{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T04:03:47Z","timestamp":1793333027345,"version":"4.5.0"},"reference-count":38,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2024,4,9]],"date-time":"2024-04-09T00:00:00Z","timestamp":1712620800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2024,4,9]],"date-time":"2024-04-09T00:00:00Z","timestamp":1712620800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100000052","name":"NIH Office of the Director","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Protein Science"],"published-print":{"date-parts":[[2024,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The Ebola virus (EBOV) is a lipid\u2010enveloped virus with a negative sense RNA genome that can cause severe and often fatal viral hemorrhagic fever. The assembly and budding of EBOV is regulated by the matrix protein, VP40, which is a peripheral protein that associates with anionic lipids at the inner leaflet of the plasma membrane. VP40 is sufficient to form virus\u2010like particles (VLPs) from cells, which are nearly indistinguishable from authentic virions. Due to the restrictions of studying EBOV in BSL\u20104 facilities, VP40 has served as a surrogate in cellular studies to examine the EBOV assembly and budding process from the host cell plasma membrane. VP40 is a dimer where inhibition of dimer formation halts budding and formation of new VLPs as well as VP40 localization to the plasma membrane inner leaflet. To better understand VP40 dimer stability and critical amino acids to VP40 dimer formation, we integrated computational approaches with experimental validation. Site saturation\/alanine scanning calculation, combined with molecular mechanics\u2010based generalized Born with Poisson\u2010Boltzmann surface area (MM\u2010GB\/PBSA) method and molecular dynamics simulations were used to predict the energetic contribution of amino acids to VP40 dimer stability and the hydrogen bonding network across the dimer interface. These studies revealed several previously unknown interactions and critical residues predicted to impact VP40 dimer formation. In vitro and cellular studies were then pursued for a subset of VP40 mutations demonstrating reduction in dimer formation (in vitro) or plasma membrane localization (in cells). Together, the computational and experimental approaches revealed critical residues for VP40 dimer stability in an alpha\u2010helical interface (between residues 106\u2013117) as well as in a loop region (between residues 52\u201361) below this alpha\u2010helical region. This study sheds light on the structural origins of VP40 dimer formation and may inform the design of a small molecule that can disrupt VP40 dimer stability.<\/jats:p>","DOI":"10.1002\/pro.4978","type":"journal-article","created":{"date-parts":[[2024,4,9]],"date-time":"2024-04-09T06:53:52Z","timestamp":1712645632000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Computational and experimental identification of keystone interactions in Ebola virus matrix protein\n                    <scp>VP40<\/scp>\n                    dimer formation"],"prefix":"10.1002","volume":"33","author":[{"given":"Yogesh","family":"Narkhede","sequence":"first","affiliation":[{"name":"Department of Chemistry and Biochemistry University of Notre Dame  Notre Dame Indiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roopashi","family":"Saxena","sequence":"additional","affiliation":[{"name":"Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious Disease Purdue University  West Lafayette Indiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tej","family":"Sharma","sequence":"additional","affiliation":[{"name":"Department of Physics Florida International University  Miami Florida USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob P.","family":"Conarty","sequence":"additional","affiliation":[{"name":"Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious Disease Purdue University  West Lafayette Indiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valentina Toro","family":"Ramirez","sequence":"additional","affiliation":[{"name":"Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious Disease Purdue University  West Lafayette Indiana USA"},{"name":"Pharmaceutical Chemistry Universidad CES  Medell\u00edn Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Balindile B.","family":"Motsa","sequence":"additional","affiliation":[{"name":"Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious Disease Purdue University  West Lafayette Indiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Souad","family":"Amiar","sequence":"additional","affiliation":[{"name":"Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious Disease Purdue University  West Lafayette Indiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheng","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Medicine University of California  San Diego California 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