Construction of an implicit membrane environment for the lattice Monte Carlo simulation of transmembrane protein.
Identifieur interne : 002565 ( Main/Exploration ); précédent : 002564; suivant : 002566Construction of an implicit membrane environment for the lattice Monte Carlo simulation of transmembrane protein.
Auteurs : Yantao Chen [République populaire de Chine] ; Mingliang Wang ; Qianling Zhang ; Jianhong LiuSource :
- Biophysical chemistry [ 1873-4200 ] ; 2010.
Descripteurs français
- KwdFr :
- Interactions hydrophobes et hydrophiles, Liaison hydrogène, Lipides membranaires (), Membrane artificielle, Modèles moléculaires, Méthode de Monte-Carlo, Pliage des protéines, Protéines de l'enveloppe virale (), Protéines de la matrice virale (), Protéines membranaires (), Simulation numérique, Thermodynamique.
- MESH :
- Interactions hydrophobes et hydrophiles, Liaison hydrogène, Lipides membranaires, Membrane artificielle, Modèles moléculaires, Méthode de Monte-Carlo, Pliage des protéines, Protéines de l'enveloppe virale, Protéines de la matrice virale, Protéines membranaires, Simulation numérique, Thermodynamique.
English descriptors
- KwdEn :
- Computer Simulation, Hydrogen Bonding, Hydrophobic and Hydrophilic Interactions, Membrane Lipids (chemistry), Membrane Proteins (chemistry), Membranes, Artificial, Models, Molecular, Monte Carlo Method, Protein Folding, Thermodynamics, Viral Envelope Proteins (chemistry), Viral Matrix Proteins (chemistry).
- MESH :
Abstract
Due to the complexity of biological membrane, computer simulation of transmembrane protein's folding is challenging. In this paper, an implicit biological membrane environment has been constructed in lattice space, in which the lipid chains and water molecules were represented by the unoccupied lattice sites. The biological membrane was characterized with three features: stronger hydrogen bonding interaction, membrane lateral pressure, and lipophobicity index for the amino acid residues. In addition to the hydrocarbon core spanning region and the water solution, the lipid interface has also been represented in this implicit membrane environment, which was proved to be effective for the transmembrane protein's folding. The associated Monte Carlo simulations have been performed for SARS-CoV E protein and M2 protein segment (residues 18-60) of influenza A virus. It was found that the coil-helix transition of the transmembrane segment occurred earlier than the coil-globule transition of the two terminal domains. The folding process and final orientation of the amphipathic helical block in water solution are obviously influenced by its corresponding hydrophobicity/lipophobicity. Therefore, this implicit membrane environment, though in lattice space, can make an elaborate balance between different driving forces for the membrane protein's folding, thus offering a potential means for the simulation of transmembrane protein oligomers in feasible time.
DOI: 10.1016/j.bpc.2009.12.008
PubMed: 20079964
Affiliations:
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last="Wang">Mingliang Wang</name></author><author><name sortKey="Zhang, Qianling" sort="Zhang, Qianling" uniqKey="Zhang Q" first="Qianling" last="Zhang">Qianling Zhang</name></author><author><name sortKey="Liu, Jianhong" sort="Liu, Jianhong" uniqKey="Liu J" first="Jianhong" last="Liu">Jianhong Liu</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2010">2010</date><idno type="RBID">pubmed:20079964</idno><idno type="pmid">20079964</idno><idno type="doi">10.1016/j.bpc.2009.12.008</idno><idno type="wicri:Area/PubMed/Corpus">001767</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001767</idno><idno type="wicri:Area/PubMed/Curation">001767</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001767</idno><idno type="wicri:Area/PubMed/Checkpoint">001698</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001698</idno><idno 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Engineering, Shenzhen University, Shenzhen 518060</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Wang, Mingliang" sort="Wang, Mingliang" uniqKey="Wang M" first="Mingliang" last="Wang">Mingliang Wang</name></author><author><name sortKey="Zhang, Qianling" sort="Zhang, Qianling" uniqKey="Zhang Q" first="Qianling" last="Zhang">Qianling Zhang</name></author><author><name sortKey="Liu, Jianhong" sort="Liu, Jianhong" uniqKey="Liu J" first="Jianhong" last="Liu">Jianhong Liu</name></author></analytic><series><title level="j">Biophysical chemistry</title><idno type="eISSN">1873-4200</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computer Simulation</term><term>Hydrogen Bonding</term><term>Hydrophobic and Hydrophilic Interactions</term><term>Membrane Lipids (chemistry)</term><term>Membrane Proteins (chemistry)</term><term>Membranes, Artificial</term><term>Models, Molecular</term><term>Monte Carlo Method</term><term>Protein Folding</term><term>Thermodynamics</term><term>Viral Envelope Proteins (chemistry)</term><term>Viral Matrix Proteins (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Interactions hydrophobes et hydrophiles</term><term>Liaison hydrogène</term><term>Lipides membranaires ()</term><term>Membrane artificielle</term><term>Modèles moléculaires</term><term>Méthode de Monte-Carlo</term><term>Pliage des protéines</term><term>Protéines de l'enveloppe virale ()</term><term>Protéines de la matrice virale ()</term><term>Protéines membranaires ()</term><term>Simulation numérique</term><term>Thermodynamique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Membrane Lipids</term><term>Membrane Proteins</term><term>Viral Envelope Proteins</term><term>Viral Matrix Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Simulation</term><term>Hydrogen Bonding</term><term>Hydrophobic and Hydrophilic Interactions</term><term>Membranes, Artificial</term><term>Models, Molecular</term><term>Monte Carlo Method</term><term>Protein Folding</term><term>Thermodynamics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Interactions hydrophobes et hydrophiles</term><term>Liaison hydrogène</term><term>Lipides membranaires</term><term>Membrane artificielle</term><term>Modèles moléculaires</term><term>Méthode de Monte-Carlo</term><term>Pliage des protéines</term><term>Protéines de l'enveloppe virale</term><term>Protéines de la matrice virale</term><term>Protéines membranaires</term><term>Simulation numérique</term><term>Thermodynamique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Due to the complexity of biological membrane, computer simulation of transmembrane protein's folding is challenging. In this paper, an implicit biological membrane environment has been constructed in lattice space, in which the lipid chains and water molecules were represented by the unoccupied lattice sites. The biological membrane was characterized with three features: stronger hydrogen bonding interaction, membrane lateral pressure, and lipophobicity index for the amino acid residues. In addition to the hydrocarbon core spanning region and the water solution, the lipid interface has also been represented in this implicit membrane environment, which was proved to be effective for the transmembrane protein's folding. The associated Monte Carlo simulations have been performed for SARS-CoV E protein and M2 protein segment (residues 18-60) of influenza A virus. It was found that the coil-helix transition of the transmembrane segment occurred earlier than the coil-globule transition of the two terminal domains. The folding process and final orientation of the amphipathic helical block in water solution are obviously influenced by its corresponding hydrophobicity/lipophobicity. Therefore, this implicit membrane environment, though in lattice space, can make an elaborate balance between different driving forces for the membrane protein's folding, thus offering a potential means for the simulation of transmembrane protein oligomers in feasible time.</div></front></TEI><affiliations><list><country><li>République populaire de Chine</li></country><region><li>Guangdong</li></region><settlement><li>Shenzhen</li></settlement></list><tree><noCountry><name sortKey="Liu, Jianhong" sort="Liu, Jianhong" uniqKey="Liu J" first="Jianhong" last="Liu">Jianhong Liu</name><name sortKey="Wang, Mingliang" sort="Wang, Mingliang" uniqKey="Wang M" first="Mingliang" last="Wang">Mingliang Wang</name><name sortKey="Zhang, Qianling" sort="Zhang, Qianling" uniqKey="Zhang Q" first="Qianling" last="Zhang">Qianling Zhang</name></noCountry><country name="République populaire de Chine"><region name="Guangdong"><name sortKey="Chen, Yantao" sort="Chen, Yantao" uniqKey="Chen Y" first="Yantao" last="Chen">Yantao Chen</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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