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PDBsum entry 1hxt
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Membrane protein
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PDB id
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1hxt
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Contents |
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* Residue conservation analysis
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DOI no:
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Biochemistry
40:6319-6325
(2001)
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PubMed id:
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Role of charged residues at the OmpF porin channel constriction probed by mutagenesis and simulation.
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P.S.Phale,
A.Philippsen,
C.Widmer,
V.P.Phale,
J.P.Rosenbusch,
T.Schirmer.
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ABSTRACT
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The channel constriction of OmpF porin, a pore protein in the bacterial outer
membrane, is highly charged due to the presence of three arginines (R42, R82,
and R132) and two acidic residues (D113 and E117). The influence of these
charges on ion conductance, ion selectivity, and voltage gating has been studied
with mutants D113N/E117Q, R42A/R82A/R132A/D113N/E117Q, and V18K/G131K, which
were designed to remove or add protein charge at the channel constriction. The
crystal structures revealed no or only local changes compared to wild-type OmpF,
thus allowing a comparative study. The single-channel conductance of the
isosteric D113N/E117Q variant was found to be 2-fold reduced, and that of the
pentuple mutant was 70% of the wild-type value, despite a considerably larger
pore cross section. Ion selectivity was drastically altered by the mutations
with cation/anion permeability ratios ranging from 1 to 12. Ion flow through
these and eight other mutants, which have been characterized previously, was
simulated by Brownian dynamics based on the detailed crystal structures. The
calculated ion selectivity and relative channel conductance values agree well
with the experimental data. This demonstrates that ion translocation through
porin is mainly governed by pore geometry and charge, the two factors that are
properly represented in the simulations.
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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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M.Queralt-Martín,
E.García-Giménez,
S.Mafé,
and
A.Alcaraz
(2011).
Divalent cations reduce the pH sensitivity of OmpF channel inducing the pK(a) shift of key acidic residues.
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Phys Chem Chem Phys,
13,
563-569.
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V.M.Aguilella,
M.Queralt-Martín,
M.Aguilella-Arzo,
and
A.Alcaraz
(2011).
Insights on the permeability of wide protein channels: measurement and interpretation of ion selectivity.
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Integr Biol (Camb),
3,
159-172.
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B.Wager,
A.Baslé,
and
A.H.Delcour
(2010).
Disulfide bond tethering of extracellular loops does not affect the closure of OmpF porin at acidic pH.
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Proteins,
78,
2886-2894.
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D.A.Hill,
and
S.A.Desai
(2010).
Malaria parasite mutants with altered erythrocyte permeability: a new drug resistance mechanism and important molecular tool.
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Future Microbiol,
5,
81-97.
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G.Kefala,
C.Ahn,
M.Krupa,
L.Esquivies,
I.Maslennikov,
W.Kwiatkowski,
and
S.Choe
(2010).
Structures of the OmpF porin crystallized in the presence of foscholine-12.
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Protein Sci,
19,
1117-1125.
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PDB codes:
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M.Vrouenraets,
and
H.Miedema
(2010).
The ionization state of D37 in E. coli porin OmpF and the nature of conductance fluctuations in D37 mutants.
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Eur Biophys J,
39,
1563-1571.
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O.Dyachok,
P.Zhabyeyev,
and
T.F.McDonald
(2010).
Electroporation-induced inward current in voltage-clamped guinea pig ventricular myocytes.
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J Membr Biol,
238,
69-80.
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A.Alcaraz,
E.M.Nestorovich,
M.L.López,
E.García-Giménez,
S.M.Bezrukov,
and
V.M.Aguilella
(2009).
Diffusion, Exclusion, and Specific Binding in a Large Channel: A Study of OmpF Selectivity Inversion.
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Biophys J,
96,
56-66.
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A.H.Delcour
(2009).
Outer membrane permeability and antibiotic resistance.
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Biochim Biophys Acta,
1794,
808-816.
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A.Schulte,
S.Ruamchan,
P.Khunkaewla,
and
W.Suginta
(2009).
The outer membrane protein VhOmp of Vibrio harveyi: pore-forming properties in black lipid membranes.
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J Membr Biol,
230,
101-111.
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J.Huff,
M.Pavlenok,
S.Sukumaran,
and
M.Niederweis
(2009).
Functions of the periplasmic loop of the porin MspA from Mycobacterium smegmatis.
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J Biol Chem,
284,
10223-10231.
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M.Aguilella-Arzo,
A.Andrio,
V.M.Aguilella,
and
A.Alcaraz
(2009).
Dielectric saturation of water in a membrane protein channel.
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Phys Chem Chem Phys,
11,
358-365.
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S.Pezeshki,
C.Chimerel,
A.N.Bessonov,
M.Winterhalter,
and
U.Kleinekathöfer
(2009).
Understanding ion conductance on a molecular level: an all-atom modeling of the bacterial porin OmpF.
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Biophys J,
97,
1898-1906.
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Y.Zhu,
T.Guo,
J.E.Park,
X.Li,
W.Meng,
A.Datta,
M.Bern,
S.K.Lim,
and
S.K.Sze
(2009).
Elucidating in vivo structural dynamics in integral membrane protein by hydroxyl radical footprinting.
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Mol Cell Proteomics,
8,
1999-2010.
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A.A.Bokhari,
T.Solomon,
and
S.A.Desai
(2008).
Two distinct mechanisms of transport through the plasmodial surface anion channel.
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J Membr Biol,
226,
27-34.
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C.Chimerel,
L.Movileanu,
S.Pezeshki,
M.Winterhalter,
and
U.Kleinekathöfer
(2008).
Transport at the nanoscale: temperature dependence of ion conductance.
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Eur Biophys J,
38,
121-125.
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E.Yamashita,
M.V.Zhalnina,
S.D.Zakharov,
O.Sharma,
and
W.A.Cramer
(2008).
Crystal structures of the OmpF porin: function in a colicin translocon.
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EMBO J,
27,
2171-2180.
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PDB codes:
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J.Cervera,
A.G.Komarov,
and
V.M.Aguilella
(2008).
Rectification properties and pH-dependent selectivity of meningococcal class 1 porin.
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Biophys J,
94,
1194-1202.
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M.Pagel,
V.Simonet,
J.Li,
M.Lallemand,
B.Lauman,
and
A.H.Delcour
(2007).
Phenotypic characterization of pore mutants of the Vibrio cholerae porin OmpU.
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J Bacteriol,
189,
8593-8600.
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A.A.Sobko,
E.A.Kotova,
Y.N.Antonenko,
S.D.Zakharov,
and
W.A.Cramer
(2006).
Lipid dependence of the channel properties of a colicin E1-lipid toroidal pore.
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J Biol Chem,
281,
14408-14416.
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C.Danelon,
E.M.Nestorovich,
M.Winterhalter,
M.Ceccarelli,
and
S.M.Bezrukov
(2006).
Interaction of zwitterionic penicillins with the OmpF channel facilitates their translocation.
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Biophys J,
90,
1617-1627.
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D.Ho,
S.Chang,
and
C.D.Montemagno
(2006).
Fabrication of biofunctional nanomaterials via Escherichia coli OmpF protein air/water interface insertion/integration with copolymeric amphiphiles.
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Nanomedicine,
2,
103-112.
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H.Miedema,
M.Vrouenraets,
J.Wierenga,
B.Eisenberg,
T.Schirmer,
A.Baslé,
and
W.Meijberg
(2006).
Conductance and selectivity fluctuations in D127 mutants of the bacterial porin OmpF.
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Eur Biophys J,
36,
13-22.
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H.Miedema,
M.Vrouenraets,
J.Wierenga,
D.Gillespie,
B.Eisenberg,
W.Meijberg,
and
W.Nonner
(2006).
Ca2+ selectivity of a chemically modified OmpF with reduced pore volume.
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Biophys J,
91,
4392-4400.
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M.Vrouenraets,
J.Wierenga,
W.Meijberg,
and
H.Miedema
(2006).
Chemical modification of the bacterial porin OmpF: gain of selectivity by volume reduction.
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Biophys J,
90,
1202-1211.
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O.Onaca,
M.Nallani,
S.Ihle,
A.Schenk,
and
U.Schwaneberg
(2006).
Functionalized nanocompartments (Synthosomes): limitations and prospective applications in industrial biotechnology.
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Biotechnol J,
1,
795-805.
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S.Varma,
S.W.Chiu,
and
E.Jakobsson
(2006).
The influence of amino acid protonation states on molecular dynamics simulations of the bacterial porin OmpF.
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Biophys J,
90,
112-123.
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A.Alcaraz,
E.M.Nestorovich,
M.Aguilella-Arzo,
V.M.Aguilella,
and
S.M.Bezrukov
(2004).
Salting out the ionic selectivity of a wide channel: the asymmetry of OmpF.
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Biophys J,
87,
943-957.
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H.Miedema,
A.Meter-Arkema,
J.Wierenga,
J.Tang,
B.Eisenberg,
W.Nonner,
H.Hektor,
D.Gillespie,
and
W.Meijberg
(2004).
Permeation properties of an engineered bacterial OmpF porin containing the EEEE-locus of Ca2+ channels.
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Biophys J,
87,
3137-3147.
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M.Ceccarelli,
C.Danelon,
A.Laio,
and
M.Parrinello
(2004).
Microscopic Mechanism of Antibiotics Translocation through a Porin.
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Biophys J,
87,
58-64.
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S.Varma,
and
E.Jakobsson
(2004).
Ionization states of residues in OmpF and mutants: effects of dielectric constant and interactions between residues.
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Biophys J,
86,
690-704.
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D.P.Tieleman,
V.Borisenko,
M.S.Sansom,
and
G.A.Woolley
(2003).
Understanding pH-dependent selectivity of alamethicin K18 channels by computer simulation.
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Biophys J,
84,
1464-1469.
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E.M.Nestorovich,
T.K.Rostovtseva,
and
S.M.Bezrukov
(2003).
Residue ionization and ion transport through OmpF channels.
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Biophys J,
85,
3718-3729.
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H.Nikaido
(2003).
Molecular basis of bacterial outer membrane permeability revisited.
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Microbiol Mol Biol Rev,
67,
593-656.
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M.Niederweis
(2003).
Mycobacterial porins--new channel proteins in unique outer membranes.
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Mol Microbiol,
49,
1167-1177.
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U.Zachariae,
V.Helms,
and
H.Engelhardt
(2003).
Multistep mechanism of chloride translocation in a strongly anion-selective porin channel.
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Biophys J,
85,
954-962.
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B.Corry,
M.Hoyles,
T.W.Allen,
M.Walker,
S.Kuyucak,
and
S.H.Chung
(2002).
Reservoir boundaries in Brownian dynamics simulations of ion channels.
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Biophys J,
82,
1975-1984.
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B.Roux
(2002).
Theoretical and computational models of ion channels.
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Curr Opin Struct Biol,
12,
182-189.
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C.Andersen,
E.Koronakis,
C.Hughes,
and
V.Koronakis
(2002).
An aspartate ring at the TolC tunnel entrance determines ion selectivity and presents a target for blocking by large cations.
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Mol Microbiol,
44,
1131-1139.
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K.M.Robertson,
and
D.P.Tieleman
(2002).
Molecular basis of voltage gating of OmpF porin.
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Biochem Cell Biol,
80,
517-523.
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M.J.Rodríguez-Marañón,
R.M.Bush,
E.M.Peterson,
T.Schirmer,
and
L.M.de la Maza
(2002).
Prediction of the membrane-spanning beta-strands of the major outer membrane protein of Chlamydia.
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Protein Sci,
11,
1854-1861.
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R.R.Gabdoulline,
and
R.C.Wade
(2002).
Biomolecular diffusional association.
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Curr Opin Struct Biol,
12,
204-213.
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S.Bransburg-Zabary,
E.Nachliel,
and
M.Gutman
(2002).
Gauging of the PhoE channel by a single freely diffusing proton.
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Biophys J,
83,
2987-3000.
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S.Bransburg-Zabary,
E.Nachliel,
and
M.Gutman
(2002).
A fast in silico simulation of ion flux through the large-pore channel proteins.
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Biophys J,
83,
3001-3011.
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T.K.Rostovtseva,
E.M.Nestorovich,
and
S.M.Bezrukov
(2002).
Partitioning of differently sized poly(ethylene glycol)s into OmpF porin.
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Biophys J,
82,
160-169.
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U.Zachariae,
A.Koumanov,
H.Engelhardt,
and
A.Karshikoff
(2002).
Electrostatic properties of the anion selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins.
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Protein Sci,
11,
1309-1319.
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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
