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PDBsum entry 1dwz
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Prion protein
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PDB id
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1dwz
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Contents |
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* Residue conservation analysis
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DOI no:
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Proc Natl Acad Sci U S A
97:8334-8339
(2000)
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PubMed id:
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NMR structure of the bovine prion protein.
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F.López Garcia,
R.Zahn,
R.Riek,
K.Wüthrich.
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ABSTRACT
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The NMR structures of the recombinant 217-residue polypeptide chain of the
mature bovine prion protein, bPrP(23-230), and a C-terminal fragment,
bPrP(121-230), include a globular domain extending from residue 125 to residue
227, a short flexible chain end of residues 228-230, and an N-terminal flexibly
disordered "tail" comprising 108 residues for the intact protein and 4 residues
for bPrP(121-230), respectively. The globular domain contains three
alpha-helices comprising the residues 144-154, 173-194, and 200-226, and a short
antiparallel beta-sheet comprising the residues 128-131 and 161-164. The
best-defined parts of the globular domain are the central portions of the
helices 2 and 3, which are linked by the only disulfide bond in bPrP.
Significantly increased disorder and mobility is observed for helix 1, the loop
166-172 leading from the beta-strand 2 to helix 2, the end of helix 2 and the
following loop, and the last turn of helix 3. Although there are characteristic
local differences relative to the conformations of the murine and Syrian hamster
prion proteins, the bPrP structure is essentially identical to that of the human
prion protein. On the other hand, there are differences between bovine and human
PrP in the surface distribution of electrostatic charges, which then appears to
be the principal structural feature of the "healthy" PrP form that might affect
the stringency of the species barrier for transmission of prion diseases between
humans and cattle.
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Selected figure(s)
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Figure 1.
Fig. 1. (a) Cartoon of the three-dimensional structure of
the intact bPrP(23-230). Helices are green,  -strands are
cyan, segments with nonregular secondary structure within the
C-terminal domain are yellow, and the flexibly disordered "tail"
of residues 23-121 is represented by 108 yellow dots, each of
which represents a residue of the tail (the numeration for hPrP
is used, and the insertions and deletions are placed according
to the alignment in ref. 23). (b) Stereo-view of an all-heavy
atom presentation of the globular domain in bPrP(23-230), with
residues 121-230, in the same orientation as in a. The backbone
is shown as a green spline function through the C^  positions,
hydrophobic side chains are yellow, and polar and charged side
chains are violet. (c and d) Surface views of the globular
domains of bPrP and hPrP, respectively. The orientation of the
molecule is slightly changed relative to a, so that the residue
186 is approximately in the center. The electrostatic surface
potential is indicated in red (negative charge), white
(neutral), and blue (positive charge). The figures were prepared
with the program MOLMOL (42).
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Figure 5.
Fig. 5. Data characterizing the internal mobility of the
globular domain of bPrP. (a) Steady-state 15N{1H}-NOEs of
bPrP(121-230), where Leu-125 is the first residue with a
positive NOE. (b) Longitudinal 15N spin-relaxation times,
T[1](15N). (c) Transverse 15N spin-relaxation times, T[2](15N).
The arrow indicates an upper limit for T[2](15N) of the residues
166-172. The locations of the regular secondary structure
elements are indicated in a.
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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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R.Tycko
(2011).
Solid-state NMR studies of amyloid fibril structure.
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Annu Rev Phys Chem,
62,
279-299.
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A.Qualtieri,
E.Urso,
M.Le Pera,
T.Sprovieri,
S.Bossio,
A.Gambardella,
and
A.Quattrone
(2010).
Proteomic profiling of cerebrospinal fluid in Creutzfeldt-Jakob disease.
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Expert Rev Proteomics,
7,
907-917.
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B.Sweeting,
M.Q.Khan,
A.Chakrabartty,
and
E.F.Pai
(2010).
Structural factors underlying the species barrier and susceptibility to infection in prion disease.
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Biochem Cell Biol,
88,
195-202.
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C.A.Tabrett,
C.F.Harrison,
B.Schmidt,
S.A.Bellingham,
T.Hardy,
Y.H.Sanejouand,
A.F.Hill,
and
P.J.Hogg
(2010).
Changing the solvent accessibility of the prion protein disulfide bond markedly influences its trafficking and effect on cell function.
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Biochem J,
428,
169-182.
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C.J.Sigurdson,
K.P.Nilsson,
S.Hornemann,
G.Manco,
N.Fernández-Borges,
P.Schwarz,
J.Castilla,
K.Wüthrich,
and
A.Aguzzi
(2010).
A molecular switch controls interspecies prion disease transmission in mice.
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J Clin Invest,
120,
2590-2599.
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G.Ilc,
G.Giachin,
M.Jaremko,
Å..Jaremko,
F.Benetti,
J.Plavec,
I.Zhukov,
and
G.Legname
(2010).
NMR structure of the human prion protein with the pathological Q212P mutation reveals unique structural features.
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PLoS One,
5,
e11715.
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PDB code:
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G.Rossetti,
G.Giachin,
G.Legname,
and
P.Carloni
(2010).
Structural facets of disease-linked human prion protein mutants: a molecular dynamic study.
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Proteins,
78,
3270-3280.
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H.Zhao,
X.Y.Wang,
W.Zou,
and
Y.P.Zhang
(2010).
Prion protein gene (PRNP) polymorphisms in native Chinese cattle.
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Genome,
53,
138-145.
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N.Daude,
V.Ng,
J.C.Watts,
S.Genovesi,
J.P.Glaves,
S.Wohlgemuth,
G.Schmitt-Ulms,
H.Young,
J.McLaurin,
P.E.Fraser,
and
D.Westaway
(2010).
Wild-type Shadoo proteins convert to amyloid-like forms under native conditions.
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J Neurochem,
113,
92.
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S.Lee,
L.Antony,
R.Hartmann,
K.J.Knaus,
K.Surewicz,
W.K.Surewicz,
and
V.C.Yee
(2010).
Conformational diversity in prion protein variants influences intermolecular beta-sheet formation.
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EMBO J,
29,
251-262.
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PDB codes:
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W.C.Guest,
N.R.Cashman,
and
S.S.Plotkin
(2010).
Electrostatics in the stability and misfolding of the prion protein: salt bridges, self energy, and solvation.
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Biochem Cell Biol,
88,
371-381.
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Y.Wen,
J.Li,
M.Xiong,
Y.Peng,
W.Yao,
J.Hong,
and
D.Lin
(2010).
Solution structure and dynamics of the I214V mutant of the rabbit prion protein.
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PLoS One,
5,
e13273.
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PDB code:
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A.Nazabal,
S.Hornemann,
A.Aguzzi,
and
R.Zenobi
(2009).
Hydrogen/deuterium exchange mass spectrometry identifies two highly protected regions in recombinant full-length prion protein amyloid fibrils.
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J Mass Spectrom,
44,
965-977.
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C.J.Sigurdson,
K.P.Nilsson,
S.Hornemann,
M.Heikenwalder,
G.Manco,
P.Schwarz,
D.Ott,
T.Rülicke,
P.P.Liberski,
C.Julius,
J.Falsig,
L.Stitz,
K.Wüthrich,
and
A.Aguzzi
(2009).
De novo generation of a transmissible spongiform encephalopathy by mouse transgenesis.
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Proc Natl Acad Sci U S A,
106,
304-309.
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C.Soto
(2009).
Constraining the loop, releasing prion infectivity.
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Proc Natl Acad Sci U S A,
106,
10-11.
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D.B.O'Sullivan,
C.E.Jones,
S.R.Abdelraheim,
M.W.Brazier,
H.Toms,
D.R.Brown,
and
J.H.Viles
(2009).
Dynamics of a truncated prion protein, PrP(113-231), from (15)N NMR relaxation: order parameters calculated and slow conformational fluctuations localized to a distinct region.
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Protein Sci,
18,
410-423.
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E.D.Walter,
D.J.Stevens,
A.R.Spevacek,
M.P.Visconte,
A.Dei Rossi,
and
G.L.Millhauser
(2009).
Copper binding extrinsic to the octarepeat region in the prion protein.
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Curr Protein Pept Sci,
10,
529-535.
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E.Gralka,
D.Valensin,
K.Gajda,
D.Bacco,
L.Szyrwiel,
M.Remelli,
G.Valensin,
W.Kamasz,
W.Baranska-Rybak,
and
H.Kozłowski
(2009).
Copper(II) coordination outside the tandem repeat region of an unstructured domain of chicken prion protein.
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Mol Biosyst,
5,
497-510.
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F.Benetti,
and
G.Legname
(2009).
De novo mammalian prion synthesis.
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Prion,
3,
213-219.
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J.Y.Shin,
J.I.Shin,
J.S.Kim,
Y.S.Yang,
Y.K.Shin,
K.K.Kim,
S.Lee,
and
D.H.Kweon
(2009).
Disulfide bond as a structural determinant of prion protein membrane insertion.
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Mol Cells,
27,
673-680.
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O.Julien,
S.Chatterjee,
A.Thiessen,
S.P.Graether,
and
B.D.Sykes
(2009).
Differential stability of the bovine prion protein upon urea unfolding.
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Protein Sci,
18,
2172-2182.
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R.A.Moore,
L.M.Taubner,
and
S.A.Priola
(2009).
Prion protein misfolding and disease.
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Curr Opin Struct Biol,
19,
14-22.
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S.H.Bae,
G.Legname,
A.Serban,
S.B.Prusiner,
P.E.Wright,
and
H.J.Dyson
(2009).
Prion proteins with pathogenic and protective mutations show similar structure and dynamics.
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Biochemistry,
48,
8120-8128.
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S.Hornemann,
B.Christen,
C.von Schroetter,
D.R.Pérez,
and
K.Wüthrich
(2009).
Prion protein library of recombinant constructs for structural biology.
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FEBS J,
276,
2359-2367.
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C.J.Sigurdson
(2008).
A prion disease of cervids: chronic wasting disease.
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Vet Res,
39,
41.
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C.K.Schneider,
and
U.Kalinke
(2008).
Toward biosimilar monoclonal antibodies.
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Nat Biotechnol,
26,
985-990.
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E.Birkmann,
and
D.Riesner
(2008).
Prion infection: seeded fibrillization or more?
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Prion,
2,
67-72.
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K.D.Kedarisetti,
S.Dick,
and
L.Kurgan
(2008).
Searching for Factors that Distinguish Disease-Prone and Disease-Resistant Prions via Sequence Analysis.
|
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Bioinform Biol Insights,
2,
133-144.
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K.Elfrink,
J.Ollesch,
J.Stöhr,
D.Willbold,
D.Riesner,
and
K.Gerwert
(2008).
Structural changes of membrane-anchored native PrP(C).
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Proc Natl Acad Sci U S A,
105,
10815-10819.
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L.Ronga,
P.Palladino,
G.Saviano,
T.Tancredi,
E.Benedetti,
R.Ragone,
and
F.Rossi
(2008).
Structural characterization of a neurotoxic threonine-rich peptide corresponding to the human prion protein alpha 2-helical 180-195 segment, and comparison with full-length alpha 2-helix-derived peptides.
|
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J Pept Sci,
14,
1096-1102.
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M.B.Oboznaya,
N.M.Vladimirova,
M.A.Titova,
T.D.Volkova,
D.O.Koroev,
A.A.Ryabokon,
A.A.Egorov,
S.S.Rybakov,
and
O.M.Vol'pina
(2008).
[Production of monoclonal antibodies to the prion protein and their characterization.]
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Bioorg Khim,
34,
754-763.
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S.E.Encalada,
K.L.Moya,
S.Lehmann,
and
R.Zahn
(2008).
The role of the prion protein in the molecular basis for synaptic plasticity and nervous system development.
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J Mol Neurosci,
34,
9.
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S.Noinville,
J.F.Chich,
and
H.Rezaei
(2008).
Misfolding of the prion protein: linking biophysical and biological approaches.
|
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Vet Res,
39,
48.
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V.B.Grigoriev,
S.L.Kalnov,
A.N.Pokidyshev,
V.V.Tsibezov,
M.V.Balandina,
R.A.Gibadulin,
O.A.Verkhovsky,
and
S.M.Klimenko
(2008).
Fibrillization of recombinant bovine prion protein (rec-PrP) in vitro.
|
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Dokl Biochem Biophys,
420,
112-114.
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W.Shin,
B.Lee,
S.Hong,
C.Ryou,
and
M.Kwon
(2008).
Cloning and expression of a prion protein (PrP) gene from Korean bovine (Bos taurus coreanae) and production of rabbit anti-bovine PrP antibody.
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Biotechnol Lett,
30,
1705-1711.
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Y.Okemoto-Nakamura,
Y.Yamakawa,
K.Hanada,
K.Tanaka,
M.Miura,
I.Tanida,
M.Nishijima,
and
K.Hagiwara
(2008).
Synthetic fibril peptide promotes clearance of scrapie prion protein by lysosomal degradation.
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Microbiol Immunol,
52,
357-365.
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A.Pastore,
and
A.Zagari
(2007).
A structural overview of the vertebrate prion proteins.
|
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Prion,
1,
185-197.
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C.W.Lennon,
H.D.Cox,
S.P.Hennelly,
S.J.Chelmo,
and
M.A.McGuirl
(2007).
Probing structural differences in prion protein isoforms by tyrosine nitration.
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Biochemistry,
46,
4850-4860.
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O.Lupi,
and
M.A.Peryassu
(2007).
An emerging concept of prion infections as a form of transmissible cerebral amyloidosis.
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Prion,
1,
223-227.
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Y.Arii,
H.Yamaguchi,
and
S.Fukuoka
(2007).
Production of a soluble recombinant prion protein fused to blue fluorescent protein without refolding or detergents in Escherichia coli cells.
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Biosci Biotechnol Biochem,
71,
2511-2514.
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A.Strom,
S.Diecke,
G.Hunsmann,
and
A.W.Stuke
(2006).
Identification of prion protein binding proteins by combined use of far-Western immunoblotting, two dimensional gel electrophoresis and mass spectrometry.
|
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Proteomics,
6,
26-34.
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E.Langella,
R.Improta,
O.Crescenzi,
and
V.Barone
(2006).
Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pK(a) calculations and molecular dynamics simulations.
|
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Proteins,
64,
167-177.
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E.Leclerc,
H.Serban,
S.B.Prusiner,
D.R.Burton,
and
R.A.Williamson
(2006).
Copper induces conformational changes in the N-terminal part of cell-surface PrPC.
|
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Arch Virol,
151,
2103-2109.
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L.Ronga,
B.Tizzano,
P.Palladino,
R.Ragone,
E.Urso,
M.Maffia,
M.Ruvo,
E.Benedetti,
and
F.Rossi
(2006).
The prion protein: Structural features and related toxic peptides.
|
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Chem Biol Drug Des,
68,
139-147.
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N.Kachel,
W.Kremer,
R.Zahn,
and
H.R.Kalbitzer
(2006).
Observation of intermediate states of the human prion protein by high pressure NMR spectroscopy.
|
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BMC Struct Biol,
6,
16.
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N.Piening,
P.Weber,
T.Högen,
M.Beekes,
H.Kretzschmar,
and
A.Giese
(2006).
Photo-induced crosslinking of prion protein oligomers and prions.
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Amyloid,
13,
67-77.
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S.Osváth,
M.Jäckel,
G.Agócs,
P.Závodszky,
G.Köhler,
and
J.Fidy
(2006).
Domain interactions direct misfolding and amyloid formation of yeast phosphoglycerate kinase.
|
| |
Proteins,
62,
909-917.
|
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T.P.Knowles,
and
R.Zahn
(2006).
Enhanced stability of human prion proteins with two disulfide bridges.
|
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Biophys J,
91,
1494-1500.
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A.Barducci,
R.Chelli,
P.Procacci,
and
V.Schettino
(2005).
Misfolding pathways of the prion protein probed by molecular dynamics simulations.
|
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Biophys J,
88,
1334-1343.
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A.D.Gossert,
S.Bonjour,
D.A.Lysek,
F.Fiorito,
and
K.Wüthrich
(2005).
Prion protein NMR structures of elk and of mouse/elk hybrids.
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Proc Natl Acad Sci U S A,
102,
646-650.
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PDB codes:
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A.D.van Dijk,
S.J.de Vries,
C.Dominguez,
H.Chen,
H.X.Zhou,
and
A.M.Bonvin
(2005).
Data-driven docking: HADDOCK's adventures in CAPRI.
|
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Proteins,
60,
232-238.
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B.Tizzano,
P.Palladino,
A.De Capua,
D.Marasco,
F.Rossi,
E.Benedetti,
C.Pedone,
R.Ragone,
and
M.Ruvo
(2005).
The human prion protein alpha2 helix: a thermodynamic study of its conformational preferences.
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Proteins,
59,
72-79.
|
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D.A.Lysek,
C.Schorn,
L.G.Nivon,
V.Esteve-Moya,
B.Christen,
L.Calzolai,
C.von Schroetter,
F.Fiorito,
T.Herrmann,
P.Güntert,
and
K.Wüthrich
(2005).
Prion protein NMR structures of cats, dogs, pigs, and sheep.
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Proc Natl Acad Sci U S A,
102,
640-645.
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PDB codes:
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D.La Mendola,
R.P.Bonomo,
G.Impellizzeri,
G.Maccarrone,
G.Pappalardo,
A.Pietropaolo,
E.Rizzarelli,
and
V.Zito
(2005).
Copper(II) complexes with chicken prion repeats: influence of proline and tyrosine residues on the coordination features.
|
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J Biol Inorg Chem,
10,
463-475.
|
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E.Ben-Zeev,
N.Kowalsman,
A.Ben-Shimon,
D.Segal,
T.Atarot,
O.Noivirt,
T.Shay,
and
M.Eisenstein
(2005).
Docking to single-domain and multiple-domain proteins: old and new challenges.
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PDB code:
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PDB codes:
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
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