---------- Forwarded message --------- From: Arpita Goswami <bt.arp...@gmail.com> Date: Sun, Sep 8, 2024, 03:11 Subject: Re: [ccp4bb] Studying hydrogen bonding network by neutron diffraction in sample with D2O To: John R Helliwell <jrhelliw...@gmail.com>
Dear Dr. John and others, Good day! Thank you all for the clarifications, corrections and discussions! I suppose since the kinetics is slower, protein interactions with water like hydration, ligands which bind through water networks etc should be slower! The paper also mentions a case of a missing water in the active site of a perdeuterated enzyme from another study! But overall the final structure should be the same so no problem in using D2O for these studies! Our protein is not perdeuterated, only enriched with D2O during crystallization! So hopefully if it diffracts, not much changes will be observed! Thank you all! Best regards, Arpita On Fri, Sep 6, 2024 at 11:53 PM John R Helliwell <jrhelliw...@gmail.com> wrote: > Dear Tim, and Arpita and Doeke, > Basically structure is not affected (as evidenced by our Fisher and > Helliwell database survey in Acta Cryst) but kinetics is affected ie > everything is slower in D2O and can thereby be toxic. > Greetings > John > Emeritus Professor John R Helliwell DSc > > > On 6 Sep 2024, at 16:02, Tim Grüne <tim.gru...@univie.ac.at> wrote: > > > > Hi Doeke, > > if I remember correctly, D2O is poisonous and bacteria grow with reduced > growth rate. > > The effect of the greater mass may not be totally insignificant. > > Best, > > Tim > > Am 06.09.2024 15:25, schrieb Hekstra, Doeke Romke: > >> Hi Arpita, > >> H and D have the same number of electrons (1). The D nucleus has an > >> extra neutron, changing its mass and therefore its vibrational energy > >> levels. That can affect hydrogen bonding patterns, although I would > >> expect the effect to be relatively minor (see e.g. Fisher and > >> Helliwell, Acta Cryst A A64: 359-367 (2008)). > >> Best, Doeke > >> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Arpita > >> Goswami > >> Sent: Thursday, September 5, 2024 11:12 PM > >> To: CCP4BB@JISCMAIL.AC.UK > >> Subject: [ccp4bb] Studying hydrogen bonding network by neutron > >> diffraction in sample with D2O > >> Dear all, > >> Good morning, Sorry for the off-topic question. > >> There is a protein crystal sample in which water bonding networks by > >> certain species to be studied by neutron diffraction, not exactly > >> within the protein. But between the subunits of the protein. Now it is > >> mandatory to use some D2O for the preparation of samples. Now my > >> question is will there be drastic differences between the hydration > >> patterns of this sample and original sample without D2O? For example, > >> some change in positions and interacting partners of the hydrated > >> species of interest with respect to the protein surface? Since > >> deuterium has 2 electrons instead of one as in protium? > >> We know D2O is regularly used for such experiments in Neutron > >> diffraction and in NMR as well. Please let me know your expert > >> opinions. > >> Thank you. > >> Best Regards, > >> Arpita > >> ------------------------- > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 [1] > >> ------------------------- > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > >> Links: > >> ------ > >> [1] > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMKOIsdAAHocfxcg&m=l-WnMj1_g2JW-6G31zEb7Kda6UHqQeExjhYiqsRkkE-f0TGFAKf71pWTr4HpWuuw&s=kfsGmxIcTXtuSeUtJFc_5SEg7Gg92Oq2Nw353lcNiqI&e= > > > > -- > > -- > > Tim Gruene > > Head of the Centre for X-ray Structure Analysis > > Faculty of Chemistry > > University of Vienna > > > > Phone: +43-1-4277-70202 > > > > GPG Key ID = A46BEE1A > > > > ######################################################################## > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
