Author Archives: Phil

Global anxiety, summed up by NY Times artist Nicholas Konrad

This image (which I reproduce here under fair use guidance) appears in this mornings New York Times in the article “The Global Coronavirus Crisis in Poised to Get Much, Much Worse”. The artist, Nicholas Konrad, really drives in the point!

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This coronavirus is toast

The orange slices are the Spike proteins.  The toast represents antibody molecules that have bound to the surface of the virus, creating immunoresistance for the host.  This, after all, is where our hopes lie:  Gaining immunity and making the virus … Continue reading

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Thanks committee members!

Thanks to all who pitched in with some important 10th week committee work: Show tables committee.  We have tables! Our show ballot committee.  Clever categories! Our show poster committee.  Splendid artistic view of a Nobel prize winning ion channel structure discovered by Rod MacKinnon . The artist … Continue reading

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Origami revolution

The original show has been taken down from the PBS/Nova site, but here’s a youtube capture. We’ll watch the first few minutes and then skip ahead to 20:30 where David Baker demonstrates some origami-like aspects of protein folding.

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OMSI Exhibit — Must see!

Raha is just back from visiting the Art of Brick exhibition at OMSI (in Portland).  Check it out!

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Standalone 3D viewers for proteins

The widely used pymol is available here. Highly recommended for adjusting your view as you work on your protein portraits projects.

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Let’s visit the Linus Pauling Collection

Chris Petersen will host a tour of the collection on Tuesday of Week 8 (May 23) at 10 am.  We’ll meet at the library 5th floor (Special Collections). Read about Pauling’s discovery of the alpha helix here.  

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Week 2 Animation Assignment

This week please post a protein example from the Molecule of the Month and include an idea of how the dynamics of that protein could be conveyed artistically! Here’s a quick rundown of the artwork we looked at on Tuesday … Continue reading

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McGill and Johnson interviewed by David Goodsell

“Images of molecules are becoming more and more common in educational and entertainment media. These pictures are often created by computer graphics artists using state-of-the-art programs such as Maya and Cinema4D. However, the methods used to import PDB structures into … Continue reading

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The waltz

Let’s look some more at the art and science of protein translation:                                 The waltz of polypeptides                 … Continue reading

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The Best Scientific Image Of The Year Was A Hand-Painted Watercolor of Ebola Virus by David Goodsell

Check it out!

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Boyer’s early portrait (model) of ATPsynthase

http://www.jbc.org/content/277/42/39045 This is a portrait of ATP synthase, circa 1979.  Circular motion was not an intrinsic requirement for this model, but the picture compels us to imagine a pinwheel-like motion relative to the central axis, does it not?

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Example post. X marks the spot

This is an example post. This is also a great example of an artist’s view of a chromosome! Krista Shapton is the artist.  Her work can be found at kshapton.com

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“Transporter” by Rebecca Kamen

Hi again, I couldn’t resist… here’s another beautiful 3D portrait by Rebbeca Kamen: I appreciate very much an artist who is inspired by science! On Monday, please remind me to tell you a beautiful story about Bonnie Hall (1931–2004) who … Continue reading

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Looking forward to next week and having our blog working properly

Hi students, I have alerted the experts to our problem and hope to get our technology problem figured out by Monday.  And so, if over the weekend you happen to receive a request to join the blog, please, if you … Continue reading

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Tinkering on the theme of a sandwich

In the CATH classification system, the “Mainly Beta” parent node (at the C level) has a child node known as “Sandwich” (at the A level) whose representative domain structures include over 18,000 known structures.  That’s a lot of sandwiches. Looking … Continue reading

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Tinkering

Why it is good to tinker (according to Francois Jacob) In 1977, Francois Jacob, fresh from his pioneering studies of gene transcription with Jacques Monod, delivered a stimulating lecture on the topic of Molecular and Evolutionary Tinkering at UC Berkeley (later published … Continue reading

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Topology in 2D and 3D — The Rossmann fold

     

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Examples of protein domains classified by CATH

Some of the architectures new to CATH since 1997:   From: Nucleic Acids Res. 2009 January; 37(Database issue): D310–D314. “CATH (class, architecture, topology, homology) is a hierarchical protein domain classification (1) where domains are classified manually by curators, guided by prediction … Continue reading

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The unlabeled set of amino acid side-chains

This set of the twenty amino acid side-chains doesn’t have the names listed.  You can quiz yourself to help you learn the names and predict the chemical properties of these different structures.  Example:  Which are the hydrophilic side-chains?  Which of … Continue reading

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The twenty amino acids

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Really great posts

Rather than comment on each separate label, here’s a hip hip hooray for all of you who have posted your label so far!  Very very nice!

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Example project label

Here’s an example label for a Protein Portrait of hemoglobin, a molecule that definitely is on my all-time favorites list. Protein:  Hemoglobin Artist:  Phil McFadden Take a breath… where did it go?  Hemoglobin, the vividly red oxygen-carrying protein of our … Continue reading

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Spread the word!

Mark your calendar – BB399H Protein Portraits Art Competition Students enrolled in BB399H will display their Protein Portraits artwork from Tuesday through Friday of Week 10 in SLUG 2, STAG 032 (May 31 – June 3). Please come see these … Continue reading

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Views of integrase

HIV integrase (the recent molecule of the month) is known from its close structural kin.  The following is the abstract of the recent “putting it all together” article that appeared in the scientific journal Nucleic Acids Research (2009 by Cherepanov … Continue reading

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The big picture

Today let’s discuss protein form from the top down.  That is not the conventional direction taken in biochemistry courses where we usually begin with the elementary building blocks and work our way up.  (I’m fighting laryngitis this morning, so for … Continue reading

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Saying hello

Please follow these directions: 1.  Log in to this blog using your onid name (this is a university blog that only allows authors who have onid accounts).  Choose a username nickname for your blog posts, such as “phil”. 2.  Choose … Continue reading

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Photographs and summer exhibit

I have taken photos of everyone’s work of art.  You’ll find those posted here by summer’s end.  But if you are really dying to renew that special bond with your protein, you can find most of the artworks on display … Continue reading

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GFP label

GFP is composed of a barrel of beta sheets and a light-emitting chromophore within.  By teaming up with aequorin (which glows blue), GFP produces the eery green light that jellyfish are known for.  GFP has found many uses, from fluorescent … Continue reading

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Paper protein models?

Remember how Pauling first modeled the alpha helix?  By discovering the optimum folding of a sheet of paper. Easy, if you know origami. Here’s a “when art meets science” video explanation from Robert Lang, a highly inventive sort of person… … Continue reading

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Exhibit labels

As agreed on Monday, let’s each post the labeling information for our portraits.  Try to have this done by Friday.  Here’s a template you can use, in italics: Protein:  Hemoglobin Artist:  Phil McFadden Take a breath… where did it go? … Continue reading

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HIV protease, woof woof!

Perryman, et al (2005) labeled the enzyme as if it were a bulldog.

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Here’s another one!

I have added a link to “May_k” on our side-bar of protein artists —> Below is the p53 tumor promoter (2OCJ) in a dancing mood!

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Painters and hats

Edgar Degas and Gustav Klimt really knew fashion hats…

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Spirals indeed

Callia made a good suggestion.  Check out the spirals she found.  On Wednesday, we’ll practice making left-handed and right-handed spirals since you’ll need that skill to build alpha helices with the proper handedness.

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Good idea about the banana

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Adding new posts

Hi everyone, I have finally signed everyone up as an author.  You should each now try to author a new post.  Log in with the username and password you received by email.  Change your profile if you want  to give … Continue reading

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Side chains of amino acids

Most biology and biochemistry textbooks have a table showing the twenty amino acids found in proteins.  Here’s a figure you can use to quiz your knowledge:

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Day one, Spring term 2010

On Monday we’ll meet each other, share a few stories, and fill in some details in our course syllabus.

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Protein portraits on display

I have set up your exhibits in the library of the Biochemistry and Biophysics Department (second floor Ag Life Sci Bldg). Come by and take a look if you have a chance. You can pick up your protein anytime.  Those … Continue reading

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