Protein Structure Modelling Group

Alexander V. Efimov

Ph.D 1983, D.Sc. 1995.

Group Leader 1998.

Deputy Director of the Institute 2002-2015.


         Super-secondary structures or structural motifs have been one of the main subjects of our recent and current investigations. Structural motifs of a given type found in unrelated proteins may have the same overall fold despite their α-helices and/or β-strands being of different lengths, their connection regions differing in length and conformation and their sequences lacking homology. Some simple structural motifs of a given type are shown to have practically the same sequence patterns for the key hydrophobic, hydrophilic and glycine residues, no matter whether these structures are found in homologous proteins or not. Several novel structural motifs, for example, abcd-unit (1982), α-α-corner (1984), 3β-corner (1992), some structural motifs containing S-like β-sheets (1993, 1998), five-segment and seven-segment α/β-motifs (1997) etc. have been found and described in this group (for reviews, see, e.g., Efimov A.V. (1993) Progr. Biophys. Mol. Biol. 60, 201-239; Efimov A.V. (1994) Structure 2, 999-1002).

        The second scope of research involves protein structure modelling based on construction and analysis of structural trees for proteins. The structural motifs having unique overall folds and a unique handedness are taken as the starting structures in modelling or the root structures of the trees. The larger protein structures are obtained by stepwise addition of α-helices and/or β-strands to the root structural motif taking into account a restricted set of rules inferred from known principles of protein structure. A scheme that includes all the intermediate and final structures connected by lines showing possible pathways of structure growing is represented as a structural tree. Several structural trees for large protein superfamilies, such as α-proteins with the aligned and orthogonal β-sheet packing, α-proteins, two-layer and three-layer α/β-proteins etc.have been constructed  ( The structural trees is a good tool for searching of all possible protein folds and folding pathways as well as for structure comparison and protein classification (for details, see e.g., Efimov, A.V. (1997) Proteins 28, 241-260; Efimov, A.V. (1998) FEBS Lett. 437, 246-250).

        In addition, the packing of α-helices and/or β-sheets is studied in the group. A model for the packing of α-helices which takes into account the principle of close packing and the chemical nature of side chains has been developed. The role that buried polar side chains play in the specificity of α-helix packing is also analysed (for a recent review, see Efimov, A.V. (1999) FEBS Lett. 463, 3-6).

       The fourth direction is associated with the development of a new method for the functional identification of hypothetical protein structures, which is being developed jointly with foreign colleagues from Canada and the UK. Hypothetical proteins include proteins for which the spatial structure is known, but the function is unknown. There are currently more than 2,500 such structures in the Protein Data Bank. Using the proposed approach, it is possible to determine the structural class of a given protein, its function, and describe the features of the active center. It is also possible to identify other homologous proteins of unknown structure. We have identified five different hypothetical protein structures and about four hundred and eighty homologous sequences found in GenBank.

Site of the Protein Structure Modeling Group 

Rusian version page