Structural Characterization of the Human Proteome

Abstract

This paper reports an analysis of the encoded proteins (the proteome) of the genomes of human, fly, worm, yeast, and representatives of bacteria and archaea in terms of the three-dimensional structures of their globular domains together with a general sequence-based study. We show that 39% of the human proteome can be assigned to known structures. We estimate that for 77% of the proteome, there is some functional annotation, but only 26% of the proteome can be assigned to standard sequence motifs that characterize function. Of the human protein sequences, 13% are transmembrane proteins, but only 3% of the residues in the proteome form membrane-spanning regions. There are substantial differences in the composition of globular domains of transmembrane proteins between the proteomes we have analyzed. Commonly occurring structural superfamilies are identified within the proteome. The frequencies of these superfamilies enable us to estimate that 98% of the human proteome evolved by domain duplication, with four of the 10 most duplicated superfamilies specific for multicellular organisms. The zinc-finger superfamily is massively duplicated in human compared to fly and worm, and occurrence of domains in repeats is more common in metazoa than in single cellular organisms. Structural superfamilies over-and underrepresented in human disease genes have been identified. Data and results can be downloaded and analyzed via web-based applications at http://www.sbg. bio.ic.ac.uk.[Supplemental material is available online at http://www.genome.org.]The interpretation and exploitation of the wealth of biological knowledge that can be derived from the human genome (Lander et al. 2001;Venter et al. 2001) requires an analysis of the three-dimensional structures and the functions of the encoded proteins (the proteome). Comparison of this analysis with those of other eukaryotic and prokaryotic proteomes will identify which structural and functional features are common and which confer species specificity. In this paper, we present an integrated analysis of the proteomes of human and 13 other species considering the folds of globular domains, the presence of transmembrane proteins, and the extent to which the proteomes can be functionally annotated. This integrated approach enables us to consider the relationship between these different aspects of annotation and thereby enhance previous analyses of the human and other proteomes (e.g., Koonin et al. 2000;Frishman et al. 2001;Iliopoulos et al. 2001), including the seminal papers reporting the human genome sequence (Lander et al. 2001;Venter et al. 2001).A widely used first step in a bioinformatics-based functional annotation is to identify known sequence motifs and domains from manually curated databases such as PFAM/ INTERPRO (Bateman et al. 2000) and PANTHER (Venter et al. 2001). This strategy was used in the original analyses of the human proteome (Lander et al. 2001;Venter et al. 2001). These annotations tend to be reliable, as these libraries have been carefully constructed to avoid ...

Fold Designability, Distribution and Disease

“…This phenomenon is consistent with the idea that relatively young folds may not have had enough time to procreate families, thus obscuring trends between these attributes. Early structural characterization of the human proteome indicated significant differences in SCOP superfamily composition between disease and non-disease proteins [24]. In this and a previous work [7], it was found that disease proteins tend to have folds with fewer families than non-disease proteins (see Protocol S2).…”

Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome

“…27 Unsurprisingly, there are numerous examples of variant TMEM proteins in human genetic disorders, [28][29][30][31][32][33][34] and in that context, we do gain pathomechanistic clues about the disorder. We have reported enrichment of TMEM domains in the ciliary proteome, 35 raising the possibility that the present constellation of phenotypes could be part of the ciliopathy spectrum.…”

Structural and Functional Characterization of Gene Products Encoded in the Human Genome by Homology Detection

“…Similar attempts have been made in the past by Muller et al (38). They have used PSI-BLAST for much of their analysis, apart from IMPALA, to assign structural/functional domains.…”