Abstract Evolutionarily related proteins have similar sequences. Such similarity is called homology and can be described using substitution matrices such as Blosum 60. Naturally occurring homologous proteins usually have similar stable tertiary structures and this fact is used in so-called homology modeling. In contrast, the artificial protein designed by the Regan group has 50% identical sequence to the B1 domain of Streptococcal IgG-binding protein and a structure similar to the protein Rop. In this study, we asked the question whether artificial similar protein sequences (pseudohomologs) tend to encode similar protein structures, such as proteins existing in nature. To answer this question, we designed sets of protein sequences (pseudohomologs) homologous to sequences having known three-dimensional structures (template structures), same number of identities, same composition and equal level of homology, according to Blosum 60 substitution matrix as the known natural homolog. We compared the structural features of homologs and pseudohomologs by fitting them to the template structure. The quality of such structures was evaluated by threading potentials. The packing quality was measured using three-dimensional homology models. The packing quality of the models was worse for the “pseudohomologs” than for real homologs. The native homologs have better threading potentials (indicating better sequence-structure fit) in the native structure than the designed sequences. Therefore, we have shown that threading potentials and proper packing are evolutionarily more strongly conserved than sequence homology measured using the Blosum 60 matrix. Our results indicate that three-dimensional protein structure is evolutionarily more conserved than expected due to sequence conservation.
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