2016 was an incredibly exciting year for membrane protein research with the publication of many groundbreaking structures. These included the CCR2(1) and CCR9(2) chemokine receptors, the M1 and M4 muscarinic acetylcholine receptors(3), the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)(4), the two-pore channel TPC1(5), the TRPV6 calcium channel(6), and the STRA6 retinol receptor(7), to name a few.
Using data from Steve White’s “Membrane Proteins of Known 3D Structure” database(8), we curated all of the unique protein structures and mined each publication for additional information, including which detergents were used in the preparation of these proteins. In total, 85 unique membrane protein structures were deposited in 2016 – the most in any single year. This brings the overall total of unique structures to 671. Here, we’ll take a closer look at the unique structures published in 2016, and provide some detailed analysis about what detergents were utilized in these studies.
Of these 85 unique structures, 64 were determined by X-ray crystallography, 18 by Cryo-EM, and 3 by NMR (Figure 1). Of interesting note is the increase in the number of unique structures determined by Cryo-EM from last year (10 total in 2015), pointing to the increasing utility of this method for membrane protein structural biology.
Once again, we looked at which detergents were used most frequently for membrane protein solubilization, purification, and crystallization*. Like last year, DDM (30%) and DDM / CHS (25%) were used in the extraction of the majority of the proteins (Figure 2). The other commonly used detergents for membrane protein solubilization include Elugent (11%) and DM (5%). For purification, we observe similar trends, with DDM (32%) and DDM / CHS (24%) being used the most (Figure 3). Although popular for protein solubilization, Elugent was only used in the purification of one protein. Other detergents used commonly for protein purification include LDAO (9%), DM (7%), Digitonin (5%), OG (5%), and LMNG / CHS (4%).
Lastly, we looked at which detergents were used in the final purification step and the structure determination experiments (Figure 4). Interestingly, over 25 different detergents were used in this step, once again highlighting the important effect detergent choice has in structure determination efforts. Once again, DDM (16%) was used in the majority of structures; however, it was used much less than in the solubilization and purification steps. C8E4 (13%) was the next most frequently used detergent, possibly a consequence of the large number (20) of ß-barrel proteins determined last year. Like last year, C8E4 was only used in the structure determination of ß-barrel proteins. Other commonly used detergents for structure determination include DDM / CHS (12%), DM (8%), OG (8%), LMNG (5%), and Digitonin (5%).
If you want to compare trends in detergent usage from year to year, have a look at our analysis we did last year for membrane protein structures published in 2015. Additionally, we are still in the process of generating detergent usage data for all 671 (and counting) unique membrane protein structures. When finished, we’re planning on making this database public and available on our website – stay tuned!
*Note: 9 proteins did not use any detergents for solubilization, purification, and structure determination (5EFR, 5FMW, 2YOC, 5KUD, 5JYN, 5HKK, 5IMW, 5IMY, 5B49).
- Zheng, Y., et al. (2016) Nature 540(7633), 458-461.
- Oswald, C., et al. (2016) Nature 540(7633), 462-465.
- Thai, D. M., et al. (2016) Nature 531(7594), 335-340.
- Zhang, Z. and Chen, J. (2016) Cell 167(6), 1586-1597.
- Kintzer, A. F. and Stroud, R. M. (2016) Nature 531(7593), 258-262.
- Saotome, K., et al. (2016) Nature 534(7608), 506-511.
- Chen, Y., et al. (2016) Science 353(6302) pii: aad8266. doi: 10.1126/science.aad8266.
- Membrane Proteins of Known 3D Structure. Steven White Laboratory. Accessed 01/13/2017: http://blanco.biomol.uci.edu/mpstruc/