Folding Properties of Cytosine Monophosphate Kinase from E. coli Indicate Stabilization through an Additional Insert in the NMP Binding Domain

Beitlich, T.; Lorenz, Thorsten; Reinstein, Jochen

doi:10.1371/journal.pone.0078384

Cited by 3 publications

(3 citation statements)

References 51 publications

(77 reference statements)

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“…Our predicted folding pathway (SI Appendix, Fig. S6D) is in agreement with previous studies, which show that DHFR folds in multiple steps with fast relaxation times and no significant off-pathway intermediates (41,42).…”

Section: Kinetic Modeling Predicts That Vectorial Synthesis Helps Marr Cir-supporting

confidence: 91%

“…S5). Our simulations predict that nonnative kinetic traps lead to very slow CMK folding, consistent with previous experimental findings that the protein refolds on timescales of minutes (41). We further For each protein, the native structure (A-D, Top) and a sample structure that has yet to undergo the rate-limiting folding step (A-D, Bottom) are shown, with C-terminal nonnative contacts that must be broken prior to this step highlighted in red.…”

Section: Kinetic Modeling Predicts That Vectorial Synthesis Helps Marr Cir-supporting

confidence: 86%

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Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps

Bitran

Jacobs

Zhai

et al. 2020

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

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Many large proteins suffer from slow or inefficient folding in vitro. It has long been known that this problem can be alleviated in vivo if proteins start folding cotranslationally. However, the molecular mechanisms underlying this improvement have not been well established. To address this question, we use an all-atom simulation-based algorithm to compute the folding properties of various large protein domains as a function of nascent chain length. We find that for certain proteins, there exists a narrow window of lengths that confers both thermodynamic stability and fast folding kinetics. Beyond these lengths, folding is drastically slowed by nonnative interactions involving C-terminal residues. Thus, cotranslational folding is predicted to be beneficial because it allows proteins to take advantage of this optimal window of lengths and thus avoid kinetic traps. Interestingly, many of these proteins’ sequences contain conserved rare codons that may slow down synthesis at this optimal window, suggesting that synthesis rates may be evolutionarily tuned to optimize folding. Using kinetic modeling, we show that under certain conditions, such a slowdown indeed improves cotranslational folding efficiency by giving these nascent chains more time to fold. In contrast, other proteins are predicted not to benefit from cotranslational folding due to a lack of significant nonnative interactions, and indeed these proteins’ sequences lack conserved C-terminal rare codons. Together, these results shed light on the factors that promote proper protein folding in the cell and how biomolecular self-assembly may be optimized evolutionarily.

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Section: Kinetic Modeling Predicts That Vectorial Synthesis Helps Marr Cir-supporting

confidence: 91%

Section: Kinetic Modeling Predicts That Vectorial Synthesis Helps Marr Cir-supporting

confidence: 86%

Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps

Bitran

Jacobs

Zhai

et al. 2020

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

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“…Each N-BAR monomer contains four proline residues which are all in the trans -conformation in the native state. In principle, all of the Xaa-Pro peptide bonds can produce slow isomerization reactions because in the unfolded state an equilibrium between the cis and trans conformation can evolve[ 40 , 55 ]. The ratio between both conformations is determined by the preceding amino acid.…”

Section: Discussionmentioning

confidence: 99%

Protein Folding Mechanism of the Dimeric AmphiphysinII/Bin1 N-BAR Domain

Gruber

Balbach

2015

PLoS ONE

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The human AmphyphisinII/Bin1 N-BAR domain belongs to the BAR domain superfamily, whose members sense and generate membrane curvatures. The N-BAR domain is a 57 kDa homodimeric protein comprising a six helix bundle. Here we report the protein folding mechanism of this protein as a representative of this protein superfamily. The concentration dependent thermodynamic stability was studied by urea equilibrium transition curves followed by fluorescence and far-UV CD spectroscopy. Kinetic unfolding and refolding experiments, including rapid double and triple mixing techniques, allowed to unravel the complex folding behavior of N-BAR. The equilibrium unfolding transition curve can be described by a two-state process, while the folding kinetics show four refolding phases, an additional burst reaction and two unfolding phases. All fast refolding phases show a rollover in the chevron plot but only one of these phases depends on the protein concentration reporting the dimerization step. Secondary structure formation occurs during the three fast refolding phases. The slowest phase can be assigned to a proline isomerization. All kinetic experiments were also followed by fluorescence anisotropy detection to verify the assignment of the dimerization step to the respective folding phase. Based on these experiments we propose for N-BAR two parallel folding pathways towards the homodimeric native state depending on the proline conformation in the unfolded state.

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Co-translational folding allows misfolding-prone proteins to circumvent deep kinetic traps

Bitran

Jacobs²,

Zhai³

et al. 2019

Preprint

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Many large proteins suffer from slow or inefficient folding in vitro.Here, we provide evidence that this problem can be alleviated in vivo if proteins start folding co-translationally. Using an all-atom simulation-based algorithm, we compute the folding properties of various large protein domains as a function of nascent chain length, and find that for certain proteins, there exists a narrow window of lengths that confers both thermodynamic stability and fast folding kinetics. Beyond these lengths, folding is drastically slowed by non-native interactions involving C-terminal residues. Thus, cotranslational folding is predicted to be beneficial because it allows proteins to take advantage of this optimal window of lengths and thus avoid kinetic traps. Interestingly, many of these proteins' sequences contain conserved rare codons that may slow down synthesis at this optimal window, suggesting that synthesis rates may be evolutionarily tuned to optimize folding. Using kinetic modelling, we show that under certain conditions, such a slowdown indeed improves co-translational folding efficiency by giving these nascent chains more time to fold. In contrast, other proteins are predicted not to benefit from co-translational folding due to a lack of significant non-native interactions, and indeed these proteins' sequences lack conserved C-terminal rare codons. Together, these results shed light on the factors that promote proper protein folding in the cell, and how biomolecular self-assembly may be optimized evolutionarily.

show abstract

Folding Properties of Cytosine Monophosphate Kinase from E. coli Indicate Stabilization through an Additional Insert in the NMP Binding Domain

Cited by 3 publications

References 51 publications

Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps

Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps

Protein Folding Mechanism of the Dimeric AmphiphysinII/Bin1 N-BAR Domain

Co-translational folding allows misfolding-prone proteins to circumvent deep kinetic traps

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