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Title of Journal: Theor Chem Acc

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Abbravation: Theoretical Chemistry Accounts

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Springer-Verlag

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10.1007/s10778-008-0093-3

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1432-2234

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Why similar protein sequences encode similar three

Authors: Szymon Kaczanowski Piotr Zielenkiewicz
Publish Date: 2009/10/23
Volume: 125, Issue: 3-6, Pages: 643-650
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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 socalled homology modeling In contrast the artificial protein designed by the Regan group has 50 identical sequence to the B1 domain of Streptococcal IgGbinding 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 threedimensional 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 threedimensional 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 sequencestructure 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 threedimensional protein structure is evolutionarily more conserved than expected due to sequence conservation

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