Please see: Dym, O., Song, W., Felder, C., Roth, E., Shnyrov, V., Ashani, Y., Xu, Y., Joosten, R. P., Weiner, L., Sussman, J. L. & Silman, I. The impact of crystallization conditions on structure-based drug design: A case study on the methylene blue/acetylcholinesterase complex. Protein Sci. 25, 1096-1114 (2016).
Structure-based drug design utilizes apoprotein or complex structures retrieved from the PDB. >57% of crystallographic PDB entries were obtained with polyethylene glycols (PEGs) as precipitant and/or as cryoprotectant, but <6% of these report presence of individual ethyleneglycol oligomers. We report a case in which ethyleneglycol oligomers' presence in a crystal structure markedly affected the bound ligand's position. Specifically, we compared the positions of methylene blue and decamethonium in acetylcholinesterase complexes obtained using isomorphous crystals precipitated with PEG200 or ammonium sulfate. The ligands' positions within the active-site gorge in complexes obtained using PEG200 are influenced by presence of ethyleneglycol oligomers in both cases bound to W84 at the gorge's bottom, preventing interaction of the ligand's proximal quaternary group with its indole. Consequently, both ligands are ∼3.0Å further up the gorge than in complexes obtained using crystals precipitated with ammonium sulfate, in which the quaternary groups make direct π-cation interactions with the indole. These findings have implications for structure-based drug design, since data for ligand-protein complexes with polyethylene glycol as precipitant may not reflect the ligand's position in its absence, and could result in selecting incorrect drug discovery leads. Docking methylene blue into the structure obtained with PEG200, but omitting the ethyleneglycols, yields results agreeing poorly with the crystal structure; excellent agreement is obtained if they are included. Many proteins display features in which precipitants might lodge. It will be important to investigate presence of precipitants in published crystal structures, and whether it has resulted in misinterpreting electron density maps, adversely affecting drug design. and the cover image showing the PEG molecules, in blue with their surrounding electron density, near the bound ligand, methylene blue, in pink. best regards Joel [cid:[email protected]] -------------------------------------------------------------------------------- Prof. Joel L. Sussman [email protected]<mailto:[email protected]> www.weizmann.ac.il/~joel<http://www.weizmann.ac.il/~joel> Dept. of Structural Biology tel: +972 (8) 934 6309 proteopedia.org<http://www.weizmann.ac.il/~joel> Weizmann Institute of Science fax: +972 (8) 934 6312 Rehovot 76100 ISRAEL mob: +972 (50) 510 9600 --------------------------------------------------------------------------------- On 2Apr, 2019, at 4:12, Zhen Luo <[email protected]<mailto:[email protected]>> wrote: Hi everyone, Thank you very much for your help and time. A PEG fragment indeed seems to fit into the density. Thanks again! <image001.png> Best regards, Zhen From: CCP4 bulletin board <[email protected]<mailto:[email protected]>> on behalf of Zhen Luo <[email protected]<mailto:[email protected]>> Reply-To: Zhen Luo <[email protected]<mailto:[email protected]>> Date: Tuesday, 2 April 2019 at 9:01 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [ccp4bb] unidentified crescent-shaped electron density Dear all, Could you please shed some light on what this crescent-shaped density around the lysine side chain might belong to? I now have two unrelated protein structures where this kind of density can be found surrounding a lysine side chain. <image002.png><image003.png> <image004.png><image005.png> 2FOFC maps were contoured at around 1.5 sigma, FOFC map at 3 sigma. One protein was crystallised in 0.1 M CaCl2 and 20% PEG 3350; the other in 10% PEG 20000, 20% PEG MME 550, 0.03 M CaCl2/MgCl2, 0.1 M MES/imidazole. Protein buffers contained 0.025 M HEPES and 0.15 M NaCl. None of these fitted in well. Could it be cleaved PEG? Any suggestion would be greatly appreciated. Thanks in advance! Best regards, Zhen Luo School of Chemistry and Molecular Biosciences The University of Queensland, Australia ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
