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PDBsum entry 3ci2
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Serine protease inhibitor
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PDB id
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3ci2
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Contents |
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* Residue conservation analysis
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J Mol Biol
222:621-635
(1991)
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PubMed id:
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Refinement of the three-dimensional solution structure of barley serine proteinase inhibitor 2 and comparison with the structures in crystals.
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S.Ludvigsen,
H.Y.Shen,
M.Kjaer,
J.C.Madsen,
F.M.Poulsen.
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ABSTRACT
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The three-dimensional structure of barley serine proteinase inhibitor, CI-2, has
been determined using nuclear magnetic resonance spectroscopy. The present
structure determination is a refinement of the structure previously determined
by us, using in the present case stereo-specific assignments, and a virtually
complete set of assignments of the two-dimensional nuclear Overhauser spectrum.
The structure determination is based on the identification of more than 1300
nuclear Overhauser effects, of which 961 were used in the structure calculation
as distance restraints, and on 94 dihedral angle restraints, of which 31 are for
chi 1 angles in defined chiral centers. These have been used to calculate a
series of 20 three-dimensional structures using a combination of distance
geometry, simulated annealing and restrained molecular dynamics. Each of the 20
structures was in agreement within less than 0.5 A of each of the distance
restraints and with all dihedral angle restraints. When compared to the
geometric average structure of the 20 refined structures the root-mean-square
differences for the backbone atoms were 0.8 (+/- 0.2) A and for all atoms were
1.6 (+/- 0.2) A. By comparison, the values obtained for the structures
determined previously were 1.4 (+/- 0.2) A and 2.1 (+/- 0.1) A, respectively.
The structures were also compared to the structure determined in the crystalline
state by X-ray diffraction showing root-mean-square differences of 1.6 (+/- 0.2)
A and 2.8 (+/- 0.2) A for the backbone and all atoms, respectively. Common
features of the solution structure and the two crystal structures are the
four-stranded beta-structure, composed of a pair of parallel strands, and three
pairs of antiparallel beta-strands flanked on one side by a 12-residue
alpha-helix and on the other side by a loop containing the serine proteinase
binding site. The new analysis of the structure has revealed an additional pair
of antiparallel beta-strands, consisting of residues 65 to 67 and 81 to 83, that
was not seen in either of the crystal structures or the previous solution
structure. Identification of this was based on nuclear magnetic resonance
evidence for the hydrogen bond (67HN to 81CO) not reported previously. Also the
presence of a bifurcated hydrogen bond involving Phe69 CO and HN atoms of Ala77
and Gln78 was observed in solution but not in crystals. Minor differences
between the two structures were observed in the phi-angles of residues Met59 and
Glu60 in the inhibitory site.
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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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P.J.Farber,
and
A.Mittermaier
(2008).
Side chain burial and hydrophobic core packing in protein folding transition states.
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Protein Sci,
17,
644-651.
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R.Day,
and
V.Daggett
(2007).
Direct observation of microscopic reversibility in single-molecule protein folding.
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J Mol Biol,
366,
677-686.
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A.Pintar,
and
S.Pongor
(2005).
The "first in-last out" hypothesis on protein folding revisited.
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Proteins,
60,
584-590.
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J.J.Hill,
E.Y.Shalaev,
and
G.Zografi
(2005).
Thermodynamic and dynamic factors involved in the stability of native protein structure in amorphous solids in relation to levels of hydration.
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J Pharm Sci,
94,
1636-1667.
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R.Day,
and
V.Daggett
(2005).
Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent.
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Protein Sci,
14,
1242-1252.
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R.Day,
and
V.Daggett
(2005).
Ensemble versus single-molecule protein unfolding.
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Proc Natl Acad Sci U S A,
102,
13445-13450.
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T.Diercks,
M.Daniels,
and
R.Kaptein
(2005).
Extended flip-back schemes for sensitivity enhancement in multidimensional HSQC-type out-and-back experiments.
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J Biomol NMR,
33,
243-259.
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H.Fan,
and
A.E.Mark
(2003).
Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study.
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Proteins,
53,
111-120.
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Z.Gáspári,
A.Patthy,
L.Gráf,
and
A.Perczel
(2002).
Comparative structure analysis of proteinase inhibitors from the desert locust, Schistocerca gregaria.
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Eur J Biochem,
269,
527-537.
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PDB codes:
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D.Laurents,
J.M.Pérez-Cañadillas,
J.Santoro,
M.Rico,
D.Schell,
C.N.Pace,
and
M.Bruix
(2001).
Solution structure and dynamics of ribonuclease Sa.
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Proteins,
44,
200-211.
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PDB code:
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S.L.Kazmirski,
K.B.Wong,
S.M.Freund,
Y.J.Tan,
A.R.Fersht,
and
V.Daggett
(2001).
Protein folding from a highly disordered denatured state: the folding pathway of chymotrypsin inhibitor 2 at atomic resolution.
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Proc Natl Acad Sci U S A,
98,
4349-4354.
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K.R.Roesler,
and
A.G.Rao
(2000).
A single disulfide bond restores thermodynamic and proteolytic stability to an extensively mutated protein.
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Protein Sci,
9,
1642-1650.
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N.Kurt,
and
T.Haliloğlu
(1999).
Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations.
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Proteins,
37,
454-464.
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R.Mohana-Borges,
J.Lima Silva,
and
G.de Prat-Gay
(1999).
Protein folding in the absence of chemical denaturants. Reversible pressure denaturation of the noncovalent complex formed by the association of two protein fragments.
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J Biol Chem,
274,
7732-7740.
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R.L.Foord,
and
R.J.Leatherbarrow
(1998).
Effect of osmolytes on the exchange rates of backbone amide protons in proteins.
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Biochemistry,
37,
2969-2978.
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J.Liu,
O.Prakash,
M.Cai,
Y.Gong,
Y.Huang,
L.Wen,
J.J.Wen,
J.K.Huang,
and
R.Krishnamoorthi
(1996).
Solution structure and backbone dynamics of recombinant Cucurbita maxima trypsin inhibitor-V determined by NMR spectroscopy.
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Biochemistry,
35,
1516-1524.
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PDB code:
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G.De Prat Gay,
J.Ruiz-Sanz,
J.L.Neira,
L.S.Itzhaki,
and
A.R.Fersht
(1995).
Folding of a nascent polypeptide chain in vitro: cooperative formation of structure in a protein module.
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Proc Natl Acad Sci U S A,
92,
3683-3686.
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A.Li,
and
V.Daggett
(1994).
Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2.
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Proc Natl Acad Sci U S A,
91,
10430-10434.
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D.E.Otzen,
L.S.Itzhaki,
N.F.elMasry,
S.E.Jackson,
and
A.R.Fersht
(1994).
Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding.
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Proc Natl Acad Sci U S A,
91,
10422-10425.
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Y.Harpaz,
N.Elmasry,
A.R.Fersht,
and
K.Henrick
(1994).
Direct observation of better hydration at the N terminus of an alpha-helix with glycine rather than alanine as the N-cap residue.
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Proc Natl Acad Sci U S A,
91,
311-315.
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PDB codes:
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M.Billeter
(1992).
Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals.
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Q Rev Biophys,
25,
325-377.
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S.Ludvigsen,
and
F.M.Poulsen
(1992).
Positive theta-angles in proteins by nuclear magnetic resonance spectroscopy.
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J Biomol NMR,
2,
227-233.
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W.J.Chazin
(1992).
NMR structures and methodology.
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Curr Opin Biotechnol,
3,
326-332.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
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
codes are
shown on the right.
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Links
