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In the multi-domain protein adenylate kinase, domain insertion facilitates cooperative folding while accommodating function at domain interfaces.

Giri Rao VV, Gosavi S - PLoS Comput. Biol. (2014)

Bottom Line: Folding cooperativity, the all or nothing folding of a protein, can reduce this aggregation propensity.In AKE, these interactions help promote conformational dynamics limited catalysis.Finally, using structural bioinformatics, we suggest that domain insertion may also facilitate the cooperative folding of other multi-domain proteins.

View Article: PubMed Central - PubMed

Affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.

ABSTRACT
Having multiple domains in proteins can lead to partial folding and increased aggregation. Folding cooperativity, the all or nothing folding of a protein, can reduce this aggregation propensity. In agreement with bulk experiments, a coarse-grained structure-based model of the three-domain protein, E. coli Adenylate kinase (AKE), folds cooperatively. Domain interfaces have previously been implicated in the cooperative folding of multi-domain proteins. To understand their role in AKE folding, we computationally create mutants with deleted inter-domain interfaces and simulate their folding. We find that inter-domain interfaces play a minor role in the folding cooperativity of AKE. On further analysis, we find that unlike other multi-domain proteins whose folding has been studied, the domains of AKE are not singly-linked. Two of its domains have two linkers to the third one, i.e., they are inserted into the third one. We use circular permutation to modify AKE chain-connectivity and convert inserted-domains into singly-linked domains. We find that domain insertion in AKE achieves the following: (1) It facilitates folding cooperativity even when domains have different stabilities. Insertion constrains the N- and C-termini of inserted domains and stabilizes their folded states. Therefore, domains that perform conformational transitions can be smaller with fewer stabilizing interactions. (2) Inter-domain interactions are not needed to promote folding cooperativity and can be tuned for function. In AKE, these interactions help promote conformational dynamics limited catalysis. Finally, using structural bioinformatics, we suggest that domain insertion may also facilitate the cooperative folding of other multi-domain proteins.

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Related in: MedlinePlus

Absolute contact order (ACO), chain length and packing fraction of insert-discontinuous domain pairs from the Pfam-A database.We extract 1713 protein chains from Pfam which have an inserted domain and an associated PDB ID and a chainID. For each chain the (A) ACO, (B) the chain length and (C) the packing fraction of the inserted ( = x) and the discontinuous domains ( = y) are calculated separately and marked as filled grey circles at the (x, y) point. The ACO, chain length and packing fraction for a majority of the insert-discontinuous domain pairs lie above the y = x line (marked in black in A–C). Fig. S6 represents the same data coloured according to the Pfam family of the inserted domain and corroborates this inference at the Pfam family level.
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pcbi-1003938-g008: Absolute contact order (ACO), chain length and packing fraction of insert-discontinuous domain pairs from the Pfam-A database.We extract 1713 protein chains from Pfam which have an inserted domain and an associated PDB ID and a chainID. For each chain the (A) ACO, (B) the chain length and (C) the packing fraction of the inserted ( = x) and the discontinuous domains ( = y) are calculated separately and marked as filled grey circles at the (x, y) point. The ACO, chain length and packing fraction for a majority of the insert-discontinuous domain pairs lie above the y = x line (marked in black in A–C). Fig. S6 represents the same data coloured according to the Pfam family of the inserted domain and corroborates this inference at the Pfam family level.

Mentions: We extract the structures of diverse families of multi-domain proteins with inserts (36 inserted domain families in total) from the Pfam database [39] and calculate three structural parameters, which have previously been correlated with the folding properties of single domain proteins (Fig. 8). For each protein chain (there are a total of 1713 chains), we compare the structural parameters of the inserted domain to those of the discontinuous domain in order to understand if domain insertion can stabilize the inserted domain and increase folding cooperativity in other multi-domain proteins. Further details of the data collation and analysis are given in the SI Methods.


In the multi-domain protein adenylate kinase, domain insertion facilitates cooperative folding while accommodating function at domain interfaces.

Giri Rao VV, Gosavi S - PLoS Comput. Biol. (2014)

Absolute contact order (ACO), chain length and packing fraction of insert-discontinuous domain pairs from the Pfam-A database.We extract 1713 protein chains from Pfam which have an inserted domain and an associated PDB ID and a chainID. For each chain the (A) ACO, (B) the chain length and (C) the packing fraction of the inserted ( = x) and the discontinuous domains ( = y) are calculated separately and marked as filled grey circles at the (x, y) point. The ACO, chain length and packing fraction for a majority of the insert-discontinuous domain pairs lie above the y = x line (marked in black in A–C). Fig. S6 represents the same data coloured according to the Pfam family of the inserted domain and corroborates this inference at the Pfam family level.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230728&req=5

pcbi-1003938-g008: Absolute contact order (ACO), chain length and packing fraction of insert-discontinuous domain pairs from the Pfam-A database.We extract 1713 protein chains from Pfam which have an inserted domain and an associated PDB ID and a chainID. For each chain the (A) ACO, (B) the chain length and (C) the packing fraction of the inserted ( = x) and the discontinuous domains ( = y) are calculated separately and marked as filled grey circles at the (x, y) point. The ACO, chain length and packing fraction for a majority of the insert-discontinuous domain pairs lie above the y = x line (marked in black in A–C). Fig. S6 represents the same data coloured according to the Pfam family of the inserted domain and corroborates this inference at the Pfam family level.
Mentions: We extract the structures of diverse families of multi-domain proteins with inserts (36 inserted domain families in total) from the Pfam database [39] and calculate three structural parameters, which have previously been correlated with the folding properties of single domain proteins (Fig. 8). For each protein chain (there are a total of 1713 chains), we compare the structural parameters of the inserted domain to those of the discontinuous domain in order to understand if domain insertion can stabilize the inserted domain and increase folding cooperativity in other multi-domain proteins. Further details of the data collation and analysis are given in the SI Methods.

Bottom Line: Folding cooperativity, the all or nothing folding of a protein, can reduce this aggregation propensity.In AKE, these interactions help promote conformational dynamics limited catalysis.Finally, using structural bioinformatics, we suggest that domain insertion may also facilitate the cooperative folding of other multi-domain proteins.

View Article: PubMed Central - PubMed

Affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.

ABSTRACT
Having multiple domains in proteins can lead to partial folding and increased aggregation. Folding cooperativity, the all or nothing folding of a protein, can reduce this aggregation propensity. In agreement with bulk experiments, a coarse-grained structure-based model of the three-domain protein, E. coli Adenylate kinase (AKE), folds cooperatively. Domain interfaces have previously been implicated in the cooperative folding of multi-domain proteins. To understand their role in AKE folding, we computationally create mutants with deleted inter-domain interfaces and simulate their folding. We find that inter-domain interfaces play a minor role in the folding cooperativity of AKE. On further analysis, we find that unlike other multi-domain proteins whose folding has been studied, the domains of AKE are not singly-linked. Two of its domains have two linkers to the third one, i.e., they are inserted into the third one. We use circular permutation to modify AKE chain-connectivity and convert inserted-domains into singly-linked domains. We find that domain insertion in AKE achieves the following: (1) It facilitates folding cooperativity even when domains have different stabilities. Insertion constrains the N- and C-termini of inserted domains and stabilizes their folded states. Therefore, domains that perform conformational transitions can be smaller with fewer stabilizing interactions. (2) Inter-domain interactions are not needed to promote folding cooperativity and can be tuned for function. In AKE, these interactions help promote conformational dynamics limited catalysis. Finally, using structural bioinformatics, we suggest that domain insertion may also facilitate the cooperative folding of other multi-domain proteins.

Show MeSH
Related in: MedlinePlus