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Chameleon sequences in neurodegenerative diseases

Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequen...

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Autores principales: Bahramali, Golnaz, Goliaei, Bahram, Minuchehr, Zarrin, Salari, Ali
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier Inc. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7124260/
https://www.ncbi.nlm.nih.gov/pubmed/26920059
http://dx.doi.org/10.1016/j.bbrc.2016.01.187
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author Bahramali, Golnaz
Goliaei, Bahram
Minuchehr, Zarrin
Salari, Ali
author_facet Bahramali, Golnaz
Goliaei, Bahram
Minuchehr, Zarrin
Salari, Ali
author_sort Bahramali, Golnaz
collection PubMed
description Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.
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spelling pubmed-71242602020-04-06 Chameleon sequences in neurodegenerative diseases Bahramali, Golnaz Goliaei, Bahram Minuchehr, Zarrin Salari, Ali Biochem Biophys Res Commun Article Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases. Elsevier Inc. 2016-03-25 2016-02-23 /pmc/articles/PMC7124260/ /pubmed/26920059 http://dx.doi.org/10.1016/j.bbrc.2016.01.187 Text en Copyright © 2016 Elsevier Inc. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Bahramali, Golnaz
Goliaei, Bahram
Minuchehr, Zarrin
Salari, Ali
Chameleon sequences in neurodegenerative diseases
title Chameleon sequences in neurodegenerative diseases
title_full Chameleon sequences in neurodegenerative diseases
title_fullStr Chameleon sequences in neurodegenerative diseases
title_full_unstemmed Chameleon sequences in neurodegenerative diseases
title_short Chameleon sequences in neurodegenerative diseases
title_sort chameleon sequences in neurodegenerative diseases
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7124260/
https://www.ncbi.nlm.nih.gov/pubmed/26920059
http://dx.doi.org/10.1016/j.bbrc.2016.01.187
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