{"id":105,"date":"2016-09-03T15:09:37","date_gmt":"2016-09-03T15:09:37","guid":{"rendered":"http:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/?page_id=105"},"modified":"2018-10-30T16:41:46","modified_gmt":"2018-10-30T16:41:46","slug":"peripheral-membrane-proteins","status":"publish","type":"page","link":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/?page_id=105","title":{"rendered":"Peripheral Membrane Proteins"},"content":{"rendered":"<p>Implicit membrane modeling allows facile determination of the binding orientation of a peripheral membrane protein to a membrane. Typically, we take the crystal structure and place it on the membrane surface at 6 different orientations. We then run a few ns of MD simulations. In some cases we observe that the protein always reorients to adopt the same final orientation. In other cases, the final orientation from the 6 simulations can be different, in which case we can compare their effective energies to determine which one is optimal. This approach has been applied to a Fatty Acid Binding Protein (Ref. 1) and to a membrane-bound proteinase (Ref. 3).<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignright wp-image-112 \" src=\"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/wp-content\/uploads\/2016\/09\/FABP-890x1024.gif\" alt=\"FABP\" width=\"462\" height=\"531\" srcset=\"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/wp-content\/uploads\/2016\/09\/FABP-890x1024.gif 890w, https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/wp-content\/uploads\/2016\/09\/FABP-261x300.gif 261w, https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/wp-content\/uploads\/2016\/09\/FABP-768x884.gif 768w\" sizes=\"auto, (max-width: 462px) 100vw, 462px\" \/><\/p>\n<p>The transfer of palmitate from the membrane bound holo-IFABP to the membrane via the helical portal region. The membrane is represented by the rectangle; the upper surface corresponds to the plane of smeared charge; the lower surface is the hydrocarbon\/headgroup boundary.<\/p>\n<p>A similar approach was used to determine the membrane-bound structure of a-synuclein, a membrane that aggregates in Parkinson\u2019s disease (Ref. 2). The protein was built as an ideal, straight a-helix and remained so during the simulations, although it exhibited considerable flexibility near the middle. The periodicity of the helix was analyzed and was found to be 11\/3, instead of the 18\/5 typically observed in aqueous helices.<\/p>\n<p>&nbsp;<\/p>\n<p><strong>References<\/strong><\/p>\n<ol>\n<li>Mihajlovic, M., Lazaridis, T. &#8220;Modeling fatty acid delivery from intestinal fatty acid binding protein to a membrane&#8221;, <em>Prot. Sci.<\/em> , 16:2042-55 (2007)<\/li>\n<li>Mihajlovic, M., Lazaridis, T. &#8220;Membrane-bound structure and energetics of alpha-synuclein&#8221;, <em>Proteins<\/em> , 70:761-78 (2008)<\/li>\n<li>Hajjar, E., Mihajlovic, M., Witko-Sarsat, V., Lazaridis, T., Reuter &#8220;Computational prediction of the binding site of proteinase 3 to the plasma membrane&#8221;, <em>Proteins<\/em> , 71:1655-69 (2008)<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"<p>Implicit membrane modeling allows facile determination of the binding orientation of a peripheral membrane protein to a membrane. Typically, we take the crystal structure and place it on the membrane surface at 6 different orientations. We then run a few ns of MD simulations. In some cases we observe that the protein always reorients to <a href=\"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/?page_id=105\" rel=\"nofollow\"><span class=\"sr-only\">Read more about Peripheral Membrane Proteins<\/span>[&hellip;]<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-fullwidth.php","meta":{"footnotes":""},"class_list":["post-105","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=\/wp\/v2\/pages\/105","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=105"}],"version-history":[{"count":7,"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=\/wp\/v2\/pages\/105\/revisions"}],"predecessor-version":[{"id":279,"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=\/wp\/v2\/pages\/105\/revisions\/279"}],"wp:attachment":[{"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=105"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}