [8], and between the N-terminal domains of human γD-crystallin when linked in a synthetic oligomer [10].


Structural Determinants of Misfolding in Multidomain Proteins.

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

Misfolding mechanism of tandem domains.The schematic shows the native-like stable intermediates populated en route to native folding (upper) or misfolding (lower), and used to explain single-molecule and ensemble folding kinetics [12]. The correctly folded dimer (c) is formed from the unfolded chain (a) via an intermediate (b) in which either of the domains folds natively. The misfolded dimers (e) form via initial formation of a domain-swapped “central domain” (d) formed by the central regions of the sequence, followed by a “terminal domain” formed by the terminal regions of the sequence. The blue and red dots indicate the N- and C- terminal respectively, in each case. The N- and C-terminal halves of the chain are also coloured in blue and red respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi.1004933.g001: Misfolding mechanism of tandem domains.The schematic shows the native-like stable intermediates populated en route to native folding (upper) or misfolding (lower), and used to explain single-molecule and ensemble folding kinetics [12]. The correctly folded dimer (c) is formed from the unfolded chain (a) via an intermediate (b) in which either of the domains folds natively. The misfolded dimers (e) form via initial formation of a domain-swapped “central domain” (d) formed by the central regions of the sequence, followed by a “terminal domain” formed by the terminal regions of the sequence. The blue and red dots indicate the N- and C- terminal respectively, in each case. The N- and C-terminal halves of the chain are also coloured in blue and red respectively.
Mentions: Protein misfolding and aggregation are well-known for their association with amyloidosis and other diseases [1, 2]. Proteins with two or more domains are abundant in higher organisms, accounting for up to 70% of all eukaryotic proteins, and domain-repeat proteins in particular occupy a fraction up to 20% of the proteomes in multicellular organisms [3, 4], therefore their folding is of considerable relevance [5]. Since there is often some sequence similarity between domains with the same structure, it is easily possible to imagine that multidomain proteins containing repeats of domains with the same fold might be susceptible to misfolding. Indeed, misfolding of multidomain proteins has been observed in many protein families [6]. Single molecule techniques have been particularly powerful for studying folding/misfolding of such proteins, in particular Förster resonance energy transfer (FRET) and atomic force microscopy (AFM). For instance, recent studies using single-molecule FRET, in conjunction with coarse-grained simulations, have revealed the presence of domain-swapped misfolded states in tandem repeats of the immunoglobulin-like domain I27 from the muscle protein Titin [7] (an example is shown in Fig 1e). Domain-swapping [2] involves the exchange of secondary structure elements between two protein domains with the same structure. Remarkably, these misfolded states are stable for days, much longer than the unfolding time of a single Titin domain. The domain-swapped misfolds identified in the Titin I27 domains are also consistent with earlier observations of misfolding in the same protein by AFM, although not given a structural interpretation at the time [8]. In addition, AFM experiments have revealed what appears to be a similar type of misfolding in polyproteins consisting of eight tandem repeats of the same fibronectin type III domain from tenascin (TNfn3) [9], as well as in native constructs of tenascin [8], and between the N-terminal domains of human γD-crystallin when linked in a synthetic oligomer [10].

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.