Structural motifs are closed into cycles in proteins

Left-handed βαβ-units: frequency of occurrence and arrangement in protein structure

Communicated by Ramaswamy H. Sarma.

Structural motifs in which β-strands are clipped together with the П-like module

In this study, the structural motifs that can be represented as combinations of small motifs such as β-hairpins, S-, and Z-like β-sheets and βαβ-units, and the П-like module are described and analyzed. The П-module consists of connected elements of the β-strand-loop-β-strand type arranged in space so that its overall fold resembles a clip or the Greek letter П. In proteins, the П-module itself and the structural motifs containing it exhibit unique overall folds and have specific sequence patterns of the key hydrophobic, hydrophilic and glycine residues. All this together enables us to conclude that these structural motifs can fold independently of the remaining part of the molecule and can act as nuclei and/or "ready-made" building blocks in protein folding.

[Two mechanisms of protein folding: theoretical analysis]

In the present study, two possible mechanisms of protein folding are analized. One of them is based on the hypothesis that at the first step of protein folding a nucleus is formed and then the remaining part of the molecule or domain is folded around it. For example, β-proteins containing 3β-corners can fold in this way. According to the other mechanism, the three-dimensional structure of proteins is formed as a result of interactions between "ready-made" building blocks. Analysis of structural features of the 3β-corners and features of their amino asid sequences enable us to conclude that the 3β-corner can fold into its unique structure per se and can act as a nucleus or "ready-made" building block in protein folding. The larger protein structures can be obtained by stepwise addition of β-strands to the 3β-corner in accordance with a restricted set of rules as shown in the corresponding structural tree, which is available at http://strees.protres.ru/. On the other hand, complementary interactions of the two 3β-corners can result in formation of the fold that is observed in the serine protease domain and similar proteins.

Exploring the evolution of protein function in Archaea

Background

Despite recent progress in studies of the evolution of protein function, the questions what were the first functional protein domains and what were their basic building blocks remain unresolved. Previously, we introduced the concept of elementary functional loops (EFLs), which are the functional units of enzymes that provide elementary reactions in biochemical transformations. They are presumably descendants of primordial catalytic peptides.

Results

We analyzed distant evolutionary connections between protein functions in Archaea based on the EFLs comprising them. We show examples of the involvement of EFLs in new functional domains, as well as reutilization of EFLs and functional domains in building multidomain structures and protein complexes.

Conclusions

Our analysis of the archaeal superkingdom yields the dominating mechanisms in different periods of protein evolution, which resulted in several levels of the organization of biochemical function. First, functional domains emerged as combinations of prebiotic peptides with the very basic functions, such as nucleotide/phosphate and metal cofactor binding. Second, domain recombination brought to the evolutionary scene the multidomain proteins and complexes. Later, reutilization and de novo design of functional domains and elementary functional loops complemented evolution of protein function.

Super-secondary structures and modeling of protein folds

A characteristic feature of the polypeptide chain is its ability to form a restricted set of commonly occurring folding units composed of two or more elements of secondary structure that are adjacent along the chain. Some of these super-secondary structures exhibit a unique handedness and a unique overall fold irrespective of whether they occur in homologous or nonhomologous proteins. Such super-secondary structures are of particular value since they can be used as starting structures in protein modeling. The larger protein folds can be obtained by stepwise addition of other secondary structural elements to the starting structures taking into account a set of simple rules inferred from known principles of protein structure.