The Urfold: Structural similarity just above the superfold level?

Area of Science:

• Structural Biology
• Bioinformatics
• Computational Biology

Background:

• Classical protein structure classification includes levels like architecture and topology.
• Extensive three-dimensional structural similarity exists beyond the fold level, suggesting an intermediate granularity.
• Existing models struggle to reconcile phenomena like significant structural overlap and fold space continuity.

Purpose of the Study:

• To introduce and qualitatively explore the concept of an intermediate level of protein structural granularity, termed the "Urfold."
• To propose the Urfold as a new conceptual approach for protein structural analysis and classification.
• To provide a framework for reconciling debated phenomena in protein structure and evolution.

Main Methods:

• Qualitative introduction of the Urfold concept.
• Examination of architectural identity despite topological variability.
• Conceptual analysis of structural similarity in protein evolution.

Main Results:

• Identification of a potential intermediate level of protein structural granularity.
• Proposal of the Urfold as a unifying concept for protein structure classification.
• Laying the groundwork for a generalized framework for protein structure-function evolution.

Conclusions:

• The Urfold concept offers a novel perspective on protein structural analysis and classification.
• This intermediate level may help reconcile long-standing debates in structural biology.
• The Urfold has the potential to synthesize various models of protein evolution into a consistent framework.