Study on the influences of palindromes in protein coding sequences on the folding rates of peptide chains.
Identifieur interne : 000A73 ( 2020/Analysis ); précédent : 000A72; suivant : 000A74Study on the influences of palindromes in protein coding sequences on the folding rates of peptide chains.
Auteurs : Rui-Fang Li [République populaire de Chine] ; Hong LiSource :
- Protein and peptide letters [ 1875-5305 ] ; 2010.
Descripteurs français
- KwdFr :
- Analyse de séquence de protéine, Biologie informatique (), Composition en bases nucléiques, Hepacivirus, Modèles linéaires, Pliage des protéines, Protéines virales (), Protéines virales (métabolisme), Structure secondaire des protéines, Séquence d'acides aminés, Séquences répétées inversées (génétique), Séquences répétées inversées (physiologie), VIH (Virus de l'Immunodéficience Humaine), Virus de l'hépatite B, Virus du SRAS.
- MESH :
- génétique : Séquences répétées inversées.
- métabolisme : Protéines virales.
- physiologie : Séquences répétées inversées.
- Analyse de séquence de protéine, Biologie informatique, Composition en bases nucléiques, Hepacivirus, Modèles linéaires, Pliage des protéines, Protéines virales, Structure secondaire des protéines, Séquence d'acides aminés, VIH (Virus de l'Immunodéficience Humaine), Virus de l'hépatite B, Virus du SRAS.
English descriptors
- KwdEn :
- Amino Acid Sequence, Base Composition, Computational Biology (methods), HIV, Hepacivirus, Hepatitis B virus, Inverted Repeat Sequences (genetics), Inverted Repeat Sequences (physiology), Linear Models, Protein Folding, Protein Structure, Secondary, SARS Virus, Sequence Analysis, Protein, Viral Proteins (chemistry), Viral Proteins (metabolism).
- MESH :
- chemical , chemistry : Viral Proteins.
- genetics : Inverted Repeat Sequences.
- chemical , metabolism : Viral Proteins.
- methods : Computational Biology.
- physiology : Inverted Repeat Sequences.
- Amino Acid Sequence, Base Composition, HIV, Hepacivirus, Hepatitis B virus, Linear Models, Protein Folding, Protein Structure, Secondary, SARS Virus, Sequence Analysis, Protein.
Abstract
Taking all the proteins of four virus genomes as samples, the segments of alpha-helix and beta-strand in proteins of the four viruses were obtained. Linear regression analyses between the average polarities and the folding rates of peptide chains were performed for alpha-helices and beta-strands respectively. The results indicated that the folding rates show significant positive linear correlation for alpha-helices and negative linear correlation for beta-strands with the average polarities. Based on the corresponding protein coding sequences of these amino acid segments, the influences of GC content of palindromes and palindrome densities in protein coding segments on the relations between the folding rates and the average polarities were studied. Results showed that the folding rates correlated positively with the GC content of palindromes and the palindrome density, and protein coding sequences do carry the information which can influence the folding rates of peptide chains or protein structures. Our analysis indicated that this kind of effects mostly comes from the information palindrome structure itself or from the synonymous codon usage, but not from the translation information from codons to amino acids.
DOI: 10.2174/092986610791306652
PubMed: 20205658
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 001737
- to stream PubMed, to step Curation: 001737
- to stream PubMed, to step Checkpoint: 001585
- to stream Ncbi, to step Merge: 002091
- to stream Ncbi, to step Curation: 002091
- to stream Ncbi, to step Checkpoint: 002091
- to stream Main, to step Merge: 002473
- to stream Main, to step Curation: 002440
- to stream Main, to step Exploration: 002440
- to stream 2020, to step Extraction: 000A73
Links to Exploration step
pubmed:20205658Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Study on the influences of palindromes in protein coding sequences on the folding rates of peptide chains.</title><author><name sortKey="Li, Rui Fang" sort="Li, Rui Fang" uniqKey="Li R" first="Rui-Fang" last="Li">Rui-Fang Li</name><affiliation wicri:level="1"><nlm:affiliation>School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021</wicri:regionArea><wicri:noRegion>Hohhot 010021</wicri:noRegion></affiliation></author><author><name sortKey="Li, Hong" sort="Li, Hong" uniqKey="Li H" first="Hong" last="Li">Hong Li</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2010">2010</date><idno type="RBID">pubmed:20205658</idno><idno type="pmid">20205658</idno><idno type="doi">10.2174/092986610791306652</idno><idno type="wicri:Area/PubMed/Corpus">001737</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001737</idno><idno type="wicri:Area/PubMed/Curation">001737</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001737</idno><idno type="wicri:Area/PubMed/Checkpoint">001585</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001585</idno><idno type="wicri:Area/Ncbi/Merge">002091</idno><idno type="wicri:Area/Ncbi/Curation">002091</idno><idno type="wicri:Area/Ncbi/Checkpoint">002091</idno><idno type="wicri:Area/Main/Merge">002473</idno><idno type="wicri:Area/Main/Curation">002440</idno><idno type="wicri:Area/Main/Exploration">002440</idno><idno type="wicri:Area/2020/Extraction">000A73</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Study on the influences of palindromes in protein coding sequences on the folding rates of peptide chains.</title><author><name sortKey="Li, Rui Fang" sort="Li, Rui Fang" uniqKey="Li R" first="Rui-Fang" last="Li">Rui-Fang Li</name><affiliation wicri:level="1"><nlm:affiliation>School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021</wicri:regionArea><wicri:noRegion>Hohhot 010021</wicri:noRegion></affiliation></author><author><name sortKey="Li, Hong" sort="Li, Hong" uniqKey="Li H" first="Hong" last="Li">Hong Li</name></author></analytic><series><title level="j">Protein and peptide letters</title><idno type="eISSN">1875-5305</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Base Composition</term><term>Computational Biology (methods)</term><term>HIV</term><term>Hepacivirus</term><term>Hepatitis B virus</term><term>Inverted Repeat Sequences (genetics)</term><term>Inverted Repeat Sequences (physiology)</term><term>Linear Models</term><term>Protein Folding</term><term>Protein Structure, Secondary</term><term>SARS Virus</term><term>Sequence Analysis, Protein</term><term>Viral Proteins (chemistry)</term><term>Viral Proteins (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence de protéine</term><term>Biologie informatique ()</term><term>Composition en bases nucléiques</term><term>Hepacivirus</term><term>Modèles linéaires</term><term>Pliage des protéines</term><term>Protéines virales ()</term><term>Protéines virales (métabolisme)</term><term>Structure secondaire des protéines</term><term>Séquence d'acides aminés</term><term>Séquences répétées inversées (génétique)</term><term>Séquences répétées inversées (physiologie)</term><term>VIH (Virus de l'Immunodéficience Humaine)</term><term>Virus de l'hépatite B</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Inverted Repeat Sequences</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Séquences répétées inversées</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines virales</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Séquences répétées inversées</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Inverted Repeat Sequences</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Base Composition</term><term>HIV</term><term>Hepacivirus</term><term>Hepatitis B virus</term><term>Linear Models</term><term>Protein Folding</term><term>Protein Structure, Secondary</term><term>SARS Virus</term><term>Sequence Analysis, Protein</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence de protéine</term><term>Biologie informatique</term><term>Composition en bases nucléiques</term><term>Hepacivirus</term><term>Modèles linéaires</term><term>Pliage des protéines</term><term>Protéines virales</term><term>Structure secondaire des protéines</term><term>Séquence d'acides aminés</term><term>VIH (Virus de l'Immunodéficience Humaine)</term><term>Virus de l'hépatite B</term><term>Virus du SRAS</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Taking all the proteins of four virus genomes as samples, the segments of alpha-helix and beta-strand in proteins of the four viruses were obtained. Linear regression analyses between the average polarities and the folding rates of peptide chains were performed for alpha-helices and beta-strands respectively. The results indicated that the folding rates show significant positive linear correlation for alpha-helices and negative linear correlation for beta-strands with the average polarities. Based on the corresponding protein coding sequences of these amino acid segments, the influences of GC content of palindromes and palindrome densities in protein coding segments on the relations between the folding rates and the average polarities were studied. Results showed that the folding rates correlated positively with the GC content of palindromes and the palindrome density, and protein coding sequences do carry the information which can influence the folding rates of peptide chains or protein structures. Our analysis indicated that this kind of effects mostly comes from the information palindrome structure itself or from the synonymous codon usage, but not from the translation information from codons to amino acids.</div></front></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><noCountry><name sortKey="Li, Hong" sort="Li, Hong" uniqKey="Li H" first="Hong" last="Li">Hong Li</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Li, Rui Fang" sort="Li, Rui Fang" uniqKey="Li R" first="Rui-Fang" last="Li">Rui-Fang Li</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/SrasV1/Data/2020/Analysis
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000A73 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/2020/Analysis/biblio.hfd -nk 000A73 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= SrasV1
|flux= 2020
|étape= Analysis
|type= RBID
|clé= pubmed:20205658
|texte= Study on the influences of palindromes in protein coding sequences on the folding rates of peptide chains.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/2020/Analysis/RBID.i -Sk "pubmed:20205658" \
| HfdSelect -Kh $EXPLOR_AREA/Data/2020/Analysis/biblio.hfd \
| NlmPubMed2Wicri -a SrasV1
| This area was generated with Dilib version V0.6.33. |  |