The week in Structures – 8th May 2013 #PDB

May 8, 2013

Week #2: Trying to jumpstart our immune system to fight off HIV. 

Fighting the good fight against HIV.

In this weeks PDB releases, we see a couple of HIV-antibody structures, continuing the work of the Kwong and Mascola labs in the NIH. In 2011, these labs released a paper (published in Science) studying various antibodies that recognises and neutralise HIV-1. If you can recall your high school biology classes, antibody recognition of an invading pathogen is the first step in activating the immune system that hopefully results in successfully fighting off the infection. This work has been further developed with papers this year in Cell and Nature – Prolific and important work!

The structure shown below contains the “FAb fragment” (gold & bronze cartoon) of the antibody bound to gp120 (the big blue blob).

Antibody recognition of HIV gp120 - a surface marker of the HIV virus. After PDB # 4JB9

Antibody recognition of HIV gp120 – a surface marker of the HIV virus. After PDB # 4JB9

Glycoprotein 120 (gp120) is a component of the HIV surface spikes – which recognise a range of different molecules on the surface of our cells and initiate infection. It is because of the this that gp120 is an attractive vaccine candidate – however, recombinant gp120 has failed deliver results in clinical trials, and it is hoped that by studying antibody-gp120 interactions and perhaps by designing a novel gp120-dervied antigen, an effective HIV vaccine can be developed.

Presumably the authors discuss the relevance of their findings in the paper (not released at the time of writing here) in the context of HIV treatment and rational vaccine design. (PDB codes 4JB9 and 4J6R). (EDIT: Other work in the same edition of Science discuss similar topics, here and an article “Rational HIV Immunogen design to targets specific germline B-cell receptors.”)

Other structures of note this week at the excellently named “star domain of quaking protein in complex with RNA” and some work looking at the mechanism by which angiopoietin 1 and 2 interact with the Tie2 receptor tyrosine kinase ([paper] | [PDB] ), which might lead to therapeutics that prevent tumours growing their own blood supplies (angiogenesis blockers).

The week in Structures – 1st May 2013 #PDB

May 1, 2013

The first in a (hopefully) weekly series of reviews of interesting structures in latest PDB release**.

High-resolution* Cryo-EM models of Human and Drosophilia Ribosomes!

Proteins are the major molecular players in life as we know it – they are the chemists, the engineers, the messengers and the defenders of life. They make new chemical compounds that we need, they break old compounds down so that we might re-use them – they transmit messages between different cells and tissues and help identify invading pathogens. In short – proteins do pretty much everything, and as such are the subject of intense study and scrutiny.

What better subject for the first of my PDB release highlight posts, than the Ribosome – a vast (at least at a molecular level) and ancient molecular machines that are responsible for the synthesis of proteins in our cells. The (perhaps outdated) “central dogma” of biology is that DNA is transcribed to mRNA, which is translated into protein, and the proteins then go and do everything. Anger et al have released 5Å resolution Cryo-EM-derived models of human and drosophila (Fruit Fly) ribosomes – they are so vast that they have to be split across several PDB files each…

Human (3J3A, 3J3D, 3J3B, 3J3F)

Drosophila (3J38, 3J3C, 3J39, 3J3E)

We're gonna need a bigger boat.

… and so complex as to defy creation of a clear and crisp picture.

The Paper concerning these is due to be published in Nature, but is not available at the time of writing (EDIT – Now it is – here (£)). Presumably, along with the methods  employed in what must be a massive modelling task, there will be some discussion of the differences between these two eukaryotic ribosomes, and the prokaryotic ribosome structures that were the subject of the 2009 Nobel Prize for Chemistry.

Other highlights in this weeks crop of 287 PDB releases include yet more BACE-inhibitor complexes (potential lead compounds for Altzheimer‘s treatments) and CDK2 and CDK8 -inhibitor complexes, which may be lead to novel anti-cancer therapies.

*ok – 5Å might not be great for crystallography, but for our Cryo-EM-based friends, this is pushing the limits and is clearly the result of a great deal of hard work and a massive amount of particle picking.

** The PDB is the “Protein Data Bank” – all structures of proteins/DNA and related molecules are deposited into the PDB and then made available to everyone (for free) prior to or at the time of publication of the paper that describes the work pertaining to the structure. The PDB issues new releases every Wednesday morning (UK time).

[Journal Club] – “Identification of a central role for complement in osteoarthritis”

April 3, 2013

In a little experiment, I’m going to do a journal club style blog post. I’m going to look at a paper, explain why I like it, and how I think it could be improved. If you like it, “like it” and I may do more. 

The paper I am going to look at is “Identification of a central role for complement in osteoarthritis” by Wang et al, published in Nature Medicine in December 2011. [PUBMED|PDF|F1000] I chose this because it is a pretty big paper in my field, and it is a damn good paper (but it is not without flaws).

The paper explores the hypothesis that the complement immune system is involved in the development of osteoarthritis (OA) (a degenerative disease of our joints).

The authors show that the presence of markers of complement activation in samples from (human) patients, such as “C3a des arg” and “C5b-9″ (the membrane attack complex), correlate with osteoarthritis (fig1 b&c).

The membrane attack complex (or MAC) is the final step of the complement immune cascade, and is a complex of proteins that in high levels punches holes in cells and kills them.

They also show that patients with osteoarthritis make more complement activating proteins and less complement inhibiting protein in the synovium of their joints when compared to healthy patients (fig1 e).

Having demonstrated a correlation between complement activation and osteoarthritis in human samples, Wang et al go on to explore this in mouse models of arthritis.

They show that if you knockout the genes for complement components C5 and C6 in mice (preventing the formation of the MAC), these mice develop less severe arthritis (as measured by cartilage degradation) in surgically-induced arthritis (fig2).

The also show that in mice lacking CD59, a natural inhibitor of complement, cartilage degradation is more severe.

These genetic models support the authors’ hypothesis that complement activation might enhance osteoarthritis progression/severity.

•Mice that can’t ACTIVATE MAC have LESS cartilage damage in OA models
•Mice that can’t REGULATE MAC have MORE cartilage damage in OA models

They then show in human chondrocytes (cartilage producing cells)(in cell culture) that extracts of arthritic cartilage or certain proteins (such as fibromodulin) known to be over-produced in arthritis can induce the production of the MAC.

And they show that low (“sub-lytic”) levels of MAC can make normal chondrocytes (but not C5 deficient chondrocytes) produce proteins known to degrade cartilage, such as ADAMTS-4 and -5, but also some Matrix MetalloProteases (MMPs).

Again, this observation supports the hypothesis that complement activation (that culminates in MAC formation) can induce osteoarthritis.

All in all, a very comprehensive paper, and a fantastic piece of work, and I’ve deliberately ignored some parts of the paper to simplify the story.

There are however, a few chinks in the armour.

1) All mice models of arthritis were surgical models – i.e surgery was performed on the mice that caused them to develop arthritis. No “sham-surgery” controls were performed (or if they were, they weren’t mentioned, which seems odd).

Given that it is known that surgery can induce complement activation, this control absolutely should have been done.

Other models of arthritis (such as proteoglycan induced arthritis) were not explored.

2) They should have looked for the products of ADAMTS induced cartilage degradation in the arthritis mice. Antibodies that recognise the breakdown products (so-called “NITEGE”) are available and could be used in immuno-histochemistry to see if/where ADAMTS-mediated cartilage damage is occurring. (H/T to Jen in our lab who pointed this out).

3) None of the subjective cartilage degradation scoring was blinded. This is a potential source of bias.

I still think that the hypothesis explored in this paper is a good one, and that complement activation is almost certainly part of the complicated puzzle of osteoarthritis pathology, but ideally I’d like to see a follow-up paper that included some of these extra experiments.

[PODCAST] – Me on Dessert Lionel Discs

March 21, 2013
Damn good coffee, and hot!

Damn good coffee, and hot! (Photo credit: photojenni)

Self promotion, dead ahead!

I have been fortunate enough to have been interviewed by @Astrondrew of  Sound of Science for episode 5 of the Dessert Lionel Discs podcast :-D

In it I talk about how I got into science, who inspired me to do science, and what exactly I do as part of my day job. I also talk Pink Floyd, Crystals, Twin Peaks and damn fine coffee.

Please listen, and I hope you enjoy!

[TALK] Studying Life at a Molecular Level!

March 3, 2013
Caffeine. One of nature's many triumphs.

Caffeine. One of nature’s many triumphs.


I am talking about how we understand what we understand about the molecular nature of life!

It will be just like “Wonders of Life” but with less silhouetted  pointing up a mountain, and more pictures of molecules and crystals and me.

The talk is on Tuesday 12th March, 2013 at the Hope Street Hotel, on Hope Street, in Liverpool – doors open at 730pm.

There is a facebook event page here. See you there.

Wonders of LIFE Drinking Game Rules

January 27, 2013

In which I re-hash an old blog post for some exceptionally cheap japes. 

BBC2. 9pm. 27th Jan 2013.


Take 1 finger of drink when Prof Cox says:

  • “Millions”
  • Evolution
  • Inherited
  • Quantum
  • “Probability”
  • “Vast”
  • “Epic”
  • Gregor Mendel” or “Mendelian Inheritance”
  • DNA
  • Primordial Soup
  • When ever Brian shouts at us from a moving vehicle. (Double for a flying vehicle – h/t @Markgfh)
  • Whenever you see time lapse footage of the sky or clouds (like this) – h/t @MrMMarsh

Take 2 fingers of drink for:

Take 3 fingers of drink for:

  • “Trillions*”
  • Any mention of crystallography or model of a protein/DNA structure. (Just because, OK!?)

Half-a-pint for:

  • Any side-swipe at pseudoscience – creationism, homeopathy, astrology, etc

Finish your drink whenever you see Brian in silhouette up a mountain somewhere.



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