How a Spatial Arrangement of Secondary Structure Elements Is Dispersed in the Universe of Protein Folds

Shintaro Minami,Kengo Sawada,George Chikenji,Yang Zhang

doi:10.1371/journal.pone.0107959

Shintaro Minami, Kengo Sawada + Show 2 more

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https://doi.org/10.1371/journal.pone.0107959

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Journal: PloS one	Publication Date: Sep 22, 2014
Citations: 16	License type: CC BY 4.0

Affiliation: Nagoya University

Abstract

It has been known that topologically different proteins of the same class sometimes share the same spatial arrangement of secondary structure elements (SSEs). However, the frequency by which topologically different structures share the same spatial arrangement of SSEs is unclear. It is important to estimate this frequency because it provides both a deeper understanding of the geometry of protein folds and a valuable suggestion for predicting protein structures with novel folds. Here we clarified the frequency with which protein folds share the same SSE packing arrangement with other folds, the types of spatial arrangement of SSEs that are frequently observed across different folds, and the diversity of protein folds that share the same spatial arrangement of SSEs with a given fold, using a protein structure alignment program MICAN, which we have been developing. By performing comprehensive structural comparison of SCOP fold representatives, we found that approximately 80% of protein folds share the same spatial arrangement of SSEs with other folds. We also observed that many protein pairs that share the same spatial arrangement of SSEs belong to the different classes, often with an opposing N- to C-terminal direction of the polypeptide chain. The most frequently observed spatial arrangement of SSEs was the 2-layer α/β packing arrangement and it was dispersed among as many as 27% of SCOP fold representatives. These results suggest that the same spatial arrangements of SSEs are adopted by a wide variety of different folds and that the spatial arrangement of SSEs is highly robust against the N- to C-terminal direction of the polypeptide chain.

Highlights

The protein fold is defined by the number, spatial arrangement, and topological connectivity of secondary structure elements (SSEs) [1]
What types of spatial arrangements of SSEs are frequently observed across fold space? We investigated the types of protein folds having large numbers of structural neighbors depending on the alignment scheme
We clarified the frequency with which protein folds share the same SSE packing arrangement with other folds, the types of spatial arrangement of SSEs that are frequently observed across different folds, and the diversity of protein folds that share the same spatial arrangement of SSEs with a given fold, using the protein structure alignment program MICAN

Summary

Introduction

The protein fold is defined by the number, spatial arrangement, and topological connectivity of secondary structure elements (SSEs) [1]. Existing protein folds resulted from both physicochemical interactions and evolutionary selection. Some aspects of the physics or geometry of protein folds, such as the nature of spatial arrangement of SSEs, remain less understood. We studied the geometrical aspects of protein structures by focusing on the spatial arrangement of SSEs. As the primary subject of this study, we should clarify our definition of the term ‘‘spatial arrangement of SSEs.’’ This term will imply the relative atomic positions of the backbone atoms within SSEs for which their connectivity and the N- to C- terminal direction are ignored

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