Analysis of the Local Sequences of Folding Sites in β Sandwich Proteins with Inter-Residue Average Distance Statistics

Abstract

Abstract:The sequences of azurin and titin, sandwich proteins, are analyzed based on inter-residue average distance statistics. A kind of predicted contact map based on inter-residue average distance statistics (Average Distance Map, ADM) is used to pinpoint regions of possible compact regions for two proteins. We compare predicted compact regions with the positions of the residues with experimental high values for these proteins reported in the literature. The results reveal that the regions predicted by ADMs correspond to the positions of residues with the high value. Furthermore, we perform random sampling of 3D conformations using these protein sequences with a potential derived from inter-residue average distance statistics. It is demonstrated that the residues with highest contact frequency during the simulations qualitatively correspond to the residues with the highest values for these proteins. Importantly, analysis with inter-residue average distance statistics predicts the properties of folding processes of the sandwich proteins starting from only sequence information.

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…”

Analyses of Sequences of (β/α) Barrel Proteins Based on the Inter-Residue Average Distance Statistics to Elucidate Folding Processes

“…This part grows to the final native structure. -Sandwich proteins such as titin, azurin (Ishizuka & Kikuchi, 2011) and so on, proteins in the c-type lysozyme fold (Nakajima & Kikuchi, 2007), sandwich proteins (Matsuoka & Kikuchi, unpublished) such as ribosomal protein S6, and so on may belong to this category. In this case, the ADM for a protein tends to predict the location of folding cores which should aggregate into the larger hydrophobic core.…”

“…One clear folding unit and a short relatively weak one are predicted for a protein in the globin family (Kawai et al, 2011). The sequence of a sandwich protein is predicted to contain two folding units, and this is interpreted to mean that these two portions merge into a larger block in the protein and form a native-like structure (Ishizuka & Kikuchi, 2011). Thus, it is interesting to see how our method predicts for the sequence of a ( / ) barrel protein and how its folding process can be interpreted from the predictions.…”