{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T14:53:34Z","timestamp":1786978414844,"version":"build-2736575974"},"reference-count":13,"publisher":"Wiley","issue":"10","license":[{"start":{"date-parts":[[2019,8,7]],"date-time":"2019-08-07T00:00:00Z","timestamp":1565136000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Protein Science"],"published-print":{"date-parts":[[2019,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Recently Bekker et al. [Bekker G\u2010J et al. Protein Sci. 2019;28:429\u2013438.] described a computational strategy of applying molecular\u2010dynamics simulations to estimate the relative stabilities of single\u2010domain antibodies, and utilized their method to design changes with the aim of increasing the stability of a single\u2010domain antibody with a known crystal structure. The structure from which they generated potentially stabilizing mutations is an anti\u2010cholera toxin single domain antibody selected from a na\u00efve library which has relatively low thermal stability, reflected by a melting point of 48\u00b0C. Their work was purely theoretical, so to examine their predictions, we prepared the parental and predicted stabilizing mutant single domain antibodies and examined their thermal stability, ability to refold and affinity. We found that the mutation that improved stability the most (~7\u00b0C) was one which changed an amino acid in CDR1 from an asparagine to an aspartic acid. This change unfortunately was also accompanied by a reduction in affinity. Thus, while their modeling did appear to successfully predict stabilizing mutations, introducing mutations in the binding regions is problematic. Of further interest, the mutations selected via their high temperature simulations, did improve refolding, suggesting that they were successful in stabilizing the structure at high temperatures and thereby decrease aggregation. Our result should permit them to reassess and refine their model and may one day lead to a useful\n                    <jats:italic>in silico<\/jats:italic>\n                    approach to protein stabilization.\n                  <\/jats:p>","DOI":"10.1002\/pro.3692","type":"journal-article","created":{"date-parts":[[2019,7,25]],"date-time":"2019-07-25T04:38:47Z","timestamp":1564029527000},"page":"1909-1912","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Experimental evaluation of single\u2010domain antibodies predicted by molecular dynamics simulations to have elevated thermal stability"],"prefix":"10.1002","volume":"28","author":[{"given":"Dan","family":"Zabetakis","sequence":"first","affiliation":[{"name":"Center for Biomolecular Science and Engineering Naval Research Laboratory  Washington District of Columbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa C.","family":"Shriver\u2010Lake","sequence":"additional","affiliation":[{"name":"Center for Biomolecular Science and Engineering Naval Research Laboratory  Washington District of Columbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark A.","family":"Olson","sequence":"additional","affiliation":[{"name":"Systems and Structural Biology Division USAMRIID  Frederick Maryland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ellen R.","family":"Goldman","sequence":"additional","affiliation":[{"name":"Center for Biomolecular Science and Engineering Naval Research Laboratory  Washington District of Columbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7545-9893","authenticated-orcid":false,"given":"George P.","family":"Anderson","sequence":"additional","affiliation":[{"name":"Center for Biomolecular Science and Engineering Naval Research Laboratory  Washington District of Columbia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2019,8,7]]},"reference":[{"key":"e_1_2_5_2_1","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2017.00865"},{"key":"e_1_2_5_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2008.01.022"},{"key":"e_1_2_5_4_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0115405"},{"key":"e_1_2_5_5_1","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3546"},{"key":"e_1_2_5_6_1","doi-asserted-by":"publisher","DOI":"10.1021\/ac0610053"},{"key":"e_1_2_5_7_1","first-page":"90","article-title":"Structure of a low\u2010melting\u2010temperature anti\u2010cholera toxin: Llama VHH domain","volume":"69","author":"Legler PM","year":"2013","journal-title":"Acta 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