2MEI

CONTRIBUTION OF HYDROPHOBIC EFFECT TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Contribution of amino acid substitutions at two different interior positions to the conformational stability of human lysozyme

Funahashi, J.Takano, K.Yamagata, Y.Yutani, K.

(1999) Protein Eng 12: 841-850

  • DOI: 10.1093/protein/12.10.841
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • To elucidate correlative relationships between structural change and thermodynamic stability in proteins, a series of mutant human lysozymes modified at two buried positions (Ile56 and Ile59) were examined. Their thermodynamic parameters of denaturat ...

    To elucidate correlative relationships between structural change and thermodynamic stability in proteins, a series of mutant human lysozymes modified at two buried positions (Ile56 and Ile59) were examined. Their thermodynamic parameters of denaturation and crystal structures were studied by calorimetry and X-ray crystallography. The mutants at positions 56 and 59 exhibited different responses to a series of amino acid substitutions. The changes in stability due to substitutions showed a linear correlation with changes in hydrophobicity of substituted residues, having different slopes at each mutation site. However, the stability of each mutant was found to be represented by a unique equation involving physical properties calculated from mutant structures. By fitting present and previous stability data for mutant human lysozymes substituted at various positions to the equation, the magnitudes of the hydrophobicity of a carbon atom and the hydrophobicity of nitrogen and neutral oxygen atoms were found to be 0.178 and -0.013 kJ/mol.A(2), respectively. It was also found that the contribution of a hydrogen bond with a length of 3.0 A to protein stability was 5.1 kJ/mol and the entropy loss of newly introduction of a water molecules was 7.8 kJ/mol.


    Related Citations: 
    • Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme: Calorimetry and X-Ray Analysis of Six Tyr-->Phe Mutants
      Yamagata, Y., Kubota, M., Sumikawa, Y., Funahashi, J., Takano, K., Fujii, S., Yutani, K.
      () To be published --: --
    • Contribution of the Hydrophobic Effect to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analyses of the Nine Valine to Alanine Mutants
      Takano, K., Yamagata, Y., Fujii, S., Yutani, K.
      (1997) Biochemistry 36: 688
    • Contribution of Water Molecules in the Interior of a Protein to the Conformational Stability
      Takano, K., Funahashi, J., Yamagata, Y., Fujii, S., Yutani, K.
      (1997) J Mol Biol 274: 132
    • The Structure, Stability, and Folding Process of Amyloidogenic Mutant Human Lysozyme
      Funahashi, J., Takano, K., Ogasahara, K., Yamagata, Y., Yutani, K.
      (1996) J Biochem 120: 1216
    • Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants
      Takano, K., Ogasahara, K., Kaneda, H., Yamagata, Y., Fujii, S., Kanaya, E., Kikuchi, M., Oobatake, M., Yutani, K.
      (1995) J Mol Biol 254: 62

    Organizational Affiliation

    Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
A
130Homo sapiensMutation(s): 1 
Gene Names: LYZLZM
EC: 3.2.1.17
Find proteins for P61626 (Homo sapiens)
Go to UniProtKB:  P61626
NIH Common Fund Data Resources
PHAROS  P61626
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.13α = 90
b = 61.23β = 90
c = 33.57γ = 90
Software Package:
Software NamePurpose
PROCESSdata collection
PROCESSdata reduction
X-PLORmodel building
X-PLORrefinement
PROCESSdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-07-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance