 |
PDBsum entry 1hqj
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
De novo protein
|
PDB id
|
|
|
|
1hqj
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
De novo protein
|
|
|
Title:
|
|
Crystal structure of a de novo designed trimeric coiled-coil peptide
|
|
Structure:
|
|
Zju-glu-leu-glu-ala-arg-ile-arg-glu-leu-glu-ala-arg-ile- lys-nh2. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Engineered: yes
|
|
Source:
|
|
Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Other_details: neosystem
|
|
Biol. unit:
|
|
Trimer (from
)
|
|
Resolution:
|
|
|
1.20Å
|
R-factor:
|
0.170
|
R-free:
|
0.223
|
|
|
Authors:
|
|
P.Burkhard,M.Meier,A.Lustig
|
|
Key ref:
|
|
P.Burkhard
et al.
(2000).
Design of a minimal protein oligomerization domain by a structural approach.
Protein Sci,
9,
2294-2301.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
18-Dec-00
|
Release date:
|
14-Mar-01
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
No UniProt id for this chain
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Protein Sci
9:2294-2301
(2000)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Design of a minimal protein oligomerization domain by a structural approach.
|
|
P.Burkhard,
M.Meier,
A.Lustig.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Because of the simplicity and regularity of the alpha-helical coiled coil
relative to other structural motifs, it can be conveniently used to clarify the
molecular interactions responsible for protein folding and stability. Here we
describe the de novo design and characterization of a two heptad-repeat peptide
stabilized by a complex network of inter- and intrahelical salt bridges.
Circular dichroism spectroscopy and analytical ultracentrifugation show that
this peptide is highly alpha-helical and 100% dimeric tinder physiological
buffer conditions. Interestingly, the peptide was shown to switch its
oligomerization state from a dimer to a trimer upon increasing ionic strength.
The correctness of the rational design principles used here is supported by
details of the atomic structure of the peptide deduced from X-ray
crystallography. The structure of the peptide shows that it is not a molten
globule but assumes a unique, native-like conformation. This de novo peptide
thus represents an attractive model system for the design of a molecular
recognition system.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
H.GradiĊĦar,
and
R.Jerala
(2011).
De novo design of orthogonal peptide pairs forming parallel coiled-coil heterodimers.
|
| |
J Pept Sci,
17,
100-106.
|
|
|
|
|
|
|
L.E.Kapinos,
P.Burkhard,
H.Herrmann,
U.Aebi,
and
S.V.Strelkov
(2011).
Simultaneous formation of right- and left-handed anti-parallel coiled-coil interfaces by a coil2 fragment of human lamin A.
|
| |
J Mol Biol,
408,
135-146.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
Z.Ji,
C.Song,
X.Lu,
and
J.Wang
(2011).
Two coiled-coil regions of Xanthomonas oryzae pv. oryzae harpin differ in oligomerization and hypersensitive response induction.
|
| |
Amino Acids,
40,
381-392.
|
|
|
|
|
|
|
B.Apostolovic,
M.Danial,
and
H.A.Klok
(2010).
Coiled coils: attractive protein folding motifs for the fabrication of self-assembled, responsive and bioactive materials.
|
| |
Chem Soc Rev,
39,
3541-3575.
|
|
|
|
|
|
|
J.P.Kirwan,
and
R.S.Hodges
(2010).
Critical interactions in the stability control region of tropomyosin.
|
| |
J Struct Biol,
170,
294-306.
|
|
|
|
|
|
|
P.Guardado-Calvo,
G.C.Fox,
A.L.Llamas-Saiz,
and
M.J.van Raaij
(2009).
Crystallographic structure of the {alpha}-helical triple coiled-coil domain of avian reovirus S1133 fibre.
|
| |
J Gen Virol,
90,
672-677.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
T.A.Pimentel,
Z.Yan,
S.A.Jeffers,
K.V.Holmes,
R.S.Hodges,
and
P.Burkhard
(2009).
Peptide nanoparticles as novel immunogens: design and analysis of a prototypic severe acute respiratory syndrome vaccine.
|
| |
Chem Biol Drug Des,
73,
53-61.
|
|
|
|
|
|
|
W.C.Pomerantz,
E.B.Hadley,
C.G.Fry,
and
S.H.Gellman
(2009).
In situ monitoring of backbone thioester exchange by 19F NMR.
|
| |
Chembiochem,
10,
2177-2181.
|
|
|
|
|
|
|
H.E.Huttunen-Hennelly,
and
J.C.Sherman
(2008).
An investigation into the native-like properties of de novo designed cavitand-based four-helix bundle proteins.
|
| |
Biopolymers,
90,
37-50.
|
|
|
|
|
|
|
M.Kreiner,
Z.Li,
J.Beattie,
S.M.Kelly,
H.J.Mardon,
and
C.F.van der Walle
(2008).
Self-assembling multimeric integrin alpha5beta1 ligands for cell attachment and spreading.
|
| |
Protein Eng Des Sel,
21,
553-560.
|
|
|
|
|
|
|
S.Raman,
G.Machaidze,
A.Lustig,
U.Aebi,
and
P.Burkhard
(2006).
Structure-based design of peptides that self-assemble into regular polyhedral nanoparticles.
|
| |
Nanomedicine,
2,
95.
|
|
|
|
|
|
|
R.A.Kammerer,
D.Kostrewa,
P.Progias,
S.Honnappa,
D.Avila,
A.Lustig,
F.K.Winkler,
J.Pieters,
and
M.O.Steinmetz
(2005).
A conserved trimerization motif controls the topology of short coiled coils.
|
| |
Proc Natl Acad Sci U S A,
102,
13891-13896.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.M.Mason,
and
K.M.Arndt
(2004).
Coiled coil domains: stability, specificity, and biological implications.
|
| |
Chembiochem,
5,
170-176.
|
|
|
|
|
|
|
R.A.Kammerer,
D.Kostrewa,
J.Zurdo,
A.Detken,
C.García-Echeverría,
J.D.Green,
S.A.Müller,
B.H.Meier,
F.K.Winkler,
C.M.Dobson,
and
M.O.Steinmetz
(2004).
Exploring amyloid formation by a de novo design.
|
| |
Proc Natl Acad Sci U S A,
101,
4435-4440.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.C.Kwok,
and
R.S.Hodges
(2004).
Effect of chain length on coiled-coil stability: decreasing stability with increasing chain length.
|
| |
Biopolymers,
76,
378-390.
|
|
|
|
|
|
|
D.L.Lee,
S.Ivaninskii,
P.Burkhard,
and
R.S.Hodges
(2003).
Unique stabilizing interactions identified in the two-stranded alpha-helical coiled-coil: crystal structure of a cortexillin I/GCN4 hybrid coiled-coil peptide.
|
| |
Protein Sci,
12,
1395-1405.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
Y.B.Yu
(2002).
Coiled-coils: stability, specificity, and drug delivery potential.
|
| |
Adv Drug Deliv Rev,
54,
1113-1129.
|
|
|
|
|
|
|
V.De Marco,
P.Burkhard,
N.Le Bot,
I.Vernos,
and
A.Hoenger
(2001).
Analysis of heterodimer formation by Xklp3A/B, a newly cloned kinesin-II from Xenopus laevis.
|
| |
EMBO J,
20,
3370-3379.
|
|
|
|
|
|
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.
|
|
Links
