Author Archives: Phil

Check out this knot review: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4556803/?report=reader

in proteins??

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!

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.  

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

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 →

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 →

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 →

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 →

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 →

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 →

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!

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 →

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 →

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 →

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 →

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 →

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 →

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 →

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 →

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 →

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

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!

Edgar Degas and Gustav Klimt really knew fashion hats…

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.

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 →

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: