{"id":157,"date":"2018-05-03T11:23:36","date_gmt":"2018-05-03T09:23:36","guid":{"rendered":"https:\/\/site.uit.no\/cube\/?page_id=157"},"modified":"2018-05-03T13:10:09","modified_gmt":"2018-05-03T11:10:09","slug":"wp3-substrate-binding","status":"publish","type":"page","link":"https:\/\/site.uit.no\/cube\/about\/wp3-substrate-binding\/","title":{"rendered":"WP3 Substrate binding"},"content":{"rendered":"<p><img fetchpriority=\"high\" decoding=\"async\" class=\"wp-image-184  alignright\" src=\"https:\/\/site.uit.no\/cube\/wp-content\/uploads\/sites\/364\/2018\/05\/binding_cycle-300x240.png\" alt=\"\" width=\"411\" height=\"329\" srcset=\"https:\/\/site.uit.no\/cube\/wp-content\/uploads\/sites\/364\/2018\/05\/binding_cycle-300x240.png 300w, https:\/\/site.uit.no\/cube\/wp-content\/uploads\/sites\/364\/2018\/05\/binding_cycle-768x615.png 768w, https:\/\/site.uit.no\/cube\/wp-content\/uploads\/sites\/364\/2018\/05\/binding_cycle.png 927w\" sizes=\"(max-width: 411px) 100vw, 411px\" \/>The ability to go beyond current state of the art with respect to substrate binding free energies in biological\u00a0systems will be pursued in two directions. The linear interaction energy (LIE) method is appealing due to its\u00a0simplicity, and estimates the absolute binding free energy as a difference in ligand-surrounding interaction\u00a0energies in the bound and free state.\u00a0The applicability of the LIE method to different temperatures must be\u00a0examined first. That is, there are indications that the electrostatic scaling coefficient is temperature\u00a0dependent. Once the free energies of binding have been successfully calculated, high precision van\u2019t Hoff\u00a0plots will be calculated, immediately yielding the enthalpy and entropy of binding without directly\u00a0evaluating the terms.<\/p>\n<p>If the LIE method fails to predict enthalpies and entropies of ligand binding for test systems, we will instead\u00a0use the free energy perturbation (FEP) approach to calculate relative free energies of binding. These will again be\u00a0examined at different temperatures to construct van\u2019t Hoff plots, but now only relative changes in enthalpies\u00a0and entropies between different substrates will be obtained.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The ability to go beyond current state of the art with respect to substrate binding free energies in biological\u00a0systems will be pursued in two directions. The linear interaction energy (LIE) method is appealing due to its\u00a0simplicity, and estimates the absolute &hellip; <a href=\"https:\/\/site.uit.no\/cube\/about\/wp3-substrate-binding\/\">Continued<\/a><\/p>\n","protected":false},"author":862,"featured_media":0,"parent":26,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-fullwidth.php","meta":{"footnotes":""},"class_list":["post-157","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/site.uit.no\/cube\/wp-json\/wp\/v2\/pages\/157","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/site.uit.no\/cube\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/site.uit.no\/cube\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/site.uit.no\/cube\/wp-json\/wp\/v2\/users\/862"}],"replies":[{"embeddable":true,"href":"https:\/\/site.uit.no\/cube\/wp-json\/wp\/v2\/comments?post=157"}],"version-history":[{"count":3,"href":"https:\/\/site.uit.no\/cube\/wp-json\/wp\/v2\/pages\/157\/revisions"}],"predecessor-version":[{"id":185,"href":"https:\/\/site.uit.no\/cube\/wp-json\/wp\/v2\/pages\/157\/revisions\/185"}],"up":[{"embeddable":true,"href":"https:\/\/site.uit.no\/cube\/wp-json\/wp\/v2\/pages\/26"}],"wp:attachment":[{"href":"https:\/\/site.uit.no\/cube\/wp-json\/wp\/v2\/media?parent=157"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}