{"id":1497,"date":"2008-09-17T14:28:28","date_gmt":"2008-09-17T18:28:28","guid":{"rendered":"https:\/\/engineering.jhu.edu\/magazine-archive\/?p=1497"},"modified":"2014-12-17T14:28:57","modified_gmt":"2014-12-17T19:28:57","slug":"final-exam-5","status":"publish","type":"post","link":"https:\/\/engineering.jhu.edu\/magazine-archive\/2008\/09\/final-exam-5\/","title":{"rendered":"Final Exam"},"content":{"rendered":"
\"Final<\/a>
This protein-protein complex was created by graduate student Sid Chaudhury by docking the unbound crystal structure of the enzyme alpha-chymotrypsin and the ensemble of nuclear magnetic resonance (NMR) structures of the inhibitor eglin-C. Using PyRosetta, students learn to fold, dock, and design proteins.<\/figcaption><\/figure>\n

In the new course<\/strong> Design of Biological Molecules and Systems, undergraduates learn to design and build proteins. Or at least they get to try.<\/p>\n

The course, split into two seven-week sessions, is co-taught by assistant professor Jeff Gray and associate professor Marc Ostermeier, both of Chemical and Biomolecular Engineering. \u201cIn my half of the course,\u201d says Gray, \u201cstudents apply rational thought and physics to the design of a protein, using computational methods to read and manipulate 3-D structures.\u201d Making it all possible is PyRosetta, a computer program Gray helped to develop that marries a programming language called Python with Rosetta, the leading research tool for protein structure prediction and design.<\/p>\n

Fundamentally, a protein\u2019s function is dictated by its structure (or shape), which is determined by its gene sequence. \u201cStructure is interesting to engineers because it\u2019s like driving a car and then opening up the engine and seeing how it works,\u201d says Gray. By using computer models to adjust and tweak the model\u2019s sequence and shape, students change its theoretical function.<\/p>\n

However, since a protein is a complicated system of thousands of atoms, the calculations the students must perform often become inexact. \u201cMany forces are very carefully balanced by nature and because calculating them can be tricky, we end up having to approximate things like the effect of water or the electrostatic energy,\u201d says Gray. That complexity often prevents the students from designing a protein that could survive in real life, so, halfway through the semester, Ostermeier takes over with a different method. Their new mission: to learn how proteins evolve and function in real cells.<\/p>\n

\u201cMy approach is quantitative and rational, while Marc\u2019s is more experimental by trial and error,\u201d Gray says. \u201cHowever,\u201d he adds with a laugh, \u201chis usually works and mine doesn\u2019t.\u201d<\/p>\n

\u201cWe use evolution as our design tool,\u201d Ostermeier says. \u201cYou put a protein into a scenario such that if it doesn\u2019t do what you want it to, it doesn\u2019t survive the process. It\u2019s survival of the fittest.\u201d Through readings and lectures, the students learn about such experimental methods and techniques that, essentially, take an approach opposite to Gray\u2019s: by forcing a protein to evolve function and later determining its sequence and shape. By the semester\u2019s end, the students know how to design proteins theoretically in Gray\u2019s lab and, in Ostermeier\u2019s, the methods and techniques that can be used to build them through experimentation.<\/p>\n

\u201cUltimately, if engineers could build proteins that perform specific tasks,\u201d Gray says, \u201cthey could potentially do things like make better drugs, make proteins that destroy agents in biological weapons, build biosensors that detect environmental contaminants, or make better enzymes for biofuels. The applications could be incredible.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"

In the new course Design of Biological Molecules and Systems, undergraduates learn to design and build proteins. Or at least they get to try. The course, split into two seven-week sessions, is co-taught by assistant professor Jeff Gray and associate professor Marc Ostermeier, both of Chemical and Biomolecular Engineering. \u201cIn my half of the course,\u201d…<\/p>\n","protected":false},"author":4,"featured_media":1498,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[33],"tags":[],"class_list":["post-1497","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-final-exam","issue-fall-2008"],"acf":[],"yoast_head":"\nFinal Exam - JHU Engineering Magazine<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/engineering.jhu.edu\/magazine-archive\/2008\/09\/final-exam-5\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Final Exam - JHU Engineering Magazine\" \/>\n<meta property=\"og:description\" content=\"In the new course Design of Biological Molecules and Systems, undergraduates learn to design and build proteins. 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