-
1
-
-
0033942874
-
Structure and function of bacterial outer membrane proteins: Barrels in a nutshell
-
Koebnik R, Locher KP, Van Gelder P. 2000. Structure and function of bacterial outer membrane proteins: barrels in a nutshell. Mol Microbiol 37:239-253.
-
(2000)
Mol Microbiol
, vol.37
, pp. 239-253
-
-
Koebnik, R.1
Locher, K.P.2
Van Gelder, P.3
-
2
-
-
50249128194
-
Structural biology of membrane-intrinsic b-barrel enzymes: Sentinels of the bacterial outer membrane
-
Bishop RE. 2008. Structural biology of membrane-intrinsic b-barrel enzymes: sentinels of the bacterial outer membrane. Biochim Biophys Acta 1778:1881-1896.
-
(2008)
Biochim Biophys Acta
, vol.1778
, pp. 1881-1896
-
-
Bishop, R.E.1
-
3
-
-
0032832765
-
Outer membrane protein A of E. coli folds into detergent micelles, but not in the presence of monomeric detergent
-
Kleinschmidt JH, Wiener MC, Tamm LK. 1999. Outer membrane protein A of E. coli folds into detergent micelles, but not in the presence of monomeric detergent. Prot Sci 8:2065-2071.
-
(1999)
Prot Sci
, vol.8
, pp. 2065-2071
-
-
Kleinschmidt, J.H.1
Wiener, M.C.2
Tamm, L.K.3
-
4
-
-
0037984384
-
Folding and insertion of the outer membrane protein OmpA is assisted by the chaperone Skp and by lipopolysaccharide
-
Bulieris PV, Behrens S, Holst O, Kleinschmidt JH. 2003. Folding and insertion of the outer membrane protein OmpA is assisted by the chaperone Skp and by lipopolysaccharide. J Biol Chem 278:9092-9099.
-
(2003)
J Biol Chem
, vol.278
, pp. 9092-9099
-
-
Bulieris, P.V.1
Behrens, S.2
Holst, O.3
Kleinschmidt, J.H.4
-
5
-
-
33646727775
-
Folding kinetics of the outer membrane proteins OmpA and FomA into phospholipid bilayers
-
Kleinschmidt JH. 2006. Folding kinetics of the outer membrane proteins OmpA and FomA into phospholipid bilayers. Chem Phys Lipids 141:30-47.
-
(2006)
Chem Phys Lipids
, vol.141
, pp. 30-47
-
-
Kleinschmidt, J.H.1
-
6
-
-
33745737498
-
Membrane elastic fluctuations and the insertion and tilt of beta-barrel proteins
-
Marsh D, Shanmugavadivu B, Kleinschmidt JH. 2006. Membrane elastic fluctuations and the insertion and tilt of beta-barrel proteins. Biophys J 91:227-232.
-
(2006)
Biophys J
, vol.91
, pp. 227-232
-
-
Marsh, D.1
Shanmugavadivu, B.2
Kleinschmidt, J.H.3
-
8
-
-
7044247850
-
Folding and assembly of b-barrel membrane proteins
-
Tamm LK, Hong H, Liang B. 2004. Folding and assembly of b-barrel membrane proteins. Biochim Biophys Acta 1666:250-263.
-
(2004)
Biochim Biophys Acta
, vol.1666
, pp. 250-263
-
-
Tamm, L.K.1
Hong, H.2
Liang, B.3
-
9
-
-
33750255413
-
Electrostatic couplings in OmpA ion-channel gating suggest a mechanism for pore opening
-
Hong H, Szabo G, Tamm LK. 2006. Electrostatic couplings in OmpA ion-channel gating suggest a mechanism for pore opening. Nature Chem Biol 2:627-635.
-
(2006)
Nature Chem Biol
, vol.2
, pp. 627-635
-
-
Hong, H.1
Szabo, G.2
Tamm, L.K.3
-
10
-
-
34447135007
-
Role of aromatic side chains in the folding and thermodynamic stability of integral membrane proteins
-
Hong HD, Park S, Jimenez RHF, Rinehart D, Tamm LK. 2007. Role of aromatic side chains in the folding and thermodynamic stability of integral membrane proteins. J Am Chem Soc 129:8320-8327.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 8320-8327
-
-
Hong, H.D.1
Park, S.2
Jimenez, R.H.F.3
Rinehart, D.4
Tamm, L.K.5
-
11
-
-
44949145433
-
Incorporation of outer membrane protein OmpG in lipid membranes: Protein-lipid interactions and beta-barrel orientation
-
Anbazhagan V, Qu J, Kleinschmidt JH, Marsh D. 2008. Incorporation of outer membrane protein OmpG in lipid membranes: protein-lipid interactions and beta-barrel orientation. Biochem 47:6189-6198.
-
(2008)
Biochem
, vol.47
, pp. 6189-6198
-
-
Anbazhagan, V.1
Qu, J.2
Kleinschmidt, J.H.3
Marsh, D.4
-
12
-
-
55549120907
-
b-Barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro
-
Burgess NK, Dao TP, Stanley AM, Fleming KG. 2008. b-Barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro. J Biol Chem 283:26748-26758.
-
(2008)
J Biol Chem
, vol.283
, pp. 26748-26758
-
-
Burgess, N.K.1
Dao, T.P.2
Stanley, A.M.3
Fleming, K.G.4
-
13
-
-
4143131241
-
A hydrocarbon ruler measures palmitate in the enzymatic acylation of endotoxin
-
Ahn VE, Lo EI, Engel CK, Chen L, Hwang PM, Kay LE, Bishop RE, Prive' GG. 2004. A hydrocarbon ruler measures palmitate in the enzymatic acylation of endotoxin. EMBO J 23:2931-2941.
-
(2004)
EMBO J
, vol.23
, pp. 2931-2941
-
-
Ahn, V.E.1
Lo, E.I.2
Engel, C.K.3
Chen, L.4
Hwang, P.M.5
Kay, L.E.6
Bishop, R.E.7
Prive', G.G.8
-
14
-
-
0037108964
-
Solution structure and dynamics of the outer membrane enzyme PagP by NMR
-
Hwang PM, Choy WY, Lo EI, Chen L, Forman-Kay JD, Raetz CRH, Prive' GG, Bishop RE, Kay LE. 2002. Solution structure and dynamics of the outer membrane enzyme PagP by NMR. Proc Nat Acad Sci USA 99:13560-13565.
-
(2002)
Proc Nat Acad Sci USA
, vol.99
, pp. 13560-13565
-
-
Hwang, P.M.1
Choy, W.Y.2
Lo, E.I.3
Chen, L.4
Forman-Kay, J.D.5
Raetz, C.R.H.6
Prive', G.G.7
Bishop, R.E.8
Kay, L.E.9
-
15
-
-
0032538292
-
Lipid A acylation and bacterial resistance against vertebrate antimicrobial peptides
-
Guo L, Lim KB, Poduje CM, Daniel M, Gunn JS, Hackett M, Miller SI. 1998. Lipid A acylation and bacterial resistance against vertebrate antimicrobial peptides. Cell 95:189-198.
-
(1998)
Cell
, vol.95
, pp. 189-198
-
-
Guo, L.1
Lim, K.B.2
Poduje, C.M.3
Daniel, M.4
Gunn, J.S.5
Hackett, M.6
Miller, S.I.7
-
16
-
-
2442544458
-
3-O-deacylation of lipid A by PagL, a PhoP/PhoQ-regulated deacylase of Salmonella typhimurium, modulates signaling through Tolllike receptor 4
-
Kawasaki K, Ernst RK, Miller SI. 2004. 3-O-deacylation of lipid A by PagL, a PhoP/PhoQ-regulated deacylase of Salmonella typhimurium, modulates signaling through Tolllike receptor 4. J Biol Chem 279:20044-20048.
-
(2004)
J Biol Chem
, vol.279
, pp. 20044-20048
-
-
Kawasaki, K.1
Ernst, R.K.2
Miller, S.I.3
-
17
-
-
3042707182
-
The integral membrane enzyme PagP alternates between two dynamically distinct states
-
Hwang PM, Bishop RE, Kay LE. 2004. The integral membrane enzyme PagP alternates between two dynamically distinct states. Proc Natl Acad Sci USA 101:9618-9623.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 9618-9623
-
-
Hwang, P.M.1
Bishop, R.E.2
Kay, L.E.3
-
18
-
-
23744436588
-
The lipid A palmitoyltransferase PagP: Molecular mechanisms and role in bacterial pathogenesis
-
Bishop RE. 2005. The lipid A palmitoyltransferase PagP: molecular mechanisms and role in bacterial pathogenesis. Molec Microbiol 57:900-912.
-
(2005)
Molec Microbiol
, vol.57
, pp. 900-912
-
-
Bishop, R.E.1
-
19
-
-
34748822875
-
The N-terminal helix is a post-assembly clamp in the bacterial outer membrane protein PagP
-
Huysmans GHM, Radford SE, Brockwell DJ, Baldwin SA. 2007. The N-terminal helix is a post-assembly clamp in the bacterial outer membrane protein PagP. J Mol Biol 373:529-540.
-
(2007)
J Mol Biol
, vol.373
, pp. 529-540
-
-
Huysmans, G.H.M.1
Radford, S.E.2
Brockwell, D.J.3
Baldwin, S.A.4
-
21
-
-
49549083949
-
Membrane proteins: Molecular dynamics simulations
-
Lindahl E, Sansom MSP. 2008. Membrane proteins: molecular dynamics simulations. Curr Opin Struct Biol 18:425-431.
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 425-431
-
-
Lindahl, E.1
Sansom, M.S.P.2
-
22
-
-
0027136282
-
Comparative protein modeling by satisfaction of spatial restraints
-
Sali A, Blundell TL. 1993. Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 234:779-815.
-
(1993)
J Mol Biol
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
23
-
-
0033810049
-
Modeling of loops in protein structures
-
Fiser A, Kinh Gian Do R, Sali A. 2000. Modeling of loops in protein structures. Prot Sci 9:1753-1773.
-
(2000)
Prot Sci
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Kinh Gian, D.R.2
Sali, A.3
-
24
-
-
0025398721
-
WhatIf-a molecular modeling and drug design program
-
Vriend G. 1990. WhatIf-a molecular modeling and drug design program. J Mol Graph 8:52-56.
-
(1990)
J Mol Graph
, vol.8
, pp. 52-56
-
-
Vriend, G.1
-
25
-
-
0024278357
-
Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds
-
Roseman MA. 1988. Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds. J Mol Biol 200:513-522.
-
(1988)
J Mol Biol
, vol.200
, pp. 513-522
-
-
Roseman, M.A.1
-
27
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
Pullman B, editor, Dordrecht: Reidel. p
-
Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. 1981. Interaction models for water in relation to protein hydration. In: Pullman B, editor. Intermolecular forces. Dordrecht: Reidel. p. 331-342.
-
(1981)
Intermolecular forces
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
Hermans, J.4
-
28
-
-
0038724257
-
Membrane protein dynamics vs. environment: Simulations of OmpA in a micelle and in a bilayer
-
Bond PJ, Sansom MSP. 2003. Membrane protein dynamics vs. environment: simulations of OmpA in a micelle and in a bilayer. J Mol Biol 329:1035-1053.
-
(2003)
J Mol Biol
, vol.329
, pp. 1035-1053
-
-
Bond, P.J.1
Sansom, M.S.P.2
-
29
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl E, Hess B, van der Spoel D. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Molec Model 7:306-317.
-
(2001)
J Molec Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
30
-
-
0003544049
-
-
Biomos & Hochschulverlag AG an der ETH Zurich, Groningen & Zurich
-
van Gunsteren WF, Kruger P, Billeter SR, Mark AE, Eising AA, Scott WRP, Huneberger PH, Tironi IG. 1996. Biomolecular simulation: the GROMOS96 Manual and User Guide. Biomos & Hochschulverlag AG an der ETH Zurich, Groningen & Zurich.
-
(1996)
Biomolecular simulation: The GROMOS96 Manual and User Guide
-
-
van Gunsteren, W.F.1
Kruger, P.2
Billeter, S.R.3
Mark, A.E.4
Eising, A.A.5
Scott, W.R.P.6
Huneberger, P.H.7
Tironi, I.G.8
-
31
-
-
33846823909
-
Particle mesh Ewald-an N.log(N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L. 1993. Particle mesh Ewald-an N.log(N) method for Ewald sums in large systems. J Chem Phys 98:10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
32
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. 1984. Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-3690.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
34
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern-recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
37
-
-
2942564158
-
The simulation approach to bacterial outer membrane proteins
-
Bond PJ, Sansom MSP. 2004. The simulation approach to bacterial outer membrane proteins. Mol Memb Biol 21:151-162.
-
(2004)
Mol Memb Biol
, vol.21
, pp. 151-162
-
-
Bond, P.J.1
Sansom, M.S.P.2
-
38
-
-
38149112637
-
Outer membrane proteins: Comparing X-ray and NMR structures by MD simulations in lipid bilayers
-
Cox K, Bond PJ, Grottesi A, Baaden M, Sansom MSP. 2007. Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers. Eur Biophys J 37:131-141.
-
(2007)
Eur Biophys J
, vol.37
, pp. 131-141
-
-
Cox, K.1
Bond, P.J.2
Grottesi, A.3
Baaden, M.4
Sansom, M.S.P.5
-
40
-
-
10044244661
-
Lipidprotein interactions of integral membrane proteins: A comparative simulation study
-
Deol SS, Bond PJ, Domene C, Sansom MSP. 2004. Lipidprotein interactions of integral membrane proteins: a comparative simulation study. Biophys J 87:3737-3749.
-
(2004)
Biophys J
, vol.87
, pp. 3737-3749
-
-
Deol, S.S.1
Bond, P.J.2
Domene, C.3
Sansom, M.S.P.4
-
41
-
-
33947384532
-
Monotopic enzymes and lipid bilayers: A comparative study
-
Fowler PW, Balali-Mood K, Deol S, Coveney PV, Sansom MSP. 2007. Monotopic enzymes and lipid bilayers: a comparative study. Biochem 46:3108-3115.
-
(2007)
Biochem
, vol.46
, pp. 3108-3115
-
-
Fowler, P.W.1
Balali-Mood, K.2
Deol, S.3
Coveney, P.V.4
Sansom, M.S.P.5
-
42
-
-
0034284386
-
How proteins adapt to a membrane-water interface
-
Killian JA, von Heijne G. 2000. How proteins adapt to a membrane-water interface. Trends Biochem Sci 25:429-434.
-
(2000)
Trends Biochem Sci
, vol.25
, pp. 429-434
-
-
Killian, J.A.1
von Heijne, G.2
-
43
-
-
12344330612
-
A study of the membrane-water interface region of membrane proteins
-
Granseth E, von Heijne G, Elofsson A. 2005. A study of the membrane-water interface region of membrane proteins. J Mol Biol 346:377-385.
-
(2005)
J Mol Biol
, vol.346
, pp. 377-385
-
-
Granseth, E.1
von Heijne, G.2
Elofsson, A.3
-
44
-
-
41449119304
-
Coarse-grained MD simulations of membrane protein-bilayer self-assembly
-
Scott KA, Bond PJ, Ivetac A, Chetwynd AP, Khalid S, Sansom MSP. 2008. Coarse-grained MD simulations of membrane protein-bilayer self-assembly. Structure 16:621-630.
-
(2008)
Structure
, vol.16
, pp. 621-630
-
-
Scott, K.A.1
Bond, P.J.2
Ivetac, A.3
Chetwynd, A.P.4
Khalid, S.5
Sansom, M.S.P.6
-
45
-
-
14644398554
-
Orientation of b-barrel proteins OmpA and FhuA in lipid membranes. Chain length dependence from infrared dichroism
-
Ramakrishnan M, Qu J, Pocanschi CL, Kleinschmidt JH, Marsh D. 2005. Orientation of b-barrel proteins OmpA and FhuA in lipid membranes. Chain length dependence from infrared dichroism. Biochem 44:3515-3523.
-
(2005)
Biochem
, vol.44
, pp. 3515-3523
-
-
Ramakrishnan, M.1
Qu, J.2
Pocanschi, C.L.3
Kleinschmidt, J.H.4
Marsh, D.5
-
46
-
-
0037114710
-
Molecular structure of the outer bacterial membrane of Pseudomonas aeruginosa via classical simulation
-
Shroll RM, Straatsma TP. 2002. Molecular structure of the outer bacterial membrane of Pseudomonas aeruginosa via classical simulation. Biopolymers 65:395-407.
-
(2002)
Biopolymers
, vol.65
, pp. 395-407
-
-
Shroll, R.M.1
Straatsma, T.P.2
-
47
-
-
45849124632
-
Assessment of the convergence of molecular dynamics simulations of lipopolysaccharide membranes
-
Soares TA, Straatsma TP. 2008. Assessment of the convergence of molecular dynamics simulations of lipopolysaccharide membranes. Molec Simul 34:295-307.
-
(2008)
Molec Simul
, vol.34
, pp. 295-307
-
-
Soares, T.A.1
Straatsma, T.P.2
|