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PDBsum entry 1b7l
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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.1.17
- lysozyme.
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Reaction:
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Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
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Protein Eng
12:663-672
(1999)
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PubMed id:
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Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes.
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K.Takano,
M.Ota,
K.Ogasahara,
Y.Yamagata,
K.Nishikawa,
K.Yutani.
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ABSTRACT
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The stability profile of mutant protein (SPMP) (Ota,M., Kanaya,S. and
Nishikawa,K., 1995, J. Mol. Biol., 248, 733-738) estimates the changes in
conformational stability due to single amino acid substitutions using a
pseudo-energy potential developed for evaluating structure-sequence
compatibility in the structure prediction method, the 3D-1D compatibility
evaluation. Nine mutant human lysozymes expected to significantly increase in
stability from SPMP were constructed, in order to experimentally verify the
reliability of SPMP. The thermodynamic parameters for denaturation and crystal
structures of these mutant proteins were determined. One mutant protein was
stabilized as expected, compared with the wild-type protein. However, the others
were not stabilized even though the structural changes were subtle, indicating
that SPMP overestimates the increase in stability or underestimates negative
effects due to substitution. The stability changes in the other mutant human
lysozymes previously reported were also analyzed by SPMP. The correlation of the
stability changes between the experiment and prediction depended on the types of
substitution: there were some correlations for proline mutants and
cavity-creating mutants, but no correlation for mutants related to side-chain
hydrogen bonds. The present results may indicate some additional factors that
should be considered in the calculation of SPMP, suggesting that SPMP can be
refined further.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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L.Fernández,
J.Caballero,
J.I.Abreu,
and
M.Fernández
(2007).
Amino acid sequence autocorrelation vectors and Bayesian-regularized genetic neural networks for modeling protein conformational stability: gene V protein mutants.
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Proteins,
67,
834-852.
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A.Mozo-Villarías,
J.Cedano,
and
E.Querol
(2006).
Hydrophobicity density profiles to predict thermal stability enhancement in proteins.
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Protein J,
25,
529-535.
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J.Cheng,
A.Randall,
and
P.Baldi
(2006).
Prediction of protein stability changes for single-site mutations using support vector machines.
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Proteins,
62,
1125-1132.
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K.Saraboji,
M.M.Gromiha,
and
M.N.Ponnuswamy
(2006).
Average assignment method for predicting the stability of protein mutants.
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Biopolymers,
82,
80-92.
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Y.Hioki,
K.Ogasahara,
S.J.Lee,
J.Ma,
M.Ishida,
Y.Yamagata,
Y.Matsuura,
M.Ota,
M.Ikeguchi,
S.Kuramitsu,
and
K.Yutani
(2004).
The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors.
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Eur J Biochem,
271,
2624-2635.
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PDB code:
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H.Minagawa,
J.Shimada,
and
H.Kaneko
(2003).
Effect of mutations at Glu160 and Val198 on the thermostability of lactate oxidase.
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Eur J Biochem,
270,
3628-3633.
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A.L.Lomize,
M.Y.Reibarkh,
and
I.D.Pogozheva
(2002).
Interatomic potentials and solvation parameters from protein engineering data for buried residues.
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Protein Sci,
11,
1984-2000.
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J.Higo,
and
M.Nakasako
(2002).
Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites, solvent density, and solvent dipole.
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J Comput Chem,
23,
1323-1336.
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PDB code:
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K.Takano,
Y.Yamagata,
and
K.Yutani
(2001).
Role of non-glycine residues in left-handed helical conformation for the conformational stability of human lysozyme.
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Proteins,
44,
233-243.
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PDB codes:
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K.Takano,
Y.Yamagata,
and
K.Yutani
(2001).
Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein.
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Proteins,
45,
274-280.
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PDB codes:
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M.Joniau,
P.Haezebrouck,
K.Noyelle,
and
H.Van Dael
(2001).
Structural basis for the appearance of a molten globule state in chimeric molecules derived from lysozyme and alpha-lactalbumin.
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Proteins,
44,
1.
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J.Funahashi,
K.Takano,
Y.Yamagata,
and
K.Yutani
(2000).
Role of surface hydrophobic residues in the conformational stability of human lysozyme at three different positions.
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Biochemistry,
39,
14448-14456.
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PDB codes:
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K.Takano,
Y.Yamagata,
and
K.Yutani
(2000).
Role of amino acid residues at turns in the conformational stability and folding of human lysozyme.
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Biochemistry,
39,
8655-8665.
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PDB codes:
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K.Takano,
K.Tsuchimori,
Y.Yamagata,
and
K.Yutani
(1999).
Effect of foreign N-terminal residues on the conformational stability of human lysozyme.
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Eur J Biochem,
266,
675-682.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
