Evolution of protein structural classes and protein sequence families

Abstract

In protein structure space, protein structures cluster into four elongated regions when mapped based solely on similarity among the 3D structures. These four regions correspond to the four major classes of present-day proteins defined by the contents of secondary structure types and their topological arrangement. Evolution of and restriction to these four classes suggest that, in most cases, the evolution of genes may have been constrained or selected to those genetic changes that results in structurally stable proteins occupying one of the four ''allowed'' regions of the protein structure space, ''structural selection,'' an important component of natural selection in gene evolution. Our studies on tracing the ''common structural ancestor'' for each protein sequence family of known structure suggest that: (i) recently emerged proteins belong mostly to three classes; (ii) the proteins that emerged earlier evolved to gain a new class; and (iii) the proteins that emerged earliest evolved to become the present-day proteins in the four major classes, with the fourth-class proteins becoming the most dominant population. Furthermore, our studies also show that not all present-day proteins evolved from one single set of proteins in the last common ancestral organism, but new common ancestral proteins were ''born'' at different evolutionary times, not traceable to one or two ancestral proteins: ''the multiple birth model'' for the evolution of protein sequence families.protein fold classes ͉ common structural ancestor ͉ evolutionary age ͉ protein structure universe

Global view of the protein universe

“…Previous work showed that the alpha/beta domains are older (19), more stable (36), more frequently involved in domain fusion events (32), and are associated with high functional diversity (20). Our analysis shows two additional unique features of these domains: they lie in a tightly connected region of protein space and their motifs mix-and-join with a wider range of motifs.…”

“…[19][20][21]. By coloring the points according to domain characteristics, one can visually identify global properties of the protein universe (19,20). However, a map representation in low-dimensional Euclidean space implicitly suggests that similarity among domains is transitive (i.e., that similarity within the pairs AB and BC implies that AC is similar too); we know that this is often not the case (6).…”

“…An alternative approach is to study the protein universe via maps--where domains are represented by points in two or three dimensions, placed so that the distances between them depend on the dissimilarity between their corresponding domains (e.g., refs. [19][20][21]. By coloring the points according to domain characteristics, one can visually identify global properties of the protein universe (19,20).…”

On-line hierarchy of general linear models for selecting and ranking the best predicted protein structures

“…We appreciate the anonymous reviewers' suggestions and efforts a conservative estimate, there are more than 10 10 proteins on earth [2] in addition to the engineered ones. The importance of the knowledge of proteins shape, the abundance of proteins of unknown structures, and the limitations of the experimental methods have all contributed to the need for the computational methods to predict the three dimensional shape of proteins.…”

Classifi cation of Protein Structural Classes using Isoluecine and Lysine Amino Acids

“…The Automated Protein Subfamily Identification and Classification by (Brown et al, 2007) enables improved specificity of functional inference and facilitates prediction of functional shifts in new sequences. (Choi and Kim, 2006) address by evolution of protein structural classes and protein sequence families. They were report on the development of an efficient sub-graph mining technique and its application to finding characteristic sub-structural patterns within protein structural families.…”