Protein space: A natural method for realizing the nature of protein universe

Chenglong Yu South Australian Health and Medical Research Institute Mo Deng Shiu-Yuen Cheng Shek-Chung Yau Rong L. He Stephen S.-T. Yau

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1703.42001

Journal of Theoretical Biology, 318, 197-204, 2013
Current methods cannot tell us what the nature of the protein universe is concretely. They are based on different models of amino acid substitution and multiple sequence alignment which is an NP-hard problem and requires manual intervention. Protein structural analysis also gives a direction for mapping the protein universe. Unfortunately, now only a minuscule fraction of proteins' 3-dimensional structures are known. Furthermore, the phylogenetic tree representations are not unique for any existing tree construction methods. Here we develop a novel method to realize the nature of protein universe. We show the protein universe can be realized as a protein space in 60-dimensional Euclidean space using a distance based on a normalized distribution of amino acids. Every protein is in one-to-one correspondence with a point in protein space, where proteins with similar properties stay close together. Thus the distance between two points in protein space represents the biological distance of the corresponding two proteins. We also propose a natural graphical representation for inferring phylogenies. The representation is natural and unique based on the biological distances of proteins in protein space. This will solve the fundamental question of how proteins are distributed in the protein universe.
Natural vector; Phylogeny; Protein universe
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@inproceedings{chenglong2013protein,
  title={Protein space: A natural method for realizing the nature of protein universe},
  author={Chenglong Yu, Mo Deng, Shiu-Yuen Cheng, Shek-Chung Yau, Rong L. He, and Stephen S.-T. Yau},
  url={http://archive.ymsc.tsinghua.edu.cn/pacm_paperurl/20170313205042128528672},
  booktitle={Journal of Theoretical Biology},
  volume={318},
  pages={197-204},
  year={2013},
}
Chenglong Yu, Mo Deng, Shiu-Yuen Cheng, Shek-Chung Yau, Rong L. He, and Stephen S.-T. Yau. Protein space: A natural method for realizing the nature of protein universe. 2013. Vol. 318. In Journal of Theoretical Biology. pp.197-204. http://archive.ymsc.tsinghua.edu.cn/pacm_paperurl/20170313205042128528672.
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