On the relationship between the sequence conservation and the packing density profiles of the protein complexes

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2013-07, Vol.81 (7), p.1192-1199
• Main Authors: Chang, Chih-Min, Huang, Yu-Wen, Shih, Chien-Hua, Hwang, Jenn-Kang
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Binding Sites; Catalytic Domain; Conserved Sequence; Databases, Protein; Evolution, Molecular; Multiprotein Complexes - chemistry; protein structure; Proteins - chemistry; Sequence Alignment; sequence conservation; Structure-Activity Relationship; weighted contact number
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.24268

We have recently showed that the weighted contact number profiles (or the packing density profiles) of proteins are well correlated with those of the corresponding sequence conservation profiles. The results suggest that a protein structure may contain sufficient information about sequence conservation comparable to that derived from multiple homologous sequences. However, there are ambiguities concerning how to compute the packing density of the subunit of a protein complex. For the subunits of a complex, there are different ways to compute its packing density – one including the packing contributions of the other subunits and the other one excluding their contributions. Here we selected two sets of enzyme complexes. Set A contains complexes with the active sites comprising residues from multiple subunits, while set B contains those with the active sites residing on single subunits. In Set A, if the packing density profile of a subunit is computed considering the contributions of the other subunits of the complex, it will agree better with the sequence conservation profile. But in Set B the situations are reversed. The results may be due to the stronger functional and structural constraints on the evolution processes on the complexes of Set A than those of Set B to maintain the enzymatic functions of the complexes. The comparison of the packing density and the sequence conservation profiles may provide a simple yet potentially useful way to understanding the structural and evolutionary couplings between the subunits of protein complexes. Proteins 2013; 81:1192–1199. © 2013 Wiley Periodicals, Inc.