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PDBsum entry 1j4m
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De novo protein
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PDB id
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1j4m
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DOI no:
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Proc Natl Acad Sci U S A
99:614-619
(2002)
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PubMed id:
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Combinatorial approaches: a new tool to search for highly structured beta-hairpin peptides.
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M.T.Pastor,
M.López de la Paz,
E.Lacroix,
L.Serrano,
E.Pérez-Payá.
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ABSTRACT
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Here we present a combinatorial approach to evolve a stable beta-hairpin fold in
a linear peptide. Starting with a de novo-designed linear peptide that shows a
beta-hairpin structure population of around 30%, we selected four positions to
build up a combinatorial library of 20(4) sequences. Deconvolution of the
library using circular dichroism reduced such a sequence complexity to 36
defined sequences. Circular dichroism and NMR of these peptides resulted in the
identification of two linear 14-aa-long peptides that in plain buffered
solutions showed a percentage of beta-hairpin structure higher than 70%. Our
results show how combinatorial approaches can be used to obtain highly
structured peptide sequences that could be used as templates in which
functionality can be introduced.
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Selected figure(s)
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Figure 4.
Fig. 4. Observed conformational C  H chemical
shift increments (   [C  H])
relative to the chemical shifts of the unfolded state for
peptides MBH12 (black bars; Aa^4 is W) and MBH36 (gray bars;
Aa^4 is Y).
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Figure 5.
Fig. 5. Schematic diagram of the structure of peptides
MBH12 and MBH36 in solution. The observed NOEs in water are
shown as thick lines.
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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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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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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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D.Matthes,
and
B.L.de Groot
(2009).
Secondary structure propensities in peptide folding simulations: a systematic comparison of molecular mechanics interaction schemes.
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Biophys J,
97,
599-608.
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T.Bereau,
and
M.Deserno
(2009).
Generic coarse-grained model for protein folding and aggregation.
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J Chem Phys,
130,
235106.
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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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D.Pantoja-Uceda,
M.T.Pastor,
J.Salgado,
A.Pineda-Lucena,
and
E.Pérez-Payá
(2008).
Design of a bivalent peptide with two independent elements of secondary structure able to fold autonomously.
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J Pept Sci,
14,
845-854.
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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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P.Mora,
R.J.Carbajo,
A.Pineda-Lucena,
M.M.Sánchez del Pino,
and
E.Pérez-Payá
(2008).
Solvent-exposed residues located in the beta-sheet modulate the stability of the tetramerization domain of p53--a structural and combinatorial approach.
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Proteins,
71,
1670-1685.
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PDB codes:
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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.
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Proteins,
66,
860-868.
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PDB codes:
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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.
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Proteins,
69,
285-296.
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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.
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Chembiochem,
8,
880-883.
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PDB code:
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B.M.Huyghues-Despointes,
X.Qu,
J.Tsai,
and
J.M.Scholtz
(2006).
Terminal ion pairs stabilize the second beta-hairpin of the B1 domain of protein G.
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Proteins,
63,
1005-1017.
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G.Malet,
A.G.Martín,
M.Orzáez,
M.J.Vicent,
I.Masip,
G.Sanclimens,
A.Ferrer-Montiel,
I.Mingarro,
A.Messeguer,
H.O.Fearnhead,
and
E.Pérez-Payá
(2006).
Small molecule inhibitors of Apaf-1-related caspase- 3/-9 activation that control mitochondrial-dependent apoptosis.
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Cell Death Differ,
13,
1523-1532.
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A.Nusrat,
G.T.Brown,
J.Tom,
A.Drake,
T.T.Bui,
C.Quan,
and
R.J.Mrsny
(2005).
Multiple protein interactions involving proposed extracellular loop domains of the tight junction protein occludin.
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Mol Biol Cell,
16,
1725-1734.
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M.T.Pastor,
A.Giménez-Giner,
and
E.Pérez-Payá
(2005).
The role of an aliphatic-aromatic interaction in the stabilization of a model beta-hairpin peptide.
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Chembiochem,
6,
1753-1756.
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R.S.Armen,
B.M.Bernard,
R.Day,
D.O.Alonso,
and
V.Daggett
(2005).
Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases.
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Proc Natl Acad Sci U S A,
102,
13433-13438.
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H.Mira,
M.Vilar,
V.Esteve,
M.Martinell,
M.J.Kogan,
E.Giralt,
D.Salom,
I.Mingarro,
L.Peñarrubia,
and
E.Pérez-Payá
(2004).
Ionic self-complementarity induces amyloid-like fibril formation in an isolated domain of a plant copper metallochaperone protein.
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BMC Struct Biol,
4,
7.
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M.S.Searle,
and
B.Ciani
(2004).
Design of beta-sheet systems for understanding the thermodynamics and kinetics of protein folding.
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Curr Opin Struct Biol,
14,
458-464.
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M.T.Pastor,
P.Mora,
A.Ferrer-Montiel,
and
E.Pérez-Payá
(2004).
Design of bioactive and structurally well-defined peptides from conformationally restricted libraries.
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Biopolymers,
76,
357-365.
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C.M.Santiveri,
M.Rico,
M.A.Jiménez,
M.T.Pastor,
and
E.Pérez-Payá
(2003).
Insights into the determinants of beta-sheet stability: 1H and 13C NMR conformational investigation of three-stranded antiparallel beta-sheet-forming peptides.
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J Pept Res,
61,
177-188.
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S.Hutschenreiter,
L.Neumann,
U.Rädler,
L.Schmitt,
and
R.Tampé
(2003).
Metal-chelating amino acids as building blocks for synthetic receptors sensing metal ions and histidine-tagged proteins.
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Chembiochem,
4,
1340-1344.
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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
codes are
shown on the right.
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Links
