Molecular Systems Biology 6; Article number 414; doi:10.1038/msb.2010.65
Citation: Molecular Systems Biology 6:414
& 2010 EMBO and Macmillan Publishers Limited All rights reserved 1744-4292/10
www.molecularsystemsbiology.com
An interdomain sector mediating allostery in Hsp70
molecular chaperones
Robert G Smock1, Olivier Rivoire2, William P Russ3, Joanna F Swain1,6, Stanislas Leibler2,4, Rama Ranganathan3,* and
Lila M Gierasch1,5,*
1
Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA, 2 Laboratory of Living Matter, Rockefeller University, New York,
NY, USA, 3 Department of Pharmacology and Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA, 4 Simons Center
for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA and 5 Department of Chemistry, University of Massachusetts, Amherst, MA, USA
6
Present address: Adnexus, a BMS R&D Co., Waltham, MA 02453, USA
* Corresponding authors. R Ranganathan, Department of Pharmacology, Green Center for Systems Biology, University of Texas Southwestern Medical Center,
6001 Forest Park Boulevard, Dallas, TX 75390-9050, USA. Tel.: þ 1 214 645 5955; Fax: þ 1 214 645 5965; E-mail: rama.ranganathan@utsouthwestern.edu or
LM Gierasch, Department of Biochemistry and Molecular Biology and Department of Chemistry, 1224 Lederle Graduate Research Tower, University of Massachusetts,
Amherst 710 N. Pleasant St., Amherst, MA 01003, USA. Tel.: þ 1 413 545 6094; Fax: þ 1 413 545 1289; E-mail: gierasch@biochem.umass.edu
Received 3.3.10; accepted 20.5.10
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.
Molecular Systems Biology 6: 414; published online 21 September 2010; doi:10.1038/msb.2010.65
Subject Categories: bioinformatics; structural biology
Keywords: allostery; chaperone; co-evolution; SCA; sector
This is an open-access article distributed under the terms of the Creative Commons Attribution
Noncommercial Share Alike 3.0 Unported License, which allows readers to alter, transform, or build upon
the article and then distribute the resulting work under the same or similar license to this one. The work must
be attributed back to the original author and commercial use is not permitted without specific permission.
Introduction
Allosteric coupling, the process by which spatially distant sites
on proteins functionally interact, is a defining biological
property of many proteins, but the underlying structural basis
remains difficult to understand (Smock and Gierasch, 2009).
The central problem is the difficulty of detecting the pattern of
cooperative functional interactions between amino-acid residues in protein structures. One approach to this problem is to
analyze the correlated evolution of amino acids in a protein
family—the expected statistical signature of conserved cooperative actions of amino acids (e.g. Lockless and Ranganathan, 1999; Kass and Horovitz, 2002; Liu et al, 2008).
Recently, an approach for the global analysis of correlated
evolution in protein families has been introduced (Estabrook
et al, 2005; Russ et al, 2005; Socolich et al, 2005; Lee et al,
2008), and the results imply a new and potentially general
& 2010 EMBO and Macmillan Publishers Limited
architecture of amino-acid interactions within protein
domains. The basic finding is that most residues evolve nearly
independently, whereas a small fraction of residues is
collectively coupled to form functional units called sectors
(Halabi et al, 2009). A characteristic of sectors is structural
connectivity; a contiguous system of sector residues within the
protein core often connects distant surfaces in the threedimensional structure. Thus, at least within single protein
domains, sectors provide a structural basis for explaining
functional properties of proteins such as allosteric coupling.
However, the principle of co-evolution of protein residues
that underlies the sectors is not limited to the coupling of
amino acids within a single domain. Indeed, allosteric
coupling (or signal transmission) between two or more protein
domains is a common finding in studies of cellular function.
This suggests the existence of sectors—units of evolutionary
selection—that are shared between different non-homologous
Molecular Systems Biology 2010 1
An interdomain sector mediating allostery
RG Smock et al
A
Substrate-binding domain
Nucleotide-binding domain
IIB
Lid subdomain
IB
ATP-binding
site
Substrate-binding
site
IIA
IA
-sandwich core
Interdomain
linker
Crossing helices
B
Lid subdomain
ATP-binding
site
Substrate-binding
site
β-sandwich core
Figure 1 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 b-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 b-sandwich, and loss of substratebinding affinity.
protein domains. For example, a sector spanning two domains
could couple a functional site on one protein domain to a
functional site on a second protein domain. Such sectors could
explain conserved aspects of allosteric coupling.
The Hsp70 molecular chaperones—a large and diverse
family of allosteric two-domain proteins—present an excellent
case study to test this concept. Hsp70 proteins interact with
substrate proteins at a C-terminal substrate-binding domain,
but both the affinity and kinetics of substrate binding are
controlled by the activity of an N-terminal nucleotide-binding
domain (Figure 1A). Specifically, exchange of ADP for ATP in
the N-terminal domain reduces the binding affinity for
substrates at the C-terminal domain and is accompanied by
significant conformational change and interdomain docking
(Mayer and Bukau, 2005; Rist et al, 2006; Swain et al, 2007;
Bertelsen et al, 2009). The structure of the ATP-bound state of
the Escherichia coli Hsp70, DnaK, is yet unsolved, but we made
a model by homology-based methods and simulated-annealing molecular dynamics using the crystal structure of ATPbound Hsp110 from yeast (Liu and Hendrickson, 2007)
(Figure 1B; Supplementary Figure 8). This model illustrates
the large conformational change in the substrate-binding
2 Molecular Systems Biology 2010
domain associated with ATP binding in the nucleotide-binding
domain, and indicates the expected interaction surface
between the two Hsp70 domains. The allosteric cycle is
completed when the intrinsic ATPase activity of the nucleotide-binding domain reverses the conformational rearrangement, returning the Hsp70 to an ADP-bound configuration
suitable for another round of substrate binding and release.
The overall family of Hsp70-like proteins that comprises the
Hsp70s and the Hsp110s, homologs that contain both domains
and as indicated above, are regarded as structural models for
Hsp70s (Easton et al, 2000). However, despite their sequence
similarity, the Hsp110 proteins have evolved to be nonallosteric, such that the nucleotide-binding domain remains
stably bound to ATP and does not appear to regulate the
substrate-binding domain. Consistent with these findings,
Hsp110s are incapable of folding substrate proteins on their
own through cycles of nucleotide exchange and hydrolysis
(Shaner and Morano, 2007).
Here, we present a new application of the statistical coupling
analysis (SCA) to sequences of the Hsp70-like family in which
we take advantage of the functional divergence of Hsp70s and
Hsp110s to reveal patterns of co-evolution that can be
& 2010 EMBO and Macmillan Publishers Limited
An interdomain sector mediating allostery
RG Smock et al
associated with interdomain allostery (see Box 1). The
identification of a group of co-evolving residues that show
structural contiguity between the two Hsp70 domains provides
testable hypotheses about allosteric function in these molecular chaperones and introduces methods that may be
applicable for more generally characterizing co-evolution
within and between protein domains.
Results
A sector associated with Hsp70 allostery
To identify sectors in Hsp70, we used the SCA to compute a
weighted correlation matrix, C̃, that describes the co-evolution
of every pair of amino-acid positions in the Hsp70/110 family.
The essence of sector identification is to analyze the nonrandom correlations in the C̃ matrix to find collectively
evolving groups of residues. One approach to do this is
spectral decomposition, in which sectors are defined by the
pattern of residue contribution to the top few eigenmodes of
the C̃ matrix (Halabi et al, 2009). Importantly, sector
identification by this method proceeds without presupposing
the function of sectors; such properties are then assigned
through experimental study.
Analysis of the Hsp70/110 protein family suggests a more
targeted strategy for analysis of the C̃ matrix in which we take
advantage of the functional divergence of allosteric mechanism between Hsp70 and Hsp110 proteins to guide sector
identification. The basic idea is to simultaneously evaluate the
pattern of divergence between sequences in a protein family
and the pattern of co-evolution between amino-acid positions
(Casari et al, 1995; Lichtarge et al, 1996). This can be
performed in the framework of SCA using a mathematical
method known as singular value decomposition (see Box 1). If
the pattern of sequence divergence classifies members of a
protein family according to distinctions in a functional
mechanism (e.g. allostery), then we can identify the group of
co-evolving residues that correspond to this mechanism. We
describe this approach here in context of the Hsp70/110 family
(see Box 1, Materials and methods, and SOM for additional
details). Given a weighted binarized sequence alignment (X̃)
comprised of M sequences (rows) and L positions (columns),
we can compute the following two correlation matrices:
1
1
C~ ¼ X~T X~ and S~ ¼ X~X~T ;
M
L
where C̃ is the SCA correlation matrix between positions and S̃
is a correlation matrix between sequences. The singular value
decomposition of X̃ is:
X~ ¼ USV T ;
in which columns of U are eigenvectors of S̃, columns of V are
eigenvectors of C̃, and S is related to the eigenvalues of these
matrices. Importantly, this decomposition allows a direct
mapping between each principal axis of sequence variation (a
column in U) and the corresponding principal axis of
positional co-evolution (the same column in V). If functionally
distinct sequences segregate along an axis of sequence
variation, then the positions that underlie this divergence are
defined in the corresponding axis of positional co-evolution.
& 2010 EMBO and Macmillan Publishers Limited
Examination of the top principal axes of sequence variation
for the Hsp70/110 family (see Materials and methods) shows in
fact a clear separation of the allosteric (Hsp70) and nonallosteric (Hsp110) members into two distinct clusters
(Figure 2A). This axis of separation between the two subfamilies is identified in an unbiased manner using an
algorithm for independent component analysis (see Materials
and methods; Supplementary information). The corresponding axis of the C̃ matrix of positional correlations reveals a
protein sector comprising a small fraction of Hsp70/110
positions (B20%, 115 sector out of 605 total residues) that
underlie the separation of Hsp70 and Hsp110 family members
(Figure 2B). The sector positions derive roughly equally from
the nucleotide-binding domain (in blue, 56 positions;
Figure 2B) and the substrate-binding domain (in green, 59
positions; Figure 2B) showing co-evolution of residues in both
domains to form a single unit of evolutionary selection. Consistent with the finding that allosteric coupling is a property of
the Hsp70 sub-family, positions comprising this sector are
more conserved within the Hsp70 sub-family than in the
Hsp110 sub-family (Supplementary Figure 5). Taken together,
these results define an interdomain sector in the Hsp70 subfamily that is associated with the allosteric mechanism.
Structural interpretation of the Hsp70 sector
What is the structural interpretation of this Hsp70 sector? NMR
(Swain et al, 2007; Bertelsen et al, 2009) and tryptophan
fluorescence (Moro et al, 2003) data in DnaK, the E. coli Hsp70,
show that in the ADP-bound state, the nucleotide-binding and
substrate-binding domains are dissociated and largely independent. In contrast, upon ATP binding, the nucleotidebinding domain undergoes conformational rearrangement,
participates in the interdomain interface, and promotes
substrate release from the substrate-binding domain
(Wilbanks et al, 1995; Moro et al, 2003; Mayer and Bukau,
2005; Swain et al, 2007).
To examine the spatial arrangement of the Hsp70 sector in
the ATP-bound state, we represented sector residues on the
Sse1-derived model for the DnaK Hsp70 (Supplementary
Figure 7). Consistent with a function in allosteric coupling,
residues comprising the Hsp70 sector form a physically
contiguous network of atoms linking the ATP-binding site to
the substrate-binding site, passing through the interdomain
interface (Figure 2C). The physical connectivity is remarkable
given that only a small fraction of overall Hsp70 residues is
involved (Figure 2B). Prior work showed that sparse but
connected clusters of amino acids forming sectors link
distantly positioned functional sites within individual protein
domains (Lockless and Ranganathan, 1999; Socolich et al,
2005; Halabi et al, 2009). This work extends this result to show
that functionally coupled but non-homologous protein domains can share a single sector that connects their respective
functional sites through a protein–protein interface.
Functional studies of Hsp70 allostery
Does the Hsp70 sector represent the mechanism of allosteric
coupling between the nucleotide-binding domain and
substrate-binding domain? A number of biochemical and
Molecular Systems Biology 2010 3
An interdomain sector mediating allostery
RG Smock et al
Box 1 SCA overview
The aim of SCA is to examine the joint conservation of all pairs of amino-acid positions in a protein family to identify sectors—groups of
sequence positions that mutually co-evolve in a protein family. As previously described (Halabi et al, 2009), the basic process is to start with
a large and diverse multiple sequence alignment (MSA) of a protein family comprising M sequences by L positions, and to compute an
L L-weighted correlation matrix (C̃, the SCA matrix) that describes the co-evolution of all pairs of sequence positions. When sequences
are diverged to such an equal extent (i.e. homogeneously) that distinct sub-families are not clearly evident, sector identification amounts
to identifying positions that group in the top eigenmodes of the SCA correlation matrix. Here, we extend this approach to the case of
‘inhomogeneous’ sequence alignments in which functionally distinct sub-families of sequences can be identified in the MSA. Such functional
structure in alignments can facilitate sector identification because of mathematical methods that provide a direct mapping between patterns of
sequence divergence and patterns of positional covariation.
Step 1: Definition of alignment and correlation matrices
In general, an MSA can be described as a three-dimensional binary tensor Xasi (M L 20) whose elements are 1 if sequence s contains aminoacid a at position i and 0 if not (A). To use the mathematical methods below, we reduce the MSA to an M L two-dimensional binary matrix
Xsi by only including the terms in Xasi representing the most prevalent amino-acid at each position, a process we term the ‘binary
approximation’ of the MSA. We next compute a weighted, normalized alignment
X~si ¼ fi ðXsi hXsi i Þ
ð1Þ
s
where fi is related to the conservation of position i in the MSA and is the weighting function used in the current implementation of SCA (B,
and see SOM and Materials and methods), and /XsiSs represents the average value of Xsi over all sequences. In effect, weighting by fi provides
a measure of the significance of amino-acid occurrences and correlation in the MSA. From the X̃ matrix representation of the MSA, two
~ which
correlation matrices can then be computed: S~ ¼ L1X~X~T , which is a fi-weighted version of a sequence correlation matrix, and C~ ¼ M1 X~T X,
is a fi-weighted version of a positional correlation matrix (i.e. the SCA matrix).
The use of the binary approximation of the MSA is a necessary simplification for usage of the specific mathematical methods for sector
analysis in this work (described below). Generalization of the methods to consider the full alignment will be a subject of future work. However,
we note that for instances such as the Hsp70/110 family in which the function of interest (e.g. allostery) is a property of a major sub-family,
sector identification is robust to the binary approximation (Halabi et al, 2009).
Step 2: Mapping modes of sequence covariation and positional covariation
To relate the divergence of sub-families of sequences to the correlated evolution of groups of positions, we use the method of singular value
decomposition. In this method, the M L binary matrix X̃ can be written as a product of three matrices: X̃¼USVT, where U is an M M matrix
whose columns contain the eigenvectors of S̃, the sequence correlation matrix, and V is an L L matrix whose columns contain the
eigenvectors of C̃, the SCA positional correlation matrix. S is a diagonal M L matrix of so-called ‘singular values’ that are related to the
eigenvalues of the S̃ and C̃ matrices.
The important concept is that if an eigenmode of the sequence correlation matrix (a column of U, |UnS) reveals a separation of two classes of
sequences, then the corresponding eigenmode of the positional correlation matrix (a column of V, |VnS) will reveal the positions that primarily
contribute to this sequence divergence. However, in general, the eigenvectors of the S̃ or C̃ matrix need not represent statistically independent
modes of sequence correlation or of positional correlation. For example, examination of the top three modes of the U matrix for the Hsp70/110
family (|U1y3S, C) reveals the existence of distinct sub-families of sequences (in different colors), but fails to clearly separate these
sub-families along the orthogonal eigenvectors. To better represent the divergence of the sub-families, we used a simple implementation of
independent component analysis (ICA), a method specifically designed to transform the k top eigenmodes of a correlation matrix into k
maximally independent components. Application of ICA to the significant top eigenmodes of the Hsp70/110 family (see SOM and Materials
and methods) indeed shows the separation of the sequences in the MSA into a few major sub-families that now largely separate along
orthogonal independent components (|US1y3S), D).
4 Molecular Systems Biology 2010
& 2010 EMBO and Macmillan Publishers Limited
An interdomain sector mediating allostery
RG Smock et al
Box 1 Continued
Application of the same ICA-transformation computed for the U matrix to the k top eigenmodes of the C̃ matrix (|V1ykS) then provides a
corresponding transformation to define the positions responsible for the directions of sequence variation observed in panel D. Thus, we can
identify correlated groups of sequence positions that are responsible for the divergence of groups of sequences.
In the main paper, Figure 2A shows the first independent component of the S̃ matrix for the family of Hsp70/110 proteins (|US1S), which
reveals a clear separation of the family into two groups—one that includes the allosteric Hsp70-like proteins (white, orange, and cyan in panels
C and D, and black in Figure 2A) and one that includes the non-allosteric Hsp110-like proteins (purple, panels C and D, and gray in Figure 2A).
The corresponding first independent component of the positional correlation matrix C̃ (|VS1S) reveals the positions most responsible for this
sequence divergence (Figure 2B), and identifies the allosteric sector.
A
Non-allosteric
Allosteric
C
Number
200
100
ATP
0
–0.15
Number
B
–0.1
–0.05
⏐U s1〉,
sequence correlations
0
0.05
0
75
50
25
0
–0.05
Substrate-binding site
0.1
⏐V s1〉, positional correlations
Figure 2 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 B20%). 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.
& 2010 EMBO and Macmillan Publishers Limited
Molecular Systems Biology 2010 5
An interdomain sector mediating allostery
RG Smock et al
A
B
ATP
Q152
K155
T199
E201
E171
D326
V218
F216
T199
E217
D201
C
D
Lid subdomain
G405
T403
E444
E444
T428
K414
Substrate
P466
N415
S398
L392
L391
L390
Substrate
L392
L390
Interdomain linker
ATP
E
Interdomain linker
Q152
I462
N415
D326
Substrate-binding
site
Figure 3 Evidence for a function of the Hsp70 sector in allosteric coupling. Examination of sector positions in the nucleotide-binding domain (blue) and in the substratebinding domain (green) reveals many experimentally characterized sites implicated in allostery (colored in red; see text for details) (A) In the ATP-binding site, sector
residues include determinants of nucleotide hydrolysis and nucleotide-mediated conformational change. (B) At nucleotide-binding domain surface contacting the
substrate-binding domain, a patch of sector residues includes many known to perturb allostery upon mutation. (C) In the substrate-binding domains, the sector contains
residues both proximal and distal from the substrate-binding site, and includes the functionally critical interdomain linker (390–392). (D) At the substrate-binding domain
surface that comprises the interface with the nucleotide-binding domain, sector residues include many that display defects in allostery upon mutation. (E) Across the
interdomain interface, mutation at residues Q152 and F216 (not shown) partially suppress the loss-of-function mutations at position 462 on the substrate-binding domain.
Also shown are positions 415 and 326, sector residues that contact across the interdomain interface and are previously untested with regard to allosteric function.
genetic studies on a variety of Hsp70s provide a basis for this
assessment. Within the nucleotide-binding domain, sector
positions include catalytic residues E171 and D201, the
mutation of which impairs ATP-induced conformational
change (Johnson and McKay, 1999), and T199, the mutation
of which stabilizes ATP-induced conformational change
(Buchberger et al, 1995), among other sites, making direct
contact with bound nucleotide (Figure 3A). Studies of isolated
bacterial Hsp70 nucleotide-binding domains have shown ATPdependent reorientation of all four sub-domains (Zhang and
Zuiderweg, 2004; Bhattacharya et al, 2009), and the sector
6 Molecular Systems Biology 2010
spans all of the sub-domain interfaces. In particular, actin and
Hsp70 retain sequence conservation at nucleotide-binding
loops and adjacent crossing helices that form an interface
between sub-domains 1A and 2A (Figure 1A) (Bork et al,
1992). Actin responds to bound nucleotide through an ATPdependent shearing motion between sub-domains 1A and 2A
(Schuler, 2001), and this structural region is a focal point of
Hsp70 sector mapping. These findings are consistent with the
view that at least in part, the co-evolution of sector positions
may be related to the anisotropic physical coupling of amino
acids within the protein structure. A similar empirical relation& 2010 EMBO and Macmillan Publishers Limited
An interdomain sector mediating allostery
RG Smock et al
B
Dilution factor: 101
102
103
104
105
Wild type
∆dnaK
D326V
N415G
ATPase activity
(mol ATP/mol DnaK/min)
C
Normalized intensity (a.u.)
A
1.00
–ATP
0.95
0.90
0.80
D326V, N415G
+ATP
0.75
0.70
330
335
340
345
Wavelength (nm)
350
Wild type
+ATP
D
0.25
ADP state
0.20
0.15
ADP
ATP
ATP state
ATP hydrolysis
0.10
+substrate
0.05
0.00
Wild type
Fold stimulation: 7.2X
D326V or N415G
D326V
3.1X
N415G
3.6X
Figure 4 Experimental test of sector-based predictions of allosteric mechanism. (A) A stress-response assay, showing that though wild-type DnaK efficiently rescues
growth in an E. coli dnaK knockout strain at heat-shock conditions (431C), DnaK variants D326V and N415G do not. (B) Fluorescence of the sole tryptophan residue in
DnaK is diagnostic for ATP-dependent interdomain docking. DnaK D326V and N415G display normal tryptophan fluorescence in the absence of ATP, but only a partial
conversion of the ensemble to the ATP state based on blue shift and intensity (wild type, black; D326V, blue; N415G, red). (C) The sector mutations distal from the ATPbinding site cause elevated basal ATPase activities (gray) and reduced stimulation by the substrate peptide p5 (p5-stimulated rates in white; fold stimulation below plot).
(D) These data can be explained by a two-state model in which sector mutants are partially defective in the formation of the docked, ATP-bound Hsp70 conformation.
ship has been noted between distributed physical interactions
and the sector-mediating specificity in the S1A serine
proteases (Halabi et al, 2009).
Moreover, the crossing helices form a solvent-accessible
cleft between sub-domains 1A and 2A in actin-like nucleotidebinding domains. In actin, the cleft mediates interaction with
allosteric effector proteins (Dominguez, 2004), whereas in
Hsp70/110, the cleft is proposed to act as an intramolecularbinding surface for the interdomain linker (Jiang et al, 2007;
Liu and Hendrickson, 2007; Swain et al, 2007). In the allosteric
Hsp70 sector that our analysis describes, the cleft surface is
lined with sector residues (e.g. Y145, D148, K155, E217 and
V218; see Figure 3B), and mutation at these sites is reported to
perturb Hsp70 allostery (Gassler et al, 1998; Vogel et al, 2006).
The conserved interdomain linker sequence motif 389VLLL392
in the sector stimulates ATPase activity when present on
truncated nucleotide-binding domain constructs (Swain et al,
2007) and its mutation impairs interdomain allostery in fulllength Hsp70 (Figure 3C and D) (Laufen et al, 1999; Vogel
et al, 2006). Binding of the linker to the cleft below the crossing
helices is postulated to be important to the formation
of the domain-docked state, bringing the substrate-binding
domain into proximity to the nucleotide-binding domain
(Swain et al, 2007).
Sector positions within the substrate-binding domain
comprise a structurally contiguous set of atoms that extends
from the substrate-binding site through the protein core to a
solvent-exposed region that includes the interdomain linker
(Figure 3C and D). The functional significance of the sector is
supported by several previous observations. Sector residue
K414 is centered in the domain surface patch, making multiple
interdomain contacts in the docked state. Previous work
& 2010 EMBO and Macmillan Publishers Limited
showed that this residue has a critical function in allosteric
signal transmission as mutation at this site blocked interdomain docking and allostery (Montgomery et al, 1999).
A substrate-binding domain sector position (I462) has been
shown to have an epistatic relationship with sector positions in
the nucleotide-binding domain (Q152 and F216): mutation of
I462 to Asn is lethal in the yeast Hsp70 Ssc1, but is partially
suppressed by nucleotide-binding domain mutations Q152L or
F216L (Figure 3E) (Davis et al, 1999). There is also evidence
that structural regions not essential for allosteric coupling are
not involved in the interdomain sector; the substrate-binding
domain lid is nearly absent in sector residues, and a DnaK
variant lacking the lid retains core allosteric function (Swain
et al, 2006). Interestingly, several sector positions within the
substrate-binding domain experience large NMR chemical shift
changes upon binding of a peptide substrate (S398, T403, G405,
T428, D431, I438, F457, L459, G468) (Swain et al, 2006). In
addition, mutation of sector residues far from the substratebinding site (S398, G400, G443, E444, L459) reduces substratebinding affinity (Figure 3C and D) (Burkholder et al, 1996).
The physical and functional connectivity of a single
co-evolutionary sector across domains provides strong support for the proposal that the sector mediates the allosteric
coupling central to the basic biological activity of Hsp70.
Direct experimental analysis of the interdomain
sector
Knowledge of the interdomain sector provides new hypotheses
for further experimental testing. For example, residues D326
and N415 are sector positions that display interdomain
Molecular Systems Biology 2010 7
An interdomain sector mediating allostery
RG Smock et al
contact, but no previous experiment has tested their involvement in interdomain allostery (Figure 3; Supplementary
Figure 7). Therefore, we made conservative mutations based
on amino-acid frequencies at these positions in Hsp70
sequences and measured the effect on interdomain allostery
both in vivo and in vitro. A direct test for the influence of sector
mutants on organism fitness is provided by the ability of DnaK
to promote E. coli growth at elevated temperature (Bukau and
Walker, 1990). For example, strains of E. coli in which the
chromosomal copy of DnaK is deleted grow very weakly after
heat shock, but are rescued by expression of wild-type DnaK
from a plasmid (Figure 4A). In contrast, the D326V or N415G
DnaK variants fail to complement the DnaK knockout strain
upon heat shock, showing that these positions are critical for
Hsp70 activity.
The origin of these cellular defects was investigated by
purifying the mutant DnaK proteins and using biochemical
tests of allosteric function in vitro. DnaK D326Vand N415G are
soluble, natively folded and thermally stable in the absence of
ATP and substrate (Supplementary Figure 9). The fluorescence
of the sole intrinsic tryptophan residue in DnaK is diagnostic
for ATP-dependent interdomain docking because it displays a
characteristic blue shift and intensity quench upon interdomain interaction (Moro et al, 2003). DnaK D326V and N415G
show the same tryptophan fluorescence spectrum as wild-type
DnaK in the absence of nucleotide, indicating that W102 is in
its normal chemical environment in the undocked state.
However, the extents of W102 fluorescence blue shifting and
intensity quenching upon addition of ATP are reduced relative
to wild type (Figure 4B). The same trends are observed for wild
type and mutants when W102 accessibility is assessed by
acrylamide quenching (Supplementary Figure 10). These
findings are characteristic of a specific defect in ATP-induced
conformational change and domain docking in the point
mutants. In addition, functional Hsp70 allostery entails an
approximately seven-fold stimulation of ATPase activity upon
binding of peptide to the substrate-binding domain. Relative to
wild-type DnaK, D326Vand N415G show significantly elevated
basal ATPase rates and only approximately three-fold stimulation by peptide (Figure 4C). Given these data and the
knowledge that ATP hydrolysis is the rate-limiting step of the
reaction cycle (McCarty et al, 1995), the likely interpretation is
that the sector mutants shift the normal DnaK conformational
equilibrium from the ATP-induced, domain-docked state to the
more independent domain arrangement characteristic of the
ADP state (Figure 4D).
These findings are consistent with the hypothesis that these
two sector positions are important for stabilizing the interdomain interface and mediating allosteric communication
between domains. More generally, these data provide further
evidence that Hsp70 sector analysis has predictive value in
describing an interdomain allosteric network.
distantly positioned functional sites on two distinct protein
domains. As per previous reports (Lockless and Ranganathan,
1999; Socolich et al, 2005; Halabi et al, 2009), the sector is
sparse, such that only a small fraction of total amino acids in
the protein are involved, and physically contiguous, so that the
ATP-binding site on the nucleotide-binding domain is connected to the substrate-binding site on the substrate-binding
domain through a continuous network of interacting amino
acids. The identification of the sector provides a clear basis for
directing new experiments toward a more complete understanding of the mechanism and evolutionary divergence of
allostery in these proteins. For example, Hsp70s use diverse cochaperones in team-assisted functions and many sector
positions emerging as an allosteric surface for interdomain
allostery in Hsp70s also have a function in J-domain binding
and J-mediated ATPase stimulation (Gassler et al, 1998; Suh
et al, 1998; Vogel et al, 2006; Jiang et al, 2007).
This work adds an important new finding with regard to the
concept of protein sectors. Previous work showed that
multiple quasi-independent sectors are possible within a
single protein domain, each of which contributes to a different
aspect of function (Halabi et al, 2009). Here, we show that a
single sector can also exist to functionally couple two different,
non-homologous protein domains. This result emphasizes the
point that sectors are simply defined as units of selection,
without regard to hierarchies of structural organization. An
interesting possibility that follows is that sectors could
physically join and co-evolve across protein–protein interfaces
in order to mediate the coupling of activities between
proteins—the essence of signal transmission and allosteric
regulation. Indeed, this idea has been recently used to design
a synthetic two-domain allosteric protein (Lee et al, 2008),
and a similar concept was used to map regions involved
in controlling the specificity of bacterial two-component
signaling systems (Skerker et al, 2008). It will be interesting
to further test the notion that interaction between protein
sectors is a process through which allostery between proteins
might evolve.
Materials and methods
Multiple sequence alignment
Hsp70/110 sequences were obtained by combining the non-redundant
results of PSI-BLAST (Altschul et al, 1997) searches queried with E. coli
DnaK, human Hsc70, and yeast Sse1. Sequences were aligned
automatically (Thompson et al, 1994) and by manual structure-based
methods (Doolittle et al, 1996). Non-Hsp70/110 sequences were
removed based on their anomalous length or sequence identity. Any
sequence sharing 495% similarity to another sequence was removed
to distribute sampling. The final alignment was large (926 sequences)
and diverse (unconserved sites approached random amino-acid
distributions).
Statistical coupling analysis
Discussion
In summary, we show that sequence analysis alone of the
Hsp70/110 molecular chaperone family identifies a group of
co-evolving residues, a sector, that is responsible for the core
function of the Hsp70 proteins—allosteric coupling between
8 Molecular Systems Biology 2010
As in previous work (Halabi et al, 2009), the alignment is binarized in
an M by L matrix X with Xsi¼1, if the most frequent amino-acid at
position i is present in sequence s, and Xsi¼0 otherwise; M is here the
number of sequences (rows of X) and L the number of positions
(columns of X). The definition of the SCA matrix C̃ involves positionspecific weights fi that quantify the degree
of conservation of each
position i: fi ¼ ln fi ð1 qðai Þ Þ=ð1 fi Þqðai Þ , where fi represents the
& 2010 EMBO and Macmillan Publishers Limited
An interdomain sector mediating allostery
RG Smock et al
frequency of the prevalent amino-acid ai at position i, and qðai Þ a
background frequency for this amino-acid. A weighted alignment X̃ is
defined with X̃si¼fi(X̃sifi). The SCA matrix C̃ is the L by L matrix of
correlations between positions given by C̃¼X̃TX̃/M, where X̃T denotes
the transpose of X̃. Similarly, S̃¼X̃X̃T/L gives an M by M matrix of
correlations between sequences. The eigenvectors of C̃ and S̃ form the
columns of two orthogonal matrices, V and U, which are related
through the singular value decomposition of X̃: X̃¼USVT, where S is a
diagonal matrix.
An independent component analysis provides a linear transformation Ws that maps the top three eigenvectors of S̃ into three maximally
independent axes of sequence variations (see Supplementary information for algorithmic details). One of these three directions, the
M-dimensional vector U1s , is found to discriminate the non-allosteric
sequences from the rest of the sequences in the alignment (Figure 2A).
Applying the same linear transformation Ws to the top three
eigenvectors of C̃ defines a direction of positional variations, the
L-dimensional vector V1s , which indicates the positions underlying the
discrimination. The allosteric sector is defined as the positions i
making significant contribution to V1s , that is i V1s Xe, where e¼0.05
corresponds to a threshold of statistical significance (Figure 2B).
Structural modeling
The ATP-bound Saccharomyces cerevisiae Sse1 structure and a
sequence alignment between Sse1 (Hsp110) and DnaK (Hsp70) (Liu
and Hendrickson, 2007) were used to generate a homology model of
DnaK(ATP) using Modeller (Sali and Blundell, 1993). Molecular
dynamics simulations were carried out using the Gromacs platform
and Gromos96 force field (Hess et al, 2008). The structural model was
truncated at residue 531, and ATP, magnesium, and potassium ions
coordinated in the active site were included. An ATP topology file
provided by an earlier study (Colombo et al, 2008) was used. The
system was solvated in a box with at least 12 Å spacing from protein
atoms to the edge of the box. Net charge was neutralized with
potassium ions and energy was minimized by steepest descents
followed by short position-restrained molecular dynamics to equilibrate water molecules at 300 K. In the production of molecular
dynamics simulation, a simulated-annealing protocol cycled through
temperature gradients based on previous work on a smaller system
(Lindorff-Larsen et al, 2005): 300–400 K over 150 ps, 400–350 K over
150 ps, 350–300 K over 500 ps, and 300 K held for 100 ps. Berendsen
temperature coupling, Parrinello–Rahman pressure coupling, and a
periodic boundary condition were used. All trajectory analysis was performed within the Gromacs package. Atomic RMSD fluctuations were
analyzed by principal component analysis, and cosine content of the first
component indicated that motions within the RMSD plateau region were
dominated by diffusion (Hess, 2002). To avoid over-interpretation,
structural clustering was performed on the trajectory such that the entire
RMSD plateau region was defined as a single cluster (4.7–53 ns) to
determine a median structure, and correlated motions within this region
were not investigated further on the basis of cooperativity. PyMol was
used for molecular visualization (Delano, 2002).
Heat-shock assay
Plasmid pMS119 containing a wild-type E. coli dnaK gene insertion was
used as a template for site-directed mutagenesis (Montgomery et al, 1999).
Plasmids were transformed into temperature-sensitive E. coli BB1553 cells
(DdnaK52, sidB1) (Bukau and Walker, 1990). Single colonies were grown
overnight in LB in the presence of antibiotics at 301C, and each growth’s
optical density at 600 nm was normalized to 0.2 by dilution with LB media.
Growths were serially diluted 10-fold in water pre-equilibrated at 431C,
spotted onto growth media plates at 431C, and placed in an incubator at
the same temperature for 15 h. Leaky expression of the pMS119 tac
promoter was sufficient to achieve nearly optimal growth rescue by
plasmid-encoded DnaK in LB media without IPTG induction.
Purification of proteins and peptides
E. coli DnaK was prepared similarly as previously described
(Montgomery et al, 1999), except that E. coli BB1553 cells were used
& 2010 EMBO and Macmillan Publishers Limited
and grown at 301C. In a modified two-column purification, the first
anion exchange column was used with buffers at pH 7.4. In the second
column, DnaK was eluted from ATP agarose with 2 mM ADP. KCl
replaced NaCl in all purification buffers. Crude p5 peptide
(CLLLSAPRR) was purchased from Genscript and purified by HPLC
using a diphenyl column with elution at B30% acetronitrile and 70%
water; mass spectrometry confirmed the identity of the peptide.
ATPase activity
Steady-state ATPase activity was measured in an enzyme-coupled
system as previously described (Montgomery et al, 1999). The ATPase
activity of 1 mM DnaK plus or minus 100 mM p5 at 301C was measured
on a Biotek Gen5 platereader using Costar 3631 plates. Measurements
were taken 3–5 times for each DnaK and auto-hydrolysis sample.
W102 fluorescence
DnaK W102 fluorescence and acrylamide quenching were measured
similarly as previously described (Moro et al, 2003). Measurements
were taken at room temperature in a Photon Technology International
fluorometer at 295 nm excitation wavelength with 4 nm slit widths on
both excitation and emission sides. For each sample, spectra were
averaged over 10 acquisitions and normalized to an intensity of 1.0
before the addition of ATP. Faster 15 s scans showed the same spectral
trends, indicating that ATP hydrolysis was not a complicating factor
during the measurement.
Circular dichroism
Measurements were taken as previously described (Montgomery et al,
1999) using a Jasco J-715 spectrophotomer. Wavelength scans were
measured at 301C using 2 mM DnaK in 10 mM potassium phosphate
buffer at pH 7.6. Temperature melts were measured at 222 nm using
2 mM DnaK in 10 mM potassium phosphate buffer, 1 mM MgCl2 and
1 mM ADP, pH 7.6.
Supplementary information
Supplementary information is available at the Molecular Systems
Biology website (http://www.nature.com/msb).
Acknowledgements
This study was supported by grants from NIH (LMG), the Robert A
Welch foundation (RR), the Green Center for Systems Biology (RR),
and a Simons Foundation fellowship from Rockefeller University (OR).
Computational resources were funded by NSF and NIH.
Conflict of interest
The authors declare that they have no conflict of interest.
References
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W,
Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation
of protein database search programs. Nucleic Acids Res 25: 3389–3402
Bertelsen EB, Chang L, Gestwicki JE, Zuiderweg ERP (2009) Solution
conformation of wild-type E. coli Hsp70 (DnaK) chaperone
complexed with ADP and substrate. Proc Natl Acad Sci USA 106:
8471–8476
Bhattacharya A, Kurochkin AV, Yip GNB, Zhang Y, Bertelsen EB,
Zuiderweg ERP (2009) Allostery in Hsp70 chaperones is transduced
by subdomain rotations. J Mol Biol 388: 475–490
Molecular Systems Biology 2010 9
An interdomain sector mediating allostery
RG Smock et al
Bork P, Sander C, Valencia A (1992) An ATPase domain common to
prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat
shock proteins. Proc Natl Acad Sci USA 89: 7290–7294
Buchberger A, Theyssen H, Schroder H, McCarty JS, Virgallita G,
Milkereit P, Reinstein J, Bukau B (1995) Nucleotide-induced
conformational changes in the ATPase and substrate binding
domains of the DnaK chaperone provide evidence for
interdomain communication. J Biol Chem 270: 16903–16910
Bukau B, Walker GC (1990) Mutations altering heat shock specific
subunit of RNA polymerase suppress major cellular defects of E.
coli mutants lacking the DnaK chaperone. EMBO J 9: 4027–4036
Burkholder WF, Zhao X, Zhu X, Hendrickson WA, Gragerov A, Gottesman
ME (1996) Mutations in the C-terminal fragment of DnaK affecting
peptide binding. Proc Natl Acad Sci USA 93: 10632–10637
Casari G, Sander C, Valencia A (1995) A method to predict functional
residues in proteins. Nat Struct Biol 2: 171–178
Colombo G, Morra G, Meli M, Verkhivker G (2008) Understanding
ligand-based modulation of the Hsp90 molecular chaperone dynamics
at atomic resolution. Proc Natl Acad Sci USA 105: 7976–7981
Davis JE, Voisine C, Craig EA (1999) Intragenic suppressors of Hsp70
mutants: interplay between the ATPase- and peptide-binding
domains. Proc Natl Acad Sci USA 96: 9269–9276
Delano WL (2002) The PyMol Molecular Graphics System. Palo Alto,
CA, USA: Delano Scientific
Dominguez R (2004) Actin-binding proteins—a unifying hypothesis.
Trends Biochem Sci 29: 572–578
Doolittle RF, Abelson JN, Simon MI (1996) Computer methods for
macromolecular sequence analysis. In Methods Enzymol, Doolittle
RF (ed), Vol. 266, pp 497–598. San Diego: Academic Press
Easton DP, Kaneko Y, Subjeck JR (2000) The Hsp110 and Grp1 70 stress
proteins: newly recognized relatives of the Hsp70s. Cell Stress
Chaperones 5: 276–290
Estabrook RA, Luo J, Purdy MM, Sharma V, Weakliem P, Bruice TC,
Reich NO (2005) Statistical coevolution analysis and molecular
dynamics: identification of amino acid pairs essential for catalysis.
Proc Natl Acad Sci USA 102: 994–999
Gassler CS, Buchberger A, Laufen T, Mayer MP, Schroder H, Valencia A,
Bukau B (1998) Mutations in the DnaK chaperone affecting interaction
with the DnaJ cochaperone. Proc Natl Acad Sci USA 95: 15229–15234
Halabi N, Rivoire O, Leibler S, Ranganathan R (2009) Protein sectors:
evolutionary units of three-dimensional structure. Cell 138: 774–786
Hess B (2002) Convergence of sampling in protein simulations. Phys
Rev E Stat Nonlin Soft Matter Phys 65: 031910
Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4:
algorithms for highly efficient, load-balanced, and scalable
molecular simulation. J Chem Theory Comput 4: 435–447
Jiang J, Maes EG, Taylor AB, Wang L, Hinck AP, Lafer EM, Sousa R
(2007) Structural basis of J cochaperone binding and regulation of
Hsp70. Mol Cell 28: 422–433
Johnson ER, McKay DB (1999) Mapping the role of active site
residues for transducing an ATP-induced conformational change in
the bovine 70-kDa heat shock cognate protein. Biochemistry 38:
10823–10830
Kass I, Horovitz A (2002) Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Proteins 48: 611–617
Laufen T, Mayer MP, Beisel C, Klostermeier D, Mogk A, Reinstein J,
Bukau B (1999) Mechanism of regulation of hsp70 chaperones by
DnaJ cochaperones. Proc Natl Acad Sci USA 96: 5452–5457
Lee J, Natarajan M, Nashine VC, Socolich M, Vo T, Russ WP, Benkovic
SJ, Ranganathan R (2008) Surface sites for engineering allosteric
control in proteins. Science 322: 438–442
Lichtarge O, Bourne HR, Cohen FE (1996) An evolutionary trace
method defines binding surfaces common to protein families. J Mol
Biol 257: 342–358
Lindorff-Larsen K, Best RB, Depristo MA, Dobson CM, Vendruscolo M
(2005) Simultaneous determination of protein structure and
dynamics. Nature 433: 128–132
Liu Q, Hendrickson WA (2007) Insights into Hsp70 chaperone activity
from a crystal structure of the yeast Hsp110 Sse1. Cell 131: 106–120
10 Molecular Systems Biology 2010
Liu Y, Eyal E, Bahar I (2008) Analysis of correlated mutations in HIV-1
protease using spectral clustering. Bioinformatics 24: 1243–1250
Lockless SW, Ranganathan R (1999) Evolutionarily conserved pathways
of energetic connectivity in protein families. Science 286: 295–299
Mayer M, Bukau B (2005) Hsp70 chaperones: cellular functions and
molecular mechanism. Cell Mol Life Sci 62: 670–684
McCarty JS, Buchberger A, Reinstein J, Bukau B (1995) The role of ATP
in the functional cycle of the DnaK chaperone system. J Mol Biol
249: 126–137
Montgomery DL, Morimoto RI, Gierasch LM (1999) Mutations in the
substrate binding domain of the Escherichia coli 70 kDa molecular
chaperone, DnaK, which alter substrate affinity or interdomain
coupling. J Mol Biol 286: 915–932
Moro F, Fernandez V, Muga A (2003) Interdomain interaction through
helices A and B of DnaK peptide binding domain. FEBS Lett 533:
119–123
Rist W, Graf C, Bukau B, Mayer MP (2006) Amide hydrogen exchange
reveals conformational changes in Hsp70 chaperones important for
allosteric regulation. J Biol Chem 281: 16493–16501
Russ WP, Lowery DM, Mishra P, Yaffe MB, Ranganathan R (2005)
Natural-like function in artificial WW domains. Nature 437: 579–583
Sali A, Blundell TL (1993) Comparative protein modelling by
satisfaction of spatial restraints. J Mol Biol 234: 779–815
Schuler H (2001) ATPase activity and conformational changes in the
regulation of actin. Biochim Biophys Acta 1549: 137–147
Shaner L, Morano KA (2007) All in the family: atypical Hsp70
chaperones are conserved modulators of Hsp70 activity. Cell Stress
Chaperones 12: 1–8
Skerker JM, Perchuk BS, Siryapron A, Lubin EA, Ashenberg O,
Gouilian M, Laub MT (2008) Rewiring the specificity of twocomponent signal transduction systems. Cell 133: 1043–1054
Smock RG, Gierasch LM (2009) Sending signals dynamically. Science
324: 198–203
Socolich M, Lockless SW, Russ WP, Lee H, Gardner KH, Ranganathan R
(2005) Evolutionary information for specifying a protein fold.
Nature 437: 512–518
Suel GM, Lockless SW, Wall MA, Ranganathan R (2003) Evolutionarily
conserved networks of residues mediate allosteric communication
in proteins. Nat Struct Biol 10: 59–69
Suh W-C, Burkholder WF, Lu CZ, Zhao X, Gottesman ME, Gross CA
(1998) Interaction of the Hsp70 molecular chaperone, DnaK, with
its cochaperone DnaJ. Proc Natl Acad Sci USA 95: 15223–15228
Swain JF, Dinler G, Sivendran R, Montgomery DL, Stotz M, Gierasch
LM (2007) Hsp70 chaperone ligands control domain association via
an allosteric mechanism mediated by the interdomain linker.
Mol Cell 26: 27–39
Swain JF, Schulz EG, Gierasch LM (2006) Direct comparison of a stable
isolated Hsp70 substrate-binding domain in the empty and
substrate-bound states. J Biol Chem 281: 1605–1611
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving
the sensitivity of progressive multiple sequence alignment through
sequence weighting, position-specific gap penalties and weight
matrix choice. Nucleic Acids Res 22: 4673–4680
Vogel M, Bukau B, Mayer MP (2006) Allosteric regulation of Hsp70
chaperones by a proline switch. Mol Cell 21: 359–367
Wilbanks SM, Chen L, Tsuruta H, Hodgson KO, McKay DB (1995)
Solution small-angle X-ray scattering study of the molecular
chaperone Hsc70 and its subfragments. Biochemistry 34: 12095–12106
Zhang Y, Zuiderweg ERP (2004) The 70-kDa heat shock protein
chaperone nucleotide-binding domain in solution unveiled as a
molecular machine that can reorient its functional subdomains.
Proc Natl Acad Sci USA 101: 10272–10277
Molecular Systems Biology is an open-access journal
published by European Molecular Biology Organization and Nature Publishing Group. This work is licensed under a
Creative Commons Attribution-Noncommercial-Share Alike 3.0
Unported License.
& 2010 EMBO and Macmillan Publishers Limited