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Prediction of folding mechanisms for Ig‐like beta sandwich proteins based on inter‐residue average distance statistics methods
Author(s) -
Aumpuchin Panyavut,
Kikuchi Takeshi
Publication year - 2019
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25637
Subject(s) - folding (dsp implementation) , protein folding , titin , biological system , sequence (biology) , chemistry , amino acid residue , amino acid , protein structure prediction , protein structure , peptide sequence , computational biology , crystallography , biology , biochemistry , engineering , myocyte , endocrinology , gene , electrical engineering , sarcomere
To understand the folding mechanism of a protein is one of the goals in bioinformatics study. Nowadays, it is enigmatic and difficult to extract folding information from amino acid sequence using standard bioinformatics techniques or even experimental protocols which can be time consuming. To overcome these problems, we aim to extract the initial folding unit for titin protein (Ig and fnIII domains) by means of inter‐residue average distance statistics, Average Distance Map (ADM) and contact frequency analysis ( F ‐value). TI I27 and TNfn3 domains are used to represent the Ig‐domain and fnIII‐domain, respectively. Beta‐strands 2, 3, 5, and 6 are significant for the initial folding processes of TI I27. The central strands of TNfn3 were predicted as a primary folding segment. Known 3D structure and unknown 3D structure domains were investigated by structure or non‐structure based multiple sequence alignment, respectively, to learn the conserved hydrophobic residues and predicted compact region relevant to evolution. Our results show good correspondence to experimental data, phi‐value and protection factor from H‐D exchange experiments. The significance of conserved hydrophobic residues near F ‐value peaks for structural stability using hydrophobic packing is confirmed. Our prediction methods once again could extract a folding mechanism only knowing the amino acid sequence.