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Contents |
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213 a.a.
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222 a.a.
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58 a.a.
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* Residue conservation analysis
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PDB id:
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Complex (antibody/binding protein)
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Title:
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Igg1 fab fragment (mopc21) complex with domain iii of protein g from streptococcus
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Structure:
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Igg1-kappa mopc21 fab (light chain). Chain: l. Engineered: yes. Igg1-kappa mopc21 fab (heavy chain). Chain: h. Engineered: yes. Streptococcal protein g (domain iii). Chain: a. Engineered: yes
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Source:
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Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Streptococcus sp. G148. Organism_taxid: 1324.
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Biol. unit:
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Trimer (from
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Resolution:
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Authors:
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J.P.Derrick,D.B.Wigley
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Key ref:
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J.P.Derrick
and
D.B.Wigley
(1994).
The third IgG-binding domain from streptococcal protein G. An analysis by X-ray crystallography of the structure alone and in a complex with Fab.
J Mol Biol,
243,
906-918.
PubMed id:
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Date:
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05-Aug-94
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Release date:
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03-Jun-95
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PROCHECK
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Headers
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References
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P01634
(KV5A2_MOUSE) -
Ig kappa chain V-V region MOPC 21 from Mus musculus
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Seq:
Struc:
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136 a.a.
213 a.a.*
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J Mol Biol
243:906-918
(1994)
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PubMed id:
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The third IgG-binding domain from streptococcal protein G. An analysis by X-ray crystallography of the structure alone and in a complex with Fab.
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J.P.Derrick,
D.B.Wigley.
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ABSTRACT
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Protein G is a cell surface-associated protein from Streptococcus that binds to
IgG with high affinity. We have determined the X-ray crystal structures of the
third IgG-binding domain (domain III) alone to a resolution of 1.1 A (final
R-factor of 19.3%), and in complex with an Fab fragment to 2.6 A (final R-factor
of 16.8%). The structure of domain III is similar to the lower-resolution
crystal structures of protein G domains determined previously by other
investigators, but shows some minor differences when compared with the
equivalent NMR structures. Domain III binds to the immunoglobulin by formation
of an antiparallel interaction between the second beta-strand in domain III and
the last beta-strand in the CH 1 domain. There is also a minor site of
interaction between the C-terminal end of the alpha-helix in protein G and the
first beta-strand in the CH 1 domain. Previous studies by NMR on the
interactions between protein G and IgG have concluded that different portions of
the protein G domain are involved in binding to the Fab and Fc portions. The
results presented here support these findings and permit a detailed analysis of
the recognition of Fab by protein G; formation of the complex buries a large
water-accessible area, of a magnitude comparable with that found in
antibody/antigen interactions. The majority of hydrogen bonds between the two
proteins involve main-chain atoms from the CH 1 domain. The CH 1 domain residues
that are in contact with protein G are shown to be highly conserved in
alignments of mouse and human gamma chain amino acid sequences. We conclude that
the binding site for protein G on Fab is relatively invariant across different
species and gamma chain subclasses, providing an explanation for the widespread
recognition of Fab fragments from mouse and human antibodies by protein G. The
solution of the crystal structures of domain III alone and bound to Fab has
demonstrated that there is no major structural change apparent in either protein
on formation of the complex.
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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.Vögeli,
S.Kazemi,
P.Güntert,
and
R.Riek
(2012).
Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs.
|
| |
Nat Struct Mol Biol,
19,
1053-1057.
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|
PDB code:
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E.V.Sidorin,
and
T.F.Solov'eva
(2011).
IgG-Binding Proteins of Bacteria.
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| |
Biochemistry (Mosc),
76,
295-308.
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J.R.Perilla,
O.Beckstein,
E.J.Denning,
and
T.B.Woolf
(2011).
Computing ensembles of transitions from stable states: Dynamic importance sampling.
|
| |
J Comput Chem,
32,
196-209.
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|
|
L.Cai,
D.S.Kosov,
and
D.Fushman
(2011).
Density functional calculations of backbone (15)N shielding tensors in beta-sheet and turn residues of protein G.
|
| |
J Biomol NMR,
50,
19-33.
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A.Grishaev,
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and
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Improved fitting of solution X-ray scattering data to macromolecular structures and structural ensembles by explicit water modeling.
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J Am Chem Soc,
132,
15484-15486.
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A.Lewandowska,
S.Ołdziej,
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. IV. Implication for the mechanism of folding of the parent protein.
|
| |
Biopolymers,
93,
469-480.
|
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|
|
|
|
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A.Lewandowska,
S.Ołdziej,
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.
|
| |
Proteins,
78,
723-737.
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L.Yao,
A.Grishaev,
G.Cornilescu,
and
A.Bax
(2010).
The impact of hydrogen bonding on amide 1H chemical shift anisotropy studied by cross-correlated relaxation and liquid crystal NMR spectroscopy.
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| |
J Am Chem Soc,
132,
10866-10875.
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M.J.Plevin,
D.L.Bryce,
and
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(2010).
Direct detection of CH/pi interactions in proteins.
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| |
Nat Chem,
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466-471.
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A.Skwierawska,
J.Makowska,
S.Ołdziej,
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.
|
| |
Proteins,
75,
931-953.
|
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|
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A.Skwierawska,
S.Ołdziej,
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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|
|
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|
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A.Skwierawska,
W.Zmudzińska,
S.Ołdziej,
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.
|
| |
Proteins,
76,
637-654.
|
|
|
|
|
|
|
D.A.MacKenzie,
L.E.Tailford,
A.M.Hemmings,
and
N.Juge
(2009).
Crystal structure of a mucus-binding protein repeat reveals an unexpected functional immunoglobulin binding activity.
|
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J Biol Chem,
284,
32444-32453.
|
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PDB code:
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G.R.Bowman,
and
V.S.Pande
(2009).
Simulated tempering yields insight into the low-resolution Rosetta scoring functions.
|
| |
Proteins,
74,
777-788.
|
|
|
|
|
|
|
G.R.Bowman,
and
V.S.Pande
(2009).
The roles of entropy and kinetics in structure prediction.
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| |
PLoS One,
4,
e5840.
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A.F.Pereira de Araújo,
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A.A.Bursztyn,
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(2008).
Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins.
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| |
Proteins,
70,
971-983.
|
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|
|
|
|
|
A.Skwierawska,
S.Rodziewicz-Motowidło,
S.Ołdziej,
A.Liwo,
and
H.A.Scheraga
(2008).
Conformational studies of the alpha-helical 28-43 fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus.
|
| |
Biopolymers,
89,
1032-1044.
|
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|
|
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|
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B.Vögeli,
L.Yao,
and
A.Bax
(2008).
Protein backbone motions viewed by intraresidue and sequential HN-Halpha residual dipolar couplings.
|
| |
J Biomol NMR,
41,
17-28.
|
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|
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D.J.Wilton,
R.B.Tunnicliffe,
Y.O.Kamatari,
K.Akasaka,
and
M.P.Williamson
(2008).
Pressure-induced changes in the solution structure of the GB1 domain of protein G.
|
| |
Proteins,
71,
1432-1440.
|
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PDB codes:
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G.Nodet,
D.Abergel,
and
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(2008).
Predicting NMR relaxation rates in anisotropically tumbling proteins through networks of coupled rotators.
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Chemphyschem,
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L.Cai,
D.Fushman,
and
D.S.Kosov
(2008).
Density functional calculations of 15N chemical shifts in solvated dipeptides.
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| |
J Biomol NMR,
41,
77-88.
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|
|
N.Juranić,
J.J.Dannenberg,
G.Cornilescu,
P.Salvador,
E.Atanasova,
H.C.Ahn,
S.Macura,
J.L.Markley,
and
F.G.Prendergast
(2008).
Structural dependencies of protein backbone 2JNC' couplings.
|
| |
Protein Sci,
17,
768-776.
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|
|
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|
|
N.Trbovic,
B.Kim,
R.A.Friesner,
and
A.G.Palmer
(2008).
Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation.
|
| |
Proteins,
71,
684-694.
|
|
|
|
|
|
|
A.M.Burroughs,
S.Balaji,
L.M.Iyer,
and
L.Aravind
(2007).
Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold.
|
| |
Biol Direct,
2,
18.
|
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|
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M.E.Villegas,
J.A.Vila,
and
H.A.Scheraga
(2007).
Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides.
|
| |
J Biomol NMR,
37,
137-146.
|
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|
|
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|
N.Juranić,
E.Atanasova,
J.H.Streiff,
S.Macura,
and
F.G.Prendergast
(2007).
Solvent-induced differentiation of protein backbone hydrogen bonds in calmodulin.
|
| |
Protein Sci,
16,
1329-1337.
|
|
|
|
|
|
|
P.A.Alexander,
Y.He,
Y.Chen,
J.Orban,
and
P.N.Bryan
(2007).
The design and characterization of two proteins with 88% sequence identity but different structure and function.
|
| |
Proc Natl Acad Sci U S A,
104,
11963-11968.
|
|
|
|
|
|
|
A.Shehu,
C.Clementi,
and
L.E.Kavraki
(2006).
Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations.
|
| |
Proteins,
65,
164-179.
|
|
|
|
|
|
|
G.Bouvignies,
S.Meier,
S.Grzesiek,
and
M.Blackledge
(2006).
Ultrahigh-resolution backbone structure of perdeuterated protein GB1 using residual dipolar couplings from two alignment media.
|
| |
Angew Chem Int Ed Engl,
45,
8166-8169.
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PDB code:
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M.Nanias,
C.Czaplewski,
and
H.A.Scheraga
(2006).
Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field.
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| |
J Chem Theory Comput,
2,
513-528.
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M.Samuelsson,
J.Jendholm,
S.Amisten,
S.L.Morrison,
A.Forsgren,
and
K.Riesbeck
(2006).
The IgD CH1 region contains the binding site for the human respiratory pathogen Moraxella catarrhalis IgD-binding protein MID.
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| |
Eur J Immunol,
36,
2525-2534.
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J.B.Hall,
R.Kümmerle,
and
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(2006).
Measurement of 15N relaxation in deuterated amide groups in proteins using direct nitrogen detection.
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J Biomol NMR,
36,
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A.Liwo,
M.Khalili,
and
H.A.Scheraga
(2005).
Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains.
|
| |
Proc Natl Acad Sci U S A,
102,
2362-2367.
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E.Miclet,
J.Boisbouvier,
and
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(2005).
Measurement of eight scalar and dipolar couplings for methine-methylene pairs in proteins and nucleic acids.
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J Biomol NMR,
31,
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P.Bernadó,
S.Meier,
K.Cho,
S.Grzesiek,
R.Brüschweiler,
and
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(2005).
Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings.
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| |
Proc Natl Acad Sci U S A,
102,
13885-13890.
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H.Li,
A.D.Robertson,
and
J.H.Jensen
(2005).
Very fast empirical prediction and rationalization of protein pKa values.
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| |
Proteins,
61,
704-721.
|
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|
|
H.M.Patterson,
J.A.Brannigan,
S.M.Cutting,
K.S.Wilson,
A.J.Wilkinson,
E.Ab,
T.Diercks,
R.N.de Jong,
V.Truffault,
G.E.Folkers,
and
R.Kaptein
(2005).
The structure of bypass of forespore C, an intercompartmental signaling factor during sporulation in Bacillus.
|
| |
J Biol Chem,
280,
36214-36220.
|
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PDB code:
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I.Koyama-Honda,
K.Ritchie,
T.Fujiwara,
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R.S.Kasai,
and
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(2005).
Fluorescence imaging for monitoring the colocalization of two single molecules in living cells.
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Biophys J,
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J.L.Jiménez
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| |
Proteins,
59,
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R.A.Gruppo,
L.K.Jennings,
and
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The beta3 subunit of the integrin alphaIIbbeta3 regulates alphaIIb-mediated outside-in signaling.
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| |
Blood,
105,
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Rapid hop diffusion of a G-protein-coupled receptor in the plasma membrane as revealed by single-molecule techniques.
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Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC.
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J Comput Chem,
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A.T.Alexandrescu
(2004).
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| |
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A.Fokine,
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58,
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(2002).
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| |
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(2002).
Application of green fluorescent protein to affinity electrophoresis; affinity of IgG-binding domain C from streptococcal protein G to mouse IgG1.
|
| |
Biol Pharm Bull,
25,
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J.S.Richardson,
and
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(2002).
Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation.
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| |
Proc Natl Acad Sci U S A,
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R.Kaźmierkiewicz,
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(2002).
Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method.
|
| |
J Comput Chem,
23,
715-723.
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PDB code:
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PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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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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