Re: [ccp4bb] Solvent channels
Hi Reza, I can recommend the work of Marc-Olivier Coppens and Kourosh Malek and the references therein for an interesting journey through solvent channels. David Hargreaves Associate Principal Scientist _ AstraZeneca Discovery Sciences, Structure & Biophysics Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693 David.Hargreaves @astrazeneca.com Please consider the environment before printing this e-mail -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Reza Khayat Sent: 27 June 2014 12:01 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Solvent channels Hi, I'd like to do some soaking experiments with a relatively large molecule. Can someone suggest a program/method to display the solvent channels of a crystal? We have the crystal structure. I'd like to see if the channels are large enough to allow the molecule to travel to the hypothesized binding site. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org
Re: [ccp4bb] Solvent channels
Sorry for the delayed response - The situation of 'normal' drug-lead molecule, no restriction of solvent channel access, no other hindrance to mobility, and rapid on-rates and/or/with a low Kd driving/maintaining the concentration gradient might be considered almost optimal. But let us assume that it is indeed typical, and put it in perspective: One of the remarks made previously was that even seconds can suffice (for ions). Say 5 sec. The time factor between that and the 'typical' 30 min soaking then is 360, while the factor to 10 hrs (movie time) is only 20, that is, 10 hrs being an 18x more typical soak time than 5 seconds ;-). But seriously now, why would I beat the dead 5 sec horse dead again? Because of the cautionary tales of failed 'typical' 5-sec ligand soaks where beating proteolysis by 'flash-soaking' was apparently the motivation to ignore prior odds: http://www.ruppweb.org/cvs/br/rupp_2001_NSB_questions_BotA.pdf http://www.nature.com/nsmb/journal/v16/n7/full/nsmb0709-795.html 8 years this model stayed in the literature, frequently cited and presumably used... Its little small-molecule friend did not live as long: http://pubs.acs.org/doi/pdf/10.1021/ja025109g While advertising again the perils of too short soaking and subsequent pressure for optimistic interpretation, I think that Dale's assessment of faster diffusion vs slower binding in the lysozyme-methylene blue case is correct. Maybe growing a clear crystal first in a counter diffusion tube so that it fills the entire tube, and then sticking it into the blue dye and documenting the dye diffusion in solution vs in crystal might work. Could be a summer student project... Soak boldly and stay off the twilight list, BR
[ccp4bb] AW: [ccp4bb] Solvent channels
Dear Bernard, we once worked with a series of protease inhibitors which turned out to be slow substrates, e.g. an acyl intermediate was formed that was subsequently hydrolyzed. Here we had to reduce the soaking times to below 30 minutes, otherwise we would see nothing, e.g. the large excess of added inhibitor was completely turned over. The precipitant was 25% PEG4000, which I consider a typical PEG condition. The inhibitors were the usual bunch of a few (aromatic) rings linked (unfortunately) by an amide linker. I agree with the others who reacted to your post that soaking times of 10 hrs are atypical and more likely caused by a slow Kon than by slow diffusion. Cheers, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Bernhard Rupp Gesendet: Samstag, 28. Juni 2014 10:46 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Solvent channels > Here you are starting to mix equilibrium arguments with the previous kinetic arguments. I don't think I am mixing them; both are relevant. If it cannot diffuse there, forget the kinetics - necessary but not sufficient requirement. Nonetheless, the fact that in high concentrations you can force even weak non-native binders into binding sites (but I reiterate, never in 100% occupancy, at best asymptotically approaching it) is the reason for the many buffer 'ligands' observed in structures (also basis for fragment screening.) > Your movie doesn't include any details of concentration of your dye, > nor what its binding constant is to any sites in a protein nor any mention of kon or koff. The movie does not claim to be a study of any specific ligand binding, it simply illustrates soaking. Graphs of concentration vs achievable equilibrium occupancy at different Kds are in separate figures eg 3-40. Cheers, BR Dale Tronrud > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Keller, Jacob > Sent: Friday, June 27, 2014 3:07 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Solvent channels > > And yet halides--even iodide--permeate those same lysozyme > crystals and others entirely in <30--60 sec. > > JPK > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Bernhard Rupp > Sent: Friday, June 27, 2014 9:00 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Solvent channels > > Just a remark: diffusion is a slow and random-walk process. > Particularly large molecules in viscous media (PEG anybody?) move > (diffuse) slowly in solution. To simply extrapolate from the fact that > the ligand is smaller than the solvent channels to the odds of the > presence of a ligand is a risky proposition. Positive omit difference > density after 'shoot first' as Boaz indicated is a much better indication. And shoot you probably will a lot. > > The little movie below shows how slowly even a small aromatic dye > molecule soaks into a crystal. Total time 10 hrs. > > http://www.ruppweb.org/cryscam/lysozyme_dye_small.wmv > > The literally hundreds of empty ligand structures collected in > Twilight attest to that fact. > > http://journals.iucr.org/d/issues/2013/02/00/issconts.html > > Best, BR > > Science is a way of trying not to fool yourself: The first principle > is that you must not fool yourself - and you are the easiest person to fool. > > R. Feynman, 1974 > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Boaz Shaanan > Sent: Friday, June 27, 2014 2:26 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Solvent channels > > Hi, > > I'm not aware of a program with an option to display channels in > crystals but if you use any of the currently available molecular > display program and ask to display symmetry-related molecules + > adjacent unit cells, it should give you a good enough idea of the > spaces between molecules. Using programs for calculation of > intermolecular distances would also be helpful here. > Independently of the calculation, I would try soaking first and > consult the calculations later (in the spirit of Rossmann's American > method: shoot first ask later). > > Cheers, > >Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaa...@bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Reza > Khayat [rkha...@ccny.c
Re: [ccp4bb] Solvent channels
On 27/06/14 12:00, Reza Khayat wrote: Hi, I'd like to do some soaking experiments with a relatively large molecule. Can someone suggest a program/method to display the solvent channels of a crystal? We have the crystal structure. I'd like to see if the channels are large enough to allow the molecule to travel to the hypothesized binding site. Thanks. Hi, Coot has an implementation of Smart's HOLE. Maybe you can use that? I generated some lysozyme symmetry copies and guessed a start and end point for illustration - not a great example, but I hope you get the general idea: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/screenshots/Screenshot-hole.png Paul. p.s. one thread, one topic please.
Re: [ccp4bb] Solvent channels
> Here you are starting to mix equilibrium arguments with the previous kinetic arguments. I don't think I am mixing them; both are relevant. If it cannot diffuse there, forget the kinetics - necessary but not sufficient requirement. Nonetheless, the fact that in high concentrations you can force even weak non-native binders into binding sites (but I reiterate, never in 100% occupancy, at best asymptotically approaching it) is the reason for the many buffer 'ligands' observed in structures (also basis for fragment screening.) > Your movie doesn't include any details of concentration of your dye, nor what its binding constant is to any sites in a protein nor any mention of kon or koff. The movie does not claim to be a study of any specific ligand binding, it simply illustrates soaking. Graphs of concentration vs achievable equilibrium occupancy at different Kds are in separate figures eg 3-40. Cheers, BR Dale Tronrud > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Keller, Jacob > Sent: Friday, June 27, 2014 3:07 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Solvent channels > > And yet halides--even iodide--permeate those same lysozyme > crystals and others entirely in <30--60 sec. > > JPK > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Bernhard Rupp > Sent: Friday, June 27, 2014 9:00 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Solvent channels > > Just a remark: diffusion is a slow and random-walk process. > Particularly large molecules in viscous media (PEG anybody?) move > (diffuse) slowly in solution. To simply extrapolate from the fact that > the ligand is smaller than the solvent channels to the odds of the > presence of a ligand is a risky proposition. Positive omit difference > density after 'shoot first' as Boaz indicated is a much better indication. And shoot you probably will a lot. > > The little movie below shows how slowly even a small aromatic dye > molecule soaks into a crystal. Total time 10 hrs. > > http://www.ruppweb.org/cryscam/lysozyme_dye_small.wmv > > The literally hundreds of empty ligand structures collected in > Twilight attest to that fact. > > http://journals.iucr.org/d/issues/2013/02/00/issconts.html > > Best, BR > > Science is a way of trying not to fool yourself: The first principle > is that you must not fool yourself - and you are the easiest person to fool. > > R. Feynman, 1974 > > -Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Boaz Shaanan > Sent: Friday, June 27, 2014 2:26 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Solvent channels > > Hi, > > I'm not aware of a program with an option to display channels in > crystals but if you use any of the currently available molecular > display program and ask to display symmetry-related molecules + > adjacent unit cells, it should give you a good enough idea of the > spaces between molecules. Using programs for calculation of intermolecular distances would also be helpful here. > Independently of the calculation, I would try soaking first and > consult the calculations later (in the spirit of Rossmann's American > method: shoot first ask later). > > Cheers, > >Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaa...@bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Reza > Khayat [rkha...@ccny.cuny.edu] > Sent: Friday, June 27, 2014 2:00 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Solvent channels > > Hi, > > I'd like to do some soaking experiments with a relatively large molecule. > Can someone suggest a program/method to display the solvent channels > of a crystal? We have the crystal structure. I'd like to see if the > channels are large enough to allow the molecule to travel to the > hypothesized binding site. > Thanks. > > Best wishes, > Reza > > Reza Khayat, PhD > Assistant Professor > The City College of New York > Department of Chemistry, MR-1135 > 160 Convent Avenue > New York, NY 10031 > Tel. (212) 650-6070 > www.khayatlab.org > = >
Re: [ccp4bb] Solvent channels
You can use CAVER but you would have to make all the symmetry mates as one chain in order to fool it. Still better to just do the experiment I think. Either it will work or it won't, regardless of what any software tells you. Just a wild idea : ) On Fri, Jun 27, 2014 at 5:06 PM, Yarrow Madrona wrote: > Hi Reza, > > CAVER is a great tool for this. There is a web version. You can also > download it to customize and run it in the command line. There is also a > Pymol CAVER plug in that works very well. I have even used it to analyze MD > trajectories. You can find it here: http://www.caver.cz/ > > -Yarrow > > > On Fri, Jun 27, 2014 at 4:00 AM, Reza Khayat > wrote: > >> Hi, >> >> I'd like to do some soaking experiments with a relatively large molecule. >> Can >> someone suggest a program/method to display the solvent channels of a >> crystal? We have the crystal structure. I'd like to see if the channels >> are large >> enough to allow the molecule to travel to the hypothesized binding site. >> Thanks. >> >> Best wishes, >> Reza >> >> Reza Khayat, PhD >> Assistant Professor >> The City College of New York >> Department of Chemistry, MR-1135 >> 160 Convent Avenue >> New York, NY 10031 >> Tel. (212) 650-6070 >> www.khayatlab.org >> > >
Re: [ccp4bb] Solvent channels
On 06/27/2014 06:33 AM, Bernhard Rupp wrote: > For small ion soaking for phasing purposes, partial occupancy is not a > problem. For example, a few 1/2 occupied Iodines still can phase quite well. > 1/2 a C is only 3 electrons, not that great. Add in higher displacement, and > odds are that the ligand interpretation will become difficult. Particularly > when the binding constants are poor, one will out of principle never reach > full occupancy, which further exacerbates the weak density problem. > Patience is definitely a virtue here. > > BR Here you are starting to mix equilibrium arguments with the previous kinetic arguments. If you have a weak binder you can always get full occupancy by adding enough of the compound - to determine how much, you must consider not only the binding constant but the number of binding sites in the crystal and the total volume of the drop containing your crystal. Time is not a factor. Halide ions and cryoprotectants are known to pervade crystals very rapidly, but they are usually added with "overwhelming force". Much more is added than is required to bind to every specific binding site in the crystal. The rate of diffusion, as mass flow, depends not only on viscosity but on the concentration of unbound molecules inside the crystal. When I was soaking an inhibitor into a crystal of Thermolysin I was having problems with the crystals falling apart. My belief was that the inhibitor caused a small change in cell constants and since the inhibitor first bound in a shell around the surface of the crystal strain was created and the crystal cracked. My solution was to add small aliquots of inhibitor with a long enough wait between to allow each batch to diffuse throughout the crystal. Despite waiting up to 6 hours between additions the crystals still cracked. This is when I realized that after the inhibitor bound in the outer shell of the crystal the remaining concentration of free inhibitor was one billionth (since the binding constant was nanomolar) that of the concentration of active sites and the remaining mass flow within the crystal was insignificant. Of course the next aliquot would rapidly diffuse through the occupied region of the crystal and be bound in the shell just below it, becoming trapped itself and increasing the strain. Your movie doesn't include any details of concentration of your dye, nor what its binding constant is to any sites in a protein nor any mention of kon or koff. The lack of information makes it very difficult to draw any conclusions from the experiment, but I believe the experience from many other molecules is that small molecules do move very rapidly through protein crystals, until they are caught by a binding site. I don't believe your movie represents typical diffusion of small molecules in a protein crystal. My interpretation of your movie is: 1) The dye rapidly diffuses into the crystal reaching a simple equilibrium where the concentration in the bulk solvent matches that of the outside solution. Since the protein excludes about half of the volume of the crystal the overall concentration is half that of the mother liquor and the color of the crystal is 1/2 as dark as the surrounding solution. 2) With a slow kon, the dye molecules within the crystal start binding specifically to the protein. Since the dye is aromatic it probably has to dig deep into the protein to find a binding site and this takes time. As dye is removed from the bulk solvent it is rapidly replaced by diffusion from outside the crystal, and the crystal begins to darken, eventually becoming darker than the surrounding liquid. The speed of binding is controlling the kinetics not diffusion. Dale Tronrud > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Keller, Jacob > Sent: Friday, June 27, 2014 3:07 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Solvent channels > > And yet halides--even iodide--permeate those same lysozyme crystals and > others entirely in <30--60 sec. > > JPK > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Bernhard Rupp > Sent: Friday, June 27, 2014 9:00 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Solvent channels > > Just a remark: diffusion is a slow and random-walk process. Particularly > large molecules in viscous media (PEG anybody?) move (diffuse) slowly in > solution. To simply extrapolate from the fact that the ligand is smaller > than the solvent channels to the odds of the presence of a ligand is a risky > proposition. Positive omit difference density after 'shoot first' as Boaz > indicated is a much better indication. And shoot you probably will a lot. > > The little movie below shows how slowly even a small aromatic dye mole
Re: [ccp4bb] Solvent channels
For small ion soaking for phasing purposes, partial occupancy is not a problem. For example, a few 1/2 occupied Iodines still can phase quite well. 1/2 a C is only 3 electrons, not that great. Add in higher displacement, and odds are that the ligand interpretation will become difficult. Particularly when the binding constants are poor, one will out of principle never reach full occupancy, which further exacerbates the weak density problem. Patience is definitely a virtue here. BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: Friday, June 27, 2014 3:07 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Solvent channels And yet halides--even iodide--permeate those same lysozyme crystals and others entirely in <30--60 sec. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp Sent: Friday, June 27, 2014 9:00 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Solvent channels Just a remark: diffusion is a slow and random-walk process. Particularly large molecules in viscous media (PEG anybody?) move (diffuse) slowly in solution. To simply extrapolate from the fact that the ligand is smaller than the solvent channels to the odds of the presence of a ligand is a risky proposition. Positive omit difference density after 'shoot first' as Boaz indicated is a much better indication. And shoot you probably will a lot. The little movie below shows how slowly even a small aromatic dye molecule soaks into a crystal. Total time 10 hrs. http://www.ruppweb.org/cryscam/lysozyme_dye_small.wmv The literally hundreds of empty ligand structures collected in Twilight attest to that fact. http://journals.iucr.org/d/issues/2013/02/00/issconts.html Best, BR Science is a way of trying not to fool yourself: The first principle is that you must not fool yourself - and you are the easiest person to fool. R. Feynman, 1974 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Boaz Shaanan Sent: Friday, June 27, 2014 2:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Solvent channels Hi, I'm not aware of a program with an option to display channels in crystals but if you use any of the currently available molecular display program and ask to display symmetry-related molecules + adjacent unit cells, it should give you a good enough idea of the spaces between molecules. Using programs for calculation of intermolecular distances would also be helpful here. Independently of the calculation, I would try soaking first and consult the calculations later (in the spirit of Rossmann's American method: shoot first ask later). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Reza Khayat [rkha...@ccny.cuny.edu] Sent: Friday, June 27, 2014 2:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Solvent channels Hi, I'd like to do some soaking experiments with a relatively large molecule. Can someone suggest a program/method to display the solvent channels of a crystal? We have the crystal structure. I'd like to see if the channels are large enough to allow the molecule to travel to the hypothesized binding site. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org =
[ccp4bb] AW: [ccp4bb] Solvent channels
To get a rough idea of the solvent channels, one could use coot. By displaying the symmetry molecules as Ca traces (an option hidden in the symmetry menu under "symmetry by molecule") one can set a large radius (100Å) and still rotate the display. A more accurate display can be obtained by generating a number of symmetry mates and reading them in pymol. Even in surface mode, pymol can handle quite a few complete protein molecules without getting excessively slow. However, it is just as important (or even more important) to examine whether the putative binding site is free and not involved in crystal contacts and whether enough room is available to accommodate the ligand. To be absolutely sure, the gold standard is of course still cocrystallization and with 96-well plates and crystallization robots it is not prohibitively difficult. I agree with Jacob Keller, in my experience, soaking is usually much faster than 10 hrs. unless some conformational change in the protein is necessary to let the ligand in the binding site. Nevertheless, we routinely soak overnight (24 hrs.). It is convenient and there is less risk that the structures end up in the twilight database. Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Bernhard Rupp Gesendet: Freitag, 27. Juni 2014 15:00 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Solvent channels Just a remark: diffusion is a slow and random-walk process. Particularly large molecules in viscous media (PEG anybody?) move (diffuse) slowly in solution. To simply extrapolate from the fact that the ligand is smaller than the solvent channels to the odds of the presence of a ligand is a risky proposition. Positive omit difference density after 'shoot first' as Boaz indicated is a much better indication. And shoot you probably will a lot. The little movie below shows how slowly even a small aromatic dye molecule soaks into a crystal. Total time 10 hrs. http://www.ruppweb.org/cryscam/lysozyme_dye_small.wmv The literally hundreds of empty ligand structures collected in Twilight attest to that fact. http://journals.iucr.org/d/issues/2013/02/00/issconts.html Best, BR Science is a way of trying not to fool yourself: The first principle is that you must not fool yourself - and you are the easiest person to fool. R. Feynman, 1974 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Boaz Shaanan Sent: Friday, June 27, 2014 2:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Solvent channels Hi, I'm not aware of a program with an option to display channels in crystals but if you use any of the currently available molecular display program and ask to display symmetry-related molecules + adjacent unit cells, it should give you a good enough idea of the spaces between molecules. Using programs for calculation of intermolecular distances would also be helpful here. Independently of the calculation, I would try soaking first and consult the calculations later (in the spirit of Rossmann's American method: shoot first ask later). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Reza Khayat [rkha...@ccny.cuny.edu] Sent: Friday, June 27, 2014 2:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Solvent channels Hi, I'd like to do some soaking experiments with a relatively large molecule. Can someone suggest a program/method to display the solvent channels of a crystal? We have the crystal structure. I'd like to see if the channels are large enough to allow the molecule to travel to the hypothesized binding site. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org =
Re: [ccp4bb] Solvent channels
And yet halides--even iodide--permeate those same lysozyme crystals and others entirely in <30--60 sec. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp Sent: Friday, June 27, 2014 9:00 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Solvent channels Just a remark: diffusion is a slow and random-walk process. Particularly large molecules in viscous media (PEG anybody?) move (diffuse) slowly in solution. To simply extrapolate from the fact that the ligand is smaller than the solvent channels to the odds of the presence of a ligand is a risky proposition. Positive omit difference density after 'shoot first' as Boaz indicated is a much better indication. And shoot you probably will a lot. The little movie below shows how slowly even a small aromatic dye molecule soaks into a crystal. Total time 10 hrs. http://www.ruppweb.org/cryscam/lysozyme_dye_small.wmv The literally hundreds of empty ligand structures collected in Twilight attest to that fact. http://journals.iucr.org/d/issues/2013/02/00/issconts.html Best, BR Science is a way of trying not to fool yourself: The first principle is that you must not fool yourself - and you are the easiest person to fool. R. Feynman, 1974 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Boaz Shaanan Sent: Friday, June 27, 2014 2:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Solvent channels Hi, I'm not aware of a program with an option to display channels in crystals but if you use any of the currently available molecular display program and ask to display symmetry-related molecules + adjacent unit cells, it should give you a good enough idea of the spaces between molecules. Using programs for calculation of intermolecular distances would also be helpful here. Independently of the calculation, I would try soaking first and consult the calculations later (in the spirit of Rossmann's American method: shoot first ask later). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Reza Khayat [rkha...@ccny.cuny.edu] Sent: Friday, June 27, 2014 2:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Solvent channels Hi, I'd like to do some soaking experiments with a relatively large molecule. Can someone suggest a program/method to display the solvent channels of a crystal? We have the crystal structure. I'd like to see if the channels are large enough to allow the molecule to travel to the hypothesized binding site. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org =
Re: [ccp4bb] Solvent channels
Just a remark: diffusion is a slow and random-walk process. Particularly large molecules in viscous media (PEG anybody?) move (diffuse) slowly in solution. To simply extrapolate from the fact that the ligand is smaller than the solvent channels to the odds of the presence of a ligand is a risky proposition. Positive omit difference density after 'shoot first' as Boaz indicated is a much better indication. And shoot you probably will a lot. The little movie below shows how slowly even a small aromatic dye molecule soaks into a crystal. Total time 10 hrs. http://www.ruppweb.org/cryscam/lysozyme_dye_small.wmv The literally hundreds of empty ligand structures collected in Twilight attest to that fact. http://journals.iucr.org/d/issues/2013/02/00/issconts.html Best, BR Science is a way of trying not to fool yourself: The first principle is that you must not fool yourself - and you are the easiest person to fool. R. Feynman, 1974 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Boaz Shaanan Sent: Friday, June 27, 2014 2:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Solvent channels Hi, I'm not aware of a program with an option to display channels in crystals but if you use any of the currently available molecular display program and ask to display symmetry-related molecules + adjacent unit cells, it should give you a good enough idea of the spaces between molecules. Using programs for calculation of intermolecular distances would also be helpful here. Independently of the calculation, I would try soaking first and consult the calculations later (in the spirit of Rossmann's American method: shoot first ask later). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Reza Khayat [rkha...@ccny.cuny.edu] Sent: Friday, June 27, 2014 2:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Solvent channels Hi, I'd like to do some soaking experiments with a relatively large molecule. Can someone suggest a program/method to display the solvent channels of a crystal? We have the crystal structure. I'd like to see if the channels are large enough to allow the molecule to travel to the hypothesized binding site. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org =
Re: [ccp4bb] Solvent channels
Hi, I'm not aware of a program with an option to display channels in crystals but if you use any of the currently available molecular display program and ask to display symmetry-related molecules + adjacent unit cells, it should give you a good enough idea of the spaces between molecules. Using programs for calculation of intermolecular distances would also be helpful here. Independently of the calculation, I would try soaking first and consult the calculations later (in the spirit of Rossmann's American method: shoot first ask later). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Reza Khayat [rkha...@ccny.cuny.edu] Sent: Friday, June 27, 2014 2:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Solvent channels Hi, I'd like to do some soaking experiments with a relatively large molecule. Can someone suggest a program/method to display the solvent channels of a crystal? We have the crystal structure. I'd like to see if the channels are large enough to allow the molecule to travel to the hypothesized binding site. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org
[ccp4bb] Solvent channels
Hi, I'd like to do some soaking experiments with a relatively large molecule. Can someone suggest a program/method to display the solvent channels of a crystal? We have the crystal structure. I'd like to see if the channels are large enough to allow the molecule to travel to the hypothesized binding site. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org
