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Physicochemical Position-Dependent Properties in the Protein Secondary Structures

BACKGROUND: Establishing theories for designing arbitrary protein structures is complicated and depends on understanding the principles for protein folding, which is affected by applied features. Computer algorithms can reach high precision and stability in computationally designed enzymes and binde...

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Autores principales: Saghapour, Ehsan, Sehhati, Mohammadreza
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Pasteur Institute 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6462287/
https://www.ncbi.nlm.nih.gov/pubmed/30954029
http://dx.doi.org/10.29252/.23.4.253
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author Saghapour, Ehsan
Sehhati, Mohammadreza
author_facet Saghapour, Ehsan
Sehhati, Mohammadreza
author_sort Saghapour, Ehsan
collection PubMed
description BACKGROUND: Establishing theories for designing arbitrary protein structures is complicated and depends on understanding the principles for protein folding, which is affected by applied features. Computer algorithms can reach high precision and stability in computationally designed enzymes and binders by applying informative features obtained from natural structures. METHODS: In this study, a position-specific analysis of secondary structures (α-helix, β-strand, and tight turn) was performed to reveal novel features for protein structure prediction and protein design. RESULTS: Our results showed that the secondary structures in the N-termini region tend to be more compact than C-termini. Decoying periodicity in length and distribution of amino acids in α-helices is deciphered using the curve-fitting methods. Compared with α-helix, β-strands do not show distinct periodicities in length. Also, significant differences in position-dependent distribution of physicochemical properties are shown in secondary structures. CONCLUSION: Position-specific propensities in our study underline valuable parameters that could be used by researchers in the field of structural biology, particularly protein design through site-directed mutagenesis.
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spelling pubmed-64622872019-07-01 Physicochemical Position-Dependent Properties in the Protein Secondary Structures Saghapour, Ehsan Sehhati, Mohammadreza Iran Biomed J Full Length BACKGROUND: Establishing theories for designing arbitrary protein structures is complicated and depends on understanding the principles for protein folding, which is affected by applied features. Computer algorithms can reach high precision and stability in computationally designed enzymes and binders by applying informative features obtained from natural structures. METHODS: In this study, a position-specific analysis of secondary structures (α-helix, β-strand, and tight turn) was performed to reveal novel features for protein structure prediction and protein design. RESULTS: Our results showed that the secondary structures in the N-termini region tend to be more compact than C-termini. Decoying periodicity in length and distribution of amino acids in α-helices is deciphered using the curve-fitting methods. Compared with α-helix, β-strands do not show distinct periodicities in length. Also, significant differences in position-dependent distribution of physicochemical properties are shown in secondary structures. CONCLUSION: Position-specific propensities in our study underline valuable parameters that could be used by researchers in the field of structural biology, particularly protein design through site-directed mutagenesis. Pasteur Institute 2019-07 /pmc/articles/PMC6462287/ /pubmed/30954029 http://dx.doi.org/10.29252/.23.4.253 Text en Copyright: © Iranian Biomedical Journal http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License, (http://creativecommons.org/licenses/by/3.0/) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Full Length
Saghapour, Ehsan
Sehhati, Mohammadreza
Physicochemical Position-Dependent Properties in the Protein Secondary Structures
title Physicochemical Position-Dependent Properties in the Protein Secondary Structures
title_full Physicochemical Position-Dependent Properties in the Protein Secondary Structures
title_fullStr Physicochemical Position-Dependent Properties in the Protein Secondary Structures
title_full_unstemmed Physicochemical Position-Dependent Properties in the Protein Secondary Structures
title_short Physicochemical Position-Dependent Properties in the Protein Secondary Structures
title_sort physicochemical position-dependent properties in the protein secondary structures
topic Full Length
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6462287/
https://www.ncbi.nlm.nih.gov/pubmed/30954029
http://dx.doi.org/10.29252/.23.4.253
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