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

Nakashima, Takuto; Kabata, Michirou; Kikuchi, Takeshi

doi:10.4172/jpb.1000429

Cited by 6 publications

(18 citation statements)

References 43 publications

(70 reference statements)

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“…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).…”

Section: Average Distance Map Analysis Methodsmentioning

confidence: 99%

“…It has been confirmed that a hydrophobic residue within AE5 residues of the F-value peak tends to form hydrophobic packing in the native structure of a protein. 25…”

Section: Average Distance Map Analysis Methodsmentioning

confidence: 99%

“…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.…”

Section: The Contact Frequency Analyses Based On Interresidue Averamentioning

confidence: 99%

“…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…”

Section: Introductionmentioning

confidence: 99%

“…Currently, the PdCR is regarded to be conserved when the conservation ratios exceed 70% in the same position of aligned samples. 25 3 | RESULTS…”

mentioning

confidence: 99%

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

Aumpuchin

Kikuchi

2018

Proteins

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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. K E Y W O R D S evolutionary analysis, folding, Ig-like beta sandwich proteins, inter-residue average distance statistics, titin

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Section: Average Distance Map Analysis Methodsmentioning

confidence: 99%

“…It has been confirmed that a hydrophobic residue within AE5 residues of the F-value peak tends to form hydrophobic packing in the native structure of a protein. 25…”

Section: Average Distance Map Analysis Methodsmentioning

confidence: 99%

Section: The Contact Frequency Analyses Based On Interresidue Averamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Currently, the PdCR is regarded to be conserved when the conservation ratios exceed 70% in the same position of aligned samples. 25 3 | RESULTS…”

mentioning

confidence: 99%

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

Aumpuchin

Kikuchi

2018

Proteins

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Prediction of the initial folding sites and the entire folding processes for Ig‐like beta‐sandwich proteins

2019

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Describing the whole story of protein folding is currently the main enigmatic problem in molecular bioinformatics study. Protein folding mechanisms have been intensively investigated with experimental as well as simulation techniques. Since a protein folds into its specific 3D structure from a unique amino acid sequence, it is interesting to extract as much information as possible from the amino acid sequence of a protein. Analyses based on inter‐residue average distance statistics and a coarse‐grained Gō‐model simulation were conducted on Ig and FN3 domains of a titin protein to decode the folding mechanisms from their sequence data and native structure data, respectively. The central region of all domains was predicted to be an initial folding unit, that is, stable in an early state of folding. This common feature coincides well with the experimental results and underscores the significance of the β‐sandwich proteins' common structure, namely, the key strands for folding and the Greek‐key motif, which is located in the central region. We confirmed that our sequence‐based techniques were able to predict the initial folding event just next to the denatured state and that a 3D‐based Gō‐model simulation can be used to investigate the whole process of protein folding.

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Analyses of the folding sites of irregular β-trefoil fold proteins through sequence-based techniques and Gō-model simulations

Kimura

Aumpuchin

Hamaue

et al. 2020

BMC Mol and Cell Biol

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Background: The details of the folding mechanisms have not yet been fully understood for many proteins, and it is believed that the information on the folding mechanism of a protein is encoded in its amino acid sequence. βtrefoil proteins are known to have the same 3D scaffold, namely, a threefold symmetric scaffold, despite the proteins' low sequence identity among superfamilies. In this study, we extract an initial folding unit from the amino acid sequences of irregular β-trefoil proteins by constructing an average distance map (ADM) and utilizing interresidue average distance statistics to determine the relative contact frequencies for residue pairs in terms of F values. We compare our sequence-based prediction results with the packing between hydrophobic residues in native 3D structures and a Gō-model simulation. Results: The ADM and F-value analyses predict that the N-terminal and C-terminal regions are compact and that the hydrophobic residues at the central region can be regarded as an interaction center with other residues. These results correspond well to those of the Gō-model simulations. Moreover, our results indicate that the irregular parts in the β-trefoil proteins do not hinder the protein formation. Conserved hydrophobic residues on the β5 strand are always the interaction center of packing between the conserved hydrophobic residues in both regular and irregular β-trefoil proteins. Conclusions: We revealed that the β5 strand plays an important role in β-trefoil protein structure construction. The sequence-based methods used in this study can extract the protein folding information from only amino acid sequence data, and well corresponded to 3D structure-based Gō-model simulation and available experimental results.

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

Cited by 6 publications

References 43 publications

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

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

Prediction of the initial folding sites and the entire folding processes for Ig‐like beta‐sandwich proteins

Analyses of the folding sites of irregular β-trefoil fold proteins through sequence-based techniques and Gō-model simulations

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