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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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Autores principales: Lin, Che-Hsin, Ju, Shin-Pon, Su, Jia-Wei, Li, Dai-En
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7005706/
https://www.ncbi.nlm.nih.gov/pubmed/32034260
http://dx.doi.org/10.1038/s41598-020-59144-7
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author Lin, Che-Hsin
Ju, Shin-Pon
Su, Jia-Wei
Li, Dai-En
author_facet Lin, Che-Hsin
Ju, Shin-Pon
Su, Jia-Wei
Li, Dai-En
author_sort Lin, Che-Hsin
collection PubMed
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.
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spelling pubmed-70057062020-02-18 Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches Lin, Che-Hsin Ju, Shin-Pon Su, Jia-Wei Li, Dai-En Sci Rep Article 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. Nature Publishing Group UK 2020-02-07 /pmc/articles/PMC7005706/ /pubmed/32034260 http://dx.doi.org/10.1038/s41598-020-59144-7 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Lin, Che-Hsin
Ju, Shin-Pon
Su, Jia-Wei
Li, Dai-En
Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches
title Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches
title_full Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches
title_fullStr Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches
title_full_unstemmed Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches
title_short Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches
title_sort peptide capping agent design for gold (111) facet by molecular simulation and experimental approaches
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7005706/
https://www.ncbi.nlm.nih.gov/pubmed/32034260
http://dx.doi.org/10.1038/s41598-020-59144-7
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