Dear Rasmus, Thankyou for your very useful summary of NMR being “more complex than flexibility”. The complementary roles of NMR and crystallography are important and I very recently provided a resume in section 2.3 of my Acta Cryst A article https://journals.iucr.org/a/issues/2021/03/00/ae5100/index.html which I imagine will be of keen interest. The IUCr has established a Commission on NMR Crystallography and Related Methods:- https://www.iucr.org/iucr/commissions/nmr-crystallography Best wishes, John
Emeritus Professor John R Helliwell DSc > On 27 May 2021, at 10:35, Rasmus Fogh <rhf...@globalphasing.com> wrote: > > Dear Dale, > > It is more complex than just 'flexibility', but then it is always more > complicated. Here are the main possibilities for undetermined regions: > > -1- fast, free movement - signals are easy to see, have 'random-coil' > chemical shifts, often overlap, and there are no NOEs > -2- intermediate-range exchange between several different conformations, > free/bound etc. Signals are broadened and harder to observe, NOEs even more > so. > -3- The molecule is too big and slow-moving - you might be able to observe a > domain linked by a flexible linker to a huge and invisible protein (or virus, > ...) > -4- Proximity to lanthanides or other kinds of unpaired electrons. > -5- Missing observations, due to overlapped signals combined with barely > adequate S/N ratio. > > Arguably 1) and 2) are both movement, just in different time scales - 1) can > be identified from relaxation measurements and/or chemical shifts, which > should be pretty routine. > 3) and 4) you would know about. > 5) you could check by looking at, essentially, completeness. > > Yours, > Rasmus > >> On 26/05/2021 22:06, Dale Tronrud wrote: >> Dear Boaz, >> We are likely in agreement. "Deficient NOE's for some regions (e.g. loops) >> arise from their flexibility, ..." This makes it sound like you agree that >> these deficiencies in other regions may be caused by properties other than >> flexibility. >> As an extreme example, the N-terminal region of a protein may have a broad >> distribution in the ensemble model either because this region experiences >> many conformations in solution, or because this peptide was cleaved from the >> protein at some earlier time and its absence was not recognized by the >> experimentalist. >> Dale Tronrud >>> On 5/26/2021 1:06 PM, Boaz Shaanan wrote: >>> Hi Dale and Cecil, >>> >>> This is quite a circular argument, isn't it? Deficient NOE's for some >>> regions (e.g. loops) arise from their flexibility, hence they are not as >>> well resolved as other (e.g. internal ) regions for which the number of NOE >>> is large. So they are flexible by all accounts and, not surprisingly, align >>> usually with high B-factor regions in the corresponding crystal structures. >>> In cases where such flexible regions are held by crystal contacts the >>> situations would likely be different. >>> >>> 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 >>> Fax: 972-8-647-2992 or 972-8-646-1710 / >>> // >>> // >>> / >>> >>> / >>> ------------------------------------------------------------------------ >>> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Dale >>> Tronrud <de...@daletronrud.com> >>> *Sent:* Wednesday, May 26, 2021 10:46 PM >>> *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >>> *Subject:* Re: [ccp4bb] Analysis of NMR ensembles >>> I agree with Dr Breyton. The variability in an NMR ensemble does not >>> reflect "mobility" but simply "uncertainty" in conformation. The spread >>> in coordinates in some regions simply reflects the lack of experimental >>> data which could define a single conformation. There are many reasons >>> why these data are be absent and high mobility is only one. >>> >>> Dale Tronrud >>> >>> On 5/26/2021 8:45 AM, Cécile Breyton wrote: >>>> Hello, >>>> >>>> In my understanding of NMR, the loops and terminii that adopt very >>>> different conformations in the structure ensemble rather reflect the fact >>>> that for those residues, the number of constraints is lower, thus the >>>> number of structures that fulfil the constraints is larger.... A dynamics >>>> study of the protein will be much more informative. >>>> >>>> Cécile >>>> >>>> Le 26/05/2021 à 17:29, S. Mohanty a écrit : >>>>> Hi Harry, >>>>> >>>>> The superpose/overlay of all the structures in PyMol should inform you >>>>> the rigid part of the protein as well as the flexible part. The rigid >>>>> part would have very low backbone RMSD or overlay tightly and the >>>>> flexible part (loops, N-term and C-term etc.) would not superpose >>>>> tightly. If you check literature, the dynamics of the protein may have >>>>> been studied through NMR relaxation. >>>>> >>>>> Smita >>>>> >>>>> >>>>> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB >>>>> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >>>>> >>>>> >>>>> Hi >>>>> >>>>> Given that there are plenty of people on this BB who are structural >>>>> biologists rather than “just” crystallographers, I thought someone here >>>>> might be able to help. >>>>> >>>>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >>>>> structures that fit the NOEs, is there a tool available that will give me >>>>> some idea about the bits of the structure that do not vary much (“rigid”) >>>>> and the bits that are all over the place (“flexible”)? >>>>> >>>>> Would superpose or gesamt be a good tool for this? Ideally I’d like >>>>> something that could add a figure to the B columns in a PDB file so I >>>>> could see something in QTMG (or PyMol if forced…) or do otheruseful >>>>> things with the information. >>>>> >>>>> Harry >>>>> >>>>> ######################################################################## >>>>> >>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <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 >>>>> <http://www.jiscmail.ac.uk/CCP4BB>, a >>>>> mailing list hosted by www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, >>>>> terms & conditions are >>>>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >>> <https://www.jiscmail.ac.uk/policyandsecurity/> >>>>> <https://www.jiscmail.ac.uk/policyandsecurity/ >>> <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 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 >>> <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 >>> <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by >>> www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, terms & conditions are >>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >>> <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/ > > -- > Rasmus H. Fogh Tel.: +44 (0)1223 353033 > Global Phasing Ltd., Fax.: +44 (0)1223 366889 > Sheraton House, > Castle Park, > Cambridge CB3 0AX > United Kingdom > > ######################################################################## > > 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/
