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PDBsum entry 1bus
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Proteinase inhibitor
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PDB id
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1bus
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References listed in PDB file
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Key reference
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Title
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Solution conformation of proteinase inhibitor iia from bull seminal plasma by 1h nuclear magnetic resonance and distance geometry.
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Authors
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M.P.Williamson,
T.F.Havel,
K.Wüthrich.
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Ref.
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J Mol Biol, 1985,
182,
295-315.
[DOI no: ]
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PubMed id
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Abstract
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A determination of the solution conformation of the proteinase inhibitor IIA
from bull seminal plasma (BUSI IIA) is described. Two-dimensional nuclear
Overhauser enhancement spectroscopy (NOESY) was used to obtain a list of 202
distance constraints between individually assigned hydrogen atoms of the
polypeptide chain, to identify the positions of the three disulfide bridges, and
to locate the single cis peptide bond. Supplementary geometric constraints were
derived from the vicinal spin-spin couplings and the locations of certain
hydrogen bonds, as determined by nuclear magnetic resonance (n.m.r.). Using a
new distance geometry program (DISGEO) which is capable of computing all-atom
structures for proteins the size of BUSI IIA, five conformers were computed from
the NOE distance constraints alone, and another five were computed with the
supplementary constraints included. Comparison of the different structures
computed from the n.m.r. data among themselves and with the crystal structures
of two homologous proteins shows that the global features of the conformation of
BUSI IIA (i.e. the overall dimensions of the molecule and the threading of the
polypeptide chain) were well-defined by the available n.m.r. data. In the
Appendix, we describe a preliminary energy refinement of the structure, which
showed that the constraints derived from the n.m.r. data are compatible with a
low energy spatial structure.
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Figure 2.
FIG. 2.
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Figure 7.
Figure 7. Schematic drawing of the polypeptide
backbone ``topology'' which was obtained in all 10 of te
BUS1 IIA structures computed from the n.m.r. data
presented.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1985,
182,
295-315)
copyright 1985.
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Secondary reference #1
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Title
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Secondary structure in the solution conformation of the proteinase inhibitor iia from bull seminal plasma by nuclear magnetic resonance.
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Authors
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M.P.Williamson,
D.Marion,
K.Wüthrich.
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Ref.
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J Mol Biol, 1984,
173,
341-359.
[DOI no: ]
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PubMed id
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Figure 1.
FIG. 1. Polypeptide backbone segment. The through-space distances d,. d,, d,(i, i+3) and d,(i, i+3)
used in the determination of helical structure are indicated by arrows.
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Figure 5.
FIG. 5. Contour plot of the region (0, = 4.33 to 4.50 p.p.m., co2 = X.11 to 8.36 p.p.m.) of a 360 MHz
high-resolution absorption mode CC%\ spectrum of a 0.016 M solution of BUST ITA in H,O, pH 4.9, at
45°C. The digital resolution is 2.4 Hz n w, and 0.4 Hz in w2. This spectral region contains the amide
proton-cc proton cross peaks of the 4 amino acid residues Als3, Glu4, ArglS and Cys57. Positive levels
are indicated by continuous lines and negative leves by broen lines. The arrows indicate where the
vicinal coupling costants 3JHN. for t)he 4 residues were measured.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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Assignment of the 1h nuclear magnetic resonance spectrum of the proteinase inhibitor iia from bull seminal plasma by two-Dimensional nuclear magnetic resonance at 500 mhz.
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Authors
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P.Strop,
G.Wider,
K.Wüthrich.
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Ref.
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J Mol Biol, 1983,
166,
641-665.
[DOI no: ]
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PubMed id
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Figure 8.
FIG. 8. Combined OSY-NOESY dl connectivity diagram, same spectra and same presenttion as
in Fig. 7. The connectivity patterns are indicated by unbroken lines or the following segments of the
BUSI IIA polpeptide chain : 57 to 54, 44 to 42, 35 to 34 and 3 to 2.
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Figure 10.
Fro. 10. Identification of sequentialy neighboring residues by d z connectivities in the spectral region
from 7'0 to 9-7 p.p.m, of a 500 MHz IH NOESY spectrum, which was recorded from a 0"016 M solution
of BUSI IIA i H20 at pH 4-9 and t = 18~ with a mixing time of 200 ms an a digita resolution o
48 Hz/point. This spectral region contains the diagonal paks of the bulk of he backbone amide
protons, and OEs between different amde protons are manifested b numerous cross peks, d2
connectivities between the amide protons f neighboring residues re indicated by unbroken and
broken lines and th resonance positions of the onnected amide protons are indicated on the margins
of the Figure. The uppr left triangle cntains the connectivities for the polypeptide segments 2 to 3
( .... ), 33 to ( ), 35 to 39 ( .... ) (positions of the diagonal peaks indicated on the left) and
40 to ( ) (diagonal peak positions indicated at th top of the Figue ; note that the cross peaks
42-* 43 and 43-* 44 are overlapped). Te lower right triangle contains the connectivities for the
segments 7 t 12 ( ..... ) and 19 to 21 ( .... ; assignments on the right), and 14 to 15 ad 52 to 54
( ; assignments at the bottom). For each segment ( 9 ) and ( [:> ), respectively, indicate the start
and the end of the d2 connectivity patern. hen searching or these patterns it is important that d2
connectivities are symmetrical with respect to the direction of the polypptide chain (Billete et al.,
1982) and that NH-NH NOE connectivity may thus eually well be bsered with eiher of the 2
neighboring residues in the sequence (Fig. 5). For example, the amid proton of Asn28 in BUSI IIA
has 2 connectivities to both Ser27 and Gly29. Since the NH resoance of Ser27 is at lowe field than
that of Asn28, the connecting cross peak is towads the let side on a horizontal line through the
diagonal peak of NH of As28. Gly29 NH, however, is a higher field an therefore the d2 cros peak i
observed on a vertical line through the diagonal eak o the Asn28 amide proton.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #3
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Title
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Characterization of the proteinase inhibitor iia from bull seminal plasma by 1h nuclear magnetic resonance. Stability, Amide proton exchange and mobility of aromatic residues.
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Authors
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P.Strop,
K.Wüthrich.
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Ref.
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J Mol Biol, 1983,
166,
631-640.
[DOI no: ]
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PubMed id
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Figure 1.
PETR STROP t AND Kt'aT Wt~THRI('H
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Figure 2.
Fro. 2. Plots of chemical versus 2H for th aromatic ~H n.m.r, of Tyrl, His24 and His53
in BUSI IIA. The experimental points were obtained fiom 360MHz IH n.m.r, recorded in
0-005 ~n solution of the protein in 2H20 at 25~ The p2H varied by the addition of minute
amounts of 2HCI and NaO2. The following acidity constants were obtained from non-linar least-
squares fits to one-proton ttration curves: Tyrl6 pK, 25~ -- 10-5 +_0'2: His53, pK~ TM = 64+_02; His20
and Tyr32 (not shown) not tit,-ate between and 12-0. except that His24 C4H shows a small
downfield shift in the 2H range near pK~ . of Tyu?16.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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