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An interdomain sector mediating allostery in Hsp70 molecular chaperones.

Smock RG, Rivoire O, Russ WP, Swain JF, Leibler S, Ranganathan R, Gierasch LM - Mol. Syst. Biol. (2010)

Bottom Line: Here, we generalize the statistical coupling analysis to simultaneously evaluate co-evolution between protein residues and functional divergence between sequences in protein sub-families.Applying this method in the Hsp70/110 protein family, we identify a sparse but structurally contiguous group of co-evolving residues called a 'sector', which is an attribute of the allosteric Hsp70 sub-family that links the functional sites of the two domains across a specific interdomain interface.The identification of the Hsp70 sector provides a basis for further experiments to understand the mechanism of allostery and introduces the idea that cooperativity between interacting proteins or protein domains can be mediated by shared sectors.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA.

ABSTRACT
Allosteric coupling between protein domains is fundamental to many cellular processes. For example, Hsp70 molecular chaperones use ATP binding by their actin-like N-terminal ATPase domain to control substrate interactions in their C-terminal substrate-binding domain, a reaction that is critical for protein folding in cells. Here, we generalize the statistical coupling analysis to simultaneously evaluate co-evolution between protein residues and functional divergence between sequences in protein sub-families. Applying this method in the Hsp70/110 protein family, we identify a sparse but structurally contiguous group of co-evolving residues called a 'sector', which is an attribute of the allosteric Hsp70 sub-family that links the functional sites of the two domains across a specific interdomain interface. Mutagenesis of Escherichia coli DnaK supports the conclusion that this interdomain sector underlies the allosteric coupling in this protein family. The identification of the Hsp70 sector provides a basis for further experiments to understand the mechanism of allostery and introduces the idea that cooperativity between interacting proteins or protein domains can be mediated by shared sectors.

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A model for Hsp70 interdomain allostery. (A) In the ADP-bound state, nucleotide-binding and substrate-binding domains tumble independently of one another, the hydrophobic interdomain linker is relatively exposed, the β-sandwich sub-domain is relatively ordered, the lid sub-domain is closed, and substrate binds with high affinity (PDB codes 1DKG and 1DKZ). (B) ATP binding is accompanied by conformational changes within the nucleotide-binding domain, domain docking with participation of the interdomain linker, opening of the lid sub-domain, reduction in order at the substrate-binding site within the β-sandwich, and loss of substrate-binding affinity.
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f1: A model for Hsp70 interdomain allostery. (A) In the ADP-bound state, nucleotide-binding and substrate-binding domains tumble independently of one another, the hydrophobic interdomain linker is relatively exposed, the β-sandwich sub-domain is relatively ordered, the lid sub-domain is closed, and substrate binds with high affinity (PDB codes 1DKG and 1DKZ). (B) ATP binding is accompanied by conformational changes within the nucleotide-binding domain, domain docking with participation of the interdomain linker, opening of the lid sub-domain, reduction in order at the substrate-binding site within the β-sandwich, and loss of substrate-binding affinity.

Mentions: Allostery is a biologically critical property by which distantly positioned functional surfaces on proteins functionally interact. This property remains difficult to elucidate at a mechanistic level (Smock and Gierasch, 2009) because long-range coupling within proteins arises from the cooperative action of groups of amino acids. As a case study, consider the Hsp70 molecular chaperones, a large and diverse family of two-domain allosteric proteins required for cellular viability in nearly every organism (Figure 1) (Mayer and Bukau, 2005). In the ADP-bound state, the two domains act independently, the C-terminal substrate-binding domain displays a stable configuration in which the so-called ‘lid' region is docked against the β-sandwich subdomain, and substrates bind with relatively high affinity (Figure 1A) (Moro et al, 2003; Swain et al, 2007; Bertelsen et al, 2009). Exchange of ADP for ATP in the N-terminal nucleotide-binding domain causes significant local and propagated conformational change, formation of an interface with the substrate-binding domain, opening of the lid subdomain, and a decrease in the binding affinity for substrates (Figure 1B) (Rist et al, 2006; Swain et al, 2007). Upon ATP hydrolysis by the nucleotide-binding domain, Hsp70 is returned to the ADP-bound configuration suitable for another round of substrate binding and release. This process of cyclical substrate binding and release underlies all biological functions of Hsp70 proteins.


An interdomain sector mediating allostery in Hsp70 molecular chaperones.

Smock RG, Rivoire O, Russ WP, Swain JF, Leibler S, Ranganathan R, Gierasch LM - Mol. Syst. Biol. (2010)

A model for Hsp70 interdomain allostery. (A) In the ADP-bound state, nucleotide-binding and substrate-binding domains tumble independently of one another, the hydrophobic interdomain linker is relatively exposed, the β-sandwich sub-domain is relatively ordered, the lid sub-domain is closed, and substrate binds with high affinity (PDB codes 1DKG and 1DKZ). (B) ATP binding is accompanied by conformational changes within the nucleotide-binding domain, domain docking with participation of the interdomain linker, opening of the lid sub-domain, reduction in order at the substrate-binding site within the β-sandwich, and loss of substrate-binding affinity.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2964120&req=5

f1: A model for Hsp70 interdomain allostery. (A) In the ADP-bound state, nucleotide-binding and substrate-binding domains tumble independently of one another, the hydrophobic interdomain linker is relatively exposed, the β-sandwich sub-domain is relatively ordered, the lid sub-domain is closed, and substrate binds with high affinity (PDB codes 1DKG and 1DKZ). (B) ATP binding is accompanied by conformational changes within the nucleotide-binding domain, domain docking with participation of the interdomain linker, opening of the lid sub-domain, reduction in order at the substrate-binding site within the β-sandwich, and loss of substrate-binding affinity.
Mentions: Allostery is a biologically critical property by which distantly positioned functional surfaces on proteins functionally interact. This property remains difficult to elucidate at a mechanistic level (Smock and Gierasch, 2009) because long-range coupling within proteins arises from the cooperative action of groups of amino acids. As a case study, consider the Hsp70 molecular chaperones, a large and diverse family of two-domain allosteric proteins required for cellular viability in nearly every organism (Figure 1) (Mayer and Bukau, 2005). In the ADP-bound state, the two domains act independently, the C-terminal substrate-binding domain displays a stable configuration in which the so-called ‘lid' region is docked against the β-sandwich subdomain, and substrates bind with relatively high affinity (Figure 1A) (Moro et al, 2003; Swain et al, 2007; Bertelsen et al, 2009). Exchange of ADP for ATP in the N-terminal nucleotide-binding domain causes significant local and propagated conformational change, formation of an interface with the substrate-binding domain, opening of the lid subdomain, and a decrease in the binding affinity for substrates (Figure 1B) (Rist et al, 2006; Swain et al, 2007). Upon ATP hydrolysis by the nucleotide-binding domain, Hsp70 is returned to the ADP-bound configuration suitable for another round of substrate binding and release. This process of cyclical substrate binding and release underlies all biological functions of Hsp70 proteins.

Bottom Line: Here, we generalize the statistical coupling analysis to simultaneously evaluate co-evolution between protein residues and functional divergence between sequences in protein sub-families.Applying this method in the Hsp70/110 protein family, we identify a sparse but structurally contiguous group of co-evolving residues called a 'sector', which is an attribute of the allosteric Hsp70 sub-family that links the functional sites of the two domains across a specific interdomain interface.The identification of the Hsp70 sector provides a basis for further experiments to understand the mechanism of allostery and introduces the idea that cooperativity between interacting proteins or protein domains can be mediated by shared sectors.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA.

ABSTRACT
Allosteric coupling between protein domains is fundamental to many cellular processes. For example, Hsp70 molecular chaperones use ATP binding by their actin-like N-terminal ATPase domain to control substrate interactions in their C-terminal substrate-binding domain, a reaction that is critical for protein folding in cells. Here, we generalize the statistical coupling analysis to simultaneously evaluate co-evolution between protein residues and functional divergence between sequences in protein sub-families. Applying this method in the Hsp70/110 protein family, we identify a sparse but structurally contiguous group of co-evolving residues called a 'sector', which is an attribute of the allosteric Hsp70 sub-family that links the functional sites of the two domains across a specific interdomain interface. Mutagenesis of Escherichia coli DnaK supports the conclusion that this interdomain sector underlies the allosteric coupling in this protein family. The identification of the Hsp70 sector provides a basis for further experiments to understand the mechanism of allostery and introduces the idea that cooperativity between interacting proteins or protein domains can be mediated by shared sectors.

Show MeSH
Related in: MedlinePlus