November 25, 2010
This morning I had an email message from SBS in my email box, touting the SBS 17th Annual Conference and Exhibition, to take place on March 27-31, 2011. The headline “New Keynote Speaker…” made me look further and I noticed that Hugh Rosen from TSRI is planning to give a keynote on the S1P Receptor structure:
High resolution of S1P Receptor (Sphingosine 1-Phosphate receptor) advertised for 2011 in an email from the Society formerly called Society for Biomolecular Sciences.
Not sure what exactly a Syzygy means in this context, but this announcement fits well with what I heard about Hugh’s presentation on the S1P receptor a few weeks ago at the Allosteric Modulator Drug Disvoery Congress.
Good news for 2011 in terms of GPCR structures!
Peter
Filed under:
Membrane Proteins, Structure | Posted by: Peter Nollert | Comments: 1
November 19, 2010
Yay - another GPCR structure to look at!
I just noticed that the 2.9A Dopamine D3 Receptor (in complex with Eticlopride) coordinates 3PBL have been released by the PDB earlier this week. This one will take some time to digest. My congratulations go again to the Stevens lab at TSRI. This is a great achievement, well done.
Peter
P.S. the total count of GPCRs of known structure is now six
PPS: Here's the paper in this week's Science magazine: Chien, E., Liu, W., Zhao, Q., Katritch, V., Won Han, G., Hanson, M., Shi, L., Newman, A., Javitch, J., Cherezov, V., & Stevens, R. (2010).
Structure of the Human Dopamine D3 Receptor in Complex with a D2/D3 Selective Antagonist
Science, 330 (6007), 1091-1095 DOI: 10.1126/science.1197410
Filed under:
Membrane Proteins, Structure | Posted by: Peter Nollert | Comments: 1
November 18, 2010
A lot of GPCR researchers over here in the US are preparing for next weeks' trip back to their family to celebrate Thanksgiving. At one point the topic of discussion will inevitably come to "what's going on in your field?" - the dreaded potential conversation stopper. For those of you who have had difficulties answering this question in plain language without getting caught up in jargon, you may want to check out this neat write-up in NATURE CHEMICAL BIOLOGY about the progress that has been achieved during the 'naughties' in the field of - what some people prefer to call - 'chemical biology' (why not stick with the old-fashioned term 'biochemistry'?):
Bucci M, Goodman C, & Sheppard TL (2010). A decade of chemical biology. Nature Chemical Biology, 6 (12), 847-854 PMID: 21079586
Of course GPCRs and their structure are a big deal for all of us who are working on them. So I was glad to see the structure of the beta2-adrenergic receptor listed as a 2007 milestone. This feature in Nat. Chem. Biol. also contains a separate box, explaining the actual finding and the relevance of this GPCR structure in clear language.
Definitely worth printing out and bringing along as 'supporting materials'. Just imagine: GPCRs could be a conversation starter this year.
Happy T-day,
Peter
Filed under:
Membrane Proteins, Opinion | Posted by: Peter Nollert | Comments: 1
November 6, 2010
Starting out as a GPCR dimer skeptic I have been 'converted' over the course of the past several years. For instance, one of the most impressive demonstrations of GPCR dimers in vivo I saw presented during this year's Keystone meeting on GPCRs by Nigel Birdsall: He has used single molecule imaging TIRF microscopy to monitor - beyond doubt - the formation and dissociation of muscarinic receptors in CHO cells. His movies of single receptors forming dimers are very convincing. Nigel's group can track individual receptors over time, their mobility, clustering and follow the receptor dimerization kinetics. This is a fantastic body of work.
A study by Albizu et al. then added another 'beyond doubt' qualifier: assymetric activation of Oxytocin receptors as shown with time-resolved FRET between ligands. BTW, the power of the fluorescence probes toolset that was developed and employed for this study is amazing in itself. The significance of this work though, lies in the fact that dimers were shown to exist not only in transfected cell lines, but in native tissue: Oxytocin receptor oligomers in mammary gland tissue.
So, since at least some GPCR dimers/oligomers are for real, they form new points of attack for the development of compounds that interfere with the dimerization/oligomerization processes. Developing ligands that disrupt interfaces is a particularly difficult exercise and I have not seen many success stories for supposedly simpler soluble proteins. The nicely formed ligand binding pockets in the GPCR structures that we have seen so far, are highly attractive starting points for computational-based drug discovery. But the interfaces may proof much more productive in yielding new classes of ligands.
Cheers,
Peter
Filed under:
Membrane Proteins, Opinion | Posted by: Peter Nollert | Comments: 1
October 29, 2010
I checked out the 'Faculty of 1000' to identify the most important GPCR structure papers that have been published in the past few years. This 'post publication peer review" should identify those papers that are deemed most important to the scientific community (er, the F1000 members). A simple search using the search term 'GPCR structure', limiting the results to those literature references that have received more than ten F1000 points yielded the following list:
Filed under:
Membrane Proteins, Lists, Online Tools | Posted by: Peter Nollert | Comments: 1
October 16, 2010
There's a nice write-up in GEN on the progress in the field of GPCR crystallization / structural biology and the impact this has on R&D efforts. I couldn't agree more with what Mike Hanson from Receptos says about the utility of lipidic cubic phases for the crystallization of G protein coupled receptor molecules. The List of "GPCRs of known structure" speaks for itself as it shows that the majority of the all crystal structures are based on crystals that have been grown within lipidic cubic phases.
Here at Emerald we have developed several relevant patented technologies ourselves and hold exclusive licenses to technologies that are indispensible for the practical aspects that are involved in GPCR crystallization. Some of these technologies are distributed as products via Emerald BioSystems. For instance, there is the 'Cubic LCP Cubic Kit' and the 'Cubic™ Screen', crystallization tools that are specifically designed for lipidic cubic phase - based membrane protein crystallization. These products aid researchers to set up crystallization trials with their own GPCR preparations.
Over here, at Emerald BioStructures we offer research services that apply these membrane protein crystallization technologies and tools within contract research projects. In fact, we have all the components in place to go from gene to membrane protein structure to provide our clients with unique insight into their drug targets (download a description of our membrane protein structure determination services here). At the heart of the matter, we feel that the field of membrane protein crystallography has now matured to a state where it can be applied within drug discovery projects and make a significant impact to lead optimization and to the discovery of new compounds, for instance with crystallographic fragment screening.
Soluble protein structure based drug discovery has an impressive track record of giving researchers a key advantage in their drug discvoery efforts. Demonstrating the value of crystallography for membrane proteins such as GPCRs is the logical next step.
This brings me to my shameless plug: Should you be interested in Emerald BioStructures' membrane protein structural biology services, please contact us here - or send me an email directly, I'd be happy to discuss specifics.
All the best,
Peter
Filed under:
Membrane Proteins, Crystallization, Opinion | Posted by: Peter Nollert | Comments: 0
October 8, 2010
Congratulations to Ray Stevens and team to determining and publishing the crystallographic structure of the CXCR4 Chemokine receptor in Science. The diffenent binding areas for the small molecule and peptide antagonist are nicely resolved and show extensive interactions with binding pocket residues in the 2.5 - 3.1 A crystal structures.
Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC, Hamel DJ, Kuhn P, Handel TM, Cherezov V, & Stevens RC (2010). Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science (New York, N.Y.), 330 (6007), 1066-71 PMID: 20929726
The corresponding structure files have not been released as of writing this. The PDB accession codes are: 3ODU (CXCR4-2–IT1t,P21), 3OE0 (CXCR4-3–CVX15, C2), 3OE8 (CXCR4-2–IT1t, P1), 3OE9 (CXCR4-3–IT1t, P1), and 3OE6 (CXCR4-1–IT1t, I222). The supplemental material lists a protocol that one could almost characterize as becoming 'the standard' for GPCR structure studies: expression of highly engineered construct (5 features) in Sf9 cells, membranes solubilized with a mix of dodecylmaltoside and cholesterol hemisuccinate (no detergent exchange) , His tag clipped off, PNGase treatment and crystallization in a matrix consisting of monoolein-based LCP with 6% cholesterol. All five crystal forms are stacked layers of membranes (as expected in LCP - grown crystals).
Lots of info to digest. What a feast!
Peter
Filed under:
Membrane Proteins, Crystallization, Structure | Posted by: Peter Nollert | Comments: 1
September 30, 2010
64% of the GPCR blog readers think that GPCRs are worthy a Nobel Prize. See the box on the right. Check out the timer that shows how many days and hours we're away from the announcement of the 2010 Nobel for Chemistry (the 2010 Nobel to Medicine went to Robert G. Edwards for his work on in-vitro fertilization). To spice this up a little I've set up a poll over at Emerald BioSystems. Cast your vote here on the protein target areas and find out what everybody else thinks.
All the best,
Peter
Filed under:
Membrane Proteins, Opinion | Posted by: Peter Nollert | Comments: 0
September 17, 2010
The simplest way to get at least a portion of a membrane protein structure is to 'chop off' the transmembrane portion and determine the structure of the remaining isolated, non-transmembrane domains. In GPCRs the extracellular portions, sometimes called ectodomains, of class B and class C receptors fold into in such independent domains that retain ligand binding and hence their crystallographic structures have been determined. The most recent addition to this class is the ectodomain complex of the CGRP receptor with bound antagonists, nicely covered in this teaser: RAMP-ing up Class-B GPCR ECD Structural Coverage. The table below lists this and other "Extracellular GPCR domains of known structure."
Table: Extracellular GPCR domains of known structure
|
GPCR extracellular domain structure |
PDB access code |
Resolution |
Reference |
|
CGRP receptor extracellular domain, class B ECD complex with RAMP 1 protein and antagonists Olcegepant and Telcagepant |
3N7P
3N7R
3N7S |
2.8
2.9
2.1 |
Ernst ter Haar et al.
Crystal Structure of the Ectodomain Complex of the CGRP Receptor, a Class-B GPCR, Reveals the Site of Drug Antagonism
Structure, Volume 18, Issue 9, 1083-1093, 2010 |
|
Methuselah receptor ectodomain with peptide inhibitor (Drosophila) |
1FJR |
2.3 |
West AP Jr, Llamas LL, Snow PM, Benzer S, Bjorkman PJ.
(2001)
Crystal structure of the ectodomain of Methuselah, a Drosophila G protein-coupled receptor associated with extended lifespan.
Proc.Natl.Acad.Sci.USA 98: 3744-3749 |
|
Vasoactive intestinal polypeptide Receptor 2 (human) |
2X57 |
2.1 |
To be published |
|
Parathyroid hormone receptor (PTH1R) in complex with parathyroid hormone-related protein (PTHrP) |
3H3G |
1.94 |
Pioszak et. al.
Structural basis for parathyroid hormone-related protein binding to the parathyroid hormone receptor and design of conformation-selective peptides.
(2009) J.Biol.Chem. 284: 28382-28391 |
|
GIP (gastric inhibitory polypeptide) receptor in complex with GIP hormone (human) |
2QKH |
1.9 |
Parthier et al.
Crystal structure of the incretin-bound extracellular domain of a G protein-coupled receptor
(2007) Proc.Natl.Acad.Sci.Usa 104: 13942-13947 |
|
FSH (follicle stimulating hormone) receptor in complex with the FSH hormone |
1XWD |
2.92 |
Fan, Q.R., Hendrickson, W.A.
Structure of human follicle-stimulating hormone in complex with its receptor.
(2005) Nature 433: 269-277 |
Filed under:
Membrane Proteins, Lists, Structure | Posted by: Peter Nollert | Comments: 3
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