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PDBsum entry 1brh
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* Residue conservation analysis
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DOI no:
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Biochemistry
35:4298-4305
(1996)
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PubMed id:
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Structural and energetic responses to cavity-creating mutations in hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities.
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A.M.Buckle,
P.Cramer,
A.R.Fersht.
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ABSTRACT
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We have solved the 2.0-A resolution crystal structures of four cavity-creating
Ile/Leu-->Ala mutations in the hydrophobic core of barnase and compare and
contrast the structural responses to mutation with those found for Leu-->Ala
mutations in T4 lysozyme. First, there are rearrangements of structure of
barnase that cause the cavities to collapse partly, and there is an
approximately linear relationship between the changes in stability and the
volume of the cavity similar to that found for the mutants of T4 lysozyme.
Second, although it is currently accepted that hydrophobic cavities formed on
the mutation of large hydrophobic side chains to smaller ones are not occupied
by water molecules, we found a buried water molecule in the crystal structure of
the barnase mutant Ile76-->Ala. A single hydrogen bond is formed between the
water molecule and a polar atom, the carbonyl oxygen of Phe7, in the hydrophobic
cavity that is formed on mutation. A survey of hydrophobic cavities produced by
similar mutations in different proteins reveals that they all contain a
proportion of polar atoms in their linings. The availability of such polar sites
has implications for understanding folding pathways because a solvated core is
presumed present in the transition state for folding and unfolding. Notably, the
hydrogen bond between the cavity-water and the carbonyl group of Phe7 is also a
marked early feature of very recent molecular dynamics simulations of barnase
denaturation [Caflisch, A., & Karplus, M. (1995) J. Mol. Biol. 252,
672-708]. It is possible that cavities engineered into the hydrophobic cores of
other proteins may contain water molecules, even though they cannot be detected
by crystallographic analysis.
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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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M.Bueno,
N.A.Temiz,
and
C.J.Camacho
(2010).
Novel modulation factor quantifies the role of water molecules in protein interactions.
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Proteins,
78,
3226-3234.
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T.D.Fenn,
M.J.Schnieders,
and
A.T.Brunger
(2010).
A smooth and differentiable bulk-solvent model for macromolecular diffraction.
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Acta Crystallogr D Biol Crystallogr,
66,
1024-1031.
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W.A.Baase,
L.Liu,
D.E.Tronrud,
and
B.W.Matthews
(2010).
Lessons from the lysozyme of phage T4.
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Protein Sci,
19,
631-641.
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A.Allali-Hassani,
G.A.Wasney,
I.Chau,
B.S.Hong,
G.Senisterra,
P.Loppnau,
Z.Shi,
J.Moult,
A.M.Edwards,
C.H.Arrowsmith,
H.W.Park,
M.Schapira,
and
M.Vedadi
(2009).
A survey of proteins encoded by non-synonymous single nucleotide polymorphisms reveals a significant fraction with altered stability and activity.
|
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Biochem J,
424,
15-26.
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B.W.Matthews,
and
L.Liu
(2009).
A review about nothing: are apolar cavities in proteins really empty?
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Protein Sci,
18,
494-502.
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S.Szep,
S.Park,
E.T.Boder,
G.D.Van Duyne,
and
J.G.Saven
(2009).
Structural coupling between FKBP12 and buried water.
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Proteins,
74,
603-611.
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PDB codes:
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A.C.Joerger,
and
A.R.Fersht
(2008).
Structural biology of the tumor suppressor p53.
|
| |
Annu Rev Biochem,
77,
557-582.
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A.Madhumalar,
D.J.Smith,
and
C.Verma
(2008).
Stability of the core domain of p53: insights from computer simulations.
|
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BMC Bioinformatics,
9,
S17.
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C.Mattos,
and
A.C.Clark
(2008).
Minimizing frustration by folding in an aqueous environment.
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Arch Biochem Biophys,
469,
118-131.
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E.Gabellieri,
E.Balestreri,
A.Galli,
and
P.Cioni
(2008).
Cavity-creating mutations in Pseudomonas aeruginosa azurin: effects on protein dynamics and stability.
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Biophys J,
95,
771-781.
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J.C.Rasaiah,
S.Garde,
and
G.Hummer
(2008).
Water in nonpolar confinement: from nanotubes to proteins and beyond.
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Annu Rev Phys Chem,
59,
713-740.
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A.Ausili,
B.Cobucci-Ponzano,
B.Di Lauro,
R.D'Avino,
G.Perugino,
E.Bertoli,
A.Scirè,
M.Rossi,
F.Tanfani,
and
M.Moracci
(2007).
A comparative infrared spectroscopic study of glycoside hydrolases from extremophilic archaea revealed different molecular mechanisms of adaptation to high temperatures.
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Proteins,
67,
991.
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A.C.Joerger,
and
A.R.Fersht
(2007).
Structure-function-rescue: the diverse nature of common p53 cancer mutants.
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Oncogene,
26,
2226-2242.
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L.V.Wray,
and
S.H.Fisher
(2007).
Functional analysis of the carboxy-terminal region of Bacillus subtilis TnrA, a MerR family protein.
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J Bacteriol,
189,
20-27.
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S.Somani,
C.P.Chng,
and
C.S.Verma
(2007).
Hydration of a hydrophobic cavity and its functional role: a simulation study of human interleukin-1beta.
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Proteins,
67,
868-885.
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A.Borgia,
D.Bonivento,
C.Travaglini-Allocatelli,
A.Di Matteo,
and
M.Brunori
(2006).
Unveiling a hidden folding intermediate in c-type cytochromes by protein engineering.
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J Biol Chem,
281,
9331-9336.
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PDB code:
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A.C.Joerger,
H.C.Ang,
and
A.R.Fersht
(2006).
Structural basis for understanding oncogenic p53 mutations and designing rescue drugs.
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Proc Natl Acad Sci U S A,
103,
15056-15061.
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PDB codes:
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E.Tamborini,
S.Pricl,
T.Negri,
M.S.Lagonigro,
F.Miselli,
A.Greco,
A.Gronchi,
P.G.Casali,
M.Ferrone,
M.Fermeglia,
A.Carbone,
M.A.Pierotti,
and
S.Pilotti
(2006).
Functional analyses and molecular modeling of two c-Kit mutations responsible for imatinib secondary resistance in GIST patients.
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Oncogene,
25,
6140-6146.
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M.Bueno,
L.A.Campos,
J.Estrada,
and
J.Sancho
(2006).
Energetics of aliphatic deletions in protein cores.
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Protein Sci,
15,
1858-1872.
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P.Cioni
(2006).
Role of protein cavities on unfolding volume change and on internal dynamics under pressure.
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Biophys J,
91,
3390-3396.
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A.A.Rashin,
and
A.H.Rashin
(2005).
Lattice models, packing density, and Boltzmann-like distribution of cavities in proteins.
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Proteins,
58,
547-559.
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C.Machicado,
J.López-Llano,
S.Cuesta-López,
M.Bueno,
and
J.Sancho
(2005).
Design of ligand binding to an engineered protein cavity using virtual screening and thermal up-shift evaluation.
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J Comput Aided Mol Des,
19,
421-443.
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M.D.Collins,
G.Hummer,
M.L.Quillin,
B.W.Matthews,
and
S.M.Gruner
(2005).
Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation.
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Proc Natl Acad Sci U S A,
102,
16668-16671.
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PDB codes:
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M.K.Yadav,
J.E.Redman,
L.J.Leman,
J.M.Alvarez-Gutiérrez,
Y.Zhang,
C.D.Stout,
and
M.R.Ghadiri
(2005).
Structure-based engineering of internal cavities in coiled-coil peptides.
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Biochemistry,
44,
9723-9732.
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PDB codes:
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Y.Li,
Y.Huang,
C.P.Swaminathan,
S.J.Smith-Gill,
and
R.A.Mariuzza
(2005).
Magnitude of the hydrophobic effect at central versus peripheral sites in protein-protein interfaces.
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Structure,
13,
297-307.
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PDB codes:
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A.Mittermaier,
and
L.E.Kay
(2004).
The response of internal dynamics to hydrophobic core mutations in the SH3 domain from the Fyn tyrosine kinase.
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Protein Sci,
13,
1088-1099.
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H.Kusunoki,
R.I.MacDonald,
and
A.Mondragón
(2004).
Structural insights into the stability and flexibility of unusual erythroid spectrin repeats.
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Structure,
12,
645-656.
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PDB code:
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M.J.Lachenmann,
J.E.Ladbury,
X.Qian,
K.Huang,
R.Singh,
and
M.A.Weiss
(2004).
Solvation and the hidden thermodynamics of a zinc finger probed by nonstandard repair of a protein crevice.
|
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Protein Sci,
13,
3115-3126.
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PDB code:
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P.Cioni,
E.de Waal,
G.W.Canters,
and
G.B.Strambini
(2004).
Effects of cavity-forming mutations on the internal dynamics of azurin.
|
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Biophys J,
86,
1149-1159.
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R.Thai,
G.Moine,
M.Desmadril,
D.Servent,
J.L.Tarride,
A.Ménez,
and
M.Léonetti
(2004).
Antigen stability controls antigen presentation.
|
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J Biol Chem,
279,
50257-50266.
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S.Vaitheeswaran,
H.Yin,
J.C.Rasaiah,
and
G.Hummer
(2004).
Water clusters in nonpolar cavities.
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Proc Natl Acad Sci U S A,
101,
17002-17005.
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S.Ventura,
and
L.Serrano
(2004).
Designing proteins from the inside out.
|
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Proteins,
56,
1.
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P.Saxena,
G.Yadav,
D.Mohanty,
and
R.S.Gokhale
(2003).
A new family of type III polyketide synthases in Mycobacterium tuberculosis.
|
| |
J Biol Chem,
278,
44780-44790.
|
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Z.Xu,
Y.Liu,
Y.Yang,
W.Jiang,
E.Arnold,
and
J.Ding
(2003).
Crystal structure of D-Hydantoinase from Burkholderia pickettii at a resolution of 2.7 Angstroms: insights into the molecular basis of enzyme thermostability.
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J Bacteriol,
185,
4038-4049.
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PDB code:
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I.Pozdnyakova,
J.Guidry,
and
P.Wittung-Stafshede
(2002).
Studies of Pseudomonas aeruginosa azurin mutants: cavities in beta-barrel do not affect refolding speed.
|
| |
Biophys J,
82,
2645-2651.
|
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S.Chakravarty,
A.Bhinge,
and
R.Varadarajan
(2002).
A procedure for detection and quantitation of cavity volumes proteins. Application to measure the strength of the hydrophobic driving force in protein folding.
|
| |
J Biol Chem,
277,
31345-31353.
|
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S.H.Xiang,
P.D.Kwong,
R.Gupta,
C.D.Rizzuto,
D.J.Casper,
R.Wyatt,
L.Wang,
W.A.Hendrickson,
M.L.Doyle,
and
J.Sodroski
(2002).
Mutagenic stabilization and/or disruption of a CD4-bound state reveals distinct conformations of the human immunodeficiency virus type 1 gp120 envelope glycoprotein.
|
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J Virol,
76,
9888-9899.
|
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J.Torrent,
P.Rubens,
M.Ribó,
K.Heremans,
and
M.Vilanova
(2001).
Pressure versus temperature unfolding of ribonuclease A: an FTIR spectroscopic characterization of 10 variants at the carboxy-terminal site.
|
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Protein Sci,
10,
725-734.
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J.W.O'Neill,
D.E.Kim,
D.Baker,
and
K.Y.Zhang
(2001).
Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution.
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Acta Crystallogr D Biol Crystallogr,
57,
480-487.
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PDB codes:
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J.Xu,
W.A.Baase,
M.L.Quillin,
E.P.Baldwin,
and
B.W.Matthews
(2001).
Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme.
|
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Protein Sci,
10,
1067-1078.
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PDB codes:
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T.Ohmura,
T.Ueda,
K.Ootsuka,
M.Saito,
and
T.Imoto
(2001).
Stabilization of hen egg white lysozyme by a cavity-filling mutation.
|
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Protein Sci,
10,
313-320.
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PDB codes:
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E.Dürr,
and
I.Jelesarov
(2000).
Thermodynamic analysis of cavity creating mutations in an engineered leucine zipper and energetics of glycerol-induced coiled coil stabilization.
|
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Biochemistry,
39,
4472-4482.
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E.J.Sundberg,
M.Urrutia,
B.C.Braden,
J.Isern,
D.Tsuchiya,
B.A.Fields,
E.L.Malchiodi,
J.Tormo,
F.P.Schwarz,
and
R.A.Mariuzza
(2000).
Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface.
|
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Biochemistry,
39,
15375-15387.
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PDB codes:
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G.S.Ratnaparkhi,
and
R.Varadarajan
(2000).
Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics.
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Biochemistry,
39,
12365-12374.
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PDB codes:
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H.Kono,
M.Saito,
and
A.Sarai
(2000).
Stability analysis for the cavity-filling mutations of the Myb DNA-binding domain utilizing free-energy calculations.
|
| |
Proteins,
38,
197-209.
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J.J.Dwyer,
A.G.Gittis,
D.A.Karp,
E.E.Lattman,
D.S.Spencer,
W.E.Stites,
and
B.García-Moreno E
(2000).
High apparent dielectric constants in the interior of a protein reflect water penetration.
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Biophys J,
79,
1610-1620.
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C.Martin,
V.Richard,
M.Salem,
R.Hartley,
and
Y.Mauguen
(1999).
Refinement and structural analysis of barnase at 1.5 A resolution.
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Acta Crystallogr D Biol Crystallogr,
55,
386-398.
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PDB code:
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Q.Wang,
A.M.Buckle,
N.W.Foster,
C.M.Johnson,
and
A.R.Fersht
(1999).
Design of highly stable functional GroEL minichaperones.
|
| |
Protein Sci,
8,
2186-2193.
|
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R.G.Maroun,
D.Krebs,
S.El Antri,
A.Deroussent,
E.Lescot,
F.Troalen,
H.Porumb,
M.E.Goldberg,
and
S.Fermandjian
(1999).
Self-association and domains of interactions of an amphipathic helix peptide inhibitor of HIV-1 integrase assessed by analytical ultracentrifugation and NMR experiments in trifluoroethanol/H(2)O mixtures.
|
| |
J Biol Chem,
274,
34174-34185.
|
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R.Loris,
U.Langhorst,
S.De Vos,
K.Decanniere,
J.Bouckaert,
D.Maes,
T.R.Transue,
and
J.Steyaert
(1999).
Conserved water molecules in a large family of microbial ribonucleases.
|
| |
Proteins,
36,
117-134.
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PDB codes:
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S.Channareddy,
and
N.Janes
(1999).
Direct determination of hydration in the interdigitated and ripple phases of dihexadecylphosphatidylcholine: hydration of a hydrophobic cavity at the membrane/water interface.
|
| |
Biophys J,
77,
2046-2050.
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T.Lazaridis,
and
M.Karplus
(1999).
Effective energy function for proteins in solution.
|
| |
Proteins,
35,
133-152.
|
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J.Xu,
W.A.Baase,
E.Baldwin,
and
B.W.Matthews
(1998).
The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect.
|
| |
Protein Sci,
7,
158-177.
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PDB codes:
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K.E.McAuley-Hecht,
P.K.Fyfe,
J.P.Ridge,
S.M.Prince,
C.N.Hunter,
N.W.Isaacs,
R.J.Cogdell,
and
M.R.Jones
(1998).
Structural studies of wild-type and mutant reaction centers from an antenna-deficient strain of Rhodobacter sphaeroides: monitoring the optical properties of the complex from bacterial cell to crystal.
|
| |
Biochemistry,
37,
4740-4750.
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PDB code:
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S.Palme,
R.Jaenicke,
and
C.Slingsby
(1998).
X-ray structures of three interface mutants of gammaB-crystallin from bovine eye lens.
|
| |
Protein Sci,
7,
611-618.
|
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T.Steiner,
A.M.Schreurs,
J.A.Kanters,
and
J.Kroon
(1998).
Water molecules hydrogen bonding to aromatic acceptors of amino acids: the structure of Tyr-Tyr-Phe dihydrate and a crystallographic database study on peptides.
|
| |
Acta Crystallogr D Biol Crystallogr,
54,
25-31.
|
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Y.Yamagata,
M.Kubota,
Y.Sumikawa,
J.Funahashi,
K.Takano,
S.Fujii,
and
K.Yutani
(1998).
Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six tyrosine --> phenylalanine mutants.
|
| |
Biochemistry,
37,
9355-9362.
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PDB codes:
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A.Akasako,
M.Haruki,
M.Oobatake,
and
S.Kanaya
(1997).
Conformational stabilities of Escherichia coli RNase HI variants with a series of amino acid substitutions at a cavity within the hydrophobic core.
|
| |
J Biol Chem,
272,
18686-18693.
|
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A.R.Clarke,
and
J.P.Waltho
(1997).
Protein folding and intermediates.
|
| |
Curr Opin Biotechnol,
8,
400-410.
|
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B.Lee,
and
G.Vasmatzis
(1997).
Stabilization of protein structures.
|
| |
Curr Opin Biotechnol,
8,
423-428.
|
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E.Mombelli,
M.Afshar,
P.Fusi,
M.Mariani,
P.Tortora,
J.P.Connelly,
and
R.Lange
(1997).
The role of phenylalanine 31 in maintaining the conformational stability of ribonuclease P2 from Sulfolobus solfataricus under extreme conditions of temperature and pressure.
|
| |
Biochemistry,
36,
8733-8742.
|
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G.Otting,
E.Liepinsh,
B.Halle,
and
U.Frey
(1997).
NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules.
|
| |
Nat Struct Biol,
4,
396-404.
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|
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|
|
|
|
H.R.Schroeder,
F.A.McOdimba,
J.G.Guillemette,
and
J.A.Kornblatt
(1997).
The polarity of tyrosine 67 in yeast iso-1-cytochrome c monitored by second derivative spectroscopy.
|
| |
Biochem Cell Biol,
75,
191-197.
|
|
|
|
|
|
|
J.W.Schwabe
(1997).
The role of water in protein-DNA interactions.
|
| |
Curr Opin Struct Biol,
7,
126-134.
|
|
|
|
|
|
|
K.Takano,
Y.Yamagata,
S.Fujii,
and
K.Yutani
(1997).
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.
|
| |
Biochemistry,
36,
688-698.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.M.Lopez,
and
D.Kosk-Kosicka
(1997).
Entropy-driven interactions of anesthetics with membrane proteins.
|
| |
Biochemistry,
36,
8864-8872.
|
|
|
|
|
|
|
P.C.Shaw,
S.Mulot,
S.K.Ma,
Q.F.Xu,
H.B.Yao,
S.Wu,
X.H.Lu,
and
Y.C.Dong
(1997).
Structure/function relationship study of Tyr14 and Arg22 in trichosanthin, a ribosome-inactivating protein.
|
| |
Eur J Biochem,
245,
423-427.
|
|
|
|
|
|
|
A.Bateman,
M.Jouet,
J.MacFarlane,
J.S.Du,
S.Kenwrick,
and
C.Chothia
(1996).
Outline structure of the human L1 cell adhesion molecule and the sites where mutations cause neurological disorders.
|
| |
EMBO J,
15,
6050-6059.
|
|
|
|
|
|
|
B.A.Fields,
F.A.Goldbaum,
W.Dall'Acqua,
E.L.Malchiodi,
A.Cauerhff,
F.P.Schwarz,
X.Ysern,
R.J.Poljak,
and
R.A.Mariuzza
(1996).
Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme.
|
| |
Biochemistry,
35,
15494-15503.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
E.S.Eberhardt,
P.K.Wittmayer,
B.M.Templer,
and
R.T.Raines
(1996).
Contribution of a tyrosine side chain to ribonuclease A catalysis and stability.
|
| |
Protein Sci,
5,
1697-1703.
|
|
|
|
|
|
|
J.K.Myers,
and
C.N.Pace
(1996).
Hydrogen bonding stabilizes globular proteins.
|
| |
Biophys J,
71,
2033-2039.
|
|
|
|
|
|
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
codes are
shown on the right.
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