{"id":2596,"date":"2015-09-01T13:58:19","date_gmt":"2015-09-01T12:58:19","guid":{"rendered":"http:\/\/www.blopig.com\/blog\/?p=2596"},"modified":"2015-09-01T13:59:18","modified_gmt":"2015-09-01T12:59:18","slug":"molecular-dynamics-of-antibody-cdrs","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2015\/09\/molecular-dynamics-of-antibody-cdrs\/","title":{"rendered":"Molecular Dynamics of Antibody CDRs"},"content":{"rendered":"<p>Efficient design of antibodies as therapeutic agents\u00a0requires understanding of their structure and behavior in solution.\u00a0I have recently\u00a0performed molecular dynamics simulations to investigate the flexibility and solution dynamics of complementarity determining regions (CDRs). Eight structures of the Fv region of antibody\u00a0SPE7 were found in the Protein Data Bank with identical sequences.\u00a0Twenty-five replicas of 100 ns simulations were performed on the Fvregion of one of these structures to investigate whether the CDRs\u00a0adopted the conformation of one of the other X-Ray structures. The\u00a0simulations showed the H3 and L3 loops start from one conformation and adopt another experimentally determined conformation.<\/p>\n<p>This confirms the potential of molecular dynamics to be used to\u00a0investigate antibody binding and flexibility. Further investigation\u00a0would involve simulating different systems, for example using solution NMR resolved structures, and comparing the conformations\u00a0deduced here to the canonical forms of CDR loops. Looking forward\u00a0it is hoped molecular dynamics could be used to predict the bound\u00a0conformation of an antibody from the unbound structure.<\/p>\n<p><a href=\"https:\/\/drive.google.com\/folderview?id=0ByH_C7wy5NuPflNhMEFTczN0cTlmLVBhZGlhdGZ4UmxCdnBPTWZNT20wSHgwM3ByNk9zVUU&amp;usp=sharing\" target=\"_blank\">Click here for simulation videos.<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Efficient design of antibodies as therapeutic agents\u00a0requires understanding of their structure and behavior in solution.\u00a0I have recently\u00a0performed molecular dynamics simulations to investigate the flexibility and solution dynamics of complementarity determining regions (CDRs). Eight structures of the Fv region of antibody\u00a0SPE7 were found in the Protein Data Bank with identical sequences.\u00a0Twenty-five replicas of 100 ns simulations [&hellip;]<\/p>\n","protected":false},"author":33,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[1],"tags":[],"ppma_author":[521],"class_list":["post-2596","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":521,"user_id":33,"is_guest":0,"slug":"hannahpatel","display_name":"Hannah Patel","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/475fce49714d9af7623be7dafe4a36b34bbcc765845293c995c7def372b15846?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/2596","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/33"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=2596"}],"version-history":[{"count":4,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/2596\/revisions"}],"predecessor-version":[{"id":2712,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/2596\/revisions\/2712"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=2596"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=2596"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=2596"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=2596"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}