Hi Chris, Though there is no alternative to have a co-crystal structure it does not always happened to be the ideal case where you would easily get it co-crystallized in the same condition. Soaking worked well in many cases, though definitely the answer is very dependent on a particular case to case basis as we all know. But as it seems the situation, that you have the native one crystallized, it is very quick process to check whether it is working for your system or not. If it would work that would make the rest of the story much easier and quicker.
Regarding the procedure details, you could add high concentration of ligand directly to the crystal drop but try to add the ligand carefully so that it take some time to get in contact with the protein crystals. If your ligand is water soluble that is the best scenario, if it is not and it is in DMSO try to dilute the DMSO concentration as much as possible. Just make a very high concentrated solution of your ligand with DMSO and then dilute it with water or buffer. HTH Thanks & Regards, Saugata Saugata Hazra Postdoctoral Research Associate Blanchard Lab Albert Einstein Medical College NY, USA ________________________________ From: Christopher Browning <[email protected]> To: [email protected] Sent: Thursday, September 12, 2013 6:25 AM Subject: Re: [ccp4bb] Adding ligand to crystallization drop Hi Again, Thanks for the suggestions. I just tried it at 2 ligand concentrations and the crystals seem not to mind. The drop does go a little cloudy but I can't say if this is protein precipitation, or the ligand coming out of solution. My feeling its a bit of protein because of the high DMSO conc. being added. I'll co-crystallize just to have a backup! Cheers C -- Christopher Browning, Ph. D Vertex Pharmaceuticals (Europe) Ltd 86-88 Jubilee Avenue Milton Park Abingdon Oxfordshire OX14 4RW United Kingdom Tel +44 (0) 1235 438327 [email protected] www.vrtx.com From: <Noinaj>, "Nicholas [E] (NIH/NIDDK)" <[email protected]> Date: Thursday, 12 September 2013 10:21 To: Christopher Browning <[email protected]>, "[email protected]" <[email protected]> Subject: RE: Adding ligand to crystallization drop Chris, Bottom line is that it is all dependent on how your ligand interacts with your protein, if there are any conformational changes, and how your crystals behave in such a dilution and high concentration of ligand. You just have to test it and see, no way to know for sure until you do the experiments and see. However, there are some things to look for along the way. For example, do your crystals crack after introducing the ligand or do they start to dissolve and lose their nice edges, or turn opaque? you will probably also want to do a buffer only control without ligand to ensure that the crystals are ok with the dilution and change of environment. I assume the native crystals diffract well enough to solve the structure. You would want to test crystals before any soaking and then with buffer only and then with ligand, to ensure diffraction is retained to a level useful enough for structure determination. I did quite a bit of crystal soaking in grad school and it is something you just have to try since every crystal/protein is different. my experience is that soaking can often lead to a slight loss of resolution but typically you still get the information you are seeking if the crystals survive. with that being said, soaking can sometimes lead to partial occupancy of your ligand. So if you are able to do co-xtallization, i think that would be preferred and doesn't seem like too much additional effort assuming you are getting crystals in the same conditions as with native protein only. and with co-xtallization, I often see slightly better resolution that with native protein only (not always the same condition though unfortunately). But again, no way to know how your particular protein/crystal will behave without doing some pilot experiments first. Good luck! Cheers, Nick -------------------------------- [ Nicholas Noinaj ] the Buchanan Lab Laboratory of Molecular Biology LMB-NIDDK, NIH 50 South Drive, Room 4505 Bethesda, MD 20892-8030 1-301-594-9230 (lab) 1-859-893-4789 (cell) [email protected] [ the Buchanan Lab ] http://www-mslmb.niddk.nih.gov/buchanan/ From:Christopher Browning [mailto:[email protected]] Sent: Thursday, September 12, 2013 4:37 AM To: [email protected] Subject: [ccp4bb] Adding ligand to crystallization drop Hi, I've just got a quick question about getting ligands bound to proteins in crystals. I've managed to co-crystallize my proteins with the various ligands, and I'm aware that soaking will work as well but I want to speed up the process. Would this work? If I had a bunch of crystals that have grown in their drop, can I pipette the ligand (say 0.6ul to get a desired conc.) onto the drop and just let the crystals soak that way. Any dilution that would have occurred when then readjust as the drop will be sealed again. Perhaps the crystals would get a little stressed when adding the high concentrated ligand and this method would not work…? Thanks, Chris -- Christopher Browning, Ph. D Vertex Pharmaceuticals (Europe) Ltd 86-88 Jubilee Avenue Milton Park Abingdon Oxfordshire OX14 4RW United Kingdom Tel +44 (0) 1235 438327 [email protected] www.vrtx.com This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you. Vertex Pharmaceuticals (Europe) Ltd. Registered in England and Wales, company no. 2907620 Registered Office: 86 - 88 Jubilee Avenue, Milton Park, Abingdon, Oxfordshire, OX14 4RW, UK This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you. Vertex Pharmaceuticals (Europe) Ltd. Registered in England and Wales, company no. 2907620 Registered Office: 86 - 88 Jubilee Avenue, Milton Park, Abingdon, Oxfordshire, OX14 4RW, UK
