[ccp4bb] CCPBioSim Industry Talk - 10 July

[Sarah Fegan - STFC UKRI]

Dear all,



Registration is now open for our next industry talk on 10 July 2024 at 2pm UK 
time. The talk by Steve Maginn, Chemical Computing Group / Molecular Graphics 
and Modelling Society, has the title "At the Interface of Academia and Industry 
for 35 Years... (aka - "You get less time for murder!")". Details and the free 
registration link can be found at https://www.ccpbiosim.ac.uk/chemcompgroup2024.



Abstract: I graduated with a PhD in chemistry from the University of Liverpool 
in 1989 and went straight into a research job in industry in a company that was 
then an international household name, ICI. At that time, such a role was 
considered something akin to a "job for life" - but things very soon changed. 
During the last 35 years I have spent my career working in science at the 
border between industry and academia, in a variety of both formal and informal 
roles, initially in research but moving gradually towards more commercial and 
organisational tasks in which my scientific background proved to be a strong 
asset. During this presentation, I will describe those roles and the reasoning 
behind the decisions that led to my taking them on, highlighting what I 
believe, despite ever-changing economic conditions and pressures, are the keys 
to a successful career in science; adaptability and networking.



Best wishes,

Sarah



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/

[ccp4bb] cc minor off topic protein symmetry

[Andrew Lovering]

Many thanks to Mark van Raaij for a super example - 5EFV - clear heterogeneity 
at the hinge/kink; although this then doesn't return to the 1st axis

Its interesting to contemplate proteins doing this several times in a 
physiologically "real" way (the models I'm looking at do this) - they need gly 
rich regions, much like the "crossover" in the above example.

If you have a trimeric fibre with trimeric lobes on the side, evolution has two 
choices:

  1.  Keep all chains on a common axis, make the fibre from 3 chains and the 
lobes from 3 sequential repeats on the same chain
  2.  Make all three chains make the fibre and the lobes, each contributing a 
third to any structural element

The question I posed is to do with models that clearly use choice 2...which is 
toplogically difficult - do they "choose" this to avoid sequence repeats in a 
protein?

Happy to hear more examples if you have them!

Thanks
Andy



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/

Re: [ccp4bb] Good electron density but poor affinity

[Tanner, John]

The refined crystallographic occupancy (sort of a measure of electron density 
quality) has been related to the ligand binding constant. In this study, they 
determined several structures of a protein with different concentrations of the 
ligand. The binding constant was estimated from a plot of the refined Q versus 
ligand concentration.

https://pubmed.ncbi.nlm.nih.gov/11180378/


--
John J. Tanner
Professor of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S. College Avenue
Columbia, MO 65211
573-884-1280
tanne...@missouri.edu



From: CCP4 bulletin board  on behalf of Armando Albert 

Date: Thursday, June 27, 2024 at 7:52 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Good electron density but poor affinity
WARNING: This message has originated from an External Source. This may be a 
phishing expedition that can result in unauthorized access to our IT System. 
Please use proper judgment and caution when opening attachments, clicking 
links, or responding to this email.

Dear all,
Is there any study that analyzes the relationship between the quality of the 
electron density of a ligand and its affinity?
Armando


To unsubscribe from the CCP4BB list, click the following link:
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C02%7Ctannerjj%40MISSOURI.EDU%7C116bb6bcfe0a4c65908f08dc96a7f90e%7Ce3fefdbef7e9401ba51a355e01b05a89%7C0%7C0%7C638550895386995181%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=40LiTIcLFMFMcr1%2BnWneX7XqkRBq9VQxPVnRstmb3j8%3D=0

This message was issued to members of 
https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB=05%7C02%7Ctannerjj%40MISSOURI.EDU%7C116bb6bcfe0a4c65908f08dc96a7f90e%7Ce3fefdbef7e9401ba51a355e01b05a89%7C0%7C0%7C638550895387005481%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=MYp6f%2BkNY94aQoVl9nA1iEdSqTJVMznCwnF52rasOzY%3D=0,
 a mailing list hosted by 
https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F=05%7C02%7Ctannerjj%40MISSOURI.EDU%7C116bb6bcfe0a4c65908f08dc96a7f90e%7Ce3fefdbef7e9401ba51a355e01b05a89%7C0%7C0%7C638550895387010701%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=tIeETg5Ck%2FLe3ehcnPegYBcK%2FpFuta6jyf%2FIhNQXRF4%3D=0,
 terms & conditions are available at 
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F=05%7C02%7Ctannerjj%40MISSOURI.EDU%7C116bb6bcfe0a4c65908f08dc96a7f90e%7Ce3fefdbef7e9401ba51a355e01b05a89%7C0%7C0%7C638550895387015629%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=qvn%2FOWizWl1SJ9Xw0R81L26G9fUYQYNWvKIvwcIB0oU%3D=0



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/

[ccp4bb] cc - minor off topic protein symmetry

[Andrew Lovering]

(I should note that my use of symmetry is used on the protein level rather on 
the absolute crystallographic equivalence level - imagine this trimer sat 
within a P1 cell, and that minor wobbles generate pseudosymmetry in places 
anyway - what I'm interested in is the topology of the chain at the junctions 
between two rough axes)



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/

[ccp4bb] Good electron density but poor affinity

[Armando Albert]

Dear all, 
Is there any study that analyzes the relationship between the quality of the 
electron density of a ligand and its affinity?
Armando


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/

[ccp4bb] minor off topic protein symmetry

[Andrew Lovering]

Dear wise list,

I have a question regarding protein oligomers that have multiple, differing 
axes of symmetry - stimulated by some perplexing but likely real Alphafold 
models.

I think it's the protein equivalent of this old chestnut: 
https://en.wikipedia.org/wiki/Three_utilities_problem

Consider a trimeric fibre (perhaps collagen a good starting example) - it can 
have global 3-fold symmetry, and if it breaks from this, it is then able to 
"re-obey" this symmetry later on, but that axis is approximately the same as 
the starting one. I.e. a long winding rope with a kink in the middle, and the 
protein doesn't have to do much to accommodate this.

What happens when a long protein has multiple, dissimilar axes of symmetry? 
I.e. perhaps a trimer with the start and end on the same axis, but the middle 
domain sits ~90 degrees to this (and is also a 3-fold arrangement of chains A,B 
& C). I think I'd be correct in assuming that all 3 chains cannot have the same 
conformation - is this true?
I'd argue that the protein has to unwind a little at the junctions and each 
chain takes a different path in space when migrating from axis 1> axis 2> back 
to axis 1? (think of 1 as up/down, 2 as left/right). This is because as each 
chain leaves the centre of mass of axis 1, it is a different distance away from 
the centre of mass of axis 2?

I hope that makes some sense!

So my question is, does anyone have an example PDB that does something similar, 
and were they able to trace the different chains, demonstrating the different 
conformations.

Thanks in advance - Andy



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/