I suspect that in many cases the crystal is making the news instead on reporting the actual status of bound waters in fluid conditions. One should probably be looking at NMR structures for a more valid report of bound waters. Are there any reports of the comparison of the number of bound waters in crystal structures vs NMR structures? Paul Kraft
--- On Tue, 6/17/08, Sanishvili, Ruslan <[EMAIL PROTECTED]> wrote: From: Sanishvili, Ruslan <[EMAIL PROTECTED]> Subject: Re: [ccp4bb] Structural importance of ordered water? To: CCP4BB@JISCMAIL.AC.UK Date: Tuesday, June 17, 2008, 5:16 PM Hi Richard and Colin, There are some "X-ray - visible" water networks described in 0.66 A structure of Aldose Reductase (Proteins. 2004 Jun 1;55(4):792-804) and I'm sure there are plenty of similar descriptions out there. I am not an expert by any means but I think the question of water contribution in protein stability is more complicated. If we look only at the protein and the bound to it water, our impressions may differ from when the rest of the solvent is considered. Surely protein-water system is energetically happier than protein-vacuum but I don't think protein-water is as happy as water-water. What is, for example, the penalty of removing a water molecule from water-water interactions and including it into water-protein networks? Some input from thermodynamics folks would be great here. Cheers, N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT, Bld. 436, D007 Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 [EMAIL PROTECTED] -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Nave, C (Colin) Sent: Tuesday, June 17, 2008 3:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Structural importance of ordered water? Richard Not sure about chains but mutual hydrogen bonded networks (you mention networks) between protein, water (and ligand) surely occur. I think most self respecting waters would try and form more then two hydrogen bonds (rather then just be part of a chain) though one might not see all the (perhaps transient) bonds in an x-ray structure. These networks seem to form very easily in computer simulations where their dynamic behavior can be studied. Lots on "spanning water networks". So waters could link residues a considerable distance away but some of these waters might also join to other residues (the mutual hydrogen bonded network). Of course you are asking about direct x-ray evidence and this is more difficult. Fig. 1 in http://www.lsbu.ac.uk/water/protein.html gives an example. I would hope there are more recent ones which others will identify more easily than I can. Colin -Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Richard Gillilan Sent: 17 June 2008 20:05 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Structural importance of ordered water? Direct hydrogen bonds between sidechains are obviously important to structural stability in proteins. From time to time I see cases of water-mediated bonds in which a single water molecule seems to play an important role (sometimes taking the place of a missing ligand atom in an apo structure, for example). But what about larger chains and networks of water? Assuming a structure is high enough in resolution and well-ordered enough to observe such things, has anyone systematically studied the structural importance of multiple water interactions (I do know of a paper by Faerman and Karplus back in 94, but perhaps there is more recent work). Has anyone here ever seen a plausible argument that a chain of several hydrogen-bonded waters enables residue A to interact with residue B, some considerable distance away? I have to say, I am skeptical of arguments based on water positions. Thanks Richard Gillilan MacCHESS <DIV><FONT size="1" color="gray">This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom </FONT></DIV>
