An interdomain sector mediating allostery in Hsp70 molecular chaperones

• Published in: Molecular systems biology 2010-09, Vol.6 (1), p.414-n/a
• Main Authors: Leibler, Stanislas, Smock, Robert G, Ranganathan, Rama, Swain, Joanna F, Gierasch, Lila M, Russ, William P, Rivoire, Olivier
• Format: Article
• Language: English
• Subjects: Actin; Adenosine triphosphatase; Adenosine Triphosphatases - chemistry; Adenosine Triphosphatases - metabolism; Allosteric properties; Allosteric Site; allostery; Amino acids; Bacterial Physiological Phenomena; Binding; Binding sites; chaperone; Chaperones; Circular Dichroism; Coupling (molecular); co‐evolution; Divergence; DnaK protein; E coli; EMBO10; EMBO40; Escherichia coli - metabolism; Escherichia coli Proteins - metabolism; Evolution; Heat-Shock Proteins - metabolism; HSP70 Heat-Shock Proteins - metabolism; Hsp70 protein; Models, Statistical; Molecular Chaperones - chemistry; Molecular Conformation; Mutagenesis; Peptides; Plasmids; Protein folding; Protein Structure, Tertiary; Proteins; Residues; Saccharomyces cerevisiae - metabolism; SCA; sector; Substrates
• ISSN: 1744-4292; 1744-4292
• DOI: 10.1038/msb.2010.65

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. Synopsis 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 i