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PDBsum entry 1m8m
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Structural protein
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PDB id
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1m8m
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Contents |
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* Residue conservation analysis
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PDB id:
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Structural protein
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Title:
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Solid-state mas nmr structure of the a-spectrin sh3 domain
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Structure:
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Spectrin alpha chain, brain. Chain: a. Fragment: src homology 3 domain (residues 965-1025). Synonym: spectrin, non-erythroid alpha chain, fodrin alpha chain. Engineered: yes
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Source:
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Gallus gallus. Chicken. Organism_taxid: 9031. Organ: brain. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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NMR struc:
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12 models
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Authors:
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F.Castellani,B.Van Rossum,A.Diehl,M.Schubert,K.Rehbein,H.Oschkinat
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Key ref:
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F.Castellani
et al.
(2002).
Structure of a protein determined by solid-state magic-angle-spinning NMR spectroscopy.
Nature,
420,
98.
PubMed id:
DOI:
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Date:
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25-Jul-02
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Release date:
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20-Nov-02
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PROCHECK
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Headers
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References
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P07751
(SPTN1_CHICK) -
Spectrin alpha chain, non-erythrocytic 1 from Gallus gallus
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Seq:
Struc:
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2477 a.a.
56 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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DOI no:
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Nature
420:98
(2002)
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PubMed id:
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Structure of a protein determined by solid-state magic-angle-spinning NMR spectroscopy.
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F.Castellani,
B.van Rossum,
A.Diehl,
M.Schubert,
K.Rehbein,
H.Oschkinat.
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ABSTRACT
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The determination of a representative set of protein structures is a chief aim
in structural genomics. Solid-state NMR may have a crucial role in structural
investigations of those proteins that do not easily form crystals or are not
accessible to solution NMR, such as amyloid systems or membrane proteins. Here
we present a protein structure determined by solid-state magic-angle-spinning
(MAS) NMR. Almost complete (13)C and (15)N resonance assignments for a
micro-crystalline preparation of the alpha-spectrin Src-homology 3 (SH3) domain
formed the basis for the extraction of a set of distance restraints. These
restraints were derived from proton-driven spin diffusion (PDSD) spectra of
biosynthetically site-directed, labelled samples obtained from bacteria grown
using [1,3-(13)C]glycerol or [2-(13)C]glycerol as carbon sources. This allowed
the observation of long-range distance correlations up to approximately 7 A. The
calculated global fold of the alpha-spectrin SH3 domain is based on 286
inter-residue (13)C-(13)C and six (15)N-(15)N restraints, all self-consistently
obtained by solid-state MAS NMR. This MAS NMR procedure should be widely
applicable to small membrane proteins that can be expressed in bacteria.
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Selected figure(s)
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Figure 2.
Figure 2: Assignment strategy. Regions extracted from the
spectra of Fig. 1c and d (I -VI) superimposed on a PDSD spectrum
of uniformly labelled SH3 domain (black), the latter recorded
with a short mixing time of 15 ms (ref. 5. Part of the
assignment of the long-range correlations is reported in the
figure, and the lines define the different correlation patterns.
As an example, correlations between residues L33 and V44 are
shown. The correlations between the C  and
C  signals
of V44 and C and
C  signals
of L33 are observed in panels I -III for 2-SH3, whereas
correlations between the methyl groups appear in the spectrum of
1,3-SH3 (panel IV). Of particular interest is the region around
50 p.p.m. (panel VI), where for 2-SH3 a large number of
cross-peaks due to the proline-  signals
(P20 and P54) are observed, whereas in the corresponding area of
the U-SH3 sample (see Fig. 1b), no correlations are detected. In
the upper left corner, a schematic representation of an
antiparallel -sheet
is shown. The numbering of the residues (i and j) corresponds to
the numbering in Table 1.
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Figure 3.
Figure 3: Solid-state structure of the alpha- -spectrin
SH3 domain. a, Stereo view of twelve of the fifteen
lowest-energy structures, representing the fold of the SH3
domain. The three structures with the largest r.m.s. deviation
to the average structure are not displayed. The -strand
regions are shown in blue. b, The X-ray structure^26 is shown
for comparison. In this case, the part of the -sheet
in the region 14 -17 and 23 -26 is non-ideal and therefore is
not indicated in blue.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2002,
420,
98-0)
copyright 2002.
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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.Abdine,
M.A.Verhoeven,
and
D.E.Warschawski
(2011).
Cell-free expression and labeling strategies for a new decade in solid-state NMR.
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N Biotechnol,
28,
272-276.
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C.Noirot,
B.Habenstein,
L.Bousset,
R.Melki,
B.H.Meier,
Y.Endo,
F.Penin,
and
A.Böckmann
(2011).
Wheat-germ cell-free production of prion proteins for solid-state NMR structural studies.
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N Biotechnol,
28,
232-238.
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F.Hefke,
A.Bagaria,
S.Reckel,
S.J.Ullrich,
V.Dötsch,
C.Glaubitz,
and
P.Güntert
(2011).
Optimization of amino acid type-specific (13)C and (15)N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm.
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J Biomol NMR,
49,
75-84.
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G.D.Paëpe,
J.R.Lewandowski,
A.Loquet,
M.Eddy,
S.Megy,
A.Böckmann,
and
R.G.Griffin
(2011).
Heteronuclear proton assisted recoupling.
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J Chem Phys,
134,
095101.
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G.J.Lu,
W.S.Son,
and
S.J.Opella
(2011).
A general assignment method for oriented sample (OS) solid-state NMR of proteins based on the correlation of resonances through heteronuclear dipolar couplings in samples aligned parallel and perpendicular to the magnetic field.
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J Magn Reson,
209,
195-206.
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J.Becker-Baldus,
T.F.Kemp,
J.Past,
A.Reinhold,
A.Samoson,
and
S.P.Brown
(2011).
Longer-range distances by spinning-angle-encoding solid-state NMR spectroscopy.
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Phys Chem Chem Phys,
13,
4514-4518.
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J.N.Dumez,
and
L.Emsley
(2011).
A master-equation approach to the description of proton-driven spin diffusion from crystal geometry using simulated zero-quantum lineshapes.
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Phys Chem Chem Phys,
13,
7363-7370.
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M.Bieri,
A.H.Kwan,
M.Mobli,
G.F.King,
J.P.Mackay,
and
P.R.Gooley
(2011).
Macromolecular NMR spectroscopy for the non-spectroscopist: beyond macromolecular solution structure determination.
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FEBS J,
278,
704-715.
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M.Huber,
S.Hiller,
P.Schanda,
M.Ernst,
A.Böckmann,
R.Verel,
and
B.H.Meier
(2011).
A proton-detected 4D solid-state NMR experiment for protein structure determination.
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Chemphyschem,
12,
915-918.
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PDB code:
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P.C.Shih,
G.C.Li,
K.J.Yang,
W.Chen,
and
D.L.Tzou
(2011).
Conformational analysis of steroid hormone molecules in the lipid environment - A solid-state NMR approach.
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Steroids,
76,
558-563.
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S.Tapaneeyakorn,
A.D.Goddard,
J.Oates,
C.L.Willis,
and
A.Watts
(2011).
Solution- and solid-state NMR studies of GPCRs and their ligands.
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Biochim Biophys Acta,
1808,
1462-1475.
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A.B.Nielsen,
L.A.Straasø,
A.J.Nieuwkoop,
C.M.Rienstra,
M.Bjerring,
and
N.C.Nielsen
(2010).
Broadband Heteronuclear Solid-State NMR Experiments by Exponentially Modulated Dipolar Recoupling without Decoupling.
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J Phys Chem Lett,
1,
1952-1956.
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A.M.Ruschak,
A.Velyvis,
and
L.E.Kay
(2010).
A simple strategy for ¹³C, ¹H labeling at the Ile-γ2 methyl position in highly deuterated proteins.
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J Biomol NMR,
48,
129-135.
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A.Schuetz,
C.Wasmer,
B.Habenstein,
R.Verel,
J.Greenwald,
R.Riek,
A.Böckmann,
and
B.H.Meier
(2010).
Protocols for the sequential solid-state NMR spectroscopic assignment of a uniformly labeled 25 kDa protein: HET-s(1-227).
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Chembiochem,
11,
1543-1551.
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B.Chen,
and
R.Tycko
(2010).
Structural and dynamical characterization of tubular HIV-1 capsid protein assemblies by solid state nuclear magnetic resonance and electron microscopy.
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Protein Sci,
19,
716-730.
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G.T.Debelouchina,
G.W.Platt,
M.J.Bayro,
S.E.Radford,
and
R.G.Griffin
(2010).
Intermolecular Alignment in β2-Microglobulin Amyloid Fibrils.
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J Am Chem Soc,
132,
17077-17079.
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H.Akutsu,
A.Egawa,
and
T.Fujiwara
(2010).
Atomic structure of the bacteriochlorophyll c assembly in intact chlorosomes from Chlorobium limicola determined by solid-state NMR.
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Photosynth Res,
104,
221-231.
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J.N.Dumez,
M.C.Butler,
E.Salager,
B.Elena-Herrmann,
and
L.Emsley
(2010).
Ab initio simulation of proton spin diffusion.
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Phys Chem Chem Phys,
12,
9172-9175.
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J.Strancar,
A.Kavalenka,
I.Urbancic,
A.Ljubetic,
and
M.A.Hemminga
(2010).
SDSL-ESR-based protein structure characterization.
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Eur Biophys J,
39,
499-511.
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K.Mochida,
and
K.Shinozaki
(2010).
Genomics and bioinformatics resources for crop improvement.
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Plant Cell Physiol,
51,
497-523.
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K.Takeuchi,
D.P.Frueh,
Z.Y.Sun,
S.Hiller,
and
G.Wagner
(2010).
CACA-TOCSY with alternate 13C-12C labeling: a 13Calpha direct detection experiment for mainchain resonance assignment, dihedral angle information, and amino acid type identification.
|
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J Biomol NMR,
47,
55-63.
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L.J.Sperling,
A.J.Nieuwkoop,
A.S.Lipton,
D.A.Berthold,
and
C.M.Rienstra
(2010).
High resolution NMR spectroscopy of nanocrystalline proteins at ultra-high magnetic field.
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J Biomol NMR,
46,
149-155.
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M.Weingarth,
P.Tekely,
R.Brüschweiler,
and
G.Bodenhausen
(2010).
Improving the quality of 2D solid-state NMR spectra of microcrystalline proteins by covariance analysis.
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Chem Commun (Camb),
46,
952-954.
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P.Turano,
D.Lalli,
I.C.Felli,
E.C.Theil,
and
I.Bertini
(2010).
NMR reveals pathway for ferric mineral precursors to the central cavity of ferritin.
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Proc Natl Acad Sci U S A,
107,
545-550.
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S.Cavadini
(2010).
Indirect detection of nitrogen-14 in solid-state NMR spectroscopy.
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Prog Nucl Magn Reson Spectrosc,
56,
46-77.
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S.Jehle,
P.Rajagopal,
B.Bardiaux,
S.Markovic,
R.Kühne,
J.R.Stout,
V.A.Higman,
R.E.Klevit,
B.J.van Rossum,
and
H.Oschkinat
(2010).
Solid-state NMR and SAXS studies provide a structural basis for the activation of alphaB-crystallin oligomers.
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Nat Struct Mol Biol,
17,
1037-1042.
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PDB code:
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S.Li,
Y.Zhang,
and
M.Hong
(2010).
3D (13)C-(13)C-(13)C correlation NMR for de novo distance determination of solid proteins and application to a human alpha-defensin.
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J Magn Reson,
202,
203-210.
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S.Paasch,
and
E.Brunner
(2010).
Trends in solid-state NMR spectroscopy and their relevance for bioanalytics.
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Anal Bioanal Chem,
398,
2351-2362.
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T.Vosegaard
(2010).
Challenges in numerical simulations of solid-state NMR experiments: Spin exchange pulse sequences.
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Solid State Nucl Magn Reson,
38,
77-83.
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W.T.Franks,
H.S.Atreya,
T.Szyperski,
and
C.M.Rienstra
(2010).
GFT projection NMR spectroscopy for proteins in the solid state.
|
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J Biomol NMR,
48,
213-223.
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Y.Han,
J.Ahn,
J.Concel,
I.J.Byeon,
A.M.Gronenborn,
J.Yang,
and
T.Polenova
(2010).
Solid-state NMR studies of HIV-1 capsid protein assemblies.
|
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J Am Chem Soc,
132,
1976-1987.
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Y.Zhang,
T.Doherty,
J.Li,
W.Lu,
C.Barinka,
J.Lubkowski,
and
M.Hong
(2010).
Resonance assignment and three-dimensional structure determination of a human alpha-defensin, HNP-1, by solid-state NMR.
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J Mol Biol,
397,
408-422.
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PDB code:
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A.Böckmann,
C.Gardiennet,
R.Verel,
A.Hunkeler,
A.Loquet,
G.Pintacuda,
L.Emsley,
B.H.Meier,
and
A.Lesage
(2009).
Characterization of different water pools in solid-state NMR protein samples.
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J Biomol NMR,
45,
319-327.
|
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A.B.Nielsen,
M.Bjerring,
J.T.Nielsen,
and
N.C.Nielsen
(2009).
Symmetry-based dipolar recoupling by optimal control: band-selective experiments for assignment of solid-state NMR spectra of proteins.
|
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J Chem Phys,
131,
025101.
|
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A.J.Nieuwkoop,
B.J.Wylie,
W.T.Franks,
G.J.Shah,
and
C.M.Rienstra
(2009).
Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy.
|
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J Chem Phys,
131,
095101.
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PDB code:
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A.Lange,
Z.Gattin,
H.Van Melckebeke,
C.Wasmer,
A.Soragni,
W.F.van Gunsteren,
and
B.H.Meier
(2009).
A combined solid-state NMR and MD characterization of the stability and dynamics of the HET-s(218-289) prion in its amyloid conformation.
|
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Chembiochem,
10,
1657-1665.
|
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|
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A.Lesage
(2009).
Recent advances in solid-state NMR spectroscopy of spin I = 1/2 nuclei.
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Phys Chem Chem Phys,
11,
6876-6891.
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A.McDermott
(2009).
Structure and dynamics of membrane proteins by magic angle spinning solid-state NMR.
|
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Annu Rev Biophys,
38,
385-403.
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B.J.Wylie,
C.D.Schwieters,
E.Oldfield,
and
C.M.Rienstra
(2009).
Protein structure refinement using 13C alpha chemical shift tensors.
|
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J Am Chem Soc,
131,
985-992.
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C.Herbst,
J.Herbst,
A.Kirschstein,
J.Leppert,
O.Ohlenschläger,
M.Görlach,
and
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(2009).
Design of high-power, broadband 180 degrees pulses and mixing sequences for fast MAS solid state chemical shift correlation NMR spectroscopy.
|
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J Biomol NMR,
43,
51-61.
|
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C.M.Widdifield,
and
D.L.Bryce
(2009).
Crystallographic structure refinement with quadrupolar nuclei: a combined solid-state NMR and GIPAW DFT example using MgBr(2).
|
| |
Phys Chem Chem Phys,
11,
7120-7122.
|
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D.H.Zhou,
G.Shah,
C.Mullen,
D.Sandoz,
and
C.M.Rienstra
(2009).
Proton-detected solid-state NMR spectroscopy of natural-abundance peptide and protein pharmaceuticals.
|
| |
Angew Chem Int Ed Engl,
48,
1253-1256.
|
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|
|
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F.V.Filipp,
N.Sinha,
L.Jairam,
J.Bradley,
and
S.J.Opella
(2009).
Labeling strategies for 13C-detected aligned-sample solid-state NMR of proteins.
|
| |
J Magn Reson,
201,
121-130.
|
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J.Lin,
M.J.Bayro,
R.G.Griffin,
and
N.Khaneja
(2009).
Dipolar recoupling in solid state NMR by phase alternating pulse sequences.
|
| |
J Magn Reson,
197,
145-152.
|
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J.R.Lewandowski,
G.De Paëpe,
M.T.Eddy,
and
R.G.Griffin
(2009).
(15)N-(15)N proton assisted recoupling in magic angle spinning NMR.
|
| |
J Am Chem Soc,
131,
5769-5776.
|
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J.Xu,
Y.Xue,
and
N.R.Skrynnikov
(2009).
Detection of nanosecond time scale side-chain jumps in a protein dissolved in water/glycerol solvent.
|
| |
J Biomol NMR,
45,
57-72.
|
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L.A.Straasø,
M.Bjerring,
N.Khaneja,
and
N.C.Nielsen
(2009).
Multiple-oscillating-field techniques for accurate distance measurements by solid-state NMR.
|
| |
J Chem Phys,
130,
225103.
|
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M.A.Ahmed,
V.V.Bamm,
L.Shi,
M.Steiner-Mosonyi,
J.F.Dawson,
L.Brown,
G.Harauz,
and
V.Ladizhansky
(2009).
Induced Secondary Structure and Polymorphism in an Intrinsically Disordered Structural Linker of the CNS: Solid-State NMR and FTIR Spectroscopy of Myelin Basic Protein Bound to Actin.
|
| |
Biophys J,
96,
180-191.
|
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M.Aluas,
C.Tripon,
J.M.Griffin,
X.Filip,
V.Ladizhansky,
R.G.Griffin,
S.P.Brown,
and
C.Filip
(2009).
CHHC and (1)H-(1)H magnetization exchange: analysis by experimental solid-state NMR and 11-spin density-matrix simulations.
|
| |
J Magn Reson,
199,
173-187.
|
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M.F.Brown,
K.Martínez-Mayorga,
K.Nakanishi,
G.F.Salgado,
and
A.V.Struts
(2009).
Retinal Conformation and Dynamics in Activation of Rhodopsin Illuminated by Solid-state H NMR Spectroscopy.
|
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Where a reference describes a PDB structure, the PDB
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