The study of the spatial configuration of the structures of a protein, also known as protein conformation, is pivotal to the understanding of the functioning and activation patterns of proteins, as well as their relations with the surrounding environment. In order to facilitate datadriven research on protein conformations, we present the Protein Conformation Ontology, an ongoing project which provides a structured vocabulary of terms used to represent protein conformations and related conformational changes at different levels of granularity. To the aim of testing the capabilities of the ontology, we adopted as a test case the conformational changes related to the activation of the epidermal growth factor receptor. In this paper, we discuss our initial results in modelling two different models of the epidermal growth factor receptor.
Ontology⋆
The spatial configuration of a protein is a key element to our understanding of its
functioning. The same protein, depending on the different environmental conditions it is
situated in, can fold into many different types of structures, also known as protein
conformations [
Ontologies are controlled vocabularies developed for allowing consistent semantic
interoperability of large and fragmented datasets [
A survey of BioPortal [
SO on the other hand represents protein structure at the secondary structure level, but
cannot be used to model protein conformations at an higher level of complexity. Moreover,
the scope of SO is limited to continuous sequences of amino acids, thus effectively
disregarding representation of secondary structures that include discontinuous regions [
The scope of the ontologies described above is then too narrow to fully represent the full variety of protein conformations, as well as changes in protein conformations, and warrants the creation of an ontology devoted to this particular domain. In this paper we present first results in developing the PRC, an ontology which intends to address this issue. The aim of the PRC is not only to represent protein conformations as physical structure or as structured material entities. Rather, the PRC represents conformational changes, the way in which these conformational changes take place, the way in which they are triggered and the way in which they are ordered in time. For this reason, the PRC identifies protein conformations as dispositions to adopt a certain structure. Such dispositions are realized in a process of conformational change, where the protein adopts the corresponding to the protein conformation.
The development of the PRC originated from the need to represent the conformational
changes involved in the formation of protein aggregates in neurological diseases, such as
the formation of prions associated with Creutzfeldt-Jakob disease [
PRC is developed with the aim of supporting and complying with FAIR data standards
practices [
The PRC currently contains 206 PRC-prefixed classes, which include terms representing secondary, tertiary, and quaternary conformation dispositions, as well as terms representing conformational changes, structural qualities, and material entities such as protein complexes and amino acid chains. Currently, the PRC includes many terms representing secondary structures, such as ‘beta helix’, that refer to conformations commonly found in many different protein complexes. Tertiary and quaternary structures, on the other hand, are very specific to particular protein complexes, and cannot all be represented in a single ontology. To test the capabilities of the ontology to represent tertiary and quaternary structures, we chose to represent certain specific protein complexes and their conformational changes over time and in different conditions.
The use-case we present in this paper as a test case for the PRC is the epidermal growth factor receptor (EGFR). The EGFR is a transmembrane protein responsible for regulation of a series of events such as coordination of cell growth, differentiation, and migration and which serves a role in epithelial development [17]. Other members of the EGFR protein superfamily, which share structural similarities with the EGFR, have roles in other parts of the body, such as cardiac development [17 18]. Errors in the activation of the EGFR are closely related to the formation of tumors [19]. Representing EGFR is a formidable test case for the PRC, given that the EGFR is involved in a very complex series of conformational changes including dimerization. Building an ontological model of the EGFR is then an excellent test case for any ontology that aims at representing conformations and conformational changes over time.
The EGFR is a tyrosine kinase receptor (RTK) which activates a process of phosphorylation that regulates cell production. The mechanism through which this process is activated is of particular interest for a structural study of proteins. The EGFR is activated through binding with one of its ligands, usually the epidermal growth factor (EGF), and through a complex process of conformational changes, that in some cases involve ligandinduced dimerization with another EGFR monomer [17 18 19].
Two models based on a variety of experimental data and simulations have been developed to represent the mechanism through which the EGFR activates. In one of the models, called “ligand-induced dimerization model”, two EGFR subunits dimerize after binding to EGF. In the other model, called “rotation model”, EGFR exists as a preformed dimer, and is merely activated after ligand binding occurs. Despite the rotation model having received stronger experimental confirmation in recent years, consensus has not been reached on whether the model should entirely replace the ligand-induced one [20 21]. We thus decided to include the ligand-induced and rotation models in our representation, not only because scientific consensus has not yet been reached, but also because both models may reflect reality, in that some EGFR subunits may be pre-dimerized and some not [22].
The EGFR comprises an external region that is divided into four domains, includes a transmembrane domain and a juxtamembrane domain, that connects the external domains to the tyrosine kinase domain (TKD) to a disordered carboxyl tail [18]. Each of these parts is described by a ‘material entity’ class in the PRC, along with the secondary structures it is composed of.
The process through which the EGFR activates its TKD, according to the ligand-induced dimerization model, is the following: first of all, one EGF monomer binds to an EGFR monomer, between the external domains 1 and 3 [17]. This causes domain 3 to rotate of roughly 120 degrees closer to domain 1, and the whole external part of the EGFR to undergo a radical conformational change. A beta hairpin called “dimerization arm”, part of external domain 2, is now pointing outwards and can be used to bind to another EGFR that has also undergone the same sequence of changes. The two dimerization arms must pass close to each other and bind reciprocally to a site on the external domain 2 of the opposite EGFR monomer, resulting in the formation of the external EGFR dimer [17].
As a consequence, other parts of the two EGFR monomers also bind. In particular, the intracellular TKD subunits dimerize and create an asymmetric TKD dimer. This dimer is formed through the rotation of an alpha helix in one TKD, called the alpha C helix, that interacts with an active site in the opposite TKD. As a result, the two TKDs, one assuming the role of an activator and the other the role of a receiver, will trans-phosphorylate each other.
These two processes of dimerization have been the main focus of our ontological representation. They represent a complex series of conformational changes that two different protein monomers undergo together in order to build a common quaternary structure. All of the entities described above have been represented in the ontology in the form of material entities for the parts of the EGFR, dispositions for the conformations of the EGFR, roles and processes of conformational changes. Processes in particular have been also axiomatized in order to automate reasoning, especially regarding their temporal ordering.
For example, the class “epidermal growth factor receptor ligand binding” has been made equivalent to “'protein binding' and (realizes some 'epidermal growth factor receptor with bound ligand conformation') and (precedes some 'epidermal growth factor receptor activation')”.
When needed, new ad-hoc classes were created to reflect this different process ordering, as well as corresponding new disposition classes and relative axioms. When possible, classes from the ligand-induced dimerization model were reused, for example to represent the material entities involved in the constitution of the EGFR. Similarly, two different classes are introduced to represent the ligand-induced and rotation-induced processes of activation, and each have different processes as parts.
The EGFR test case was successfully completed. The complex conformational changes that the protein complex is involved in are all represented in the PRC and properly axiomatized. Moreover, two different models for the EGFR functioning were also successfully represented and can now be coherently compared and used for querying purposes. Many subclasses of tertiary and quaternary structure were created to represent the structure of the EGFR protein complex: its disposition to connect with an EGFR ligand, its disposition to form a dimer with another EGFR monomer, its disposition to activate by rotating its dimerization arm, and so on. Further work in representing the EGFR will include linking the conformational changes in the ontology with other biological processes such as phosphorylation and extending our ontological representation of the normal forms of EGFR to include how pathological mutations alter its conformation and activation. Changes in the conformational activations of the EGFR might be related with its mis-activation in cases where the EGFR is involved with the formation of cancer [18]. Representing this process ontologically would provide an extremely helpful application of the PRC.
The PRC is aimed at representing protein conformations, how they are created as a result of various biological processes and how they inhere in different material entities. Allowing for querying of information about protein structures can also be beneficial a series of datadriven areas of research. For example, systems biology investigates biological functions based on the interactions between different parts of the whole organism. The ELIXIR platform has recently become a focal point for data-driven investigation in the field of systems biology [22]. Conformational changes depend on features of the biological environment that their bearers are situated in, and this is interestingly also the case for the EGFR [23]. Moreover, being able to differentiate between the two possible EGFR models on the basis of surrounding environmental features would reveal an extremely useful use case for an EGFR ontological representation.
The PRC is an ontology which adopts BFO as a top-level architecture and which aims at representing protein conformation, the processes they are involved in, and the material entities they depend on. The current development of the PRC includes 206 classes which represent secondary, tertiary, and quaternary structures. To test the capabilities of the PRC in representing protein conformations, we have modeled the EGFR, its dimerization process, and its activation, includes representing the two competing models of the EGFR in a coherent way. Being able to represent the complex series of conformational changes that interest the EGFR at different levels of granularity, the PRC proves to be the first successful ontology for modeling protein conformations and their changes.
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