Similar Structures to the E-to-H Helix Unit in the Globin-Like Fold are Found in Other Helical Folds

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.

Detection of Folding Sites of β-Trefoil Fold Proteins Based on Amino Acid Sequence Analyses and Structure-Based Sequence Alignment

“…These methods can predict the folding properties of proteins. We have confirmed so far that our techniques can extract information of folding mechanisms from the sequence of a protein for the following proteins: fatty acid binding proteins [25], globin-like fold proteins [26], IgG binding and albumin binding domains [27,28], immunoglobulinlike fold proteins [29], ferredoxin-like fold proteins [30], and lysozyme (to be published). Using these techniques significant parts for folding in an amino acid sequence can be detected with relatively high accuracy.…”

Prediction of folding mechanisms for Ig‐like beta sandwich proteins based on inter‐residue average distance statistics methods

“…It should be noticed that we consider the autonomous folding of a protein and compare our results to available experimental data. We have confirmed in previous studies that our prediction methods successfully extract the folding properties that well to the data from experimental analyses of following proteins: fatty acid binding proteins, 19 globin-like fold proteins, 20 IgG binding and albumin binding domains, 21 Ig-like fold proteins, 22 ferredoxin-like fold proteins, 23 beta-trafoil fold proteins, 24 and lysozyme-like superfamily proteins. 25 2 | MATERIAL AND METHOD…”

“…Such regions correspond to experimental analyzes of protein folding mechanisms. [19][20][21][22][23][24][25] The details of this method were described in the Supporting Information (Figures S1 and S2).…”

“…The F-value analysis could extract the residues with high possibility to make a contact in an early event as confirmed in previous studies. [20][21][22][23][24][25] In this study, we performed the F-value analyses of TI In TI I27, the peaks from the F-value plots were determined at positions G16, K35, E51, and H61 ( Figure 3A), and the hydrophobic residues within AE5 residues of the peak are considered as a residue which might significantly important in the initial hydrophobic collapse event (show by red dot on the F-value plots). 25 Interestingly, the core residues, F21, W34, and L58, are located near the peaks within AE5 residues.…”

Properties of Amino Acid Sequences of Lysozyme-Like Superfamily Proteins Relating to Their Folding Mechanisms

“…We have been applying a contact map based on inter-residue average distance statistics (we refer it as average distance map analysis) and a contact frequency prediction technique also based on inter-residue average distance statistics for protein folding [6,7]. Examples of the applications of these techniques to extract the information of folding mechanisms are the following proteins: fatty acid binding proteins [8], globin-like fold proteins [9], IgG binding and albumin binding domains [7,10], immunoglobulin-like fold proteins [11], ferredoxin-like fold proteins [12], and β-trefoil fold proteins (to be published). We apply these techniques to the present problem.…”