{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T16:30:20Z","timestamp":1780072220725,"version":"3.54.0"},"reference-count":60,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2023,1,30]],"date-time":"2023-01-30T00:00:00Z","timestamp":1675036800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Petchra Pra Jom Klao Ph.D. Research Scholarship from King Mongkut\u2019s University of Technology Thonburi"},{"name":"Thailand Science Research and Innovation (TSRI) Basic Research Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Atomistic molecular dynamics simulations of amyloid models, consisting of the previously reported STDY-K-peptides and K-peptides from the hen egg white lysozyme (HEWL), were performed to address the effects of charged residues and pH observed in an in vitro study. Simulation results showed that amyloid models with antiparallel configurations possessed greater stability and compactness than those with parallel configurations. Then, peptide chain stretching and ordering were measured through the end-to-end distance and the order parameter, for which the amyloid models consisting of K-peptides and the STDY-K-peptides at pH 2 displayed a higher level of chain stretching and ordering. After that, the molecular mechanics energy decomposition and the radial distribution function (RDF) clearly displayed the importance of Trp62 to the K-peptide and the STDY-K-peptide models at pH 2. Moreover, the results also displayed how the negatively charged Asp52 disrupted the interaction networks and prevented the amyloid formation from STDY-K-peptide at pH 7. Finally, this study provided an insight into the interplay between pH conditions and molecular interactions underlying the formation of amyloid fibrils from short peptides contained within the HEWL. This served as a basis of understanding towards the design of other amyloids for biomaterial applications.<\/jats:p>","DOI":"10.3390\/ijms24032626","type":"journal-article","created":{"date-parts":[[2023,1,30]],"date-time":"2023-01-30T06:06:13Z","timestamp":1675058773000},"page":"2626","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Roles of Tryptophan and Charged Residues on the Polymorphisms of Amyloids Formed by K-Peptides of Hen Egg White Lysozyme Investigated through Molecular Dynamics Simulations"],"prefix":"10.3390","volume":"24","author":[{"given":"Husnul Fuad","family":"Zein","sequence":"first","affiliation":[{"name":"Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut\u2019s University of Technology Thonburi (KMUTT), 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand"},{"name":"Department of Physics, King Mongkut\u2019s University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thana","family":"Sutthibutpong","sequence":"additional","affiliation":[{"name":"Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut\u2019s University of Technology Thonburi (KMUTT), 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand"},{"name":"Department of Physics, King Mongkut\u2019s University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand"},{"name":"Center of Excellence in Theoretical and Computational Science (TaCS-CoE), Faculty of Science, King Mongkut\u2019s University of Technology Thonburi (KMUTT), 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,1,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1146\/annurev.biochem.75.101304.123901","article-title":"Protein Misfolding, Functional Amyloid, and Human Disease","volume":"75","author":"Chiti","year":"2006","journal-title":"Annu. 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