Simple model of pH-induced protein denaturation.
Identifieur interne : 001575 ( Main/Exploration ); précédent : 001574; suivant : 001576Simple model of pH-induced protein denaturation.
Auteurs : T. Hidaka [Japon] ; A. Shimada [Japon] ; Y. Nakata [Japon] ; H. Kodama [Japon] ; H. Kurihara [Japon] ; T. Tokihiro [Japon] ; S. Ihara [Japon]Source :
- Physical review. E, Statistical, nonlinear, and soft matter physics [ 1550-2376 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
The pH-induced conformational changes of proteins are systematically studied in the framework of a hydrophobic-polar (HP) model, in which proteins are dramatically simplified as chains of hydrophobic (H) and polar (P) beads on a lattice. We express the electrostatic interaction, the principal driving force of pH-induced unfolding that is not included in the conventional HP model, as the repulsive energy term between P monomers. As a result of the exact enumeration of all of the 14- to 18-mers, it is found that lowest-energy states in many sequences change from single "native" conformations to multiple sets of "denatured" conformations with an increase in the electrostatic repulsion. The switching of the lowest-energy states occurs in quite a similar way to real proteins: it is almost always between two states, while in a small fraction of ≥16-mers it is between three states. We also calculate the structural fluctuations for all of the denatured states and find that the denatured states contain a broad range of incompletely unfolded conformations, similar to "molten globule" states referred to in acid or alkaline denatured real proteins. These results show that the proposed model provides a simple physical picture of pH-induced protein denaturation.
DOI: 10.1103/PhysRevE.92.012709
PubMed: 26274205
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 001507
- to stream PubMed, to step Curation: 001507
- to stream PubMed, to step Checkpoint: 001347
- to stream Ncbi, to step Merge: 001231
- to stream Ncbi, to step Curation: 001231
- to stream Ncbi, to step Checkpoint: 001231
- to stream Main, to step Merge: 001580
- to stream Main, to step Curation: 001575
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Simple model of pH-induced protein denaturation.</title><author><name sortKey="Hidaka, T" sort="Hidaka, T" uniqKey="Hidaka T" first="T" last="Hidaka">T. Hidaka</name><affiliation wicri:level="4"><nlm:affiliation>Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Shimada, A" sort="Shimada, A" uniqKey="Shimada A" first="A" last="Shimada">A. Shimada</name><affiliation wicri:level="4"><nlm:affiliation>Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Nakata, Y" sort="Nakata, Y" uniqKey="Nakata Y" first="Y" last="Nakata">Y. Nakata</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Kodama, H" sort="Kodama, H" uniqKey="Kodama H" first="H" last="Kodama">H. Kodama</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Kurihara, H" sort="Kurihara, H" uniqKey="Kurihara H" first="H" last="Kurihara">H. Kurihara</name><affiliation wicri:level="4"><nlm:affiliation>Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Tokihiro, T" sort="Tokihiro, T" uniqKey="Tokihiro T" first="T" last="Tokihiro">T. Tokihiro</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Ihara, S" sort="Ihara, S" uniqKey="Ihara S" first="S" last="Ihara">S. Ihara</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26274205</idno><idno type="pmid">26274205</idno><idno type="doi">10.1103/PhysRevE.92.012709</idno><idno type="wicri:Area/PubMed/Corpus">001507</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001507</idno><idno type="wicri:Area/PubMed/Curation">001507</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001507</idno><idno type="wicri:Area/PubMed/Checkpoint">001347</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001347</idno><idno type="wicri:Area/Ncbi/Merge">001231</idno><idno type="wicri:Area/Ncbi/Curation">001231</idno><idno type="wicri:Area/Ncbi/Checkpoint">001231</idno><idno type="wicri:Area/Main/Merge">001580</idno><idno type="wicri:Area/Main/Curation">001575</idno><idno type="wicri:Area/Main/Exploration">001575</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Simple model of pH-induced protein denaturation.</title><author><name sortKey="Hidaka, T" sort="Hidaka, T" uniqKey="Hidaka T" first="T" last="Hidaka">T. Hidaka</name><affiliation wicri:level="4"><nlm:affiliation>Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Shimada, A" sort="Shimada, A" uniqKey="Shimada A" first="A" last="Shimada">A. Shimada</name><affiliation wicri:level="4"><nlm:affiliation>Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Nakata, Y" sort="Nakata, Y" uniqKey="Nakata Y" first="Y" last="Nakata">Y. Nakata</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Kodama, H" sort="Kodama, H" uniqKey="Kodama H" first="H" last="Kodama">H. Kodama</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Kurihara, H" sort="Kurihara, H" uniqKey="Kurihara H" first="H" last="Kurihara">H. Kurihara</name><affiliation wicri:level="4"><nlm:affiliation>Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Tokihiro, T" sort="Tokihiro, T" uniqKey="Tokihiro T" first="T" last="Tokihiro">T. Tokihiro</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Ihara, S" sort="Ihara, S" uniqKey="Ihara S" first="S" last="Ihara">S. Ihara</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author></analytic><series><title level="j">Physical review. E, Statistical, nonlinear, and soft matter physics</title><idno type="eISSN">1550-2376</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Hydrogen-Ion Concentration</term><term>Hydrophobic and Hydrophilic Interactions</term><term>Models, Molecular</term><term>Protein Conformation</term><term>Proteolysis</term><term>Static Electricity</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Concentration en ions d'hydrogène</term><term>Conformation des protéines</term><term>Interactions hydrophobes et hydrophiles</term><term>Modèles moléculaires</term><term>Protéolyse</term><term>Électricité statique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Hydrogen-Ion Concentration</term><term>Hydrophobic and Hydrophilic Interactions</term><term>Models, Molecular</term><term>Protein Conformation</term><term>Proteolysis</term><term>Static Electricity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Concentration en ions d'hydrogène</term><term>Conformation des protéines</term><term>Interactions hydrophobes et hydrophiles</term><term>Modèles moléculaires</term><term>Protéolyse</term><term>Électricité statique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The pH-induced conformational changes of proteins are systematically studied in the framework of a hydrophobic-polar (HP) model, in which proteins are dramatically simplified as chains of hydrophobic (H) and polar (P) beads on a lattice. We express the electrostatic interaction, the principal driving force of pH-induced unfolding that is not included in the conventional HP model, as the repulsive energy term between P monomers. As a result of the exact enumeration of all of the 14- to 18-mers, it is found that lowest-energy states in many sequences change from single "native" conformations to multiple sets of "denatured" conformations with an increase in the electrostatic repulsion. The switching of the lowest-energy states occurs in quite a similar way to real proteins: it is almost always between two states, while in a small fraction of ≥16-mers it is between three states. We also calculate the structural fluctuations for all of the denatured states and find that the denatured states contain a broad range of incompletely unfolded conformations, similar to "molten globule" states referred to in acid or alkaline denatured real proteins. These results show that the proposed model provides a simple physical picture of pH-induced protein denaturation. </div></front></TEI><affiliations><list><country><li>Japon</li></country><region><li>Région de Kantō</li></region><settlement><li>Tokyo</li></settlement><orgName><li>Université de Tokyo</li></orgName></list><tree><country name="Japon"><region name="Région de Kantō"><name sortKey="Hidaka, T" sort="Hidaka, T" uniqKey="Hidaka T" first="T" last="Hidaka">T. Hidaka</name></region><name sortKey="Ihara, S" sort="Ihara, S" uniqKey="Ihara S" first="S" last="Ihara">S. Ihara</name><name sortKey="Kodama, H" sort="Kodama, H" uniqKey="Kodama H" first="H" last="Kodama">H. Kodama</name><name sortKey="Kurihara, H" sort="Kurihara, H" uniqKey="Kurihara H" first="H" last="Kurihara">H. Kurihara</name><name sortKey="Nakata, Y" sort="Nakata, Y" uniqKey="Nakata Y" first="Y" last="Nakata">Y. Nakata</name><name sortKey="Shimada, A" sort="Shimada, A" uniqKey="Shimada A" first="A" last="Shimada">A. Shimada</name><name sortKey="Tokihiro, T" sort="Tokihiro, T" uniqKey="Tokihiro T" first="T" last="Tokihiro">T. Tokihiro</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001575 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 001575 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:26274205
|texte= Simple model of pH-induced protein denaturation.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:26274205" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |