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PDBsum entry 1bdd
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Immunoglobulin-binding protein
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PDB id
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1bdd
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Immunoglobulin-binding protein
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Title:
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Staphylococcus aureus protein a, immunoglobulin-binding b domain, nmr, minimized average structure
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Structure:
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Staphylococcus aureus protein a. Chain: a. Fragment: b domain. Engineered: yes
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Source:
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Staphylococcus aureus. Organism_taxid: 1280. Gene: synthetic gene. Expressed in: escherichia coli. Expression_system_taxid: 562.
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NMR struc:
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1 models
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Authors:
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H.Gouda,H.Torigoe,A.Saito,M.Sato,Y.Arata,I.Shimada
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Key ref:
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H.Gouda
et al.
(1992).
Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures.
Biochemistry,
31,
9665-9672.
PubMed id:
DOI:
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Date:
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28-Jun-96
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Release date:
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11-Jan-97
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PROCHECK
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Headers
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References
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P38507
(SPA_STAAU) -
Immunoglobulin G-binding protein A from Staphylococcus aureus
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Seq:
Struc:
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508 a.a.
60 a.a.*
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Key: |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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DOI no:
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Biochemistry
31:9665-9672
(1992)
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PubMed id:
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Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures.
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H.Gouda,
H.Torigoe,
A.Saito,
M.Sato,
Y.Arata,
I.Shimada.
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ABSTRACT
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The three-dimensional solution structure of the recombinant B domain (FB) of
staphylococcal protein A, which specifically binds to the Fc portion of
immunoglobulin G, was determined by NMR spectroscopy and hybrid distance
geometry-dynamical simulated annealing calculations. On the basis of 692
experimental constraints including 587 distance constraints obtained from the
nuclear Overhauser effect (NOE), 57 torsion angle (phi, chi 1) constraints, and
48 constraints associated with 24 hydrogen bonds, a total of 10 converged
structures of FB were obtained. The atomic root mean square difference among the
10 converged structures is 0.52 +/- 0.10 A for the backbone atoms and 0.98 +/-
0.08 A for all heavy atoms (excluding the N-terminal segment from Thr1 to Glu9
and the C-terminal segment from Gln56 to Ala60, which are partially disordered).
FB is composed of a bundle of three alpha-helices, i.e., helix I (Gln10-His19),
helix II (Glu25-Asp37), and helix III (Ser42-Ala55). Helix II and helix III are
antiparallel to each other, whereas the long axis of helix I is tilted at an
angle of about 30 degrees with respect to those of helix II and helix III. Most
of the hydrophobic residues of FB are buried in the interior of the bundle of
the three helices. It is suggested that the buried hydrophobic residues form a
hydrophobic core, contributing to the stability of FB.(ABSTRACT TRUNCATED AT 250
WORDS)
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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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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.
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J Comput Chem,
32,
196-209.
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G.G.Maisuradze,
P.Senet,
C.Czaplewski,
A.Liwo,
and
H.A.Scheraga
(2010).
Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field.
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J Phys Chem A,
114,
4471-4485.
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T.Jin,
D.K.Tiwari,
S.Tanaka,
Y.Inouye,
K.Yoshizawa,
and
T.M.Watanabe
(2010).
Antibody-ProteinA conjugated quantum dots for multiplexed imaging of surface receptors in living cells.
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Mol Biosyst,
6,
2325-2331.
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G.G.Maisuradze,
A.Liwo,
and
H.A.Scheraga
(2009).
How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?
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Phys Rev Lett,
102,
238102.
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H.Huang,
E.Ozkirimli,
and
C.B.Post
(2009).
A Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions.
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J Chem Theory Comput,
5,
1301-1314.
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H.Kamberaj,
and
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(2009).
An optimized replica exchange molecular dynamics method.
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J Chem Phys,
130,
074906.
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H.Lammert,
A.Schug,
and
J.N.Onuchic
(2009).
Robustness and generalization of structure-based models for protein folding and function.
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Proteins,
77,
881-891.
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H.Shen,
A.Liwo,
and
H.A.Scheraga
(2009).
An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics.
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J Phys Chem B,
113,
8738-8744.
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J.Yamaguchi,
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M.Biyani,
T.Sasaki,
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T.Funatsu,
Y.Husimi,
and
N.Nemoto
(2009).
cDNA display: a novel screening method for functional disulfide-rich peptides by solid-phase synthesis and stabilization of mRNA-protein fusions.
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Nucleic Acids Res,
37,
e108.
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P.C.Whitford,
J.K.Noel,
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A.Schug,
K.Y.Sanbonmatsu,
and
J.N.Onuchic
(2009).
An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.
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Proteins,
75,
430-441.
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H.Lei,
C.Wu,
Z.X.Wang,
Y.Zhou,
and
Y.Duan
(2008).
Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations.
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J Chem Phys,
128,
235105.
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H.Yang,
J.Cao,
L.Q.Li,
X.Zhou,
Q.L.Chen,
W.T.Liao,
Z.M.Wen,
S.H.Jiang,
R.Xu,
J.A.Jia,
X.Pan,
Z.T.Qi,
and
W.Pan
(2008).
Evolutional selection of a combinatorial phage library displaying randomly-rearranged various single domains of immunoglobulin (Ig)-binding proteins (IBPs) with four kinds of Ig molecules.
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BMC Microbiol,
8,
137.
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J.Chen,
and
C.L.Brooks Iii
(2008).
Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.
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Phys Chem Chem Phys,
10,
471-481.
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J.D.Lambris,
D.Ricklin,
and
B.V.Geisbrecht
(2008).
Complement evasion by human pathogens.
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Nat Rev Microbiol,
6,
132-142.
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J.F.St-Pierre,
N.Mousseau,
and
P.Derreumaux
(2008).
The complex folding pathways of protein A suggest a multiple-funnelled energy landscape.
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J Chem Phys,
128,
045101.
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T.A.Knotts,
N.Rathore,
and
J.J.de Pablo
(2008).
An entropic perspective of protein stability on surfaces.
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Biophys J,
94,
4473-4483.
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G.Jayachandran,
V.Vishal,
A.E.García,
and
V.S.Pande
(2007).
Local structure formation in simulations of two small proteins.
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J Struct Biol,
157,
491-499.
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H.S.Lee,
J.Choi,
and
S.Yoon
(2007).
QHELIX: a computational tool for the improved measurement of inter-helical angles in proteins.
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Protein J,
26,
556-561.
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K.Cline,
and
M.McCaffery
(2007).
Evidence for a dynamic and transient pathway through the TAT protein transport machinery.
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EMBO J,
26,
3039-3049.
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P.Derreumaux,
and
N.Mousseau
(2007).
Coarse-grained protein molecular dynamics simulations.
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J Chem Phys,
126,
025101.
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S.Trebst,
and
U.H.Hansmann
(2007).
Optimized folding simulations of protein A.
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Eur Phys J E Soft Matter,
24,
311-316.
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A.W.Stumpff-Kane,
and
M.Feig
(2006).
A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes.
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Proteins,
63,
155-164.
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H.Takahashi,
M.Miyazawa,
Y.Ina,
Y.Fukunishi,
Y.Mizukoshi,
H.Nakamura,
and
I.Shimada
(2006).
Utilization of methyl proton resonances in cross-saturation measurement for determining the interfaces of large protein-protein complexes.
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J Biomol NMR,
34,
167-177.
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M.I.Gómez,
M.O'Seaghdha,
M.Magargee,
T.J.Foster,
and
A.S.Prince
(2006).
Staphylococcus aureus protein A activates TNFR1 signaling through conserved IgG binding domains.
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J Biol Chem,
281,
20190-20196.
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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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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.
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Proc Natl Acad Sci U S A,
102,
2362-2367.
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A.Schug,
T.Herges,
A.Verma,
K.H.Lee,
and
W.Wenzel
(2005).
Comparison of stochastic optimization methods for all-atom folding of the Trp-Cage protein.
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Chemphyschem,
6,
2640-2646.
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G.J.Silverman,
C.S.Goodyear,
and
D.L.Siegel
(2005).
On the mechanism of staphylococcal protein A immunomodulation.
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Transfusion,
45,
274-280.
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J.M.Carr,
and
D.J.Wales
(2005).
Global optimization and folding pathways of selected alpha-helical proteins.
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J Chem Phys,
123,
234901.
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M.Khalili,
A.Liwo,
A.Jagielska,
and
H.A.Scheraga
(2005).
Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems.
|
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J Phys Chem B,
109,
13798-13810.
|
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M.Nanias,
M.Chinchio,
S.Ołdziej,
C.Czaplewski,
and
H.A.Scheraga
(2005).
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,
26,
1472-1486.
|
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T.A.Knotts,
N.Rathore,
and
J.J.de Pablo
(2005).
Structure and stability of a model three-helix-bundle protein on tailored surfaces.
|
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Proteins,
61,
385-397.
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T.Herges,
and
W.Wenzel
(2005).
Free-energy landscape of the villin headpiece in an all-atom force field.
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Structure,
13,
661-668.
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W.Kwak,
and
U.H.Hansmann
(2005).
Efficient sampling of protein structures by model hopping.
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Phys Rev Lett,
95,
138102.
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D.Zheng,
J.M.Aramini,
and
G.T.Montelione
(2004).
Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data.
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Protein Sci,
13,
549-554.
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PDB code:
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G.Favrin,
A.Irbäck,
and
S.Wallin
(2004).
Sequence-based study of two related proteins with different folding behaviors.
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Proteins,
54,
8.
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J.Lee,
S.Y.Kim,
K.Joo,
I.Kim,
and
J.Lee
(2004).
Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing.
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| |
Proteins,
56,
704-714.
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M.Linhult,
S.Gülich,
T.Gräslund,
A.Simon,
M.Karlsson,
A.Sjöberg,
K.Nord,
and
S.Hober
(2004).
Improving the tolerance of a protein a analogue to repeated alkaline exposures using a bypass mutagenesis approach.
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Proteins,
55,
407-416.
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N.M.Grubor,
R.Shinar,
R.Jankowiak,
M.D.Porter,
and
G.J.Small
(2004).
Novel biosensor chip for simultaneous detection of DNA-carcinogen adducts with low-temperature fluorescence.
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Biosens Bioelectron,
19,
547-556.
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P.G.Wolynes
(2004).
Latest folding game results: protein A barely frustrates computationalists.
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Proc Natl Acad Sci U S A,
101,
6837-6838.
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S.Sato,
T.L.Religa,
V.Daggett,
and
A.R.Fersht
(2004).
Testing protein-folding simulations by experiment: B domain of protein A.
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Proc Natl Acad Sci U S A,
101,
6952-6956.
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PDB code:
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U.H.Hansmann
(2004).
Simulations of a small protein in a specifically designed generalized ensemble.
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Phys Rev E Stat Nonlin Soft Matter Phys,
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012902.
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A.E.García,
and
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(2003).
Folding a protein in a computer: an atomic description of the folding/unfolding of protein A.
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Proc Natl Acad Sci U S A,
100,
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J.A.Vila,
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(2003).
Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures.
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| |
Proc Natl Acad Sci U S A,
100,
14812-14816.
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and
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(2002).
An atomically detailed study of the folding pathways of protein A with the stochastic difference equation.
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| |
Proc Natl Acad Sci U S A,
99,
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(2002).
A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field.
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Proc Natl Acad Sci U S A,
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Folding of a small helical protein using hydrogen bonds and hydrophobicity forces.
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Proteins,
47,
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I.M.Frick,
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P.A.Nygren,
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T.Drakenberg,
S.Forsén,
and
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(2002).
Structure, specificity, and mode of interaction for bacterial albumin-binding modules.
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J Biol Chem,
277,
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PDB codes:
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J.E.Shea,
and
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(2001).
From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding.
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(2001).
Recognition of DNA by VH and Fv domains of an IgG anti-poly(dC) antibody with a singly mutated VH domain.
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J Mol Recognit,
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K.Kato
(2001).
[Structural basis of the interaction between immunoglobulins and Fc receptors provided by NMR spectroscopy]
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Yakugaku Zasshi,
121,
345-354.
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D.O.Alonso,
and
V.Daggett
(2000).
Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains.
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| |
Proc Natl Acad Sci U S A,
97,
133-138.
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D.P.Meininger,
M.Rance,
M.A.Starovasnik,
W.J.Fairbrother,
and
N.J.Skelton
(2000).
Characterization of the binding interface between the E-domain of Staphylococcal protein A and an antibody Fv-fragment.
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| |
Biochemistry,
39,
26-36.
|
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M.Graille,
E.A.Stura,
A.L.Corper,
B.J.Sutton,
M.J.Taussig,
J.B.Charbonnier,
and
G.J.Silverman
(2000).
Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: structural basis for recognition of B-cell receptors and superantigen activity.
|
| |
Proc Natl Acad Sci U S A,
97,
5399-5404.
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PDB code:
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N.Opalka,
R.A.Mooney,
C.Richter,
K.Severinov,
R.Landick,
and
S.A.Darst
(2000).
Direct localization of a beta-subunit domain on the three-dimensional structure of Escherichia coli RNA polymerase.
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| |
Proc Natl Acad Sci U S A,
97,
617-622.
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P.Derreumaux
(2000).
Generating ensemble averages for small proteins from extended conformations by Monte Carlo simulations.
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Phys Rev Lett,
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R.B.Hill,
D.P.Raleigh,
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and
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(2000).
De novo design of helical bundles as models for understanding protein folding and function.
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Acc Chem Res,
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The most recent references are shown first.
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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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|
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