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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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Identification of an allosteric sector in Hsp70 proteins. (A) A histogram of the Hsp70/110 sequences projected on a top axis of sequence variation derived from singular value decomposition and independent component analysis (see Box 1 Materials and methods). This axis separates family into two sub-families that correspond to the allosteric Hsp70s and the non-allosteric Hsp110s. (B) A histogram of Hsp70 residues projected on the corresponding axis of positional co-evolution, showing that a small fraction of residues is largely responsible for the sequence divergence shown in panel A (115 sector out of 605 total residues or ∼20%). This defines the Hsp70 sector. The sector nearly equally comprises residues from the nucleotide-binding domain (blue, 56 residues) and the substrate-binding domain (green, 59 residues). (C) The Hsp70 sector mapped onto a model of the ATP-bound state of E. coli DnaK. The sector forms a physically contiguous group of residues that connect the ATP-binding site in the nucleotide-binding domain (pale blue) to the substrate-binding pocket of the substrate-binding domain (yellow) through the binding interface between the two domains. Sector positions are represented as spheres and colored as in panel B. Source data is available for this figure at www.nature.com/msb.
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f2: Identification of an allosteric sector in Hsp70 proteins. (A) A histogram of the Hsp70/110 sequences projected on a top axis of sequence variation derived from singular value decomposition and independent component analysis (see Box 1 Materials and methods). This axis separates family into two sub-families that correspond to the allosteric Hsp70s and the non-allosteric Hsp110s. (B) A histogram of Hsp70 residues projected on the corresponding axis of positional co-evolution, showing that a small fraction of residues is largely responsible for the sequence divergence shown in panel A (115 sector out of 605 total residues or ∼20%). This defines the Hsp70 sector. The sector nearly equally comprises residues from the nucleotide-binding domain (blue, 56 residues) and the substrate-binding domain (green, 59 residues). (C) The Hsp70 sector mapped onto a model of the ATP-bound state of E. coli DnaK. The sector forms a physically contiguous group of residues that connect the ATP-binding site in the nucleotide-binding domain (pale blue) to the substrate-binding pocket of the substrate-binding domain (yellow) through the binding interface between the two domains. Sector positions are represented as spheres and colored as in panel B. Source data is available for this figure at www.nature.com/msb.

Mentions: To identify the allosteric sector in Hsp70, we used SCA to compute a weighted correlation matrix, C̃, that describes the co-evolution of every pair of amino-acids positions in a sequence alignment of 926 members of the Hsp70/110 family. We then applied a mathematical method known as singular value decomposition to simultaneously evaluate the pattern of divergence between sequences and the pattern of co-evolution between amino-acid positions. The basic idea is that if the pattern of sequence divergence is able to classify members of a protein family into distinct functional subgroups, then we can rigorously identify the group of co-evolving residues that correspond to the underlying mechanism. Figure 2A shows the principal axis of sequence variation in the Hsp70/110 family, showing a clear separation of the allosteric (Hsp70) and non-allosteric (Hsp110) members of this family. The corresponding axis of co-evolution between amino-acid positions reveals a subset of Hsp70/110 positions (∼20%, 115 residues out of 605 total) that underlie the divergence of Hsp70 and Hsp110 proteins (Figure 2B). These positions derive roughly equally from the nucleotide-binding domain (in blue, 56 positions) and the substrate-binding domain (in green, 59 positions) and are more conserved within the Hsp70 sub-family. These results define a protein sector that is predicted to underlie the allosteric mechanism of Hsp70.


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)

Identification of an allosteric sector in Hsp70 proteins. (A) A histogram of the Hsp70/110 sequences projected on a top axis of sequence variation derived from singular value decomposition and independent component analysis (see Box 1 Materials and methods). This axis separates family into two sub-families that correspond to the allosteric Hsp70s and the non-allosteric Hsp110s. (B) A histogram of Hsp70 residues projected on the corresponding axis of positional co-evolution, showing that a small fraction of residues is largely responsible for the sequence divergence shown in panel A (115 sector out of 605 total residues or ∼20%). This defines the Hsp70 sector. The sector nearly equally comprises residues from the nucleotide-binding domain (blue, 56 residues) and the substrate-binding domain (green, 59 residues). (C) The Hsp70 sector mapped onto a model of the ATP-bound state of E. coli DnaK. The sector forms a physically contiguous group of residues that connect the ATP-binding site in the nucleotide-binding domain (pale blue) to the substrate-binding pocket of the substrate-binding domain (yellow) through the binding interface between the two domains. Sector positions are represented as spheres and colored as in panel B. Source data is available for this figure at www.nature.com/msb.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Identification of an allosteric sector in Hsp70 proteins. (A) A histogram of the Hsp70/110 sequences projected on a top axis of sequence variation derived from singular value decomposition and independent component analysis (see Box 1 Materials and methods). This axis separates family into two sub-families that correspond to the allosteric Hsp70s and the non-allosteric Hsp110s. (B) A histogram of Hsp70 residues projected on the corresponding axis of positional co-evolution, showing that a small fraction of residues is largely responsible for the sequence divergence shown in panel A (115 sector out of 605 total residues or ∼20%). This defines the Hsp70 sector. The sector nearly equally comprises residues from the nucleotide-binding domain (blue, 56 residues) and the substrate-binding domain (green, 59 residues). (C) The Hsp70 sector mapped onto a model of the ATP-bound state of E. coli DnaK. The sector forms a physically contiguous group of residues that connect the ATP-binding site in the nucleotide-binding domain (pale blue) to the substrate-binding pocket of the substrate-binding domain (yellow) through the binding interface between the two domains. Sector positions are represented as spheres and colored as in panel B. Source data is available for this figure at www.nature.com/msb.
Mentions: To identify the allosteric sector in Hsp70, we used SCA to compute a weighted correlation matrix, C̃, that describes the co-evolution of every pair of amino-acids positions in a sequence alignment of 926 members of the Hsp70/110 family. We then applied a mathematical method known as singular value decomposition to simultaneously evaluate the pattern of divergence between sequences and the pattern of co-evolution between amino-acid positions. The basic idea is that if the pattern of sequence divergence is able to classify members of a protein family into distinct functional subgroups, then we can rigorously identify the group of co-evolving residues that correspond to the underlying mechanism. Figure 2A shows the principal axis of sequence variation in the Hsp70/110 family, showing a clear separation of the allosteric (Hsp70) and non-allosteric (Hsp110) members of this family. The corresponding axis of co-evolution between amino-acid positions reveals a subset of Hsp70/110 positions (∼20%, 115 residues out of 605 total) that underlie the divergence of Hsp70 and Hsp110 proteins (Figure 2B). These positions derive roughly equally from the nucleotide-binding domain (in blue, 56 positions) and the substrate-binding domain (in green, 59 positions) and are more conserved within the Hsp70 sub-family. These results define a protein sector that is predicted to underlie the allosteric mechanism of Hsp70.

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