Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain
The ankyrin repeat (AR) domain of IκBα consists of a cooperative folding unit of roughly four ARs (AR1-AR4) and of two weakly folded repeats (AR5 and AR6). The kinetic folding mechanism of the cooperative subdomain, IκBα 67-206, was analyzed using rapid mixing techniques. Despite its apparent archit...
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2011
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00222836_v408_n1_p163_Devries http://hdl.handle.net/20.500.12110/paper_00222836_v408_n1_p163_Devries |
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paper:paper_00222836_v408_n1_p163_Devries2023-06-08T14:48:44Z Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain α value; folding landscapeNFκB protein folding repeat protein ankyrin ankyrin 1 ankyrin 2 ankyrin 3 ankyrin 4 ankyrin 5 ankyrin 6 I kappa B alpha mutant protein unclassified drug article gene deletion gene mutation human kinetics priority journal protein analysis protein folding protein stability temperature Amino Acid Sequence Ankyrin Repeat Ankyrins Consensus Sequence Humans I-kappa B Proteins Kinetics Models, Molecular Molecular Sequence Data Mutation Protein Folding Sequence Homology, Amino Acid The ankyrin repeat (AR) domain of IκBα consists of a cooperative folding unit of roughly four ARs (AR1-AR4) and of two weakly folded repeats (AR5 and AR6). The kinetic folding mechanism of the cooperative subdomain, IκBα 67-206, was analyzed using rapid mixing techniques. Despite its apparent architectural simplicity, IκBα 67-206 displays complex folding kinetics, with two sequential on-pathway high-energy intermediates. The effect of mutations to or away from the consensus sequences of ARs on folding behavior was analyzed, particularly the GXTPLHLA motif, which have not been examined in detail previously. Mutations toward the consensus generally resulted in an increase in folding stability, whereas mutations away from the consensus resulted in decreased overall stability. We determined the free energy change upon mutation for three sequential transition state ensembles along the folding route for 16 mutants. We show that folding initiates with the formation of the interface of the outer helices of AR3 and AR4, and then proceeds to consolidate structure in these repeats. Subsequently, AR1 and AR2 fold in a concerted way in a single kinetic step. We show that this mechanism is robust to the presence of AR5 and AR6 as they do not strongly affect the folding kinetics. Overall, the protein appears to fold on a rather smooth energy landscape, where the folding mechanism conforms a one-dimensional approximation. However, we note that the AR does not necessarily act as a single folding element. © 2011 Elsevier Ltd. 2011 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00222836_v408_n1_p163_Devries http://hdl.handle.net/20.500.12110/paper_00222836_v408_n1_p163_Devries |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
α value; folding landscapeNFκB protein folding repeat protein ankyrin ankyrin 1 ankyrin 2 ankyrin 3 ankyrin 4 ankyrin 5 ankyrin 6 I kappa B alpha mutant protein unclassified drug article gene deletion gene mutation human kinetics priority journal protein analysis protein folding protein stability temperature Amino Acid Sequence Ankyrin Repeat Ankyrins Consensus Sequence Humans I-kappa B Proteins Kinetics Models, Molecular Molecular Sequence Data Mutation Protein Folding Sequence Homology, Amino Acid |
| spellingShingle |
α value; folding landscapeNFκB protein folding repeat protein ankyrin ankyrin 1 ankyrin 2 ankyrin 3 ankyrin 4 ankyrin 5 ankyrin 6 I kappa B alpha mutant protein unclassified drug article gene deletion gene mutation human kinetics priority journal protein analysis protein folding protein stability temperature Amino Acid Sequence Ankyrin Repeat Ankyrins Consensus Sequence Humans I-kappa B Proteins Kinetics Models, Molecular Molecular Sequence Data Mutation Protein Folding Sequence Homology, Amino Acid Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain |
| topic_facet |
α value; folding landscapeNFκB protein folding repeat protein ankyrin ankyrin 1 ankyrin 2 ankyrin 3 ankyrin 4 ankyrin 5 ankyrin 6 I kappa B alpha mutant protein unclassified drug article gene deletion gene mutation human kinetics priority journal protein analysis protein folding protein stability temperature Amino Acid Sequence Ankyrin Repeat Ankyrins Consensus Sequence Humans I-kappa B Proteins Kinetics Models, Molecular Molecular Sequence Data Mutation Protein Folding Sequence Homology, Amino Acid |
| description |
The ankyrin repeat (AR) domain of IκBα consists of a cooperative folding unit of roughly four ARs (AR1-AR4) and of two weakly folded repeats (AR5 and AR6). The kinetic folding mechanism of the cooperative subdomain, IκBα 67-206, was analyzed using rapid mixing techniques. Despite its apparent architectural simplicity, IκBα 67-206 displays complex folding kinetics, with two sequential on-pathway high-energy intermediates. The effect of mutations to or away from the consensus sequences of ARs on folding behavior was analyzed, particularly the GXTPLHLA motif, which have not been examined in detail previously. Mutations toward the consensus generally resulted in an increase in folding stability, whereas mutations away from the consensus resulted in decreased overall stability. We determined the free energy change upon mutation for three sequential transition state ensembles along the folding route for 16 mutants. We show that folding initiates with the formation of the interface of the outer helices of AR3 and AR4, and then proceeds to consolidate structure in these repeats. Subsequently, AR1 and AR2 fold in a concerted way in a single kinetic step. We show that this mechanism is robust to the presence of AR5 and AR6 as they do not strongly affect the folding kinetics. Overall, the protein appears to fold on a rather smooth energy landscape, where the folding mechanism conforms a one-dimensional approximation. However, we note that the AR does not necessarily act as a single folding element. © 2011 Elsevier Ltd. |
| title |
Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain |
| title_short |
Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain |
| title_full |
Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain |
| title_fullStr |
Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain |
| title_full_unstemmed |
Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain |
| title_sort |
folding kinetics of the cooperatively folded subdomain of the iκbα ankyrin repeat domain |
| publishDate |
2011 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00222836_v408_n1_p163_Devries http://hdl.handle.net/20.500.12110/paper_00222836_v408_n1_p163_Devries |
| _version_ |
1768543263552176128 |