Abstract
A protein in the globin-like fold contains six alpha-helices, A, B, E, F, G and H. Among them, the E-to-H helix unit (E, F, G and H helices) forms a compact structure. In this study, we searched similar structures to the E-to-H helix of leghomoglobin in the whole protein structure space using the Dali program. Several similar structures were found in other helical folds, such as KaiA/RbsU domain and Type III secretion system domain. These observations suggest that the E-to-H helix unit may be a common subunit in the whole protein 3D structure space. In addition, the common conserved hydrophobic residues were found among the similar structures to the E-to-H helix unit. Hydrophobic interactions between the conserved residues may stabilize the 3D structures of the unit. We also predicted the possible compact regions of the units using the average distance method.
Highlights
To elucidate how a protein folds into its unique 3D structure is a long-standing unsolved problem in molecular bioinformatics and molecular biophysics
The hit proteins could be classified into the 690 Structural Classification of Protein Database (SCOP) families, and the representative protein from each family was selected based on the criterion described in the method section, Section 4.2
The results of the present study show that the common topology of the E-to-H helix unit can be observed beyond the globin-like fold when the Dali search is performed followed by average distance map (ADM) screening to check the tendency of a partial amino acid sequence of the hit regions to form a compact structure
Summary
To elucidate how a protein folds into its unique 3D structure is a long-standing unsolved problem in molecular bioinformatics and molecular biophysics To tackle this problem, we have to know how the information of a protein’s 3D structure construction is coded in its amino acid sequence. Some protein folds have neither sequence nor functional similarity Proteins with these folds frequently appear in the structure database, that is, more than 30% of determined structures and such folds are called a “superfold” [1]. In such a case, one might ask if there is a common property in their amino acid sequences that leads to the same fold
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