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

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dc.contributor.authorYu, C.
dc.contributor.authorDeng, M.
dc.contributor.authorCheng, S.
dc.contributor.authorYau, S.
dc.contributor.authorHe, R.
dc.contributor.authorYau, S.
dc.date.issued2013
dc.descriptionData source: Supplementary materials, https://doi.org/10.1016/j.jtbi.2012.11.005
dc.description.abstractCurrent 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.
dc.identifier.citationJournal of Theoretical Biology, 2013; 318:197-204
dc.identifier.doi10.1016/j.jtbi.2012.11.005
dc.identifier.issn0022-5193
dc.identifier.issn1095-8541
dc.identifier.orcidYu, C. [0000-0002-3248-8421]
dc.identifier.urihttps://hdl.handle.net/11541.2/131869
dc.language.isoen
dc.publisherElsevier
dc.relation.fundingUS NSF DMS-1120824
dc.relation.fundingChina NSF 31271408
dc.relation.fundingTsinghua University
dc.rightsCopyright 2012 Elsevier
dc.source.urihttps://doi.org/10.1016/j.jtbi.2012.11.005
dc.subjectAnimals
dc.subjectAmino Acids
dc.subjectProteins
dc.subjectPhylogeny
dc.subjectProtein Conformation
dc.subjectAlgorithms
dc.subjectModels, Molecular
dc.subjectDatabases, Protein
dc.titleProtein space: A natural method for realizing the nature of protein universe
dc.typeJournal article
pubs.publication-statusPublished
ror.mmsid9916188090101831

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