Tuesday, 16 October 2012

3d Structure of the GDP G-protein alpha subunit

The movie below shows the 3d structure of a guanosine diphosphate (GDP) bound G protein alpha-subunit.

Gdp alpha

The small green molecule in the middle is the bound GDP.

https://www.rcsb.org/structure/1TAG

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Additional Resources

Bovine Rhodopsin

The structure of a G-protein coupled receptor is often shown as:

Screen Shot 2012 10 16 at 20 58 21

However, the crystal structure of bovine rhodopsin shows that the seven transmembrane-spanning domains actually form a tight core

Bovine rhodopsin

J. Mol. Biol. (2004) 342, 571–583 https://www.rcsb.org/structure/1U19

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3d Structure - β2AR-T4L

The structure of a G-protein coupled receptor is often shown as:

Screen Shot 2012 10 16 at 20 58 21

Which shows a receptor with the N-terminal outside the cell, seven transmembrane-spanning domains, 3 exoloops, 4 cytoloops and a C terminal inside the cell.

However, it is actually more compact, with the seven transmembrane spanning domains forming a tight core.

Beta2AR

Lower part = T4-lysozyme in place of cyto 3 Small green molecules = cholesterol; can just make out bound ligand in pocket
Science. 2007 318(5854): 1258–1265. https://www.rcsb.org/structure/2RH1

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⍺Gs and Adenylyl Cyclase

The following animation shows αGs interacting with adenylyl cyclase.

Alpha adenylyl cyclase small

The animation is also available as a slightly larger video....



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GPCR movement of TM3 and 6

I have been asked for access to a number of the movies I used in the lectures.

The following animation shows the proposed movements of transmembrane spanning domains 3 and 6 for rhodopsin and β2 adrenergic receptors.

3 6 rotation

It should be noted that other GPCRs may use different methods.

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Tuesday, 25 January 2011

Back to Basics: How do you study?

I have just read a really interesting paper in Science1, which has a very good write-up in the New York Times (New York Times: "To Really Learn, Quit Studying and Take a Test" - link) on how to study.

I am not going to discuss the findings of the paper here, but instead, I will just mention the major findings of the work.

Basically, Karpicke and Janell1 looked at how students learn. They have used a scientific approach to look at this with some carefully designed experiments. The authors looked at:

  1. Just reading
  2. Repeat reading
  3. Reading and drawing a concept map whilst consulting the text
  4. Reading and then drawing a concept map from memory (no consulting the text)
  5. Reading and then writing what you have read (without consulting the original text)

The findings, put in simple terms (as judged by testing the students a week after carrying out the original exercise), was that method 4 and 5 produced the best results. That is, read the text, and then test yourself.

I strongly recommend reading the write-up in the New York Times (link) and then tackling the original paper at Science.

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Reference:

  1. Jeffrey D. Karpicke and Janell R. Blunt "Retrieval Practice Produces More Learning than Elaborative Studying with Concept Mapping" Science 1199327 Published online 20 January 2011 [DOI:10.1126/science.1199327] link

Wednesday, 22 December 2010

The other blog.... Blogging at Scitable

Today I started blogging over at Scitable (Nature Education). The new blog can be found here.

So, why two blogs?

Well, the two blogs have two different functions:

This Blog

The function of this blog is to directly serve my teaching.

I will continue to post material here that is connected with the courses I deliver, and it will also continue to host the 'science' tweets (tweets that link to papers and articles of interest) I post.

The Scitable Blog

The Scitable Blog will be used for posts connected to the use of technology in teaching and learning.

In the Scitable Blog I plan to write about how technology can be used to teach the biosciences, and how students can use technology to help with their studies. The Scitable Blog will contain posts that are (hopefully) of use to both lecturers and students.

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm