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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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Structure, cartoon and contact map of WT AKE.(A) WT AKE (open state, PDB: 4AKE, chain A) colored by domain: CORE (grey; residues 1–29, 68–117 (CORE-N) and 161–214 (CORE-C)), NMP (green; residues 30–67) and LID (orange; residues 118–160). The conformational transitions of LID and NMP are indicated by red arrows. All structures in this article were drawn using the PyMOL Molecular Graphics System (Version 1.4.1 Schrödinger, LLC). (B) Cartoon showing the domain organization of AKE on the folded structure (top) and the sequence (bottom) colored as in A. The CORE domain is split into three grey regions because of domain insertion. (C) The C-α contact map of WT AKE. X and Y axes represent residue number. Secondary structure is shown along the axes: α helices are empty boxes and β strands are filled boxes. The contacts are colored according to their location (CORE: grey, NMP: green, LID: orange). The absolute contact order of these regions is: LID: 15.27, NMP: 10.42, CORE: 62.87, and the entire WT AKE: 46.04. The red contacts are closed state specific contacts that drive the conformational transitions.
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pcbi-1003938-g001: Structure, cartoon and contact map of WT AKE.(A) WT AKE (open state, PDB: 4AKE, chain A) colored by domain: CORE (grey; residues 1–29, 68–117 (CORE-N) and 161–214 (CORE-C)), NMP (green; residues 30–67) and LID (orange; residues 118–160). The conformational transitions of LID and NMP are indicated by red arrows. All structures in this article were drawn using the PyMOL Molecular Graphics System (Version 1.4.1 Schrödinger, LLC). (B) Cartoon showing the domain organization of AKE on the folded structure (top) and the sequence (bottom) colored as in A. The CORE domain is split into three grey regions because of domain insertion. (C) The C-α contact map of WT AKE. X and Y axes represent residue number. Secondary structure is shown along the axes: α helices are empty boxes and β strands are filled boxes. The contacts are colored according to their location (CORE: grey, NMP: green, LID: orange). The absolute contact order of these regions is: LID: 15.27, NMP: 10.42, CORE: 62.87, and the entire WT AKE: 46.04. The red contacts are closed state specific contacts that drive the conformational transitions.

Mentions: The presence of multiple domains in proteins can lead to interactions between partially folded domains and in turn to increased misfolding and aggregation [1]. Nevertheless, several multi-domain proteins fold reversibly in vitro [2], [3]. Cooperative folding, the all or nothing folding of a protein with the population of few intermediates, reduces partially folded states [4]. It has been hypothesized that folding cooperativity has evolved in proteins to avoid misfolding and decrease aggregation propensity [5]. Strong inter-domain interactions have been implicated in the cooperative folding of multi-domain proteins [1], [6]–[10]. Here, we computationally investigate the role of inter-domain interactions in the folding of the three-domain protein E. coli Adenylate kinase (AKE) (Fig. 1) and find that an altogether different method, domain insertion, promotes folding cooperativity. Domain insertion is the presence of the amino acid sequence of one domain (the inserted domain) within the sequence of another domain (the discontinuous domain) (Fig. 1B). In the three-dimensional structure, the discontinuous (along the protein chain) amino acid stretches of the discontinuous domain (Fig. 1B, bottom, grey segments) fold together into a single domain (Fig. 1B, top, grey regions).


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)

Structure, cartoon and contact map of WT AKE.(A) WT AKE (open state, PDB: 4AKE, chain A) colored by domain: CORE (grey; residues 1–29, 68–117 (CORE-N) and 161–214 (CORE-C)), NMP (green; residues 30–67) and LID (orange; residues 118–160). The conformational transitions of LID and NMP are indicated by red arrows. All structures in this article were drawn using the PyMOL Molecular Graphics System (Version 1.4.1 Schrödinger, LLC). (B) Cartoon showing the domain organization of AKE on the folded structure (top) and the sequence (bottom) colored as in A. The CORE domain is split into three grey regions because of domain insertion. (C) The C-α contact map of WT AKE. X and Y axes represent residue number. Secondary structure is shown along the axes: α helices are empty boxes and β strands are filled boxes. The contacts are colored according to their location (CORE: grey, NMP: green, LID: orange). The absolute contact order of these regions is: LID: 15.27, NMP: 10.42, CORE: 62.87, and the entire WT AKE: 46.04. The red contacts are closed state specific contacts that drive the conformational transitions.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1003938-g001: Structure, cartoon and contact map of WT AKE.(A) WT AKE (open state, PDB: 4AKE, chain A) colored by domain: CORE (grey; residues 1–29, 68–117 (CORE-N) and 161–214 (CORE-C)), NMP (green; residues 30–67) and LID (orange; residues 118–160). The conformational transitions of LID and NMP are indicated by red arrows. All structures in this article were drawn using the PyMOL Molecular Graphics System (Version 1.4.1 Schrödinger, LLC). (B) Cartoon showing the domain organization of AKE on the folded structure (top) and the sequence (bottom) colored as in A. The CORE domain is split into three grey regions because of domain insertion. (C) The C-α contact map of WT AKE. X and Y axes represent residue number. Secondary structure is shown along the axes: α helices are empty boxes and β strands are filled boxes. The contacts are colored according to their location (CORE: grey, NMP: green, LID: orange). The absolute contact order of these regions is: LID: 15.27, NMP: 10.42, CORE: 62.87, and the entire WT AKE: 46.04. The red contacts are closed state specific contacts that drive the conformational transitions.
Mentions: The presence of multiple domains in proteins can lead to interactions between partially folded domains and in turn to increased misfolding and aggregation [1]. Nevertheless, several multi-domain proteins fold reversibly in vitro [2], [3]. Cooperative folding, the all or nothing folding of a protein with the population of few intermediates, reduces partially folded states [4]. It has been hypothesized that folding cooperativity has evolved in proteins to avoid misfolding and decrease aggregation propensity [5]. Strong inter-domain interactions have been implicated in the cooperative folding of multi-domain proteins [1], [6]–[10]. Here, we computationally investigate the role of inter-domain interactions in the folding of the three-domain protein E. coli Adenylate kinase (AKE) (Fig. 1) and find that an altogether different method, domain insertion, promotes folding cooperativity. Domain insertion is the presence of the amino acid sequence of one domain (the inserted domain) within the sequence of another domain (the discontinuous domain) (Fig. 1B). In the three-dimensional structure, the discontinuous (along the protein chain) amino acid stretches of the discontinuous domain (Fig. 1B, bottom, grey segments) fold together into a single domain (Fig. 1B, top, grey regions).

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