Abstract
Proteins are involved in almost all functions in a living cell, and functions of proteins are realized by their tertiary structures. Obtaining a global perspective of the variety and distribution of protein structures lays a foundation for our understanding of the building principle of protein structures. In light of the rapid accumulation of low-resolution structure data from electron tomography and cryo-electron microscopy, here we map and classify three-dimensional (3D) surface shapes of proteins into a similarity space. Surface shapes of proteins were represented with 3D Zernike descriptors, mathematical moment-based invariants, which have previously been demonstrated effective for biomolecular structure similarity search. In addition to single chains of proteins, we have also analyzed the shape space occupied by protein complexes. From the mapping, we have obtained various new insights into the relationship between shapes, main-chain folds, and complex formation. The unique view obtained from shape mapping opens up new ways to understand design principles, functions, and evolution of proteins.
Highlights
Proteins are the primary workers in a living cell, involved in transportation, catalysis, signaling, energy production, and many other processes
We present a novel mapping of protein shapes that represents the variety and the similarities of 3D shapes of proteins and their assemblies
The mapping will be a valuable resource for artificial protein design as well as references for classifying medium- to low-resolution protein structure images of determined by cryo-electron microscopy and tomography
Summary
Proteins are the primary workers in a living cell, involved in transportation, catalysis, signaling, energy production, and many other processes. Protein structures have been classified based on their main-chain conformations and evolutionary history [4,5,6] Such classifications led to several important observations including the number of different protein folds in nature [7,8,9], distributions of folds in genomes [10,11], and the relationship between sequence and structure conservations [12]. The discovery of the limited number of folds yielded stimulating discussions on the mechanism behind it [13,14] Such studies contributed to the birth of a very successful paradigm of threading [15] and more recent fragment-based approaches [16] in protein structure prediction
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