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- W2106156629 abstract "In recent experimental studies of coupled folding and binding of IDPs investigators have adapted methods from the protein folding literature whereby point mutations are used to identify the degree to which different regions are pre-folded prior to the rate limiting step in binding and folding. These approaches assume a one-to-one correspondence between coarse-grained readouts of structure such as alpha helicity and the degree of foldedness. Our previous work demonstrated a lack of correlation between alpha-helicity and the degree of disorder within unbound IDPs. Therefore, an important first step toward mutagenesis based approaches for dissecting the mechanisms of coupled folding and binding is the design of sequences that (a) have a target alpha helicity (b) have a prescribed degree of disorder and (c) retain the residues corresponding to the binding interface. We report results from an evolution algorithm (EA) that designs sequences to meet the specified criteria. We coupled this sequence design algorithm to atomistic simulations based on the ABSINTH model to quantify residue-specific helicities for each sequence. We demonstrate our approach using the sequence of PUMA, which folds upon binding to its target protein MCL-1. In the unbound ensemble, PUMA forms two uncorrelated helical segments that partition the sequence into two halves. In the bound complex, PUMA forms a single long helix. Our design strategy successfully generates sequences that span the spectrum of conformational options for the unbound PUMA that includes sequences with uncorrelated helical segments N- and C-terminal and sequences with a single helix that spans the entire sequence length. Our approach is well suited to the design of sequences for use in experiments geared toward dissecting the mechanisms of coupled folding and binding of IDPs." @default.
- W2106156629 created "2016-06-24" @default.
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- W2106156629 date "2015-01-01" @default.
- W2106156629 modified "2023-09-28" @default.
- W2106156629 title "An Evolutionary Algorithm for the Design of Different Degrees of Secondary Structure in Intrinsically Disordered Proteins (IDPs)" @default.
- W2106156629 doi "https://doi.org/10.1016/j.bpj.2014.11.1259" @default.
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