Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches
The stochastic tunneling-basin hopping method (STUN-BH) was utilized to obtain the most stable peptide S7 configuration (Ac-Ser-Ser-Phe-Pro-Gln-Pro-Asn-CONH 2 ) adsorbed on Au(111) facet. After the most stable S7 configuration was found, molecular dynamics (MD) simulation was conducted to investigat...
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description | The stochastic tunneling-basin hopping method (STUN-BH) was utilized to obtain the most stable peptide S7 configuration (Ac-Ser-Ser-Phe-Pro-Gln-Pro-Asn-CONH
2
) adsorbed on Au(111) facet. After the most stable S7 configuration was found, molecular dynamics (MD) simulation was conducted to investigate the thermal stability between S7 and Au facet at 300 K in both vacuum and water environment. Moreover, further design sets of peptide sequences on Au(111) facet were used to compare with S7. All molecular simulations were carried out by the large-scale atomic/molecular massively parallel simulator (LAMMPS). The Amber99sb-ILDN force field was employed for modeling the interatomic interaction of peptides, and the TIP3P water was used for the water environment. The CHARMM-METAL force field was introduced to model the S7, PF8 (Ac-Pro-Phe-Ser-Pro-Phe-Ser-Pro-Phe-CONH
2
) and FS8 (Ac-Phe-Ser-Phe-Ser-Phe-Ser-Phe-Ser-CONH
2
) interactions with Au(111). The MD simulation results demonstrate that the morphology of Pro affects the adsorption stability of Phe. Therefore, we designed two sequences, PF8 and FS8, to confirm our simulation result through experiment. The present study also develops a novel low-temperature plasma synthesis method to evaluate the facet selecting performance of the designed peptide sequences of S7, PF8, and FS8. The experimental results suggest that the reduced Au atom seed is captured with the designed peptide sequences and slowing growing under room temperature for 72 hours. The experimental results are in the excellent agreement with the simulation finding that the Pro in the designed peptide sequences plays a critical role in the facet selection for Au atom stacking. |
doi_str_mv | 10.1038/s41598-020-59144-7 |
format | Article |
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2
) adsorbed on Au(111) facet. After the most stable S7 configuration was found, molecular dynamics (MD) simulation was conducted to investigate the thermal stability between S7 and Au facet at 300 K in both vacuum and water environment. Moreover, further design sets of peptide sequences on Au(111) facet were used to compare with S7. All molecular simulations were carried out by the large-scale atomic/molecular massively parallel simulator (LAMMPS). The Amber99sb-ILDN force field was employed for modeling the interatomic interaction of peptides, and the TIP3P water was used for the water environment. The CHARMM-METAL force field was introduced to model the S7, PF8 (Ac-Pro-Phe-Ser-Pro-Phe-Ser-Pro-Phe-CONH
2
) and FS8 (Ac-Phe-Ser-Phe-Ser-Phe-Ser-Phe-Ser-CONH
2
) interactions with Au(111). The MD simulation results demonstrate that the morphology of Pro affects the adsorption stability of Phe. Therefore, we designed two sequences, PF8 and FS8, to confirm our simulation result through experiment. The present study also develops a novel low-temperature plasma synthesis method to evaluate the facet selecting performance of the designed peptide sequences of S7, PF8, and FS8. The experimental results suggest that the reduced Au atom seed is captured with the designed peptide sequences and slowing growing under room temperature for 72 hours. The experimental results are in the excellent agreement with the simulation finding that the Pro in the designed peptide sequences plays a critical role in the facet selection for Au atom stacking.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/s41598-020-59144-7</identifier><identifier>PMID: 32034260</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>119/118 ; 639/301/1034/1035 ; 639/925/357/354 ; Design ; Humanities and Social Sciences ; Low temperature ; Molecular dynamics ; multidisciplinary ; Peptides ; Science ; Science (multidisciplinary) ; Simulation ; Stochasticity ; Thermal stability ; Vacuum</subject><ispartof>Scientific reports, 2020-02, Vol.10 (1), p.2090-2090, Article 2090</ispartof><rights>The Author(s) 2020</rights><rights>This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c474t-9ab3b3956ac1365478a4bbd13f5a030bcecae21690015b6677710d9cd5ca93fe3</citedby><cites>FETCH-LOGICAL-c474t-9ab3b3956ac1365478a4bbd13f5a030bcecae21690015b6677710d9cd5ca93fe3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7005706/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7005706/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,41120,42189,51576,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32034260$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lin, Che-Hsin</creatorcontrib><creatorcontrib>Ju, Shin-Pon</creatorcontrib><creatorcontrib>Su, Jia-Wei</creatorcontrib><creatorcontrib>Li, Dai-En</creatorcontrib><title>Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>The stochastic tunneling-basin hopping method (STUN-BH) was utilized to obtain the most stable peptide S7 configuration (Ac-Ser-Ser-Phe-Pro-Gln-Pro-Asn-CONH
2
) adsorbed on Au(111) facet. After the most stable S7 configuration was found, molecular dynamics (MD) simulation was conducted to investigate the thermal stability between S7 and Au facet at 300 K in both vacuum and water environment. Moreover, further design sets of peptide sequences on Au(111) facet were used to compare with S7. All molecular simulations were carried out by the large-scale atomic/molecular massively parallel simulator (LAMMPS). The Amber99sb-ILDN force field was employed for modeling the interatomic interaction of peptides, and the TIP3P water was used for the water environment. The CHARMM-METAL force field was introduced to model the S7, PF8 (Ac-Pro-Phe-Ser-Pro-Phe-Ser-Pro-Phe-CONH
2
) and FS8 (Ac-Phe-Ser-Phe-Ser-Phe-Ser-Phe-Ser-CONH
2
) interactions with Au(111). The MD simulation results demonstrate that the morphology of Pro affects the adsorption stability of Phe. Therefore, we designed two sequences, PF8 and FS8, to confirm our simulation result through experiment. The present study also develops a novel low-temperature plasma synthesis method to evaluate the facet selecting performance of the designed peptide sequences of S7, PF8, and FS8. The experimental results suggest that the reduced Au atom seed is captured with the designed peptide sequences and slowing growing under room temperature for 72 hours. The experimental results are in the excellent agreement with the simulation finding that the Pro in the designed peptide sequences plays a critical role in the facet selection for Au atom stacking.</description><subject>119/118</subject><subject>639/301/1034/1035</subject><subject>639/925/357/354</subject><subject>Design</subject><subject>Humanities and Social Sciences</subject><subject>Low temperature</subject><subject>Molecular dynamics</subject><subject>multidisciplinary</subject><subject>Peptides</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>Simulation</subject><subject>Stochasticity</subject><subject>Thermal stability</subject><subject>Vacuum</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kU9PFTEUxRujEYJ8ARemiRtcjPZ_XzcmL09AE4gm6rrpdO4MJfPasZ0h8O2pPER0QTe3yf3d03N7EHpNyXtK-OpDEVSaVUMYaaShQjT6GdpnRMiGccaeP7rvocNSLkk9khlBzUu0xxnhgimyj-AbTHPoAG_cNIU44PUAccafoIQh4j5lfJrGDh9RSt_hE-dhxu0NPk8j-GV0GX8P21rnkCJ2scPH1xPksK0SbsTracrJ-Qsor9CL3o0FDu_rAfp5cvxj87k5-3r6ZbM-a7zQYm6Ma3nLjVTOU66k0Csn2rajvJeOcNJ68A4YVYYQKlultNaUdMZ30jvDe-AH6ONOd1raLXS--shutFO15PKNTS7YfzsxXNghXVldP0cTVQWO7gVy-rVAme02FA_j6CKkpVjGJVNSGSYq-vY_9DItOdb17ijO6gakUmxH-ZxKydA_mKHE_g7S7oK0NUh7F6TVdejN4zUeRv7EVgG-A0ptxQHy37efkL0FEj2oGg</recordid><startdate>20200207</startdate><enddate>20200207</enddate><creator>Lin, Che-Hsin</creator><creator>Ju, Shin-Pon</creator><creator>Su, Jia-Wei</creator><creator>Li, Dai-En</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20200207</creationdate><title>Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches</title><author>Lin, Che-Hsin ; Ju, Shin-Pon ; Su, Jia-Wei ; Li, Dai-En</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c474t-9ab3b3956ac1365478a4bbd13f5a030bcecae21690015b6677710d9cd5ca93fe3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>119/118</topic><topic>639/301/1034/1035</topic><topic>639/925/357/354</topic><topic>Design</topic><topic>Humanities and Social Sciences</topic><topic>Low temperature</topic><topic>Molecular dynamics</topic><topic>multidisciplinary</topic><topic>Peptides</topic><topic>Science</topic><topic>Science (multidisciplinary)</topic><topic>Simulation</topic><topic>Stochasticity</topic><topic>Thermal stability</topic><topic>Vacuum</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lin, Che-Hsin</creatorcontrib><creatorcontrib>Ju, Shin-Pon</creatorcontrib><creatorcontrib>Su, Jia-Wei</creatorcontrib><creatorcontrib>Li, Dai-En</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lin, Che-Hsin</au><au>Ju, Shin-Pon</au><au>Su, Jia-Wei</au><au>Li, Dai-En</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2020-02-07</date><risdate>2020</risdate><volume>10</volume><issue>1</issue><spage>2090</spage><epage>2090</epage><pages>2090-2090</pages><artnum>2090</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>The stochastic tunneling-basin hopping method (STUN-BH) was utilized to obtain the most stable peptide S7 configuration (Ac-Ser-Ser-Phe-Pro-Gln-Pro-Asn-CONH
2
) adsorbed on Au(111) facet. After the most stable S7 configuration was found, molecular dynamics (MD) simulation was conducted to investigate the thermal stability between S7 and Au facet at 300 K in both vacuum and water environment. Moreover, further design sets of peptide sequences on Au(111) facet were used to compare with S7. All molecular simulations were carried out by the large-scale atomic/molecular massively parallel simulator (LAMMPS). The Amber99sb-ILDN force field was employed for modeling the interatomic interaction of peptides, and the TIP3P water was used for the water environment. The CHARMM-METAL force field was introduced to model the S7, PF8 (Ac-Pro-Phe-Ser-Pro-Phe-Ser-Pro-Phe-CONH
2
) and FS8 (Ac-Phe-Ser-Phe-Ser-Phe-Ser-Phe-Ser-CONH
2
) interactions with Au(111). The MD simulation results demonstrate that the morphology of Pro affects the adsorption stability of Phe. Therefore, we designed two sequences, PF8 and FS8, to confirm our simulation result through experiment. The present study also develops a novel low-temperature plasma synthesis method to evaluate the facet selecting performance of the designed peptide sequences of S7, PF8, and FS8. The experimental results suggest that the reduced Au atom seed is captured with the designed peptide sequences and slowing growing under room temperature for 72 hours. The experimental results are in the excellent agreement with the simulation finding that the Pro in the designed peptide sequences plays a critical role in the facet selection for Au atom stacking.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>32034260</pmid><doi>10.1038/s41598-020-59144-7</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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subjects | 119/118 639/301/1034/1035 639/925/357/354 Design Humanities and Social Sciences Low temperature Molecular dynamics multidisciplinary Peptides Science Science (multidisciplinary) Simulation Stochasticity Thermal stability Vacuum |
title | Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches |
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