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PDBsum entry 1zim
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Leucine zipper
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PDB id
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1zim
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Nat Struct Biol
3:1011-1018
(1996)
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PubMed id:
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Buried polar residues and structural specificity in the GCN4 leucine zipper.
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L.Gonzalez,
D.N.Woolfson,
T.Alber.
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ABSTRACT
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A conserved asparagine (Asn 16) buried in the interface of the GCN4 leucine
zipper selectively favours the parallel, dimeric, coiled-coil structure. To test
if other polar residues confer oligomerization specificity, the structural
effects of Gln and Lys substitutions for Asn 16 were characterized. Like the
wild-type peptide, the Asn 16Lys mutant formed exclusively dimers. In contrast,
Gln 16, despite its chemical similarity to Asn, allowed the peptide to form both
dimers and trimers. The Gln 16 side chain was accommodated by qualitatively
different interactions in the dimer and trimer crystal structures. These
findings demonstrate that the structural selectivity of polar residues results
not only from the burial of polar atoms, but also depends on the complementarity
of the side-chain stereochemistry with the surrounding structural environment.
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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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A.Das,
Y.Wei,
I.Pelczer,
and
M.H.Hecht
(2011).
Binding of small molecules to cavity forming mutants of a de novo designed protein.
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Protein Sci,
20,
702-711.
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J.Gee,
and
M.S.Shell
(2011).
Two-dimensional replica exchange approach for peptide-peptide interactions.
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J Chem Phys,
134,
064112.
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E.H.Bromley,
K.J.Channon,
P.J.King,
Z.N.Mahmoud,
E.F.Banwell,
M.F.Butler,
M.P.Crump,
T.R.Dafforn,
M.R.Hicks,
J.D.Hirst,
A.Rodger,
and
D.N.Woolfson
(2010).
Assembly pathway of a designed alpha-helical protein fiber.
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Biophys J,
98,
1668-1676.
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J.Diao
(2010).
Crystal structure of a super leucine zipper, an extended two-stranded super long coiled coil.
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Protein Sci,
19,
319-326.
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PDB code:
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M.D.Hartmann,
O.Ridderbusch,
K.Zeth,
R.Albrecht,
O.Testa,
D.N.Woolfson,
G.Sauer,
S.Dunin-Horkawicz,
A.N.Lupas,
and
B.H.Alvarez
(2009).
A coiled-coil motif that sequesters ions to the hydrophobic core.
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Proc Natl Acad Sci U S A,
106,
16950-16955.
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PDB codes:
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Q.Xu,
and
D.L.Minor
(2009).
Crystal structure of a trimeric form of the K(V)7.1 (KCNQ1) A-domain tail coiled-coil reveals structural plasticity and context dependent changes in a putative coiled-coil trimerization motif.
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Protein Sci,
18,
2100-2114.
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PDB codes:
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R.S.Hodges,
J.Mills,
S.McReynolds,
J.P.Kirwan,
B.Tripet,
and
D.Osguthorpe
(2009).
Identification of a unique "stability control region" that controls protein stability of tropomyosin: A two-stranded alpha-helical coiled-coil.
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J Mol Biol,
392,
747-762.
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S.S.Pendley,
Y.B.Yu,
and
T.E.Cheatham
(2009).
Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils.
|
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Proteins,
74,
612-629.
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T.R.Mack,
R.Gao,
and
A.M.Stock
(2009).
Probing the roles of the two different dimers mediated by the receiver domain of the response regulator PhoB.
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J Mol Biol,
389,
349-364.
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A.S.Burguete,
T.D.Fenn,
A.T.Brunger,
and
S.R.Pfeffer
(2008).
Rab and Arl GTPase family members cooperate in the localization of the golgin GCC185.
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Cell,
132,
286-298.
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PDB code:
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E.B.Hadley,
O.D.Testa,
D.N.Woolfson,
and
S.H.Gellman
(2008).
Preferred side-chain constellations at antiparallel coiled-coil interfaces.
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Proc Natl Acad Sci U S A,
105,
530-535.
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P.Jing,
J.S.Rudra,
A.B.Herr,
and
J.H.Collier
(2008).
Self-assembling peptide-polymer hydrogels designed from the coiled coil region of fibrin.
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Biomacromolecules,
9,
2438-2446.
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D.H.Shin,
J.S.Kim,
H.Yokota,
R.Kim,
and
S.H.Kim
(2006).
Crystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae.
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Protein Sci,
15,
921-928.
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PDB code:
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J.Liu,
Q.Zheng,
Y.Deng,
C.S.Cheng,
N.R.Kallenbach,
and
M.Lu
(2006).
A seven-helix coiled coil.
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Proc Natl Acad Sci U S A,
103,
15457-15462.
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PDB code:
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J.M.Mason,
M.A.Schmitz,
K.M.Müller,
and
K.M.Arndt
(2006).
Semirational design of Jun-Fos coiled coils with increased affinity: Universal implications for leucine zipper prediction and design.
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Proc Natl Acad Sci U S A,
103,
8989-8994.
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J.Yang,
C.Xu,
P.Kopecková,
and
J.Kopecek
(2006).
Hybrid hydrogels self-assembled from HPMA copolymers containing peptide grafts.
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Macromol Biosci,
6,
201-209.
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M.K.Yadav,
L.J.Leman,
D.J.Price,
C.L.Brooks,
C.D.Stout,
and
M.R.Ghadiri
(2006).
Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution.
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Biochemistry,
45,
4463-4473.
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PDB codes:
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P.P.Chapagain,
and
B.S.Gerstman
(2006).
Removal of kinetic traps and enhanced protein folding by strategic substitution of amino acids in a model alpha-helical hairpin peptide.
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Biopolymers,
81,
167-178.
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C.M.Taylor,
and
A.E.Keating
(2005).
Orientation and oligomerization specificity of the Bcr coiled-coil oligomerization domain.
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Biochemistry,
44,
16246-16256.
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M.K.Yadav,
J.E.Redman,
L.J.Leman,
J.M.Alvarez-Gutiérrez,
Y.Zhang,
C.D.Stout,
and
M.R.Ghadiri
(2005).
Structure-based engineering of internal cavities in coiled-coil peptides.
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Biochemistry,
44,
9723-9732.
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PDB codes:
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A.L.Lomize,
I.D.Pogozheva,
and
H.I.Mosberg
(2004).
Quantification of helix-helix binding affinities in micelles and lipid bilayers.
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Protein Sci,
13,
2600-2612.
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C.D.Deppmann,
A.Acharya,
V.Rishi,
B.Wobbes,
S.Smeekens,
E.J.Taparowsky,
and
C.Vinson
(2004).
Dimerization specificity of all 67 B-ZIP motifs in Arabidopsis thaliana: a comparison to Homo sapiens B-ZIP motifs.
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Nucleic Acids Res,
32,
3435-3445.
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J.H.Fong,
A.E.Keating,
and
M.Singh
(2004).
Predicting specificity in bZIP coiled-coil protein interactions.
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Genome Biol,
5,
R11.
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J.Holton,
and
T.Alber
(2004).
Automated protein crystal structure determination using ELVES.
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Proc Natl Acad Sci U S A,
101,
1537-1542.
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PDB codes:
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J.M.Mason,
and
K.M.Arndt
(2004).
Coiled coil domains: stability, specificity, and biological implications.
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Chembiochem,
5,
170-176.
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M.J.West,
H.M.Webb,
A.J.Sinclair,
and
D.N.Woolfson
(2004).
Biophysical and mutational analysis of the putative bZIP domain of Epstein-Barr virus EBNA 3C.
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J Virol,
78,
9431-9445.
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N.Pokala,
and
T.M.Handel
(2004).
Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation.
|
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Protein Sci,
13,
925-936.
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T.Stockner,
W.L.Ash,
J.L.MacCallum,
and
D.P.Tieleman
(2004).
Direct simulation of transmembrane helix association: role of asparagines.
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Biophys J,
87,
1650-1656.
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S.K.Sia,
and
P.S.Kim
(2003).
Protein grafting of an HIV-1-inhibiting epitope.
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Proc Natl Acad Sci U S A,
100,
9756-9761.
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W.F.DeGrado,
H.Gratkowski,
and
J.D.Lear
(2003).
How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles.
|
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Protein Sci,
12,
647-665.
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Y.Yang,
L.Fanning,
and
T.Jack
(2003).
The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins, APETALA3 and PISTILLATA.
|
| |
Plant J,
33,
47-59.
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B.Ciani,
E.G.Hutchinson,
R.B.Sessions,
and
D.N.Woolfson
(2002).
A designed system for assessing how sequence affects alpha to beta conformational transitions in proteins.
|
| |
J Biol Chem,
277,
10150-10155.
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C.Beloin,
S.McKenna,
and
C.J.Dorman
(2002).
Molecular dissection of VirB, a key regulator of the virulence cascade of Shigella flexneri.
|
| |
J Biol Chem,
277,
15333-15344.
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H.Gratkowski,
Q.H.Dai,
A.J.Wand,
W.F.DeGrado,
and
J.D.Lear
(2002).
Cooperativity and specificity of association of a designed transmembrane peptide.
|
| |
Biophys J,
83,
1613-1619.
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K.M.Campbell,
A.J.Sholders,
and
K.J.Lumb
(2002).
Contribution of buried lysine residues to the oligomerization specificity and stability of the fos coiled coil.
|
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Biochemistry,
41,
4866-4871.
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L.J.Tai,
S.M.McFall,
K.Huang,
B.Demeler,
S.G.Fox,
K.Brubaker,
I.Radhakrishnan,
and
R.I.Morimoto
(2002).
Structure-function analysis of the heat shock factor-binding protein reveals a protein composed solely of a highly conserved and dynamic coiled-coil trimerization domain.
|
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J Biol Chem,
277,
735-745.
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Y.B.Yu
(2002).
Coiled-coils: stability, specificity, and drug delivery potential.
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Adv Drug Deliv Rev,
54,
1113-1129.
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A.Ababou,
and
J.R.Desjarlais
(2001).
Solvation energetics and conformational change in EF-hand proteins.
|
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Protein Sci,
10,
301-312.
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D.L.Akey,
V.N.Malashkevich,
and
P.S.Kim
(2001).
Buried polar residues in coiled-coil interfaces.
|
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Biochemistry,
40,
6352-6360.
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PDB codes:
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H.Zhu,
S.A.Celinski,
J.M.Scholtz,
and
J.C.Hu
(2001).
An engineered leucine zipper a position mutant with an unusual three-state unfolding pathway.
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Protein Sci,
10,
24-33.
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K.Dutta,
A.Alexandrov,
H.Huang,
and
S.M.Pascal
(2001).
pH-induced folding of an apoptotic coiled coil.
|
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Protein Sci,
10,
2531-2540.
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M.Rosa-Calatrava,
L.Grave,
F.Puvion-Dutilleul,
B.Chatton,
and
C.Kedinger
(2001).
Functional analysis of adenovirus protein IX identifies domains involved in capsid stability, transcriptional activity, and nuclear reorganization.
|
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J Virol,
75,
7131-7141.
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C.L.Boon,
and
A.Chakrabartty
(2000).
Nonpolar contributions to conformational specificity in assemblies of designed short helical peptides.
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Protein Sci,
9,
1011-1023.
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D.N.Marti,
I.Jelesarov,
and
H.R.Bosshard
(2000).
Interhelical ion pairing in coiled coils: solution structure of a heterodimeric leucine zipper and determination of pKa values of Glu side chains.
|
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Biochemistry,
39,
12804-12818.
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PDB code:
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H.Ji,
C.Bracken,
and
M.Lu
(2000).
Buried polar interactions and conformational stability in the simian immunodeficiency virus (SIV) gp41 core.
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Biochemistry,
39,
676-685.
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J.M.Matthews,
T.F.Young,
S.P.Tucker,
and
J.P.Mackay
(2000).
The core of the respiratory syncytial virus fusion protein is a trimeric coiled coil.
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J Virol,
74,
5911-5920.
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M.A.Willis,
B.Bishop,
L.Regan,
and
A.T.Brunger
(2000).
Dramatic structural and thermodynamic consequences of repacking a protein's hydrophobic core.
|
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Structure,
8,
1319-1328.
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PDB codes:
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M.J.Pandya,
G.M.Spooner,
M.Sunde,
J.R.Thorpe,
A.Rodger,
and
D.N.Woolfson
(2000).
Sticky-end assembly of a designed peptide fiber provides insight into protein fibrillogenesis.
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Biochemistry,
39,
8728-8734.
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R.B.Hill,
and
W.F.DeGrado
(2000).
A polar, solvent-exposed residue can be essential for native protein structure.
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Structure,
8,
471-479.
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E.C.Johnson,
G.A.Lazar,
J.R.Desjarlais,
and
T.M.Handel
(1999).
Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin.
|
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Structure,
7,
967-976.
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PDB code:
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G.A.Lazar,
E.C.Johnson,
J.R.Desjarlais,
and
T.M.Handel
(1999).
Rotamer strain as a determinant of protein structural specificity.
|
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Protein Sci,
8,
2598-2610.
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PDB code:
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K.Wagschal,
B.Tripet,
P.Lavigne,
C.Mant,
and
R.S.Hodges
(1999).
The role of position a in determining the stability and oligomerization state of alpha-helical coiled coils: 20 amino acid stability coefficients in the hydrophobic core of proteins.
|
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Protein Sci,
8,
2312-2329.
|
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S.Nautiyal,
and
T.Alber
(1999).
Crystal structure of a designed, thermostable, heterotrimeric coiled coil.
|
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Protein Sci,
8,
84-90.
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PDB code:
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V.N.Malashkevich,
B.J.Schneider,
M.L.McNally,
M.A.Milhollen,
J.X.Pang,
and
P.S.Kim
(1999).
Core structure of the envelope glycoprotein GP2 from Ebola virus at 1.9-A resolution.
|
| |
Proc Natl Acad Sci U S A,
96,
2662-2667.
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PDB code:
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W.F.DeGrado,
C.M.Summa,
V.Pavone,
F.Nastri,
and
A.Lombardi
(1999).
De novo design and structural characterization of proteins and metalloproteins.
|
| |
Annu Rev Biochem,
68,
779-819.
|
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Z.S.Hendsch,
and
B.Tidor
(1999).
Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding.
|
| |
Protein Sci,
8,
1381-1392.
|
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E.G.Hutchinson,
R.B.Sessions,
J.M.Thornton,
and
D.N.Woolfson
(1998).
Determinants of strand register in antiparallel beta-sheets of proteins.
|
| |
Protein Sci,
7,
2287-2300.
|
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G.A.Lazar,
and
T.M.Handel
(1998).
Hydrophobic core packing and protein design.
|
| |
Curr Opin Chem Biol,
2,
675-679.
|
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J.P.Schneider,
A.Lombardi,
and
W.F.DeGrado
(1998).
Analysis and design of three-stranded coiled coils and three-helix bundles.
|
| |
Fold Des,
3,
R29-R40.
|
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N.Liu,
C.Deillon,
S.Klauser,
B.Gutte,
and
R.M.Thomas
(1998).
Synthesis, physicochemical characterization, and crystallization of a putative retro-coiled coil.
|
| |
Protein Sci,
7,
1214-1220.
|
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O.H.Pan,
and
K.Beck
(1998).
The C-terminal domain of matrilin-2 assembles into a three-stranded alpha-helical coiled coil.
|
| |
J Biol Chem,
273,
14205-14209.
|
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R.A.Kammerer,
T.Schulthess,
R.Landwehr,
A.Lustig,
J.Engel,
U.Aebi,
and
M.O.Steinmetz
(1998).
An autonomous folding unit mediates the assembly of two-stranded coiled coils.
|
| |
Proc Natl Acad Sci U S A,
95,
13419-13424.
|
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V.A.Sharma,
J.Logan,
D.S.King,
R.White,
and
T.Alber
(1998).
Sequence-based design of a peptide probe for the APC tumor suppressor protein.
|
| |
Curr Biol,
8,
823-830.
|
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J.J.Falke,
R.B.Bass,
S.L.Butler,
S.A.Chervitz,
and
M.A.Danielson
(1997).
The two-component signaling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases, and adaptation enzymes.
|
| |
Annu Rev Cell Dev Biol,
13,
457-512.
|
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K.Beck,
J.E.Gambee,
A.Kamawal,
and
H.P.Bächinger
(1997).
A single amino acid can switch the oligomerization state of the alpha-helical coiled-coil domain of cartilage matrix protein.
|
| |
EMBO J,
16,
3767-3777.
|
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K.Tan,
J.Liu,
J.Wang,
S.Shen,
and
M.Lu
(1997).
Atomic structure of a thermostable subdomain of HIV-1 gp41.
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Proc Natl Acad Sci U S A,
94,
12303-12308.
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PDB code:
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M.A.Danielson,
R.B.Bass,
and
J.J.Falke
(1997).
Cysteine and disulfide scanning reveals a regulatory alpha-helix in the cytoplasmic domain of the aspartate receptor.
|
| |
J Biol Chem,
272,
32878-32888.
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R.Wiltscheck,
R.A.Kammerer,
S.A.Dames,
T.Schulthess,
M.J.Blommers,
J.Engel,
and
A.T.Alexandrescu
(1997).
Heteronuclear NMR assignments and secondary structure of the coiled coil trimerization domain from cartilage matrix protein in oxidized and reduced forms.
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| |
Protein Sci,
6,
1734-1745.
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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
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
code is
shown on the right.
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Links
