3did Update: domain-domain and peptide-mediated interactions of known 3D structure.

Abstract

The database of 3D interacting domains (3did) is a collection of protein interactions for which high-resolution 3D structures are known. 3did exploits structural information to provide the crucial molecular details necessary for understanding how protein interactions occur. Besides interactions between globular domains, the new release of 3did also contains a hand-curated set of transient peptide-mediated interactions. The interactions are grouped in Interaction Types, based on the mode of binding, and the different binding interfaces used in each type are also identified and catalogued. A web-based tool to query 3did is available at http://3did.irbbarcelona.org.

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D300–D304
doi:10.1093/nar/gkn690
Nucleic Acids Research, 2009, Vol. 37, Database issuePublished online 25 October 2008
3did Update: domain–domain and peptide-mediated
interactions of known 3D structure
Amelie Stein1, Alejandro Panjkovich1and Patrick Aloy1,2,*
1Institute for Research in Biomedicine (IRB) and Barcelona Supercomputing Center (BSC). c/ Baldiri Reixac 10-12,
08028 Barcelona, Spain and2Institucio ´ Catalana de Recerca i Estudis Avanc ¸ats (ICREA) Pg. Lluı ´s Companys 23,
08010 Barcelona, Spain
Received September 15, 2008; Accepted September 24, 2008
ABSTRACT
The database of 3D interacting domains (3did) is a
collection of protein interactions for which high-
resolution 3D structures are known. 3did exploits
structural information to provide the crucial molecu-
lar details necessary for understanding how protein
interactions occur. Besides interactions between
globular domains, the new release of 3did also con-
tains a hand-curated set of transient peptide-
mediated interactions. The interactions are grouped
in Interaction Types, based on the mode of binding,
and the different binding interfaces used in each
type are also identified and catalogued. A web-
based tool to query 3did is available at http://
3did.irbbarcelona.org.
INTRODUCTION
Proteins are the main perpetrators of most biological pro-
cesses that take place within and between cells. However,
proteins are very social in nature and often perform their
function as part of large molecular machines, whose
action is coordinated through complex regulatory net-
works of transient protein interactions. It is thus the rela-
tionships between molecules, rather than their mere
presence, what will ultimately determine the behavior of
a biological system. Consequently, after the completion of
the first genome sequencing projects, much effort has been
devoted to unveiling protein interrelationships in a high-
throughput manner, and recent years have witnessed the
consecution of the first interactome drafts for several
model organisms, including human (1,2), setting the
bases for future systems biology initiatives (3). However,
high-throughput interaction discovery experiments indi-
cate only that two proteins interact, but do not provide
information about the molecular details or the mechanism
of the interaction. Currently, this atomic level of detail can
come only from high-resolution 3D structures, where the
residue contacts are resolved and the protein interaction
interfaces characterized. As a result, several databases
have been developed in the last years to capture and
store interactions of known 3D structure (4–6).
The database of 3D interacting domains (3did) is a col-
lection of protein–protein interactions for which a high-
resolution 3D structure has been solved. By exploring all
interactions of known structure as stored in the Protein
Data Bank (PDB) (7), we could divide them into two main
categories on the basis of their contact interfaces: domain–
domain and domain–peptide interactions (3). We also
used the finding that homologous pairs of interacting pro-
teins tend to interact in the same way (i.e. all FGFs bind
the same FGF receptor pocket) to further cluster and
classify protein interactions in Interaction Types (8),
according to their binding and interface topologies.
DOMAIN–DOMAIN INTERACTIONS
Domain–domain interactions involve the binding of two
globular domains, which creates a large contact interface
of ?2000 A˚2on average (9). These are the type of inter-
actions that usually occur in multimeric enzymes and large
multiprotein complexes, and they can be either intra- or
inter-molecular (i.e. between domains in the same or dif-
ferent proteins, respectively).
To identify all the cases of domain–domain interactions
of known 3D structure, we first assigned Pfam (10)
domains to each individual protein in the PDB. We then
computed all the physical interactions between domains
requiring at least five contacts (hydrogen bonds, electro-
static or van der Waals interactions), and removed those
lacking a significant interface as described in refs (11,12).
This procedure has proven efficient at identifying and pur-
ging interaction artifacts from crystal packing; however, it
is likely that 3did still contains some nonbiological associ-
ates. Currently, 3did contains 115559 domain–domain
interactions of known 3D structure comprising 120980
proteins. We have classified them in 4887 unique interac-
tion types according to the Pfam families mediating them.
Of these, 3535 interaction types always occur between
domains placed in different proteins (intermolecular),
*To whom correspondence should be addressed. Tel: +34 9340 39690; Fax: +34 9340 39954; Email: patrick.aloy@irbbarcelona.org
? 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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738 are only seen between domains in the same polypep-
tide chain (intramolecular) and the remaining 614 occur
both inter- and intra-molecular. When available, 3did also
contains functional information about the interacting
domains as annotated in the Gene Ontology (GO) data-
base (13).
PEPTIDE-MEDIATED INTERACTIONS
Domain–peptide, or peptide-mediated, interactions are
those where a globular domain in one protein recognizes
and binds a short linear motif in another, creating a rela-
tively small interface. Such interactions are found predo-
minantly in signaling and regulatory networks (14) and,
due to their transient nature, are much more difficult to
handle biochemically. Linear motifs are short patterns of
around 10 residues with a common function (i.e. binding
to a globular domain) that occur in otherwise unrelated
proteins. In isolation, these motifs bind their target pro-
teins with sufficient strength to establish a functional inter-
action. They are frequently found in disordered or
unstructured regions and adopt a well-defined structure
only upon binding. An example of this type of interactions
is the well-studied Src-homology-3 (SH3) domain, which
binds slightly different variants of proline-rich peptides
(e.g. [RKY]xxPxxP or PxxPx[KR]). Most of what is cur-
rently known about peptide-mediated interactions is com-
piled in the Eukaryotic Linear Motif (ELM) database
(15), which provides a literature-curated collection of
motifs and their interaction partners. Finally, it is worth
remembering that these interactions, as the domain–
domain ones, can also be intra- or inter-molecular.
Our procedure to detect all cases of peptide-mediated
protein interactions of known 3D structure was recently
described in ref. (16). In brief, we first parsed the PDB and
identified all those entries containing two or more inter-
acting proteins. We extracted all the information regard-
ing the different 66 ligands involved in peptide-mediated
interactions from the ELM database and assigned Pfam
families to all the globular domains involved in the inter-
actions via literature curation. We then assigned Pfam
families to all interactions of known 3D structure.
Whenever we identified a protein chain containing an
ELM-binding domain, we searched all contacting chains
for occurrences of the linear consensus motif. When we
found a motif match in close vicinity of the globular
domain (?10A˚) we considered it a potential domain–
peptide interaction. Finally, we went manually through
the 2200 potential hits, comparing the interacting struc-
tures to those described in the literature, and removing
false positives where the interaction was not mediated by
the consensus peptide. Because of the visual inspection, we
are confident that the interactions reported here are bio-
logically relevant. At present, 3did contains data on 829
hand-curated peptide-mediated interactions of known 3D
structure, from 611 protein pairs, involving 32 globular
domains and 51 linear motifs.
IDENTIFICATION OF INTERACTION INTERFACES
The whole concept of interaction types relies on the obser-
vation that homologous pairs of interacting proteins very
often interact in the same way, this is, using the same
binding interfaces (8). However, there are exceptions to
the norm where homologous protein pairs can interact
in a completely different manner. For instance, the inter-
action between the signaling proteins CheY and CheA-P2
differs by a rotation of 908 in different bacterial species,
Figure 1. Number of interface topologies per interaction type. Half of the interaction types in 3did always interact using the same topology, and
most of the remaining ones show only a few different topologies. For a handful of interaction types, we find over 50 interface topologies (66 for
Ras:Ras up to 199 for V-set:V-set).
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Figure 2. Motif query results. The query results for ‘LIG_SH2_SRC’ show the linear motif pattern and source database (ELM), links to the binding
domain SH2 and all 3D structures containing this motif, followed by all motifs binding SH2 along with their patterns (if available), SH2’s interface
residues and a link to the corresponding domain–motif interaction page. The network below visualizes domains and motifs interacting with
LIG_SH2_SRC as well as their interactions among each other.
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despite being close homologs (17). This is particularly rele-
vant for those proteins that have evolved to interact with
many different partners by only changing a few binding
residues, such as antibodies, ankyrin repeats, etc. (18).
To encapsulate this information into 3did, we have
computed and classified all the interaction interfaces for
each interaction type using a clustering procedure reminis-
cent of the one used by Kim et al. (19). For each interface
of a given interaction type, we identified all the contacting
residues in the two domains. We then computed a distance
matrix for all the interfaces based on the number of shared
contacts, and performed a complete linkage hierarchical
clustering analysis to discover the different modes of
interaction between the two given domains. The result is
that, for each interaction type, we are able to identify
how many different interfaces are used and how often
Figure 3. Domain–domain interactions with interface topologies. The domain–domain interaction view shows all topologies observed in 3D struc-
tures of this interaction type along with their frequencies. The ‘rainbow’ color scheme is used to visualize where interface residues lie in the sequence,
from N-terminus (blue) to C-terminus (red). Each topology has an identifier (ID) of the form ‘X:Y’, where X is the interface ID in domain 1 (PDZ
here) and Y is the interface ID of domain 2 (Trypsin here). Note that for homomeric interactions, ‘X:X’ indicates a symmetric interaction. The
interaction details provide PDB ID, domain positions, score and Z-score as well as the topology ID, linked to the topology visualization above, for
each interaction between these two domains in a known 3D structure.
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these occur. We have termed the alternative interaction
interfaces within the same interaction type Interface
Topologies, and they are stored in 3did together with the
frequency in which they occur. Although the vast majority
of known interaction types only display one or a few dif-
ferent topologies, it is also true that some families are able
to interact with many partners using a large number of
surface patches (Figure 1). It is thus important, if one
wants to model the structure of one interaction onto
another, to make sure that, for this particular interaction
type, only one interaction topology is possible or, at least,
that there is one whose occurrence clearly stands over
the rest.
3did Usage and Visualization
The standard way of accessing 3did is through the web-
based tool by querying it with a particular domain or
motif, although it can also be queried by pasting a protein
sequence or directly indicating the PDB codes or GO
terms of interest. As in previous versions, 3did will then
display all domains, or peptides, that do physically inter-
act with our domain of interest and for which the 3D
structure of the interaction is known. All interaction part-
ners will also be displayed in an interactive network
(Figure 2), where the user can choose the depth and a
color scheme based on molecular function, biological pro-
cess or cellular compartment as described by GO. The
network also gives information on the type of interaction
(domain–domain or peptide-mediated) and whether these
interactions are intra- or inter-molecular. The user can
then select a particular interaction and retrieve the specific
details stored in 3did. The output page for each domain–
domain interaction displays a table with information con-
cerning all the known 3D structures where this interaction
is found (Figure 3). The table shows the exact location of
the two domains in the 3D complex and gives empirical
potential scores and Z-scores, which provide a measure of
the number of favorable interacting residue-pairs at the
interface (11,12). The Z-score generally accounts for inter-
action specificity: the higher it is the more specific the
interaction. Finally, clicking on the rasmol (20) icon pops
up a display of the 3D complex. The two interacting
domains are colored and shown in ribbons representation
with the residues participating in the interface (i.e. making
hydrogen bonds, salt bridges or van der Waals contacts)
shown in ball-and-stick. The newest version of 3did also
includes a graphical representation of the different interac-
tion topologies for each interacting domain. This represen-
tation indicates which residues of a domain are used in a
particular interaction, as well as their frequency (Figure 3).
AVAILABILITY
A web-based tool to query 3did is available at http://
3did.irbbarcelona.org. MySQL and flat files containing
the entire database are also available through the website
for independent studies. 3did is weekly updated with new
3D structures, and major updates are implemented when-
ever new versions of Pfam or ELM are released.
FUNDING
Spanish Ministerio de Educacio ´ n y Ciencia (PSE-010000-
2007-1 and BIO2007-62426) partially; 3D-Repertoire
from the European Commission under FP6 contract
LSHG-CT-2005-512028. Funding
charge: BIO2007-62426.
foropen access
Conflict of interest statement. None declared.
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