{"id":418,"date":"2022-01-07T08:42:58","date_gmt":"2022-01-07T13:42:58","guid":{"rendered":"https:\/\/sites.temple.edu\/voelzlab\/?page_id=418"},"modified":"2022-01-07T08:42:59","modified_gmt":"2022-01-07T13:42:59","slug":"cumulative-exam-january-2022","status":"publish","type":"page","link":"https:\/\/sites.temple.edu\/voelzlab\/cumulative-exam-january-2022\/","title":{"rendered":"Cumulative Exam January 2022"},"content":{"rendered":"\n<p>January 17, 2022<br>Biochemistry Cumulative Exam<\/p>\n\n\n\n<p><strong>Topic<\/strong>: Protein structure, function, binding and computational design<\/p>\n\n\n\n<p><strong>Reading<\/strong>:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Bryan, Cassie M., Gabriel J. Rocklin, Matthew J. Bick, Alex Ford, Sonia Majri-Morrison, Ashley V. Kroll, Chad J. Miller, et al. \u201cComputational Design of a Synthetic PD-1 Agonist.\u201d Proceedings of the National Academy of Sciences 118, no. 29 (July 20, 2021): e2102164118. <a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1073\/pnas.2102164118\" target=\"_blank\">https:\/\/doi.org\/10.1073\/pnas.2102164118<\/a> <\/li><\/ul>\n\n\n\n<p>It is <span style=\"text-decoration: underline\"><em>highly<\/em><\/span> recommended that you consult the references cited in the paper (and therein) to learn more about the background and methods employed.<\/p>\n\n\n\n<p>Students may use the Bryan et al. paper listed under \u201cReading\u201d during the exam. No other materials are permitted.<\/p>\n\n\n\n<p><strong>Learning goals<\/strong>. Be able to discuss:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>The biological function of PD-1 and background on the need for synthetic agonists<\/li><li>The main experimental and computational methods used, including (but not limited to)<br>computational protein design using Rosetta; on overview of the \u201cMotifgraft\u201d and \u201cFold-From-Loops\u201d protocols used in the paper<\/li><li>yeast display and affinity maturation<\/li><li>binding and activity assays<\/li><li>Biophysical methods like CD and biolayer interferometry (BLI)<\/li><li>The work\u2019s main results and conclusions. Know what information is presented in each figure, and what conclusions the experimental data imply. (Example: Figure 2 presents a color-map of Shannon entropies \u2013 know what that is, and how to compute it)<\/li><li>Knowledge of basic biochemical principles (protein structure, energetics, stability, folding, binding affinity, kinetics) and how they apply to this study.<\/li><\/ul>\n\n\n\n<p>If you are totally unfamiliar with Rosetta and computational protein design, David Baker (HHMI, Univ. Washington) has an introductory iBiology video seminar you should watch:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Part 1: Introduction to Protein Design <a href=\"https:\/\/www.youtube.com\/watch?v=0LetJMbu7uY\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/www.youtube.com\/watch?v=0LetJMbu7uY<\/a><\/li><li>Part 2: Part 2: Design of New Protein Functions <a href=\"https:\/\/www.youtube.com\/watch?v=ZrAwWx7meTk\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/www.youtube.com\/watch?v=ZrAwWx7meTk<\/a><\/li><\/ul>\n\n\n\n<p><strong>Post-CUME review party<\/strong><\/p>\n\n\n\n<p>I will host a Biochem CUME review party on Tuesday Jan 18 at 4 pm, in BE226. If you are interested and can\u2019t make that time, let me know: voelz@temple.edu<\/p>\n","protected":false},"excerpt":{"rendered":"<p>January 17, 2022Biochemistry Cumulative Exam Topic: Protein structure, function, binding and computational design Reading: Bryan, Cassie M., Gabriel J. Rocklin, Matthew J. Bick, Alex Ford, Sonia Majri-Morrison, Ashley V. Kroll, Chad J. Miller, et al. \u201cComputational Design of a Synthetic PD-1 Agonist.\u201d Proceedings of the National Academy of Sciences 118, no. 29 (July 20, 2021): &hellip; <\/p>\n<p class=\"link-more\"><a href=\"https:\/\/sites.temple.edu\/voelzlab\/cumulative-exam-january-2022\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Cumulative Exam January 2022&#8221;<\/span><\/a><\/p>\n","protected":false},"author":1258,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-418","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/pages\/418","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/users\/1258"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/comments?post=418"}],"version-history":[{"count":0,"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/pages\/418\/revisions"}],"wp:attachment":[{"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/media?parent=418"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}