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PDBsum entry 1le0
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De novo protein
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PDB id
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1le0
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DOI no:
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Proc Natl Acad Sci U S A
98:5578-5583
(2001)
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PubMed id:
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Tryptophan zippers: stable, monomeric beta -hairpins.
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A.G.Cochran,
N.J.Skelton,
M.A.Starovasnik.
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ABSTRACT
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A structural motif, the tryptophan zipper (trpzip), greatly stabilizes the
beta-hairpin conformation in short peptides. Peptides (12 or 16 aa in length)
with four different turn sequences are monomeric and fold cooperatively in
water, as has been observed previously for some hairpin peptides. However, the
folding free energies of the trpzips exceed substantially those of all
previously reported beta-hairpins and even those of some larger designed
proteins. NMR structures of three of the trpzip peptides reveal exceptionally
well-defined beta-hairpin conformations stabilized by cross-strand pairs of
indole rings. The trpzips are the smallest peptides to adopt an unique tertiary
fold without requiring metal binding, unusual amino acids, or disulfide
crosslinks.
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Selected figure(s)
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Figure 2.
Fig. 2. Equilibrium ultracentrifugation of trpzips 1-3.
The data shown are for 60 µM peptide samples and a rotor
speed of 40 krpm. Apparent molecular weights obtained from the
slopes (assuming ideal behavior) are shown; calculated formula
weights are 1,608 for trpzips 1 and 2 and 1,648 for trpzip3.
Trpzip1 data are offset vertically (ln absorbance  0.085) for
clarity.
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Figure 5.
Fig. 5. NMR analysis of trpzip4. (A) Overlay of the COSY
fingerprint regions for the wild-type gb1 peptide (red) and
trpzip4 (black); the location of crosspeaks are indicated for
both peptides and are labeled for trpzip4. (B) Ensemble of 20
structures of trpzip 4 compared with the minimized mean
structure of the B1 domain of protein G (Protein Data Bank code
2GB1) (30); backbone atoms of protein residues 46-52 were
superposed on the mean coordinates of the ensemble, yielding a
rmsd of 0.67 Å.
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Figures were
selected
by an automated process.
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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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A.A.Deeg,
T.E.Schrader,
S.Kempter,
J.Pfizer,
L.Moroder,
and
W.Zinth
(2011).
Light-triggered aggregation and disassembly of amyloid-like structures.
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Chemphyschem,
12,
559-562.
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K.Matsuura,
H.Hayashi,
K.Murasato,
and
N.Kimizuka
(2011).
Trigonal tryptophane zipper as a novel building block for pH-responsive peptide nano-assemblies.
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Chem Commun (Camb),
47,
265-267.
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M.Gupta,
and
V.S.Chauhan
(2011).
De novo design of α,β-didehydrophenylalanine containing peptides: From models to applications.
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Biopolymers,
95,
161-173.
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N.R.Hayre,
R.R.Singh,
and
D.L.Cox
(2011).
Evaluating force field accuracy with long-time simulations of a β-hairpin tryptophan zipper peptide.
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J Chem Phys,
134,
035103.
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Y.Yamamura,
H.Hirakawa,
S.Yamaguchi,
and
T.Nagamune
(2011).
Enhancement of sortase A-mediated protein ligation by inducing a β-hairpin structure around the ligation site.
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Chem Commun (Camb),
47,
4742-4744.
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A.J.Riemen,
and
M.L.Waters
(2010).
Positional effects of phosphoserine on β-hairpin stability.
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Org Biomol Chem,
8,
5411-5417.
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A.Lewandowska,
S.OÅ‚dziej,
A.Liwo,
and
H.A.Scheraga
(2010).
Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. III. Dynamics of long-range hydrophobic interactions.
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Proteins,
78,
723-737.
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B.L.Kier,
I.Shu,
L.A.Eidenschink,
and
N.H.Andersen
(2010).
Stabilizing capping motif for beta-hairpins and sheets.
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Proc Natl Acad Sci U S A,
107,
10466-10471.
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C.M.Santiveri,
and
M.A.Jiménez
(2010).
Tryptophan residues: Scarce in proteins but strong stabilizers of β-hairpin peptides.
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Biopolymers,
94,
779-790.
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C.Zhang,
and
J.Ma
(2010).
Enhanced sampling and applications in protein folding in explicit solvent.
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J Chem Phys,
132,
244101.
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H.Wei,
Q.Shao,
and
Y.Q.Gao
(2010).
The effects of side chain hydrophobicity on the denaturation of simple beta-hairpins.
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Phys Chem Chem Phys,
12,
9292-9299.
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M.P.Hatfield,
R.F.Murphy,
and
S.Lovas
(2010).
VCD spectroscopic properties of the beta-hairpin forming miniprotein CLN025 in various solvents.
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Biopolymers,
93,
442-450.
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M.P.Hatfield,
R.F.Murphy,
and
S.Lovas
(2010).
Molecular dynamics analysis of the conformations of a beta-hairpin miniprotein.
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J Phys Chem B,
114,
3028-3037.
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M.S.Bauer,
B.Strodel,
S.N.Fejer,
E.F.Koslover,
and
D.J.Wales
(2010).
Interpolation schemes for peptide rearrangements.
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J Chem Phys,
132,
054101.
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R.D.Hills,
L.Lu,
and
G.A.Voth
(2010).
Multiscale coarse-graining of the protein energy landscape.
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PLoS Comput Biol,
6,
e1000827.
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R.Uozumi,
T.Takahashi,
T.Yamazaki,
V.Granholm,
and
H.Mihara
(2010).
Design and conformational analysis of natively folded β-hairpin peptides stabilized by nucleobase interactions.
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Biopolymers,
94,
830-842.
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S.Roy,
T.L.Jansen,
and
J.Knoester
(2010).
Structural classification of the amide I sites of a beta-hairpin with isotope label 2DIR spectroscopy.
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Phys Chem Chem Phys,
12,
9347-9357.
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A.Irback,
S.Mitternacht,
and
S.Mohanty
(2009).
An effective all-atom potential for proteins.
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PMC Biophys,
2,
2.
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A.J.Riemen,
and
M.L.Waters
(2009).
Design of highly stabilized beta-hairpin peptides through cation-pi interactions of lysine and n-methyllysine with an aromatic pocket.
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Biochemistry,
48,
1525-1531.
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A.J.Riemen,
and
M.L.Waters
(2009).
Controlling peptide folding with repulsive interactions between phosphorylated amino acids and tryptophan.
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J Am Chem Soc,
131,
14081-14087.
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A.Roy,
P.Bour,
and
T.A.Keiderling
(2009).
TD-DFT modeling of the circular dichroism for a tryptophan zipper peptide with coupled aromatic residues.
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Chirality,
21,
E163-E171.
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A.Skwierawska,
J.Makowska,
S.OÅ‚dziej,
A.Liwo,
and
H.A.Scheraga
(2009).
Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure.
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Proteins,
75,
931-953.
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A.Skwierawska,
S.OÅ‚dziej,
A.Liwo,
and
H.A.Scheraga
(2009).
Conformational studies of the C-terminal 16-amino-acid-residue fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus.
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Biopolymers,
91,
37-51.
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A.Skwierawska,
W.Zmudzińska,
S.OÅ‚dziej,
A.Liwo,
and
H.A.Scheraga
(2009).
Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. II. Interplay of local backbone conformational dynamics and long-range hydrophobic interactions in hairpin formation.
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Proteins,
76,
637-654.
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A.Vitalis,
and
R.V.Pappu
(2009).
ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions.
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J Comput Chem,
30,
673-699.
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G.Schäfer,
S.Shastri,
M.K.Verhoefen,
V.Vogel,
C.Glaubitz,
J.Wachtveitl,
and
W.Mäntele
(2009).
Characterizing the Structure and Photocycle of PR 2D Crystals with CD and FTIR Spectroscopy.
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Photochem Photobiol,
85,
529-534.
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L.Eidenschink,
B.L.Kier,
K.N.Huggins,
and
N.H.Andersen
(2009).
Very short peptides with stable folds: building on the interrelationship of Trp/Trp, Trp/cation, and Trp/backbone-amide interaction geometries.
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Proteins,
75,
308-322.
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M.Varedian,
M.Erdélyi,
A.Persson,
and
A.Gogoll
(2009).
Interplaying factors for the formation of photoswitchable beta-hairpins: the advantage of a flexible switch.
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J Pept Sci,
15,
107-113.
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Y.He,
C.Chen,
and
Y.Xiao
(2009).
United-residue (UNRES) Langevin dynamics simulations of trpzip2 folding.
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J Comput Biol,
16,
1719-1730.
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Y.He,
Y.Xiao,
A.Liwo,
and
H.A.Scheraga
(2009).
Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.
|
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J Comput Chem,
30,
2127-2135.
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Y.Mirassou,
C.M.Santiveri,
M.J.Pérez de Vega,
R.González-Muñiz,
and
M.A.Jiménez
(2009).
Disulfide bonds versus TrpTrp pairs in irregular beta-hairpins: NMR structure of vammin loop 3-derived peptides as a case study.
|
| |
Chembiochem,
10,
902-910.
|
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Y.Mu
(2009).
Dissociation aided and side chain sampling enhanced Hamiltonian replica exchange.
|
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J Chem Phys,
130,
164107.
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Y.Xiao,
C.Chen,
and
Y.He
(2009).
Folding mechanism of Beta-hairpin trpzip2: heterogeneity, transition state and folding pathways.
|
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Int J Mol Sci,
10,
2838-2848.
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Z.Cheng,
and
R.E.Campbell
(2009).
An engineered tryptophan zipper-type peptide as a molecular recognition scaffold.
|
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J Pept Sci,
15,
523-532.
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A.J.Riemen,
and
M.L.Waters
(2008).
Stabilization of the N-terminal beta-hairpin of ubiquitin by a terminal hydrophobic cluster.
|
| |
Biopolymers,
90,
394-398.
|
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B.L.Kier,
and
N.H.Andersen
(2008).
Probing the lower size limit for protein-like fold stability: ten-residue microproteins with specific, rigid structures in water.
|
| |
J Am Chem Soc,
130,
14675-14683.
|
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C.Chen,
and
Y.Xiao
(2008).
Observation of multiple folding pathways of beta-hairpin trpzip2 from independent continuous folding trajectories.
|
| |
Bioinformatics,
24,
659-665.
|
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D.Katagiri,
H.Fuji,
S.Neya,
and
T.Hoshino
(2008).
Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation.
|
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J Comput Chem,
29,
1930-1944.
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G.Settanni,
and
A.R.Fersht
(2008).
High temperature unfolding simulations of the TRPZ1 peptide.
|
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Biophys J,
94,
4444-4453.
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J.Chen,
and
C.L.Brooks Iii
(2008).
Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.
|
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Phys Chem Chem Phys,
10,
471-481.
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J.Wang,
W.Zhuang,
S.Mukamel,
and
R.Hochstrasser
(2008).
Two-dimensional infrared spectroscopy as a probe of the solvent electrostatic field for a twelve residue peptide.
|
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J Phys Chem B,
112,
5930-5937.
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K.Noy,
N.Kalisman,
and
C.Keasar
(2008).
Prediction of structural stability of short beta-hairpin peptides by molecular dynamics and knowledge-based potentials.
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BMC Struct Biol,
8,
27.
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M.Jager,
S.Deechongkit,
E.K.Koepf,
H.Nguyen,
J.Gao,
E.T.Powers,
M.Gruebele,
and
J.W.Kelly
(2008).
Understanding the mechanism of beta-sheet folding from a chemical and biological perspective.
|
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Biopolymers,
90,
751-758.
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M.S.Shell,
R.Ritterson,
and
K.A.Dill
(2008).
A test on peptide stability of AMBER force fields with implicit solvation.
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J Phys Chem B,
112,
6878-6886.
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P.Bour,
J.Kim,
J.Kapitan,
R.P.Hammer,
R.Huang,
L.Wu,
and
T.A.Keiderling
(2008).
Vibrational circular dichroism and IR spectral analysis as a test of theoretical conformational modeling for a cyclic hexapeptide.
|
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Chirality,
20,
1104-1119.
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T.C.Jansen,
and
J.Knoester
(2008).
Two-dimensional infrared population transfer spectroscopy for enhancing structural markers of proteins.
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Biophys J,
94,
1818-1825.
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T.Terada,
D.Satoh,
T.Mikawa,
Y.Ito,
and
K.Shimizu
(2008).
Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation.
|
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Proteins,
73,
621-631.
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PDB code:
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T.la Cour Jansen,
and
W.M.Ruszel
(2008).
Motional narrowing in the time-averaging approximation for simulating two-dimensional nonlinear infrared spectra.
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J Chem Phys,
128,
214501.
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Z.Cao,
and
H.Liu
(2008).
Using free energy perturbation to predict effects of changing force field parameters on computed conformational equilibriums of peptides.
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J Chem Phys,
129,
015101.
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A.J.Scotter,
M.Guo,
M.M.Tomczak,
M.E.Daley,
R.L.Campbell,
R.J.Oko,
D.A.Bateman,
A.Chakrabartty,
B.D.Sykes,
and
P.L.Davies
(2007).
Metal ion-dependent, reversible, protein filament formation by designed beta-roll polypeptides.
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| |
BMC Struct Biol,
7,
63.
|
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D.E.Dollins,
J.J.Warren,
R.M.Immormino,
and
D.T.Gewirth
(2007).
Structures of GRP94-nucleotide complexes reveal mechanistic differences between the hsp90 chaperones.
|
| |
Mol Cell,
28,
41-56.
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PDB codes:
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H.Yuki,
Y.Tanaka,
M.Hata,
H.Ishikawa,
S.Neya,
and
T.Hoshino
(2007).
Implementation of pi-pi interactions in molecular dynamics simulation.
|
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J Comput Chem,
28,
1091-1099.
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J.D.Chodera,
N.Singhal,
V.S.Pande,
K.A.Dill,
and
W.C.Swope
(2007).
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.
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| |
J Chem Phys,
126,
155101.
|
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M.Araki,
and
A.Tamura
(2007).
Transformation of an alpha-helix peptide into a beta-hairpin induced by addition of a fragment results in creation of a coexisting state.
|
| |
Proteins,
66,
860-868.
|
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PDB codes:
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M.Jäger,
M.Dendle,
A.A.Fuller,
and
J.W.Kelly
(2007).
A cross-strand Trp Trp pair stabilizes the hPin1 WW domain at the expense of function.
|
| |
Protein Sci,
16,
2306-2313.
|
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|
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|
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N.W.Luedtke,
R.J.Dexter,
D.B.Fried,
and
A.Schepartz
(2007).
Surveying polypeptide and protein domain conformation and association with FlAsH and ReAsH.
|
| |
Nat Chem Biol,
3,
779-784.
|
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|
|
|
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P.Timmerman,
W.C.Puijk,
and
R.H.Meloen
(2007).
Functional reconstruction and synthetic mimicry of a conformational epitope using CLIPS technology.
|
| |
J Mol Recognit,
20,
283-299.
|
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R.Acharya,
M.Gupta,
S.Ramakumar,
U.A.Ramagopal,
and
V.S.Chauhan
(2007).
Observation of glycine zipper and unanticipated occurrence of ambidextrous helices in the crystal structure of a chiral undecapeptide.
|
| |
BMC Struct Biol,
7,
51.
|
|
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|
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R.J.Woods,
J.O.Brower,
E.Castellanos,
M.Hashemzadeh,
O.Khakshoor,
W.A.Russu,
and
J.S.Nowick
(2007).
Cyclic modular beta-sheets.
|
| |
J Am Chem Soc,
129,
2548-2558.
|
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R.Mahalakshmi,
A.Sengupta,
S.Raghothama,
N.Shamala,
and
P.Balaram
(2007).
Tryptophan rich peptides: influence of indole rings on backbone conformation.
|
| |
Biopolymers,
88,
36-54.
|
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R.Rai,
S.Raghothama,
R.Sridharan,
and
P.Balaram
(2007).
Tuning the beta-turn segment in designed peptide beta-hairpins: construction of a stable type I' beta-turn nucleus and hairpin-helix transition promoting segments.
|
| |
Biopolymers,
88,
350-361.
|
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S.Rana,
B.Kundu,
and
S.Durani
(2007).
A mixed-alpha,beta miniprotein stereochemically reprogrammed to high-binding affinity for acetylcholine.
|
| |
Biopolymers,
87,
231-243.
|
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T.K.Chakraborty,
D.Koley,
R.Ravi,
and
A.C.Kunwar
(2007).
Synthesis and structural studies of peptides containing a mannose-derived furanoid sugar amino acid.
|
| |
Org Biomol Chem,
5,
3713-3716.
|
|
|
|
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|
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Y.Wei,
B.M.Huyghues-Despointes,
J.Tsai,
and
J.M.Scholtz
(2007).
NMR study and molecular dynamics simulations of optimized beta-hairpin fragments of protein G.
|
| |
Proteins,
69,
285-296.
|
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|
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|
|
Z.Cheng,
M.Miskolzie,
and
R.E.Campbell
(2007).
In vivo screening identifies a highly folded beta-hairpin peptide with a structured extension.
|
| |
Chembiochem,
8,
880-883.
|
|
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PDB code:
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Z.Xu,
H.H.Luo,
and
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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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