4NWH

Lysozyme UNDER 30 BAR PRESSURE OF XENON


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystallographic Studies with Xenon and Nitrous Oxide Provide Evidence for Protein-dependent Processes in the Mechanisms of General Anesthesia

Abraini, J.H.Marassio, G.David, H.N.Vallone, B.Prange, T.Colloc'h, N.

(2014) Anesthesiology 121: 1018-1027

  • DOI: https://doi.org/10.1097/ALN.0000000000000435
  • Primary Citation of Related Structures:  
    4NWE, 4NWH, 4NXA, 4NXC, 4O4T, 4O4Z

  • PubMed Abstract: 

    The mechanisms by which general anesthetics, including xenon and nitrous oxide, act are only beginning to be discovered. However, structural approaches revealed weak but specific protein-gas interactions. To improve knowledge, we performed x-ray crystallography studies under xenon and nitrous oxide pressure in a series of 10 binding sites within four proteins. Whatever the pressure, we show (1) hydrophobicity of the gas binding sites has a screening effect on xenon and nitrous oxide binding, with a threshold value of 83% beyond which and below which xenon and nitrous oxide, respectively, binds to their sites preferentially compared to each other; (2) xenon and nitrous oxide occupancies are significantly correlated respectively to the product and the ratio of hydrophobicity by volume, indicating that hydrophobicity and volume are binding parameters that complement and oppose each other's effects; and (3) the ratio of occupancy of xenon to nitrous oxide is significantly correlated to hydrophobicity of their binding sites. These data demonstrate that xenon and nitrous oxide obey different binding mechanisms, a finding that argues against all unitary hypotheses of narcosis and anesthesia, and indicate that the Meyer-Overton rule of a high correlation between anesthetic potency and solubility in lipids of general anesthetics is often overinterpreted. This study provides evidence that the mechanisms of gas binding to proteins and therefore of general anesthesia should be considered as the result of a fully reversible interaction between a drug ligand and a receptor as this occurs in classical pharmacology.


  • Organizational Affiliation

    From the Faculté de Médecine, Université de Caen Basse Normandie, Normandie-Université, Caen, France (J.H.A., G.M.); Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France (J.H.A.); Département d'Anesthésiologie, Université Laval, Quebec City, Québec, Canada (J.H.A., H.N.D.); Centre de Recherche Hôtel-Dieu de Lévis, CSSS Alphonse-Desjardins, Lévis, Québec, Canada (H.N.D.); Department of Biochemical Sciences, University of Rome La Sapienza, Rome, Italy (B.V.); LCRB UMR 8015, Université Paris Descartes-CNRS, Faculté de Pharmacie, Paris, France (T.P.); ISTCT UMR 6301, CNRS, CERVOxy group, GIP Cyceron, Caen, France (N.C.); ISTCT UMR 6301, Université de Caen Basse Normandie, Normandie-Université, Caen, France (N.C.); and ISTCT UMR 6301, CEA DSV/I2BM, Caen, France (N.C.).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.306α = 90
b = 79.306β = 90
c = 38.072γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary