Monday, 21 January 2008

Structure and mechanism of Hsp90, a heat shock protein

Heat shock proteins are over-expressed when cells are exposed to heat or stress. Their function is to help other proteins to fold "correctly" into their mature, functional forms and, as such, they are classified as "chaperones". The structures and functions of these proteins will be described in much more detail in section 8 of the PPS course ("The Protein Lifecycle").

Today (21 January), in the School of Crystallography's Monday seminar programme, Maruf Ali from the Institute of Cancer Research in London spoke about his research on the structure of the heat shock protein Hsp90. This protein is found in all kingdoms except for the Archaea; it interacts with many other proteins (known as "client proteins" to help them enter their mature, active structural forms. Hsp90 client proteins include kinases that are important targets for anti-cancer drugs - hence the ICR's interest.

Hsp90 is a three-domain protein. The N-terminal domain binds ATP, which is necessary for the protein's activity; the middle domain binds client proteins; and the C-terminal one is involved in dimerisation. Structures of each domain separately were already known when Maruf started his post-doc a few years ago; each of these domains has a fold in Scop's alpha+beta class. Maruf's work involved solving the structure of a mutated form of the intact protein bound to a co-chaperone, (Ali et al. (2006), Nature 440, 1013-1019; PDB code 2CG9). This structure gives a clear picture of a complex structure, showing how a "lid" of structure closes to enabl the client protein to bind, and supports a previously proposed model in which the N-terminal domain is also involved in dimerisation.

Try downloading the structure, loading it into Jmol or a similar program, and seeing if you can identify the three domains.

Tuesday, 15 January 2008

CCP4 2008 Study Weekend

CCP4 (Collaborative computing Project 4) is responsible for one of the main X-ray crystallography computer packages. It holds a study weekend the first weekend in January each year attended by 3-500 delegates. It is the social event of the UK protein crystallographers calendar as well as being the best methods meeting each year certainly in Europe. This year the topic was "Low Resolution Structure Determination and Validation" inspired by the retraction in Dec 2006 of five high profile structures of membrane proteins, which had been wrongly determined due to the author using an incorrect piece of software (not CCP4!) which meant that his maps were inverted ie his helices were all left handed rather than right handed. Because the resolution was low, as membrane protein crystals often are, this mistake was not immediately obvious from the maps and he forced through the refinement of right handed helices into left handed density by some dubious methods. Less was said about another structure published in Nature which essentially does not have the copies of the protein touching in the crystal as this is still under investigation by the American University from where this structure originates. Analysing these mistakes should help the community to avoid them themselves and possibly spot them as referees- all these papers had got past expert referees.
On a more positive note the first example of an ab initio (ie without a sequence homologue) prediction of a protein structure that was good enough to solve a crystal structure was presented. The main conclusion of the meeting is that the resolution of the structure is pretty much the only thing that determines the quality of the structure. Big structures at the same resolution are just as good as small structures. However big structures tend not to be at as high a resolution so that on average big structures are less well determined than small structures, but this is because they are lower resolution. Structural genomics groups are no better or worse than targetted labs at determining structures.

From a PPS point of view probably the most interesting talk was by Chris Tate from MRC in Cambridge who said that the retracted structure had to be wrong because it was incompatible with the biochemical data. Although structure is powerful, it has to be compatible with the biology. The system he worked on (EmrE) has another peculiarity in that half the protein inserts into the membrane in one direction (N terminus in) and half in the other (N terminal out) and the active molecule consists of one of each of these protein chains.

Friday, 11 January 2008

Tim Hunt's Lecture

The Institute of Structural Molecular Biology, based at Birkbeck and University College, hosted a star performer as its first seminar speaker of 2008: Tim Hunt of the Cancer Research UK London Research Institute. Tim was awarded the Nobel Prize for Physiology or Medicine in 2001, with Leland Hartwell and Paul Nurse, for his discovery of cyclins - proteins that control the expression of the cyclin-dependent kinases (CDKs) which control a cell's passage through the cell cycle. So cyclins can be described as regulators of the regulators of the cell cycle.

Maybe only a Nobel Laureate could do it. Tim started his lecture with a quick tour through several hundred years of Physics, inspired by his small daughter's (unanswered) question "Why is the sky opaque?" He introduced (or re-introduced) his audience to Schrodinger's equation and Maxwell's idea of a "field" before confessing that he didn't understand quantum mechanics: no one should ever be ashamed of admitting as much.

The cell cycle, and its control, is, like quantum mechanics, "very interesting and very complicated". Tim's critical observation, which he made studying frog oocytes, was that cell division is controlled by the concentrations of the proteins that we now know as cyclins. They were given this name because their concentration in cells goes up and down according to where those cells are in the cell cycle - whether they are growing, replicating their DNA, undergoing mitosis...

Cyclins control the progress of cells through cell division by regulating the function of cyclin dependent kinases (CDKs). By binding to CDKs, cyclins control their activation state, and active CDKs drive the cells through the cell cycle. The press release for the 2001 Nobel Prize succinctly described CDKs as the cells' "motors" and cyclins as the gear boxes that control whether cells will be in idle or overdrive.

Cyclins are all-alpha proteins (link is to the PPS material) with 5-helical cores. PDB entry 1H1S shows human cyclin A bound to CDK2.

It is impossible to do justice to such a complex topic, and lecture, in a few paragraphs. To learn more, try the resources on the Nobel website would be a good first port of call.

Happy New Year!

It must have been the way the holidays fell in the middle of the week, this year, but that was certainly a long break! But we are now back in earnest.

And I hope that none of you have forgotten what you have been learning over the long holiday. Section 5 of the course will be released on Monday 14th Jan.

And there have already been a few interesting scientific events of 2008...