PDBsum entry 2mef

Hydrolase

PDB id: 2mef

Contents

Protein chain

130 a.a.

Metals

_NA

Waters ×230

References listed in PDB file

Key reference

Title

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

Authors

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

Ref.

Protein Eng, 1999, 12, 841-850.

PubMed id

10556244

Note: In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above have been manually determined.

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 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.

Secondary reference #1

Title

Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-Ray analysis of six tyrosine --≫ phenylalanine mutants.

Authors

Y.Yamagata, M.Kubota, Y.Sumikawa, J.Funahashi, K.Takano, S.Fujii, K.Yutani.

Ref.

Biochemistry, 1998, 37, 9355-9362. [DOI no: 10.1021/bi980431i]

PubMed id

9649316

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 90%.

Secondary reference #2

Title

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.

Authors

K.Takano, Y.Yamagata, S.Fujii, K.Yutani.

Ref.

Biochemistry, 1997, 36, 688-698. [DOI no: 10.1021/bi9621829]

PubMed id

9020766

Secondary reference #3

Title

Contribution of water molecules in the interior of a protein to the conformational stability.

Authors

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

Ref.

J Mol Biol, 1997, 274, 132-142. [DOI no: 10.1006/jmbi.1997.1365]

PubMed id

9398521

Figure 2.
Figure 2. Structures in the vicinity of the residue 56 in the wild-type (a) and I56A (b) to (d), and those of the residue 59 in the wild-type (e) and I59A (f). In (c) and (d), dummy water molecules, which were estimated to be energetically favorable using the program, X-PLOR [Brunger 1992], are drawn. The dummy water molecules in (c) and (d) made hydrogen bonds with O^γ of Ser36 and an internal water molecule, respectively. The side-chain atoms of the residues 56 and 59, carbon atoms, oxygen and nitrogen atoms, interior water molecules, introduced water molecules and the dummy water molecules are represented by green, yellow, orange, blue, dark blue and purple, respectively.

Figure 3.
Figure 3. Correlation of ΔΔASA[HP] (changes in hydrophobic surface area exposed upon denaturation) with ΔΔG for the mutant proteins with empty cavities (a) and with solvated cavities (b). The mutants with solvated cavities are shown as open symbols and labeled. The mutants of the type I are represented by black filled up-triangles (with empty cavity). The black continuous line shows the linear regression of the type I mutants with empty cavity (black filled up-triangles). The mutants of the type II are represented by blue filled (with empty cavity) and open (with solvated cavity) circles. The blue broken line shows the linear regression of the type II mutants with solvated cavity (blue open circles). The mutants of the type III are represented by red filled (with empty cavity) and open (with solvated cavity) squares. The red continuous line shows the linear regression of the type III mutants with empty cavity (red filled squares). The red broken line is drawn with reference to the red continuous line. The ASA values were calculated using the procedure of [Connolly 1993].

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #4

Title

The structure, Stability, And folding process of amyloidogenic mutant human lysozyme.

Authors

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

Ref.

J Biochem (tokyo), 1996, 120, 1216-1223.

PubMed id

9010773

Secondary reference #5

Title

Contribution of hydrophobic residues to the stability of human lysozyme: calorimetric studies and X-Ray structural analysis of the five isoleucine to valine mutants.

Authors

K.Takano, K.Ogasahara, H.Kaneda, Y.Yamagata, S.Fujii, E.Kanaya, M.Kikuchi, M.Oobatake, K.Yutani.

Ref.

J Mol Biol, 1995, 254, 62-76. [DOI no: 10.1006/jmbi.1995.0599]

PubMed id

7473760

Figure 2.
Figure 2. Typical excess heat capacity curves of the mutant human lysozyme (I106V) at pH 2.70 (a), 2.92 (b), 3.04 (c), 3.10 (d), and 3.14 (e). The increments of excess heat capacity were 10 kJ/mol K.

Figure 5.
Figure 5. Stereo drawings (Johnson, 1976) showing the mutant structure in the vicinity of the mutation sites. The wild-type (open bonds) and mutant structures (filled bonds) are superimposed. (a) I23V; (b) I56V; (c) I59V; (d) I89V; and (e) I106V. Solvent water molecules are drawn as cross-circles. Broken lines indicate hydrogen bonds.

The above figures are reproduced from the cited reference with permission from Elsevier