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References listed in PDB file
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Key reference
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Title
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Analysis of the interaction between charged side chains and the alpha-Helix dipole using designed thermostable mutants of phage t4 lysozyme.
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Authors
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H.Nicholson,
D.E.Anderson,
S.Dao-Pin,
B.W.Matthews.
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Ref.
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Biochemistry, 1991,
30,
9816-9828.
[DOI no: ]
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PubMed id
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Abstract
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It was shown previously that the introduction of a negatively charged amino acid
at the N-terminus of an alpha-helix could increase the thermostability of phage
T4 lysozyme via an electrostatic interaction with the "helix dipole" [Nicholson,
H., Becktel, W. J., & Matthews, B. W. (1988) Nature 336, 651-656]. The prior
report focused on the two stabilizing substitutions Ser 38----Asp (S38D) and Asn
144----Asp (N144D). Two additional examples of stabilizing mutants, T109D and
N116D, are presented here. Both show the pH-dependent increase in thermal
stability expected for the interaction of an aspartic acid with an alpha-helix
dipole. Control mutants were also constructed to further characterize the nature
of the interaction with the alpha-helix dipole. High-resolution crystal
structure analysis was used to determine the nature of the interaction of the
substituted amino acids with the end of the alpha-helix in both the primary and
the control mutants. Control mutant S38N has stability essentially the same as
that of wild-type lysozyme but hydrogen bonding similar to that of the
stabilizing mutant S38D. This confirms that it is the electrostatic interaction
between Asp 38 and the helix dipole, rather than a change in hydrogen-bonding
geometry, that gives enhanced stability. Structural and thermodynamic analysis
of mutant T109N provide a similar control for the stabilizing replacement T109D.
In the case of mutant N116D, there was concern that the enhanced stability might
be due to a favorable salt-bridge interaction between the introduced aspartate
and Arg 119, rather than an interaction with the alpha-helix dipole. The
additivity of the stabilities of N116D and R119M seen in the double mutant
N116D/R119M indicates that favorable interactions are largely independent of
residue 119. As a further control, Asp 92, a presumed helix-stabilizing residue
in wild-type lysozyme, was replaced with Asn. This decreased the stability of
the protein in the manner expected for the loss of a favorable helix dipole
interaction. In total, five mutations have been identified that increase the
thermostability of T4 lysozyme and appear to do so by favorable interactions
with alpha-helix dipoles. As measured by the pH dependence of stability, the
strength of the electrostatic interaction between the charged groups studied
here and the helix dipole ranges from 0.6 to 1.3 kcal/mol in 150 mM KCl. In the
case of mutants S38D and N144H, NMR titration was used to measure the pKa's of
Asp 38 and His 144 in the folded structures.(ABSTRACT TRUNCATED AT 400 WORDS)
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Secondary reference #1
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Title
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Authors
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H.Nicholson,
W.Becktel,
B.W.Matthews.
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Ref.
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TO BE PUBLISHED ...
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Secondary reference #2
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Title
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Structural and thermodynamic consequences of burying a charged residue within the hydrophobic core of t4 lysozyme.
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Authors
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S.Dao-Pin,
D.E.Anderson,
W.A.Baase,
F.W.Dahlquist,
B.W.Matthews.
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Ref.
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Biochemistry, 1991,
30,
11521-11529.
[DOI no: ]
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PubMed id
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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
96%.
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Secondary reference #3
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Title
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Multiple alanine replacements within alpha-Helix 126-134 of t4 lysozyme have independent, Additive effects on both structure and stability.
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Authors
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X.J.Zhang,
W.A.Baase,
B.W.Matthews.
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Ref.
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Protein Sci, 1992,
1,
761-776.
[DOI no: ]
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PubMed id
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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
84%.
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Secondary reference #4
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Title
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Tolerance of t4 lysozyme to proline substitutions within the long interdomain alpha-Helix illustrates the adaptability of proteins to potentially destabilizing lesions.
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Authors
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U.H.Sauer,
D.P.San,
B.W.Matthews.
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Ref.
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J Biol Chem, 1992,
267,
2393-2399.
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PubMed id
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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
96%.
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Secondary reference #5
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Title
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Tolerance of t4 lysozyme to multiple xaa (right arrow) ala substitutions: a polyalanine alpha-Helix containing ten consecutive alanines
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Authors
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D.W.Heinz,
W.A.Baase,
B.W.Matthews.
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Ref.
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TO BE PUBLISHED ...
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Secondary reference #6
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Title
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Cumulative site-Directed charge-Change replacements in bacteriophage t4 lysozyme suggest that long-Range electrostatic interactions contribute little to protein stability.
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Authors
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S.Dao-Pin,
E.Söderlind,
W.A.Baase,
J.A.Wozniak,
U.Sauer,
B.W.Matthews.
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Ref.
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J Mol Biol, 1991,
221,
873-887.
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PubMed id
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Secondary reference #7
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Title
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Structural and thermodynamic analysis of the packing of two alpha-Helices in bacteriophage t4 lysozyme.
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Authors
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S.Daopin,
T.Alber,
W.A.Baase,
J.A.Wozniak,
B.W.Matthews.
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Ref.
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J Mol Biol, 1991,
221,
647-667.
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PubMed id
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Secondary reference #8
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Title
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Contributions of engineered surface salt bridges to the stability of t4 lysozyme determined by directed mutagenesis.
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Authors
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D.P.Sun,
U.Sauer,
H.Nicholson,
B.W.Matthews.
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Ref.
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Biochemistry, 1991,
30,
7142-7153.
[DOI no: ]
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PubMed id
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Secondary reference #9
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Title
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Toward a simplification of the protein folding problem: a stabilizing polyalanine alpha-Helix engineered in t4 lysozyme.
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Authors
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X.J.Zhang,
W.A.Baase,
B.W.Matthews.
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Ref.
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Biochemistry, 1991,
30,
2012-2017.
[DOI no: ]
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PubMed id
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Secondary reference #10
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Title
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Structure of a thermostable disulfide-Bridge mutant of phage t4 lysozyme shows that an engineered cross-Link in a flexible region does not increase the rigidity of the folded protein.
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Authors
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P.E.Pjura,
M.Matsumura,
J.A.Wozniak,
B.W.Matthews.
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Ref.
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Biochemistry, 1990,
29,
2592-2598.
[DOI no: ]
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PubMed id
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Secondary reference #11
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Title
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Structural studies of mutants of t4 lysozyme that alter hydrophobic stabilization.
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Authors
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M.Matsumura,
J.A.Wozniak,
D.P.Sun,
B.W.Matthews.
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Ref.
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J Biol Chem, 1989,
264,
16059-16066.
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PubMed id
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Secondary reference #12
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Title
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High-Resolution structure of the temperature-Sensitive mutant of phage lysozyme, Arg 96----His.
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Authors
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L.H.Weaver,
T.M.Gray,
M.G.Grütter,
D.E.Anderson,
J.A.Wozniak,
F.W.Dahlquist,
B.W.Matthews.
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Ref.
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Biochemistry, 1989,
28,
3793-3797.
[DOI no: ]
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PubMed id
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Secondary reference #13
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Title
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Contributions of left-Handed helical residues to the structure and stability of bacteriophage t4 lysozyme.
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Authors
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H.Nicholson,
E.Söderlind,
D.E.Tronrud,
B.W.Matthews.
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Ref.
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J Mol Biol, 1989,
210,
181-193.
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PubMed id
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Secondary reference #14
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Title
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Hydrophobic stabilization in t4 lysozyme determined directly by multiple substitutions of ile 3.
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Authors
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M.Matsumura,
W.J.Becktel,
B.W.Matthews.
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Ref.
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Nature, 1988,
334,
406-410.
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PubMed id
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Secondary reference #15
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Title
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Enhanced protein thermostability from designed mutations that interact with alpha-Helix dipoles.
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Authors
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H.Nicholson,
W.J.Becktel,
B.W.Matthews.
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Ref.
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Nature, 1988,
336,
651-656.
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PubMed id
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Secondary reference #16
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Title
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Replacements of pro86 in phage t4 lysozyme extend an alpha-Helix but do not alter protein stability.
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Authors
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T.Alber,
J.A.Bell,
D.P.Sun,
H.Nicholson,
J.A.Wozniak,
S.Cook,
B.W.Matthews.
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Ref.
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Science, 1988,
239,
631-635.
[DOI no: ]
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PubMed id
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Secondary reference #17
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Title
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Enhanced protein thermostability from site-Directed mutations that decrease the entropy of unfolding.
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Authors
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B.W.Matthews,
H.Nicholson,
W.J.Becktel.
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Ref.
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Proc Natl Acad Sci U S A, 1987,
84,
6663-6667.
[DOI no: ]
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PubMed id
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Secondary reference #18
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Title
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Structural analysis of the temperature-Sensitive mutant of bacteriophage t4 lysozyme, Glycine 156----Aspartic acid.
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Authors
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T.M.Gray,
B.W.Matthews.
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Ref.
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J Biol Chem, 1987,
262,
16858-16864.
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PubMed id
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Secondary reference #19
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Title
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Contributions of hydrogen bonds of thr 157 to the thermodynamic stability of phage t4 lysozyme.
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Authors
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T.Alber,
D.P.Sun,
K.Wilson,
J.A.Wozniak,
S.P.Cook,
B.W.Matthews.
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Ref.
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Nature, 1987,
330,
41-46.
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PubMed id
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Secondary reference #20
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Title
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Structural studies of mutants of the lysozyme of bacteriophage t4. The temperature-Sensitive mutant protein thr157----Ile.
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Authors
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M.G.Grütter,
T.M.Gray,
L.H.Weaver,
T.A.Wilson,
B.W.Matthews.
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Ref.
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J Mol Biol, 1987,
197,
315-329.
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PubMed id
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Secondary reference #21
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Title
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Structure of bacteriophage t4 lysozyme refined at 1.7 a resolution.
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Authors
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L.H.Weaver,
B.W.Matthews.
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Ref.
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J Mol Biol, 1987,
193,
189-199.
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PubMed id
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Secondary reference #22
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Title
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Temperature-Sensitive mutations of bacteriophage t4 lysozyme occur at sites with low mobility and low solvent accessibility in the folded protein.
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Authors
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T.Alber,
D.P.Sun,
J.A.Nye,
D.C.Muchmore,
B.W.Matthews.
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Ref.
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Biochemistry, 1987,
26,
3754-3758.
[DOI no: ]
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PubMed id
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Secondary reference #23
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Title
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Common precursor of lysozymes of hen egg-White and bacteriophage t4.
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Authors
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B.W.Matthews,
M.G.Grütter,
W.F.Anderson,
S.J.Remington.
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Ref.
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Nature, 1981,
290,
334-335.
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PubMed id
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Secondary reference #24
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Title
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Crystallographic determination of the mode of binding of oligosaccharides to t4 bacteriophage lysozyme: implications for the mechanism of catalysis.
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Authors
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W.F.Anderson,
M.G.Grütter,
S.J.Remington,
L.H.Weaver,
B.W.Matthews.
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Ref.
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J Mol Biol, 1981,
147,
523-543.
[DOI no: ]
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PubMed id
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Figure 4.
FIN. 4. (a) Stereo drawing showing the diterence density (lcNAc,,-native)
(b) Elert,ron density ap ith coeficients (4F,,,,.,,,,-3Fx,, 1.
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Figure 6.
FIG. 6. View of the presumed binding of a pentasaccharide in the active sik of phage Iq'sozyme.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #25
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Title
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Relation between hen egg white lysozyme and bacteriophage t4 lysozyme: evolutionary implications.
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Authors
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B.W.Matthews,
S.J.Remington,
M.G.Grütter,
W.F.Anderson.
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Ref.
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J Mol Biol, 1981,
147,
545-558.
[DOI no: ]
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PubMed id
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Figure 5.
FIG. 5. Schematic drawing comparing the saccharie-protein interaction in phage lysozyme (names
in parentheses) and hen egg white lyszyme. The hatched line illustrat,es the apparent close contact that
owu~`s hen saccharide D is in the normal chair conformat.ion.
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Figure 6.
FIG:. 6. Superosition of common elements of the phage lysozyme active site (solid bonds and names
nderlined) onto hen egg white lysozyme. (a) Mono view looking into the active site cleft. (b) Stereo
vie along z. i.e. approximately at right angles to that shown in (a).
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #26
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Title
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Structure of the lysozyme from bacteriophage t4: an electron density map at 2.4 a resolution.
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Authors
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S.J.Remington,
W.F.Anderson,
J.Owen,
L.F.Ten eyck,
C.T.Grainger,
B.W.Matthews.
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Ref.
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J Mol Biol, 1978,
118,
81-98.
[DOI no: ]
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PubMed id
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Figure 5.
FIG. 5. Schemaic illustration of the p-sheet region of T4 phage lysozyme.
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Figure 6.
FIG. 6. Conformation angls for T4 phage lysozyme; glycine residues are indicated by open
circles. he allowed regions for a hard-sphere model (Ramachandran & Sasisekharan, 1968)
are indicated by solid lines, and those preicted by a quantum mechanical method (Pullman
et ~1.. 1970) are indicated by a broken line.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #27
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Title
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Atomic coordinates for t4 phage lysozyme.
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Authors
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S.J.Remington,
L.F.Eyck,
B.W.Matthews.
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Ref.
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Biochem Biophys Res Commun, 1977,
75,
265-270.
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PubMed id
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Secondary reference #28
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Title
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Comparison of the predicted and observed secondary structure of t4 phage lysozyme.
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Author
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B.W.Matthews.
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Ref.
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Biochim Biophys Acta, 1975,
405,
442-451.
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PubMed id
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Secondary reference #29
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Title
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The three dimensional structure of the lysozyme from bacteriophage t4.
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Authors
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B.W.Matthews,
S.J.Remington.
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Ref.
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Proc Natl Acad Sci U S A, 1974,
71,
4178-4182.
[DOI no: ]
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PubMed id
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Secondary reference #30
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Title
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Letter: crystallographic data fro lysoxyme from bacteriophage t4.
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Authors
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B.W.Matthews,
F.W.Dahlquist,
A.Y.Maynard.
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Ref.
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J Mol Biol, 1973,
78,
575-576.
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PubMed id
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