[ccp4bb] Fw: Re: [ccp4bb] Structural importance of ordered water?
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 DIVFONT size=1 color=grayThis 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
Re: [ccp4bb] Fw: Re: [ccp4bb] Structural importance of ordered water?
On Wed, 18 Jun 2008, Paul Kraft wrote: Are there any reports of the comparison of the number of bound waters in crystal structures vs NMR structures? Paul Kraft this is discussed inter alia in : Mattos, C. Ringe, D., Solvent Structure, in International Tables for Crystallography (Rossman, M. G. Arnold, E., Eds). Kluwer Academic Publishers: Dordrecht p. 623-640 (2001). hth -bryan
Re: [ccp4bb] Structural importance of ordered water?
Title: Re: [ccp4bb] Fw: Re: [ccp4bb] Structural importance of ordered water? Some work has been done on collagen regardingits hydration structure: (crystal data) Bella,J.Brodsky, B. Berman, H.M.. Structure (3), 893-906 1995 (NMR) Peto, S. Gillis, P. Henri, V.P.. Biophys J. (57), 71-84, 1990 (NMR) Renou, J.P. Bonnet, M. Bielicki, G. Rochdi, A. Gatellier, P. Biopolymers (34), 1615-1626, 1994 ### Dr. Paul A. McEwan Protein Crystallography Group Office C58 Centre for Biomolecular Science University of Nottingham Nottingham NG7 2RD UK Tel: 0115 8232018 http://www.nottingham.ac.uk/pharmacy/research/medicinal-chemistry-structural-biology/structbio.php### This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Re: [ccp4bb] Structural importance of ordered water?
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sanishvili, Ruslan Sent: 17 June 2008 22:17 To: Nave, C (Colin); CCP4BB@JISCMAIL.AC.UK Cc: Richard Gillilan Subject: RE: [ccp4bb] Structural importance of ordered water? Surely protein-water system is energetically happier than protein-vacuum but I don't think protein-water is as happy as water-water. Hi, IMHO you can't make such blanket statements without some qualification. The very fact that a protein is soluble in water under given conditions implies that the protein-water interactions created upon dissolution are energetically more favourable (I'm talking about free energy of course) than the protein-protein and water-water interactions that they replace. Similarly, protein-water interactions are no doubt more favourable than a protein-vacuum interface if the protein surface in question contains H-bond donors/acceptors, but this is not true (at least not at normal pressures) if the protein surface is purely non-polar. This was convincingly demonstrated for a T4 lysozyme mutant (http://www.pnas.org/cgi/reprint/102/46/16668.pdf) where water molecules could only be induced (reversibly) to enter a large (160 Ang^3) rigid hydrophobic void in the protein's interior created by the L99A mutation by application of extreme external pressure (200 Mpascals, or 2000 x atmospheric pressure). Cheers -- Ian Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
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 DIVFONT size=1 color=grayThis 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
Re: [ccp4bb] Structural importance of ordered water?
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 DIVFONT size=1 color=grayThis 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
Re: [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). Actin gives an example of such. It has two large domains with a metal-nucleotide binding cleft between them. Without the metal-nucleotide the protein is unstable and slowly and irreversibly denatures. When a water network coming out from the Me-nucleotide is analysed (I did it manually), the reason becomes very clear - secondary and tertiary hydration shells provide a web of interactions that ultimately join the two large domains, thus, presumably, providing the stability. Dima
