Abstract
The hydrophobic core, when subjected to analysis based on the fuzzy oil drop model, appears to be a universal structural component of proteins irrespective of their secondary, supersecondary, and tertiary conformations. A study has been performed on a set of nonhomologous proteins representing a variety of CATH categories. The presence of a well-ordered hydrophobic core has been confirmed in each case, regardless of the protein’s biological function, chain length or source organism. In light of fuzzy oil drop (FOD) analysis, various supersecondary forms seem to share a common structural factor in the form of a hydrophobic core, emerging either as part of the whole protein or a specific domain. The variable status of individual folds with respect to the FOD model reflects their propensity for conformational changes, frequently associated with biological function. Such flexibility is expressed as variable stability of the hydrophobic core, along with specific encoding of potential conformational changes which depend on the properties of helices and β-folds.
Highlights
The traditional classification of secondary and supersecondary protein structures covers helical and β-fragments along with their mutual arrangement within the protein body
Attempts to introduce a detailed structural classification of domain units in large proteins have resulted in the creation of the CATH/Gene3D database, which currently contains 26 million domains arranged into 2738 families
Our analysis of diverse structures is based on the fuzzy oil drop model and shows that both secondary and supersecondary structural motifs participate in the formation of a domain- or protein-wide hydrophobic core
Summary
The traditional classification of secondary and supersecondary protein structures covers helical and β-fragments along with their mutual arrangement within the protein body. This α/β classification varies with respect to the participation of both folds in proteins, as well as their orientation. Water is the immanent condition ensuring proper folding and biological activity This is why the water participation and its influencing on protein structure is the basis for the fuzzy oil drop model applied to interpret the different structures of proteins. Our analysis of diverse structures is based on the fuzzy oil drop model and shows that both secondary and supersecondary structural motifs participate in the formation of a domain- or protein-wide hydrophobic core. The presented paper is an attempt to show the possible interpretation of structural effects which may express the role of water
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