{"id":1830,"date":"2016-04-11T00:19:41","date_gmt":"2016-04-11T07:19:41","guid":{"rendered":"http:\/\/blogs.oregonstate.edu\/psquared\/?page_id=1830"},"modified":"2026-04-08T15:06:43","modified_gmt":"2026-04-08T22:06:43","slug":"choosing-a-protein","status":"publish","type":"page","link":"https:\/\/blogs.oregonstate.edu\/psquared\/choosing-a-protein\/","title":{"rendered":"Choosing a protein to portray"},"content":{"rendered":"

Choosing a subject for a protein portrait<\/h3>\n

This week we will put on our artist caps and earnestly search the protein data bank\u00a0for subjects to portray. \u00a0There are well over 100,000 structures<\/a> on deposit in the PDB. \u00a0How to choose just one?<\/p>\n

Our interests in the science of proteins will strongly guide our choice of subject. \u00a0Most of us have encountered topics in the life sciences that have piqued our curiosity and that we have told ourselves we will study further someday. \u00a0Perhaps that day is here. \u00a0You\u00a0have seven weeks ahead of you to put together\u00a0a protein portrait for public display. \u00a0So if you are still curious about that nervous system twitch\u00a0or that flower pollen antigen you heard about in Biology 211, that may be all the incentive you need\u00a0to plunge into a deeper examination of the proteins\u00a0associated with those fondly remembered topics.<\/p>\n

\"calderThe search for a protein subject is also closely intertwined with our preferences for artistic media. \u00a0Ask yourself in which artistic medium you are talented. \u00a0And if the word “talent” is an overstatement, then ask yourself which medium you would like to play around in for the next several weeks. \u00a0If you\u00a0are a painter, say, you\u00a0may look for a certain sort of\u00a0protein subject, such as one that looks good in\u00a0the gaudy\u00a0colors of Calder’s Spiral Flowers.<\/p>\n

Or if you\u00a0have talent as a sculptor\u00a0you\u00a0may look for a different sort of subject, one whose molecular articulations\u00a0are well presented by wiring and bended metals, like Calder’s Vertical Constellation. \u00a0\"calder<\/a><\/p>\n

Or if you skipped art class in high school you may at least have stashed in the back of your closet a set of Leggo building blocks or an embroidery kit someone gave you for your birthday one year — Put that stuff to use by turning it into a protein portrait for 2016!<\/p>\n

But an equally important source of inspiration is the simple tug we may feel when we encounter a protein while thumbing through the PDB. \u00a0Check out this recently deposited structure, portrayed below by standard PDB thumbnail graphics.\u00a0Without even knowing the name of the structure or its biological function, are you not intrigued by its pinwheel\u00a0shape? \u00a0Does the appearance of the molecule take you in an artistic direction? \u00a0If so, go with\u00a0the wind!<\/p>\n

\"ImageSource=RCSB<\/a>

Click on the structure to go to its PDB page<\/p><\/div>\n

Zeroing in on a protein structure in the PDB<\/h2>\n

Let’s look up one of the\u00a0enzyme molecules that many people are interested in these days, \u00a0HMG CoA reductase. \u00a0This is the enzyme that is inhibited by the statin drugs, the drugs that block cholesterol synthesis. \u00a0One of the most informative examples of the structure of HMG CoA reductase is listed under the code name 1hwk<\/a> in the PDB. \u00a0How did I discover this enzyme molecule in the PDB? \u00a0I used the dynamic duo of online resources that every protein artist will use often:<\/p>\n