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PDBsum entry 1ip4
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References listed in PDB file
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Key reference
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Title
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Role of amino acid residues in left-Handed helical conformation for the conformational stability of a protein.
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Authors
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K.Takano,
Y.Yamagata,
K.Yutani.
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Ref.
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Proteins, 2001,
45,
274-280.
[DOI no: ]
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PubMed id
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Abstract
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Our previous study of six non-Gly to Gly/Ala mutant human lysozymes in a
left-handed helical region showed that only one non-Gly residue at a rigid site
had unfavorable strain energy as compared with Gly at the same position (Takano
et al., Proteins 2001; 44:233-243). To further examine the role of left-handed
residues in the conformational stability of a protein, we constructed ten Gly to
Ala mutant human lysozymes. Most Gly residues in human lysozyme are located in
the left-handed helix region. The thermodynamic parameters for denaturation and
crystal structures were determined by differential scanning calorimetry and
X-ray analysis, respectively. The difference in denaturation Gibbs energy
(DeltaDeltaG) for the ten Gly to Ala mutants ranged from + 1.9 to -7.5 kJ/mol,
indicating that the effect of the mutation depends on the environment of the
residue. We confirm that Gly in a left-handed region is more favorable at rigid
sites than non-Gly, but there is little difference in energetic cost between Gly
and non-Gly at flexible sites. The present results indicate that dihedral angles
in the backbone conformation and also the flexibility at the position should be
considered for analyses of protein stability, and protein structural
determination, prediction, and design.
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Figure 2.
Figure 2. Stereodrawings of the structures in the vicinity of
the mutation sites for (a) G37A, (b) G48A, (c) G68A, (d) G72A,
(e) G105A, (f) G127A, and (g) G129A of human lysozymes. The
wild-type and mutant structures are superimposed.
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Figure 3.
Figure 3. Ramachandran plot[1] of the Gly residues in the
wild-type human lysozyme structure (open squares), and each Ala
residue in the mutant structure (closed squares).
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2001,
45,
274-280)
copyright 2001.
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Secondary reference #1
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Title
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Role of non-Glycine residues in left-Handed helical conformation for the conformational stability of human lysozyme.
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Authors
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K.Takano,
Y.Yamagata,
K.Yutani.
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Ref.
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Proteins, 2001,
44,
233-243.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. Stereodrawings of the structures in the vicinity of
the mutation sites for (a) Q58G, Q58A, and wild-type; (b) H78G,
H78A, and wild-type; and (c) N118G, N118A, and wild-type human
lysozymes. Wild-type and mutant structures are superimposed.
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Figure 5.
Figure 5. Structures in the vicinity of mutation sites for
position 21 (a) wild-type, (b) R21G, and (c) R21A human
lysozymes. Thin lines and filled circles represent hydrogen
bonds and water molecules, respectively.
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The above figures are
reproduced from the cited reference
with permission from John Wiley & Sons, Inc.
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