-
2
-
-
0037064291
-
The structure of bacterial outer membrane proteins
-
DOI 10.1016/S0005-2736(02)00577-1, PII S0005273602005771
-
G.E. Schulz The structure of bacterial outer membrane proteins Biochim. Biophys. Acta Biomembr. 1565 2002 308 317 (Pubitemid 35284483)
-
(2002)
Biochimica et Biophysica Acta - Biomembranes
, vol.1565
, Issue.2
, pp. 308-317
-
-
Schulz, G.E.1
-
3
-
-
2942564158
-
The simulation approach to bacterial outer membrane proteins
-
DOI 10.1080/0968760410001699169
-
P.J. Bond, and M.S.P. Sansom The simulation approach to bacterial outer membrane proteins (Review) Mol. Membr. Biol. 21 2004 151 161 (Pubitemid 38745644)
-
(2004)
Molecular Membrane Biology
, vol.21
, Issue.3
, pp. 151-161
-
-
Bond, P.J.1
Sansom, M.S.P.2
-
4
-
-
0034996154
-
Structure of the cell envelope of corynebacteria: Importance of the non-covalently bound lipids in the formation of the cell wall permeability barrier and fracture plane
-
V. Puech, M. Chami, A. Lemassu, M.A. Laneelle, B. Schiffler, P. Gounon, N. Bayan, R. Benz, and M. Daffe Structure of the cell envelope of corynebacteria: importance of the non-covalently bound lipids in the formation of the cell wall permeability barrier and fracture plane Microbiology 147 2001 1365 1382 (Pubitemid 32454654)
-
(2001)
Microbiology
, vol.147
, Issue.5
, pp. 1365-1382
-
-
Puech, V.1
Chami, M.2
Lemassu, A.3
Laneelle, M.-A.4
Schiffler, B.5
Gounon, P.6
Bayan, N.7
Benz, R.8
Daffe, M.9
-
5
-
-
77952889716
-
Carbohydrate metabolism in Corynebacterium glutamicum and applications for the metabolic engineering of l-lysine production strains
-
B. Blombach, and G.M. Seibold Carbohydrate metabolism in Corynebacterium glutamicum and applications for the metabolic engineering of l-lysine production strains Appl. Microbiol. Biotechnol. 86 2010 1313 1322
-
(2010)
Appl. Microbiol. Biotechnol.
, vol.86
, pp. 1313-1322
-
-
Blombach, B.1
Seibold, G.M.2
-
6
-
-
49449107199
-
Direct visualization of the outer membrane of mycobacteria and corynebacteria in their native state
-
B. Zuber, M. Chami, C. Houssin, J. Dubochet, G. Griffiths, and M. Daffe Direct visualization of the outer membrane of mycobacteria and corynebacteria in their native state J. Bacteriol. 190 2008 5672 5680
-
(2008)
J. Bacteriol.
, vol.190
, pp. 5672-5680
-
-
Zuber, B.1
Chami, M.2
Houssin, C.3
Dubochet, J.4
Griffiths, G.5
Daffe, M.6
-
7
-
-
43449090997
-
A putative alpha-helical porin from Corynebacterium glutamicum
-
K. Ziegler, R. Benz, and G.E. Schulz A putative alpha-helical porin from Corynebacterium glutamicum J. Mol. Biol. 379 2008 482 491
-
(2008)
J. Mol. Biol.
, vol.379
, pp. 482-491
-
-
Ziegler, K.1
Benz, R.2
Schulz, G.E.3
-
8
-
-
75149161126
-
Reconstitution experiments and gene deletions reveal the existence of two-component major cell wall channels in the genus Corynebacterium
-
E. Barth, M.A. Barcelo, C. Klackta, and R. Benz Reconstitution experiments and gene deletions reveal the existence of two-component major cell wall channels in the genus Corynebacterium J. Bacteriol. 192 2010 786 800
-
(2010)
J. Bacteriol.
, vol.192
, pp. 786-800
-
-
Barth, E.1
Barcelo, M.A.2
Klackta, C.3
Benz, R.4
-
9
-
-
0043062677
-
PorA represents the major cell wall channel of the gram-positive bacterium Corynebacterium glutamicum
-
DOI 10.1128/JB.185.16.4779-4786.2003
-
N. Costa-Riu, A. Burkovski, R. Kramer, and R. Benz PorA represents the major cell wall channel of the gram-positive bacterium Corynebacterium glutamicum J. Bacteriol. 185 2003 4779 4786 (Pubitemid 36962285)
-
(2003)
Journal of Bacteriology
, vol.185
, Issue.16
, pp. 4779-4786
-
-
Costa-Riu, N.1
Burkovski, A.2
Kramer, R.3
Benz, R.4
-
10
-
-
0345689441
-
Identification of an anion-specific channel in the cell wall of the Gram-positive bacterium Corynebacterium glutamicum
-
DOI 10.1046/j.1365-2958.2003.03754.x
-
N. Costa-Riu, E. Maier, A. Burkovski, R. Kramer, F. Lottspeich, and R. Benz Identification of an anion-specific channel in the cell wall of the Gram-positive bacterium Corynebacterium glutamicum Mol. Microbiol. 50 2003 1295 1308 (Pubitemid 37475860)
-
(2003)
Molecular Microbiology
, vol.50
, Issue.4
, pp. 1295-1308
-
-
Costa-Riu, N.1
Maier, E.2
Burkovski, A.3
Kramer, R.4
Lottspeich, F.5
Benz, R.6
-
11
-
-
33646845510
-
Topology of the porin MspA in the outer membrane of Mycobacterium smegmatis
-
DOI 10.1074/jbc.M511642200
-
M. Mahfoud, S. Sukumaran, P. Hülsmann, K. Grieger, and M. Niederweis Topology of the porin MspA in the outer membrane of Mycobacterium smegmatis J. Biol. Chem. 281 2006 5908 5915 (Pubitemid 43847691)
-
(2006)
Journal of Biological Chemistry
, vol.281
, Issue.9
, pp. 5908-5915
-
-
Mahfoud, M.1
Sukumaran, S.2
Hulsmann, P.3
Grieger, K.4
Niederweis, M.5
-
12
-
-
0027198547
-
Tryptophans in membrane proteins: Indole ring orientations and functional implications in the gramicidin channel
-
W. Hu, K.C. Lee, and T.A. Cross Tryptophans in membrane proteins: indole ring orientations and functional implications in the gramicidin channel Biochemistry 32 1993 7035 7047 (Pubitemid 23221639)
-
(1993)
Biochemistry
, vol.32
, Issue.27
, pp. 7035-7047
-
-
Hu, W.1
Lee, K.-C.2
Cross, T.A.3
-
13
-
-
66549128460
-
The role of lipid composition for insertion and stabilization of amino acids in membranes
-
A.C.V. Johansson, and E. Lindahl The role of lipid composition for insertion and stabilization of amino acids in membranes J. Chem. Phys. 130 2009 8
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 8
-
-
Johansson, A.C.V.1
Lindahl, E.2
-
14
-
-
77749320417
-
An iris-like mechanism of pore dilation in the CorA magnesium transport system
-
N. Chakrabarti, C. Neale, J. Payandeh, E.F. Pai, and R. Pomes An iris-like mechanism of pore dilation in the CorA magnesium transport system Biophys. J. 98 2010 784 792
-
(2010)
Biophys. J.
, vol.98
, pp. 784-792
-
-
Chakrabarti, N.1
Neale, C.2
Payandeh, J.3
Pai, E.F.4
Pomes, R.5
-
15
-
-
0033932839
-
Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations
-
E. Lindahl, and O. Edholm Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations Biophys. J. 79 2000 426 433 (Pubitemid 30436758)
-
(2000)
Biophysical Journal
, vol.79
, Issue.1
, pp. 426-433
-
-
Lindahl, E.1
Edholm, O.2
-
16
-
-
0030999097
-
Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature
-
O. Berger, O. Edholm, and F. Jahnig Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature Biophys. J. 72 1997 2002 2013 (Pubitemid 27184429)
-
(1997)
Biophysical Journal
, vol.72
, Issue.5
, pp. 2002-2013
-
-
Berger, O.1
Edholm, O.2
Jahnig, F.3
-
17
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
DOI 10.1021/jp003919d
-
G.A. Kaminski, R.A. Friesner, J. Tirado-Rives, and W.L. Jorgensen Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides J. Phys. Chem. B 105 2001 6474 6487 (Pubitemid 35339015)
-
(2001)
Journal of Physical Chemistry B
, vol.105
, Issue.28
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
18
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
DOI 10.1021/ja9621760, PII S0002786396021762
-
W.L. Jorgensen, D.S. Maxwell, and J. TiradoRives Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 118 1996 11225 11236 (Pubitemid 26399746)
-
(1996)
Journal of the American Chemical Society
, vol.118
, Issue.45
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
20
-
-
84926811618
-
Constant pressure molecular dynamics for molecular systems
-
S. Nosé, and M.L. Klein Constant pressure molecular dynamics for molecular systems Mol. Phys. 50 1983 1055 1076
-
(1983)
Mol. Phys.
, vol.50
, pp. 1055-1076
-
-
Nosé, S.1
Klein, M.L.2
-
21
-
-
0019707626
-
Polymorphic transitions in single crystals: A new molecular dynamics method
-
DOI 10.1063/1.328693
-
M. Parrinello, and A. Rahman Polymorphic transitions in single crystals: a new molecular dynamics method J. Appl. Phys. 52 1981 7182 7190 (Pubitemid 12456820)
-
(1981)
Journal of Applied Physics
, vol.52
, Issue.12
, pp. 7182-7190
-
-
Parrinello, M.1
Rahman, A.2
-
22
-
-
0001538909
-
Canonical dynamics: Equilibrium phase-space distributions
-
W.G. Hoover Canonical dynamics: equilibrium phase-space distributions Phys. Rev. A 31 1985 1695
-
(1985)
Phys. Rev. A
, vol.31
, pp. 1695
-
-
Hoover, W.G.1
-
23
-
-
84943502952
-
A molecular dynamics method for simulations in the canonical ensemble
-
S.I. Nosé A molecular dynamics method for simulations in the canonical ensemble Mol. Phys. 52 1984 255 268
-
(1984)
Mol. Phys.
, vol.52
, pp. 255-268
-
-
Nosé, S.I.1
-
24
-
-
33645961739
-
A smooth particle mesh Ewald method
-
U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and L.G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 1995 8577 8593
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
25
-
-
33846823909
-
Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems
-
T. Darden, D. York, and L. Pedersen Particle mesh Ewald: an N.log(N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
26
-
-
0000202909
-
Ewald summation for systems with slab geometry
-
I.C. Yeh, and M.L. Berkowitz Ewald summation for systems with slab geometry J. Chem. Phys. 111 1999 3155 3162
-
(1999)
J. Chem. Phys.
, vol.111
, pp. 3155-3162
-
-
Yeh, I.C.1
Berkowitz, M.L.2
-
28
-
-
84986440341
-
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
-
S. Miyamoto, and P.A. Kollman Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 13 1992 952 962
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
29
-
-
0000388705
-
LINCS: A Linear Constraint Solver for molecular simulations
-
B. Hess, H. Bekker, H.J.C. Berendsen, and J. Fraaije LINCS: a linear constraint solver for molecular simulations J. Comput. Chem. 18 1997 1463 1472 (Pubitemid 127637344)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.12
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.G.E.M.4
-
31
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 2008 435 447
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
32
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
DOI 10.1002/jcc.20291
-
D. Van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, and H.J.C. Berendsen GROMACS: fast, flexible, and free J. Comput. Chem. 26 2005 1701 1718 (Pubitemid 43076182)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
-
33
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
DOI 10.1007/S008940100045
-
E. Lindahl, B. Hess, and D. van der Spoel GROMACS 3.0: a package for molecular simulation and trajectory analysis J. Mol. Model. 7 2001 306 317 (Pubitemid 36153547)
-
(2001)
Journal of Molecular Modeling
, vol.7
, Issue.8
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
34
-
-
1642485164
-
Coarse grained model for semiquantitative lipid simulations
-
S.J. Marrink, A.H. de Vries, and A.E. Mark Coarse grained model for semiquantitative lipid simulations J. Phys. Chem. B 108 2004 750 760
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 750-760
-
-
Marrink, S.J.1
De Vries, A.H.2
Mark, A.E.3
-
35
-
-
53249150686
-
Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer
-
P.J. Bond, C.L. Wee, and M.S.P. Sansom Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer Biochemistry 47 2008 11321 11331
-
(2008)
Biochemistry
, vol.47
, pp. 11321-11331
-
-
Bond, P.J.1
Wee, C.L.2
Sansom, M.S.P.3
-
36
-
-
33847242278
-
Coarse-grained molecular dynamics simulations of membrane proteins and peptides
-
P.J. Bond, J. Holyoake, A. Ivetac, S. Khalid, and M.S.P. Sansom Coarse-grained molecular dynamics simulations of membrane proteins and peptides J. Struct. Biol. 157 2007 593 605
-
(2007)
J. Struct. Biol.
, vol.157
, pp. 593-605
-
-
Bond, P.J.1
Holyoake, J.2
Ivetac, A.3
Khalid, S.4
Sansom, M.S.P.5
-
37
-
-
33644644163
-
Insertion and assembly of membrane proteins via simulation
-
DOI 10.1021/ja0569104
-
P.J. Bond, and M.S.P. Sansom Insertion and assembly of membrane proteins via simulation J. Am. Chem. Soc. 128 2006 2697 2704 (Pubitemid 43327948)
-
(2006)
Journal of the American Chemical Society
, vol.128
, Issue.8
, pp. 2697-2704
-
-
Bond, P.J.1
Sansom, M.S.P.2
-
38
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
H.J.C. Berendsen, J.P.M. Postma, W.F.V. Gunsteren, A. DiNola, and J.R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 1984 3684 3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Gunsteren, W.F.V.3
Dinola, A.4
Haak, J.R.5
-
39
-
-
33645038628
-
Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa
-
S. Khalid, P.J. Bond, S.S. Deol, and M.S.P. Sansom Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa Proteins 63 2006 6 15
-
(2006)
Proteins
, vol.63
, pp. 6-15
-
-
Khalid, S.1
Bond, P.J.2
Deol, S.S.3
Sansom, M.S.P.4
-
40
-
-
33751538074
-
Molecular dynamics simulations of a bacterial autotransporter: NalP from Neisseria meningitidis
-
DOI 10.1080/09687860600849531, PII V10M8U8GMU851684
-
S. Khalid, and M.S.P. Sansom Molecular dynamics simulations of a bacterial autotransporter: NalP from Neisseria meningitidis Mol. Membr. Biol. 23 2006 499 508 (Pubitemid 44837735)
-
(2006)
Molecular Membrane Biology
, vol.23
, Issue.6
, pp. 499-508
-
-
Khalid, S.1
Sansom, M.S.P.2
-
41
-
-
0030404988
-
HOLE: A program for the analysis of the pore dimensions of ion channel structural models
-
DOI 10.1016/S0263-7855(97)00009-X, PII S026378559700009X
-
O.S. Smart, J.G. Neduvelil, X. Wang, B.A. Wallace, and M.S.P. Sansom HOLE: a program for the analysis of the pore dimensions of ion channel structural models J. Mol. Graph. 14 1996 354 360 (Pubitemid 27302826)
-
(1996)
Journal of Molecular Graphics
, vol.14
, Issue.6
, pp. 354-360
-
-
Smart, O.S.1
Neduvelil, J.G.2
Wang, X.3
Wallace, B.A.4
Sansom, M.S.P.5
-
42
-
-
27244444569
-
Interface connections of a transmembrane voltage sensor
-
DOI 10.1073/pnas.0507618102
-
J.A. Freites, D.J. Tobias, G. von Heijne, and S.H. White Interface connections of a transmembrane voltage sensor Proc. Natl Acad. Sci. USA 102 2005 15059 15064 (Pubitemid 41513334)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.42
, pp. 15059-15064
-
-
Freites, J.A.1
Tobias, D.J.2
Von Heijne, G.3
White, S.H.4
-
44
-
-
33846785439
-
How Does a Voltage Sensor Interact with a Lipid Bilayer? Simulations of a Potassium Channel Domain
-
DOI 10.1016/j.str.2007.01.004, PII S0969212607000330
-
Z.A. Sands, and M.S.P. Sansom How does a voltage sensor interact with a lipid bilayer? Simulations of a potassium channel domain Structure 15 2007 235 244 (Pubitemid 46209817)
-
(2007)
Structure
, vol.15
, Issue.2
, pp. 235-244
-
-
Sands, Z.A.1
Sansom, M.S.P.2
-
45
-
-
41449119304
-
Coarse-grained MD simulations of membrane protein-bilayer self-assembly
-
DOI 10.1016/j.str.2008.01.014, PII S0969212608000683
-
K.A. Scott, P.J. Bond, A. Ivetac, A.P. Chetwynd, S. Khalid, and M.S.P. Sansom Coarse-grained MD simulations of membrane protein-bilayer self-assembly Structure 16 2008 621 630 (Pubitemid 351458703)
-
(2008)
Structure
, vol.16
, Issue.4
, 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
-
46
-
-
33947709389
-
Molecular dynamics simulations of inwardly rectifying (Kir) potassium channels: A comparative study
-
DOI 10.1021/bi062210f
-
S. Haider, S. Khalid, S.J. Tucker, F.M. Ashcroft, and M.S.P. Sansom Molecular dynamics simulations of inwardly rectifying (Kir) potassium channels: a comparative study Biochemistry 46 2007 3643 3652 (Pubitemid 46493465)
-
(2007)
Biochemistry
, vol.46
, Issue.12
, pp. 3643-3652
-
-
Haider, S.1
Khalid, S.2
Tucker, S.J.3
Ashcroft, F.M.4
Sansom, M.S.P.5
-
47
-
-
10044244661
-
Lipid-protein interactions of integral membrane proteins: A comparative simulation study
-
DOI 10.1529/biophysj.104.048397
-
S.S. Deol, P.J. Bond, C. Domene, and M.S.P. Sansom Lipid-protein interactions of integral membrane proteins: a comparative simulation study Biophys. J. 87 2004 3737 3749 (Pubitemid 39610530)
-
(2004)
Biophysical Journal
, vol.87
, Issue.6
, pp. 3737-3749
-
-
Deol, S.S.1
Bond, P.J.2
Domene, C.3
Sansom, M.S.P.4
-
48
-
-
77953101439
-
Membrane proteins diffuse as dynamic complexes with lipids
-
P.S. Niemela, M.S. Miettinen, L. Monticelli, H. Hammaren, P. Bjelkmar, T. Murtola, E. Lindahl, and I. Vattulainen Membrane proteins diffuse as dynamic complexes with lipids J. Am. Chem. Soc. 132 2010 7574 7575
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 7574-7575
-
-
Niemela, P.S.1
Miettinen, M.S.2
Monticelli, L.3
Hammaren, H.4
Bjelkmar, P.5
Murtola, T.6
Lindahl, E.7
Vattulainen, I.8
|