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PDBsum entry 1alc
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Calcium binding protein
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PDB id
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1alc
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Contents |
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* Residue conservation analysis
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J Mol Biol
208:99
(1989)
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PubMed id:
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Refined structure of baboon alpha-lactalbumin at 1.7 A resolution. Comparison with C-type lysozyme.
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K.R.Acharya,
D.I.Stuart,
N.P.Walker,
M.Lewis,
D.C.Phillips.
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ABSTRACT
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The solution of the structure of alpha-lactalbumin from baboon milk (Papio
cynocephalus) at 4.5 A resolution using the isomorphous replacement method has
been reported previously. Initial refinement on the basis of these
low-resolution studies was not successful because of the poor isomorphism of the
best heavy-atom derivative. Because of the striking similarity between the
structure of lysozyme and alpha-lactalbumin, a more cautious molecular
replacement approach was tried to refine the model. Using hen egg-white lysozyme
as the starting model, preliminary refinement was performed using heavily
constrained least-squares minimization in reciprocal space. The model was
further refined using stereochemical restraints at 1.7 A resolution to a
conventional crystallographic residual of 0.22 for 1141 protein atoms. In the
final model, the root-mean-square deviation from ideality for bond distances is
0.015 A, and for angle distances it is 0.027 A. The refinement was carried out
using the human alpha-lactalbumin sequence and "omit maps" calculated during the
course of refinement indicated eight possible sequence changes in the baboon
alpha-lactalbumin X-ray sequence. During the refinement, a tightly bound calcium
ion and 150 water molecules, of which four are internal, have been located. Some
of the water molecules were modelled for disordered side-chains. The
co-ordination around the calcium is a slightly distorted pentagonal bipyramid.
The Ca-O distances vary from 2.2 A to 2.6 A, representing a tight
calcium-binding loop in the structure. The calcium-binding fold only
superficially resembles the "EF-hand" and presumably has no evolutionary
relationship with other EF-hand structures. The overall structure of
alpha-lactalbumin is very similar to that of lysozyme. All large deviations
occur in the loops where all sequence deletions and insertions are found. The C
terminus appears to be rather flexible in alpha-lactalbumin compared to
lysozyme. The experimental evidence supports the earlier predictions for the
alpha-lactalbumin structure that were based upon the assumption that
alpha-lactalbumin and lysozyme have similar three-dimensional structures, with
minimal deletions and insertions. A detailed comparison of the two structures
shows striking features as well as throwing some light on the evolution of these
two proteins from a common precursor.
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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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R.C.Cheng,
and
B.S.Zhorov
(2010).
Docking of calcium ions in proteins with flexible side chains and deformable backbones.
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Eur Biophys J,
39,
825-838.
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A.C.Schmidt,
B.Fahlbusch,
and
M.Otto
(2009).
Size exclusion chromatography coupled to electrospray ionization mass spectrometry for analysis and quantitative characterization of arsenic interactions with peptides and proteins.
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J Mass Spectrom,
44,
898-910.
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C.Budiman,
K.Bando,
C.Angkawidjaja,
Y.Koga,
K.Takano,
and
S.Kanaya
(2009).
Engineering of monomeric FK506-binding protein 22 with peptidyl prolyl cis-trans isomerase. Importance of a V-shaped dimeric structure for binding to protein substrate.
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FEBS J,
276,
4091-4101.
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L.A.Munishkina,
A.Ahmad,
A.L.Fink,
and
V.N.Uversky
(2008).
Guiding protein aggregation with macromolecular crowding.
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Biochemistry,
47,
8993-9006.
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A.Vanhooren,
A.Chedad,
V.Farkas,
Z.Majer,
M.Joniau,
H.Van Dael,
and
I.Hanssens
(2005).
Tryptophan to phenylalanine substitutions allow differentiation of short- and long-range conformational changes during denaturation of goat alpha-lactalbumin.
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Proteins,
60,
118-130.
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D.Ming,
and
M.E.Wall
(2005).
Quantifying allosteric effects in proteins.
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Proteins,
59,
697-707.
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F.A.Chowdhury,
and
D.P.Raleigh
(2005).
A comparative study of the alpha-subdomains of bovine and human alpha-lactalbumin reveals key differences that correlate with molten globule stability.
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Protein Sci,
14,
89-96.
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J.Fast,
A.K.Mossberg,
C.Svanborg,
and
S.Linse
(2005).
Stability of HAMLET--a kinetically trapped alpha-lactalbumin oleic acid complex.
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Protein Sci,
14,
329-340.
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M.Mizuguchi,
A.Matsuura,
Y.Nabeshima,
K.Masaki,
M.Watanabe,
T.Aizawa,
M.Demura,
K.Nitta,
Y.Mori,
H.Shinoda,
and
K.Kawano
(2005).
Effects of the stabilization of the molten globule state on the folding mechanism of alpha-lactalbumin: a study of a chimera of bovine and human alpha-lactalbumin.
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Proteins,
61,
356-365.
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A.Kundu,
and
N.Kishore
(2004).
1,1,1,3,3,3-hexafluoroisopropanol induced thermal unfolding and molten globule state of bovine alpha-lactalbumin: calorimetric and spectroscopic studies.
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Biopolymers,
73,
405-420.
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A.Vanhooren,
K.Vanhee,
K.Noyelle,
Z.Majer,
M.Joniau,
and
I.Hanssens
(2002).
Structural basis for difference in heat capacity increments for Ca(2+) binding to two alpha-lactalbumins.
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Biophys J,
82,
407-417.
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M.Mizuguchi,
Y.Kobashigawa,
Y.Kumaki,
M.Demura,
K.Kawano,
and
K.Nitta
(2002).
Effects of a helix substitution on the folding mechanism of bovine alpha-lactalbumin.
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Proteins,
49,
95.
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T.Ohkuri,
T.Ueda,
Y.Yoshida,
Y.Abe,
N.Hamasaki,
and
T.Imoto
(2002).
A metal binding in the polypeptide chain improves the folding efficiency of a denatured and reduced protein.
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Biopolymers,
64,
106-114.
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W.Yang,
H.W.Lee,
H.Hellinga,
and
J.J.Yang
(2002).
Structural analysis, identification, and design of calcium-binding sites in proteins.
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Proteins,
47,
344-356.
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K.Horii,
M.Saito,
T.Yoda,
K.Tsumoto,
M.Matsushima,
K.Kuwajima,
and
I.Kumagai
(2001).
Contribution of Thr29 to the thermodynamic stability of goat alpha-lactalbumin as determined by experimental and theoretical approaches.
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Proteins,
45,
16-29.
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PDB codes:
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S.J.Demarest,
J.C.Horng,
and
D.P.Raleigh
(2001).
A protein dissection study demonstrates that two specific hydrophobic clusters play a key role in stabilizing the core structure of the molten globule state of human alpha-lactalbumin.
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Proteins,
42,
237-242.
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S.J.Demarest,
S.Q.Zhou,
J.Robblee,
R.Fairman,
B.Chu,
and
D.P.Raleigh
(2001).
A comparative study of peptide models of the alpha-domain of alpha-lactalbumin, lysozyme, and alpha-lactalbumin/lysozyme chimeras allows the elucidation of critical factors that contribute to the ability to form stable partially folded states.
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Biochemistry,
40,
2138-2147.
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T.Yoda,
M.Saito,
M.Arai,
K.Horii,
K.Tsumoto,
M.Matsushima,
I.Kumagai,
and
K.Kuwajima
(2001).
Folding-unfolding of goat alpha-lactalbumin studied by stopped-flow circular dichroism and molecular dynamics simulations.
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Proteins,
42,
49-65.
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W.Dzwolak,
M.Kato,
A.Shimizu,
and
Y.Taniguchi
(2001).
FTIR study on heat-induced and pressure-assisted cold-induced changes in structure of bovine alpha-lactalbumin: stabilizing role of calcium ion.
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Biopolymers,
62,
29-39.
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Y.Xue,
J.N.Liu,
Z.Sun,
Z.Ma,
C.Wu,
and
D.Zhu
(2001).
alpha-lactalbumin mutant acting as lysozyme.
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Proteins,
42,
17-22.
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C.Jegerschöld,
A.W.Rutherford,
T.A.Mattioli,
M.Crimi,
and
R.Bassi
(2000).
Calcium binding to the photosystem II subunit CP29.
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J Biol Chem,
275,
12781-12788.
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E.W.Blanch,
L.A.Morozova-Roche,
L.Hecht,
W.Noppe,
and
L.D.Barron
(2000).
Raman optical activity characterization of native and molten globule states of equine lysozyme: comparison with hen lysozyme and bovine alpha-lactalbumin.
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Biopolymers,
57,
235-248.
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M.Mizuguchi,
D.Hashimoto,
M.Sakurai,
and
K.Nitta
(2000).
Cold denaturation of alpha-lactalbumin.
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Proteins,
38,
407-413.
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T.K.Chaudhuri,
M.Arai,
T.P.Terada,
T.Ikura,
and
K.Kuwajima
(2000).
Equilibrium and kinetic studies on folding of the authentic and recombinant forms of human alpha-lactalbumin by circular dichroism spectroscopy.
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Biochemistry,
39,
15643-15651.
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T.Koshiba,
M.Yao,
Y.Kobashigawa,
M.Demura,
A.Nakagawa,
I.Tanaka,
K.Kuwajima,
and
K.Nitta
(2000).
Structure and thermodynamics of the extraordinarily stable molten globule state of canine milk lysozyme.
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Biochemistry,
39,
3248-3257.
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PDB code:
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W.Yang,
T.Tsai,
M.Kats,
and
J.J.Yang
(2000).
Peptide analogs from E-cadherin with different calcium-binding affinities.
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J Pept Res,
55,
203-215.
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D.B.Veprintsev,
M.Narayan,
S.E.Permyakov,
V.N.Uversky,
C.L.Brooks,
A.M.Cherskaya,
E.A.Permyakov,
and
L.J.Berliner
(1999).
Fine tuning the N-terminus of a calcium binding protein: alpha-lactalbumin.
|
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Proteins,
37,
65-72.
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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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W.Dzwolak,
M.Kato,
A.Shimizu,
and
Y.Taniguchi
(1999).
Fourier-transform infrared spectroscopy study of the pressure-induced changes in the structure of the bovine alpha-lactalbumin: the stabilizing role of the calcium ion.
|
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Biochim Biophys Acta,
1433,
45-55.
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G.Vanderheeren,
I.Hanssens,
K.Noyelle,
H.Van Dael,
and
M.Joniau
(1998).
The perturbations of the native state of goat alpha-lactalbumin induced by 1,1'-bis(4-anilino-5-naphthalenesulfonate) are Ca2+-dependent.
|
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Biophys J,
75,
2195-2204.
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M.Kikuchi,
K.Kawano,
and
K.Nitta
(1998).
Calcium-binding and structural stability of echidna and canine milk lysozymes.
|
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Protein Sci,
7,
2150-2155.
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N.Chandra,
K.Brew,
and
K.R.Acharya
(1998).
Structural evidence for the presence of a secondary calcium binding site in human alpha-lactalbumin.
|
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Biochemistry,
37,
4767-4772.
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PDB code:
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S.Kim,
and
J.Baum
(1998).
Electrostatic interactions in the acid denaturation of alpha-lactalbumin determined by NMR.
|
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Protein Sci,
7,
1930-1938.
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B.Kuhlman,
J.A.Boice,
W.J.Wu,
R.Fairman,
and
D.P.Raleigh
(1997).
Calcium binding peptides from alpha-lactalbumin: implications for protein folding and stability.
|
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Biochemistry,
36,
4607-4615.
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K.M.Cawthern,
M.Narayan,
D.Chaudhuri,
E.A.Permyakov,
and
L.J.Berliner
(1997).
Interactions of alpha-lactalbumin with fatty acids and spin label analogs.
|
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J Biol Chem,
272,
30812-30816.
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M.H.Zehfus
(1997).
Identification of compact, hydrophobically stabilized domains and modules containing multiple peptide chains.
|
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Protein Sci,
6,
1210-1219.
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M.Kataoka,
K.Kuwajima,
F.Tokunaga,
and
Y.Goto
(1997).
Structural characterization of the molten globule of alpha-lactalbumin by solution X-ray scattering.
|
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Protein Sci,
6,
422-430.
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M.Mizuguchi,
M.Nara,
Y.Ke,
K.Kawano,
T.Hiraoki,
and
K.Nitta
(1997).
Fourier-transform infrared spectroscopic studies on the coordination of the side-chain COO- groups to Ca2+ in equine lysozyme.
|
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Eur J Biochem,
250,
72-76.
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P.Falson,
T.Menguy,
F.Corre,
L.Bouneau,
A.G.de Gracia,
S.Soulié,
F.Centeno,
J.V.Moller,
P.Champeil,
and
M.le Maire
(1997).
The cytoplasmic loop between putative transmembrane segments 6 and 7 in sarcoplasmic reticulum Ca2+-ATPase binds Ca2+ and is functionally important.
|
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J Biol Chem,
272,
17258-17262.
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P.J.Anderson,
C.L.Brooks,
and
L.J.Berliner
(1997).
Functional identification of calcium binding residues in bovine alpha-lactalbumin.
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Biochemistry,
36,
11648-11654.
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P.K.Qasba,
and
S.Kumar
(1997).
Molecular divergence of lysozymes and alpha-lactalbumin.
|
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Crit Rev Biochem Mol Biol,
32,
255-306.
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T.E.Creighton
(1997).
How important is the molten globule for correct protein folding?
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Trends Biochem Sci,
22,
6.
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A.C.Pike,
K.Brew,
and
K.R.Acharya
(1996).
Crystal structures of guinea-pig, goat and bovine alpha-lactalbumin highlight the enhanced conformational flexibility of regions that are significant for its action in lactose synthase.
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Structure,
4,
691-703.
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PDB codes:
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G.Vanderheeren,
I.Hanssens,
W.Meijberg,
and
A.Van Aerschot
(1996).
Thermodynamic characterization of the partially unfolded state of Ca(2+)-loaded bovine alpha-lactalbumin: evidence that partial unfolding can precede Ca2+ release.
|
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Biochemistry,
35,
16753-16759.
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K.M.Cawthern,
E.Permyakov,
and
L.J.Berliner
(1996).
Membrane-bound states of alpha-lactalbumin: implications for the protein stability and conformation.
|
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Protein Sci,
5,
1394-1405.
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L.C.Wu,
B.A.Schulman,
Z.Y.Peng,
and
P.S.Kim
(1996).
Disulfide determinants of calcium-induced packing in alpha-lactalbumin.
|
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Biochemistry,
35,
859-863.
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T.M.Hendrix,
Y.Griko,
and
P.Privalov
(1996).
Energetics of structural domains in alpha-lactalbumin.
|
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Protein Sci,
5,
923-931.
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V.A.Malinovskii,
J.Tian,
J.A.Grobler,
and
K.Brew
(1996).
Functional site in alpha-lactalbumin encompasses a region corresponding to a subsite in lysozyme and parts of two adjacent flexible substructures.
|
| |
Biochemistry,
35,
9710-9715.
|
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E.Pardon,
P.Haezebrouck,
A.De Baetselier,
S.D.Hooke,
K.T.Fancourt,
J.Desmet,
C.M.Dobson,
H.Van Dael,
and
M.Joniau
(1995).
A Ca(2+)-binding chimera of human lysozyme and bovine alpha-lactalbumin that can form a molten globule.
|
| |
J Biol Chem,
270,
10514-10524.
|
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J.C.Hempel,
R.M.Fine,
M.Hassan,
W.Ghoul,
A.Guaragna,
S.C.Koerber,
Z.Li,
and
A.T.Hagler
(1995).
Conformational analysis of endothelin-1: effects of solvation free energy.
|
| |
Biopolymers,
36,
283-301.
|
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K.Takeda,
K.Ogawa,
M.Ohara,
S.Hamada,
and
Y.Moriyama
(1995).
Conformational changes of alpha-lactalbumin induced by the stepwise reduction of its disulfide bridges: the effect of the disulfide bridges on the structural stability of the protein in sodium dodecyl sulfate solution.
|
| |
J Protein Chem,
14,
679-684.
|
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|
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M.H.Zehfus
(1995).
Automatic recognition of hydrophobic clusters and their correlation with protein folding units.
|
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Protein Sci,
4,
1188-1202.
|
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P.Shih,
D.R.Holland,
and
J.F.Kirsch
(1995).
Thermal stability determinants of chicken egg-white lysozyme core mutants: hydrophobicity, packing volume, and conserved buried water molecules.
|
| |
Protein Sci,
4,
2050-2062.
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PDB codes:
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S.Gohda,
A.Shimizu,
M.Ikeguchi,
and
S.Sugai
(1995).
The superreactive disulfide bonds in alpha-lactalbumin and lysozyme.
|
| |
J Protein Chem,
14,
731-737.
|
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S.Improta,
H.Molinari,
A.Pastore,
R.Consonni,
and
L.Zetta
(1995).
Probing protein structure by solvent perturbation of NMR spectra. A comparison with photochemically induced dynamic nuclear polarization techniques applied to native alpha-lactalbumin.
|
| |
Eur J Biochem,
227,
78-86.
|
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S.Improta,
H.Molinari,
A.Pastore,
R.Consonni,
and
L.Zetta
(1995).
Probing protein structure by solvent perturbation of NMR spectra. Photochemically induced dynamic nuclear polarization and paramagnetic perturbation techniques applied to the study of the molten globule state of alpha-lactalbumin.
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| |
Eur J Biochem,
227,
87-96.
|
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D.Xie,
and
E.Freire
(1994).
Molecular basis of cooperativity in protein folding. V. Thermodynamic and structural conditions for the stabilization of compact denatured states.
|
| |
Proteins,
19,
291-301.
|
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K.R.Acharya,
D.I.Stuart,
D.C.Phillips,
H.A.McKenzie,
and
C.G.Teahan
(1994).
Models of the three-dimensional structures of echidna, horse, and pigeon lysozymes: calcium-binding lysozymes and their relationship with alpha-lactalbumins.
|
| |
J Protein Chem,
13,
569-584.
|
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L.Heginbotham,
Z.Lu,
T.Abramson,
and
R.MacKinnon
(1994).
Mutations in the K+ channel signature sequence.
|
| |
Biophys J,
66,
1061-1067.
|
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|
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L.J.Smith,
A.T.Alexandrescu,
M.Pitkeathly,
and
C.M.Dobson
(1994).
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