2MEI

CONTRIBUTION OF HYDROPHOBIC EFFECT TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.158 

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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

  • Primary Citation of Related Structures:  

  • 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 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 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 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.(Tokyo) 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: LYZ (LZM)
EC: 3.2.1.17
Find proteins for P61626 (Homo sapiens)
Go to Gene View: LYZ
Go to UniProtKB:  P61626
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.130α = 90.00
b = 61.230β = 90.00
c = 33.570γ = 90.00
Software Package:
Software NamePurpose
PROCESSdata reduction
X-PLORphasing
PROCESSdata scaling
PROCESSdata collection
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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