PMID- 22752989
OWN - NLM
STAT- MEDLINE
DCOM- 20130305
LR  - 20211021
IS  - 1097-0134 (Electronic)
IS  - 0887-3585 (Print)
IS  - 0887-3585 (Linking)
VI  - 80
IP  - 11
DP  - 2012 Nov
TI  - Crystal packing modifies ligand binding affinity: the case of aldose reductase.
PG  - 2552-61
LID - 10.1002/prot.24136 [doi]
AB  - The relationship between the structures of protein-ligand complexes existing in 
      the crystal and in solution, essential in the case of fragment-based screening by 
      X-ray crystallography (FBS-X), has been often an object of controversy. To 
      address this question, simultaneous co-crystallization and soaking of two 
      inhibitors with different ratios, Fidarestat (FID; K(d) = 6.5 nM) and IDD594 
      (594; K(d) = 61 nM), which bind to h-aldose reductase (AR), have been performed. 
      The subatomic resolution of the crystal structures allows the differentiation of 
      both inhibitors, even when the structures are almost superposed. We have 
      determined the occupation ratio in solution by mass spectrometry (MS) 
      Occ(FID)/Occ(594) = 2.7 and by X-ray crystallography Occ(FID)/Occ(594) = 0.6. The 
      occupancies in the crystal and in solution differ 4.6 times, implying that ligand 
      binding potency is influenced by crystal contacts. A structural analysis shows 
      that the Loop A (residues 122-130), which is exposed to the solvent, is flexible 
      in solution, and is involved in packing contacts within the crystal. Furthermore, 
      inhibitor 594 contacts the base of Loop A, stabilizing it, while inhibitor FID 
      does not. This is shown by the difference in B-factors of the Loop A between the 
      AR-594 and AR-FID complexes. A stable loop diminishes the entropic energy barrier 
      to binding, favoring 594 versus FID. Therefore, the effect of the crystal 
      environment should be taken into consideration in the X-ray diffraction analysis 
      of ligand binding to proteins. This conclusion highlights the need for additional 
      methodologies in the case of FBS-X to validate this powerful screening technique, 
      which is widely used.
CI  - Copyright (c) 2012 Wiley Periodicals, Inc.
FAU - Cousido-Siah, Alexandra
AU  - Cousido-Siah A
AD  - Department of Integrative Biology, IGBMC, CNRS, INSERM, Universite de Strasbourg, 
      Illkirch, France.
FAU - Petrova, Tatiana
AU  - Petrova T
FAU - Hazemann, Isabelle
AU  - Hazemann I
FAU - Mitschler, Andre
AU  - Mitschler A
FAU - Ruiz, Francesc X
AU  - Ruiz FX
FAU - Howard, Eduardo
AU  - Howard E
FAU - Ginell, Stephan
AU  - Ginell S
FAU - Atmanene, Cedric
AU  - Atmanene C
FAU - Van Dorsselaer, Alain
AU  - Van Dorsselaer A
FAU - Sanglier-Cianferani, Sarah
AU  - Sanglier-Cianferani S
FAU - Joachimiak, Andrzej
AU  - Joachimiak A
FAU - Podjarny, Alberto
AU  - Podjarny A
LA  - eng
GR  - U54 GM094585/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20120728
PL  - United States
TA  - Proteins
JT  - Proteins
JID - 8700181
RN  - 0 (Enzyme Inhibitors)
RN  - 0 (Ligands)
RN  - EC 1.1.1.21 (Aldehyde Reductase)
SB  - IM
MH  - Aldehyde Reductase/antagonists & inhibitors/*chemistry/*metabolism
MH  - Binding Sites
MH  - Crystallography, X-Ray
MH  - Enzyme Inhibitors/chemistry/metabolism
MH  - Humans
MH  - Ligands
MH  - Models, Molecular
MH  - Protein Binding
PMC - PMC4671318
MID - NIHMS738275
EDAT- 2012/07/04 06:00
MHDA- 2013/03/06 06:00
PMCR- 2015/12/07
CRDT- 2012/07/04 06:00
PHST- 2012/04/16 00:00 [received]
PHST- 2012/06/05 00:00 [revised]
PHST- 2012/06/13 00:00 [accepted]
PHST- 2012/07/04 06:00 [entrez]
PHST- 2012/07/04 06:00 [pubmed]
PHST- 2013/03/06 06:00 [medline]
PHST- 2015/12/07 00:00 [pmc-release]
AID - 10.1002/prot.24136 [doi]
PST - ppublish
SO  - Proteins. 2012 Nov;80(11):2552-61. doi: 10.1002/prot.24136. Epub 2012 Jul 28.