Abstract
The presented analysis concerns the inter-domain and inter-protein interface in protein complexes. We propose extending the traditional understanding of the protein domain as a function of local compactness with an additional criterion which refers to the presence of a well-defined hydrophobic core. Interface areas in selected homodimers vary with respect to their contribution to share as well as individual (domain-specific) hydrophobic cores. The basic definition of a protein domain, i.e., a structural unit characterized by tighter packing than its immediate environment, is extended in order to acknowledge the role of a structured hydrophobic core, which includes the interface area. The hydrophobic properties of interfaces vary depending on the status of interacting domains—In this context we can distinguish: (1) Shared hydrophobic cores (spanning the whole dimer); (2) Individual hydrophobic cores present in each monomer irrespective of whether the dimer contains a shared core. Analysis of interfaces in dystrophin and utrophin indicates the presence of an additional quasi-domain with a prominent hydrophobic core, consisting of fragments contributed by both monomers. In addition, we have also attempted to determine the relationship between the type of interface (as categorized above) and the biological function of each complex. This analysis is entirely based on the fuzzy oil drop model.
Highlights
The traditional definition of a domain refers to the local compactness criterion [1,2,3,4]
We propose an approach which regards complexation as an effect of global conformational characteristics produced by the fuzzy oil drop model (FOD) in each structural unit, as well as in multi-domain complexes and protein dimers
The main point of this paper is the recognition of a distinct interface which manifests itself as a quasi-domain comprising fragments contributed by both monomers and possessing its own hydrophobic core
Summary
The traditional definition of a domain refers to the local compactness criterion [1,2,3,4]. The innovation of the fuzzy oil drop approach rests in its ability to identify “hydrophobically ordered” domains in the protein body—Even when these domains are formed by fragments contributed by separate chains Such emergent hydrophobic cores may play a key role in ensuring proper biological activity of protein complexes, when contraction and stretching come into play [42]. The main point of this paper is the recognition of a distinct interface which manifests itself as a quasi-domain comprising fragments contributed by both monomers and possessing its own hydrophobic core Such quasi-domains have been found in dystrophin and utrophin. The main contribution of this paper is recognition of a distinct interface, which manifests itself as an independent domain, comprising fragments contributed by both monomers and possessing its own well-defined hydrophobic core Such interfaces are found in dystrophin and utrophin. Inter-domain/inter-chain contacts have been identified on the basis of the PDBSum distance criterion [51]
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