Molecule of the Month: Photoactive Yellow Protein
Researchers use synchrotrons and X-ray lasers to reveal the rapid processes of light sensing.
Seeing the Sensor
The metric terminology for expressing shorter and shorter time intervals is commonly used when discussing these types of molecular transitions.
millisecond = one thousandth of a second
microsecond = one millionth of a second
nanosecond = one billionth of a second
picosecond = one trillionth of a second
femtosecond = one quadrillionth of a second
Looking at the Hydrogens
Exploring the Structure
Snapshots of Photoactive Yellow Protein
Researchers are now developing ways to look at protein structures even faster. Currently, the fastest method is serial femtosecond crystallography. Tiny crystals of the protein are subjected to a very intense flash of x-rays from the Linac Coherent Light Source free-electron laser, which creates an instantaneous diffraction pattern and burns up the crystal in the process. Using this method, researchers have captured snapshots of PYP as the chromophore changes from trans to cis after absorbing light. The structure shown here was captured 100-400 femtoseconds after illumination. Click on the image here to view a movie of these amazing structures.
Topics for Further Discussion
- Try searching for “serial femtosecond crystallography” to see other light-absorbing proteins that have been studied this way, including bacteriorhodopsin and photosystems.
- Many other sensing proteins have domains similar to PYP, collectively called “PAS” domains. For instance, try comparing the structure of PYP to one of the light-sensing domains of phototropin, PDB entry 2z6c.
Related PDB-101 Resources
- Browse Biomolecular Structural Biology
- Browse Cellular Signaling
- 5hd3, 5hdc, 5hdd, 5hds, 5hd5: K Pande, CDM Hutchison, G Groenhof, A Aquila, JS Robinson, J Tenboer, S Basu, S Boutet, DP DePonte, M Liang, TA White, NA Zatsepin, O Yefanov, D Morozov, D Oberthuer, C Gati, G Subramanian, D James, Y Zhao, J Koralek, J Brayshaw, C Kupitz, C Conrad, S Roy-Chowdhury, JD Coe, M Metz, PL Xavier, TD Grand, JE Koglin, G Ketawala, R Fromme, V Srajer, R Henning, JCH Spence, A Ourmazd, P Schwander, U Weierstall, M Frank, P Fromme, A Barty, HN Chapman, K Moffat, JJ van Thor & M Schmidt (2016) Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein. Science 352, 725-729.
- 4b9o: F Schotte, HS Cho, VRI Kaila, H Kamikubo, N Dashdorj, ER Henry, TJ Graber, R Henning, M Wulff, G Hummer, M Kataoka & PA Anfinrud (2012) Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography. Proceedings of the National Academy of Science USA 109, 19256-19261.
- 2zoi: S Yamaguchi, H Kamikubo, K Kurihara, R Kuroki, N Niimura, N Shimizu, Y Yamazaki & M Kataoka (2009) Low-barrier hydrogen bond in photoactive yellow protein. Proceedings of the National Academy of Science USA 106, 440-444.
- 1ts0: H Ihee, S Rajagopal, V Srajer, R Pahl, S Anderson, M Schmidt, F Schotte, PA Anfinrud, M Wulff & K Moffat (2005) Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds. Proceedings of the National Academy of Science USA 102, 7145-7150.
- S Anderson, S Crosson & K Moffat (2004) Short hydrogen bonds in photoactive yellow protein. Acta Crystallographica D60, 1008-1016.
- 2pyp: UK Genick, GEO Borgstahl, K Ng, Z Ren, C Pradervand, PM Burke, V Srajer, TY Teng, W Schildkamp, DE McRee, K Moffat & ED Getzoff (1997) Structure of a protein photocycle intermediate by millisecond time-resolved crystallography. Science 275, 1471-1475.
March 2017, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2017_3