{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T12:59:58Z","timestamp":1780405198554,"version":"3.54.1"},"reference-count":31,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T00:00:00Z","timestamp":1765843200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R16GM159167-01"],"award-info":[{"award-number":["1R16GM159167-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Science Foundation","award":["2406155"],"award-info":[{"award-number":["2406155"]}]},{"name":"National Science Foundation","award":["2000296"],"award-info":[{"award-number":["2000296"]}]},{"name":"DoD Center of Excellence in AI and Machine Learning (CoE-AIML) at Howard University","award":["W911NF-20-2-0277"],"award-info":[{"award-number":["W911NF-20-2-0277"]}]},{"name":"National Institute on Minority Health and Health Disparities of the National Institutes of Health","award":["2U54MD007597"],"award-info":[{"award-number":["2U54MD007597"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Apolipoprotein E (APOE) plays a central role in lipid transport and neuronal cholesterol metabolism. Among its three major isoforms (APOE2, APOE3, and APOE4), the APOE4 variant is the strongest genetic risk factor for late-onset Alzheimer\u2019s disease (AD). However, the structural consequences of specific APOE mutations on protein stability remain poorly understood. Methods: Here, we performed computational saturation mutagenesis and molecular dynamics simulations on the non-lipidated N-terminal fragments of APOE3 and APOE4 to examine how missense mutations affect their structural stability. Results: Based on the folding energy (\u0394\u0394G) calculations, mutations G165W and L155W were particularly destabilizing in APOE4. Molecular dynamics analyses showed that these mutations altered local flexibility and compactness, particularly within the helix 4 region, a key structural element for maintaining APOE\u2019s structural integrity. Conclusions: Our findings, which are state dependent and hypothesis generating, highlight isoform-dependent differences in protein stability and identify regions of structural vulnerability within APOE. These insights enhance our understanding of APOE\u2019s conformational dynamics and may inform future studies on its role in neurodegenerative disease mechanisms.<\/jats:p>","DOI":"10.3390\/genes16121509","type":"journal-article","created":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T12:47:26Z","timestamp":1765889246000},"page":"1509","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Structural Analysis of Missense Mutations on the Stability of APOE3 and APOE4"],"prefix":"10.3390","volume":"16","author":[{"given":"Malcolm","family":"Anthony","sequence":"first","affiliation":[{"name":"Department of Biology, Howard University, Washington, DC 20059, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4436-3474","authenticated-orcid":false,"given":"Yixin","family":"Xie","sequence":"additional","affiliation":[{"name":"College of Computer Science and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jahn N.","family":"O\u2019Neil","sequence":"additional","affiliation":[{"name":"Department of Physiology & Biophysics, Howard University College of Medicine, Washington, DC 20059, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8326-9889","authenticated-orcid":false,"given":"Shaolei","family":"Teng","sequence":"additional","affiliation":[{"name":"Department of Biology, Howard University, Washington, DC 20059, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,16]]},"reference":[{"key":"ref_1","unstructured":"Alzheimer\u2019s Association (2025, October 09). 2025 Alzheimer\u2019s Disease Facts and Figures (PDF). 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