title: Sequence-related human proteins cluster by degree of evolutionary conservation.
abstract: Gene duplication followed by adaptive evolution is thought to be a central mechanism for the emergence of novel genes. To illuminate the contribution of duplicated protein-coding sequences to the complexity of the human genome, we study the connectivity of pairwise sequence-related human proteins and construct a network (N) of linked protein sequences with shared similarities. We find that (i) the connectivity distribution P (k) for k sequence-related proteins decays as a power law P (k) approximately k(-gamma) with gamma approximately 1.2 , (ii) the top rank of N consists of a single large cluster of proteins ( approximately 70%) , while bottom ranks consist of multiple isolated clusters, and (iii) structural characteristics of N show both a high degree of clustering and an intermediate connectivity ("small-world" features). We gain further insight into structural properties of N by studying the relationship between the connectivity distribution and the phylogenetic conservation of proteins in bacteria, plants, invertebrates, and vertebrates. We find that (iv) the proportion of sequence-related proteins increases with increasing extent of evolutionary conservation. Our results support that small-world network properties constitute a footprint of an evolutionary mechanism and extend the traditional interpretation of protein families.
authors.affiliation: Systems Biology Group, Department of Physiology, Charité Universitätsmedizin Berlin, Tucholskystrasse 2, 10117 Berlin, Germany. ralf.mrowka@charite.de
authors.forename: Ralf
authors.initials: R
authors.lastname: Mrowka
authors.forename: Andreas
authors.initials: A
authors.lastname: Patzak
authors.forename: Hanspeter
authors.initials: H
authors.lastname: Herzel
authors.forename: Dirk
authors.initials: D
authors.lastname: Holste
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D016000:Cluster Analysis; D017124:Conserved Sequence; D019143:Evolution, Molecular; D014644:Genetic Variation; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins