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PDBsum entry 1ypc
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Proteinase inhibitor(chymotrypsin)
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PDB id
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1ypc
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Contents |
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* Residue conservation analysis
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DOI no:
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Proc Natl Acad Sci U S A
91:311-315
(1994)
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PubMed id:
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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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Y.Harpaz,
N.Elmasry,
A.R.Fersht,
K.Henrick.
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ABSTRACT
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The structural basis for the stability of N termini of helices has been analyzed
by thermodynamic and crystallographic studies of three suitably engineered
mutants of the barley chymotrypsin inhibitor 2 with Ser, Gly, or Ala at the
N-cap position (residue 31). Each mutant has a well-organized shell of hydration
of the terminal NH groups of the helix. The three structures are virtually
superimposable (rms separations for all atoms, including the common water
molecules, are 0.15-0.17 A) and show neither changes in conformation at the site
of substitution nor changes in the crystal packing. The only changes on going
from Ser-31 to Ala-31 to Gly-31 are in the position of a water molecule
(Wat-116). This is bound to the Ser-O gamma atom in the Ser-31 structure but is
in a weak hydrogen bonding position with the NH of residue 34 (O ... N = 3.28 A)
in the Ala-31 mutant, partly replacing the strong Ser-31-O gamma ... N34
hydrogen bond (O ... N = 2.65 A). The corresponding water molecule completely
replaces the Ser hydroxyl hydrogen bond to N34 on mutation to Gly (2.74 A). The
only other change between the three structures is an additional water molecule
in the Ala-31 structure (Wat-150) that partly compensates for the weak Wat-116
... N34 hydrogen bond. Perturbation of solvation by the side chain of Ala is
consistent with earlier hypotheses on the importance of exposure of the termini
of helices to the aqueous solvent.
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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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F.F.Liu,
L.Ji,
L.Zhang,
X.Y.Dong,
and
Y.Sun
(2010).
Molecular basis for polyol-induced protein stability revealed by molecular dynamics simulations.
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J Chem Phys,
132,
225103.
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M.C.Thielges,
J.Zimmermann,
P.E.Dawson,
and
F.E.Romesberg
(2009).
The determinants of stability and folding in evolutionarily diverged cytochromes c.
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J Mol Biol,
388,
159-167.
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P.C.Whitford,
J.K.Noel,
S.Gosavi,
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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M.C.Stumpe,
and
H.Grubmüller
(2008).
Polar or apolar--the role of polarity for urea-induced protein denaturation.
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PLoS Comput Biol,
4,
e1000221.
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B.J.Bennion,
and
V.Daggett
(2004).
Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: a chemical chaperone at atomic resolution.
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Proc Natl Acad Sci U S A,
101,
6433-6438.
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B.J.Bennion,
and
V.Daggett
(2003).
The molecular basis for the chemical denaturation of proteins by urea.
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Proc Natl Acad Sci U S A,
100,
5142-5147.
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V.Daggett,
and
A.R.Fersht
(2003).
Is there a unifying mechanism for protein folding?
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Trends Biochem Sci,
28,
18-25.
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B.Li,
D.O.Alonso,
and
V.Daggett
(2002).
Stabilization of globular proteins via introduction of temperature-activated elastin-based switches.
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Structure,
10,
989-998.
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C.Baysal,
and
A.R.Atilgan
(2001).
Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2.
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Proteins,
45,
62-70.
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L.Li,
and
E.I.Shakhnovich
(2001).
Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations.
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Proc Natl Acad Sci U S A,
98,
13014-13018.
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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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A.Karimi,
M.Matsumura,
P.E.Wright,
and
H.J.Dyson
(1999).
Characterization of monomeric and dimeric B domain of Staphylococcal protein A.
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J Pept Res,
54,
344-352.
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M.Vijayakumar,
H.Qian,
and
H.X.Zhou
(1999).
Hydrogen bonds between short polar side chains and peptide backbone: prevalence in proteins and effects on helix-forming propensities.
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Proteins,
34,
497-507.
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S.J.Lahr,
A.Broadwater,
C.W.Carter,
M.L.Collier,
L.Hensley,
J.C.Waldner,
G.J.Pielak,
and
M.H.Edgell
(1999).
Patterned library analysis: a method for the quantitative assessment of hypotheses concerning the determinants of protein structure.
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Proc Natl Acad Sci U S A,
96,
14860-14865.
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D.E.Otzen,
and
A.R.Fersht
(1998).
Folding of circular and permuted chymotrypsin inhibitor 2: retention of the folding nucleus.
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Biochemistry,
37,
8139-8146.
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A.J.Doig,
M.W.MacArthur,
B.J.Stapley,
and
J.M.Thornton
(1997).
Structures of N-termini of helices in proteins.
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Protein Sci,
6,
147-155.
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O.R.Veltman,
G.Vriend,
F.Hardy,
J.Mansfeld,
B.van den Burg,
G.Venema,
and
V.G.Eijsink
(1997).
Mutational analysis of a surface area that is critical for the thermal stability of thermolysin-like proteases.
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Eur J Biochem,
248,
433-440.
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H.S.Mchaourab,
M.A.Lietzow,
K.Hideg,
and
W.L.Hubbell
(1996).
Motion of spin-labeled side chains in T4 lysozyme. Correlation with protein structure and dynamics.
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Biochemistry,
35,
7692-7704.
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M.Blaber,
J.DiSalvo,
and
K.A.Thomas
(1996).
X-ray crystal structure of human acidic fibroblast growth factor.
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Biochemistry,
35,
2086-2094.
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PDB codes:
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A.J.Doig,
and
R.L.Baldwin
(1995).
N- and C-capping preferences for all 20 amino acids in alpha-helical peptides.
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Protein Sci,
4,
1325-1336.
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C.H.Robert,
and
P.S.Ho
(1995).
Significance of bound water to local chain conformations in protein crystals.
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Proc Natl Acad Sci U S A,
92,
7600-7604.
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E.López-Hernández,
and
L.Serrano
(1995).
Empirical correlation for the replacement of Ala by Gly: importance of amino acid secondary intrinsic propensities.
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Proteins,
22,
340-349.
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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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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
