-
1
-
-
0032987478
-
Membrane protein folding and stability: Physical principles
-
White S.H., Wimley W.C. Membrane protein folding and stability: physical principles. Annu. Rev. Biophys. Biomol. 28:1999;319-365.
-
(1999)
Annu. Rev. Biophys. Biomol.
, vol.28
, pp. 319-365
-
-
White, S.H.1
Wimley, W.C.2
-
2
-
-
0033790343
-
Helical membrane protein folding, stability, and evolution
-
Popot J.L., Engelman D.M. Helical membrane protein folding, stability, and evolution. Annu. Rev. Biochem. 69:2000;881-922.
-
(2000)
Annu. Rev. Biochem.
, vol.69
, pp. 881-922
-
-
Popot, J.L.1
Engelman, D.M.2
-
4
-
-
0032744963
-
A day in the life of Dr. K. or how I learned to stop worrying and love lysozyme: A trajedy in six acts
-
von Heijine G. A day in the life of Dr. K. or how I learned to stop worrying and love lysozyme: a trajedy in six acts. J. Mol. Biol. 293:1999;367-379.
-
(1999)
J. Mol. Biol.
, vol.293
, pp. 367-379
-
-
Von Heijine, G.1
-
6
-
-
0033954256
-
The Protein Data Bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., et al. The Protein Data Bank. Nucl. Acids Res. 28:2000;235-242.
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
-
7
-
-
0036536998
-
Theoretical and computational models of ion channels
-
Roux B. Theoretical and computational models of ion channels. Curr. Opin. Struct. Biol. 12:2002;182-189.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 182-189
-
-
Roux, B.1
-
8
-
-
0036301334
-
Ions and counterions in a biological channel: A molecular dynamics simulation of ompf porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution
-
Im W., Roux B. Ions and counterions in a biological channel: a molecular dynamics simulation of ompf porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution. J. Mol. Biol. 319:2002;1177-1197.
-
(2002)
J. Mol. Biol.
, vol.319
, pp. 1177-1197
-
-
Im, W.1
Roux, B.2
-
9
-
-
0042626159
-
Structure of gramicidin a in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data
-
Allen T.W., Andersen O.S., Roux B. Structure of gramicidin a in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data. J. Am. Chem. Soc. 125:2003;9868-9877.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 9868-9877
-
-
Allen, T.W.1
Andersen, O.S.2
Roux, B.3
-
10
-
-
0038724257
-
Membrane protein dynamics versus environment: Simulations of ompa in a micelle and in a bilayer
-
Bond P.J., Sansom M.S.P. Membrane protein dynamics versus environment: simulations of ompa in a micelle and in a bilayer. J. Mol. Biol. 329:2003;1035-1053.
-
(2003)
J. Mol. Biol.
, vol.329
, pp. 1035-1053
-
-
Bond, P.J.1
Sansom, M.S.P.2
-
12
-
-
0032567163
-
Folding and translocation of the undecamer of poly-L-leucine across the water-hexane interface. A multi-nanosecond molecular dynamics study
-
Chipot C., Pohorille A. Folding and translocation of the undecamer of poly-L-leucine across the water-hexane interface. A multi-nanosecond molecular dynamics study. J. Am. Chem. Soc. 120:1998;11912-11924.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 11912-11924
-
-
Chipot, C.1
Pohorille, A.2
-
13
-
-
0035132984
-
Voltage-dependent insertion of a channel forming peptide: Molecular dynamics simulations of alamethicin at phospholipid/water and octane/water interfaces
-
Tieleman D., Berendsen H., Sansom M. Voltage-dependent insertion of a channel forming peptide: molecular dynamics simulations of alamethicin at phospholipid/water and octane/water interfaces. Biophys. J. 80:2001;331-346.
-
(2001)
Biophys. J.
, vol.80
, pp. 331-346
-
-
Tieleman, D.1
Berendsen, H.2
Sansom, M.3
-
14
-
-
0039179572
-
Ion channels, permeaion, and electrostatics: Insight into the function of KcsA
-
Roux B., Bernèche S., Im W. Ion channels, permeaion, and electrostatics: insight into the function of KcsA. Biochemistry. 39:2000;13295-13306.
-
(2000)
Biochemistry
, vol.39
, pp. 13295-13306
-
-
Roux, B.1
Bernèche, S.2
Im, W.3
-
15
-
-
0036161583
-
Electrostatic control of the membrane targeting of c2 domains
-
Murray D., Honig B. Electrostatic control of the membrane targeting of c2 domains. Mol. Cell. 9:2002;145-154.
-
(2002)
Mol. Cell
, vol.9
, pp. 145-154
-
-
Murray, D.1
Honig, B.2
-
16
-
-
0141956090
-
Generalized born model with a simple smoothing function
-
Im W., Lee M.S., Brooks C.L. III. Generalized born model with a simple smoothing function. J. Comput. Chem. 24:2003;1691-1702.
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1691-1702
-
-
Im, W.1
Lee, M.S.2
Brooks III, C.L.3
-
17
-
-
0242322528
-
An implicit membrane generalized born theory for the study of structures, stability, and interactions of membrane proteins
-
Im W., Feig M., Brooks C.L. III. An implicit membrane generalized born theory for the study of structures, stability, and interactions of membrane proteins. Biophys. J. 85:2003;2900-2918.
-
(2003)
Biophys. J.
, vol.85
, pp. 2900-2918
-
-
Im, W.1
Feig, M.2
Brooks III, C.L.3
-
18
-
-
0029099311
-
A Monte Carlo model of fd and Pf1 coat proteins in lipid membranes
-
Milik M., Skolnick J. A Monte Carlo model of fd and Pf1 coat proteins in lipid membranes. Biophys. J. 69:1995;1382-1386.
-
(1995)
Biophys. J.
, vol.69
, pp. 1382-1386
-
-
Milik, M.1
Skolnick, J.2
-
19
-
-
0037194983
-
Introducing an implicit membrane in generalized born/solvent accessibility continuum solvent models
-
Spassov V.Z., Yan L., Szalma S. Introducing an implicit membrane in generalized born/solvent accessibility continuum solvent models. J. Phys. Chem. B. 106:2002;8726-8738.
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 8726-8738
-
-
Spassov, V.Z.1
Yan, L.2
Szalma, S.3
-
20
-
-
0037339521
-
Folding in lipid membranes (film): A novel method for the prediction of small membrane protein 3d structures
-
Pellegrini-Calace M., Carotti A., Jones D.T. Folding in lipid membranes (film): a novel method for the prediction of small membrane protein 3d structures. Proteins: Struct. Funct. Genet. 50:2003;537-545.
-
(2003)
Proteins: Struct. Funct. Genet.
, vol.50
, pp. 537-545
-
-
Pellegrini-Calace, M.1
Carotti, A.2
Jones, D.T.3
-
21
-
-
0038675609
-
Effective energy functions for proteins in lipid membranes
-
Lazaridis T. Effective energy functions for proteins in lipid membranes. Proteins: Struct. Funct. Genet. 52:2003;176-192.
-
(2003)
Proteins: Struct. Funct. Genet.
, vol.52
, pp. 176-192
-
-
Lazaridis, T.1
-
22
-
-
0031578972
-
Parallel tempering algorithm for conformational studies of biological molecules
-
Hansmann U.H.E. Parallel tempering algorithm for conformational studies of biological molecules. Chem. Phys. Letters. 281:1997;140-150.
-
(1997)
Chem. Phys. Letters
, vol.281
, pp. 140-150
-
-
Hansmann, U.H.E.1
-
23
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita Y., Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Letters. 314:1999;141-151.
-
(1999)
Chem. Phys. Letters
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
24
-
-
0035909921
-
The free energy landscape for β hairpin folding in explicit water
-
Zhou R., Berne B.J., Germain R. The free energy landscape for β hairpin folding in explicit water. Proc. Natl Acad. Sci. USA. 98:2002;14931-14936.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 14931-14936
-
-
Zhou, R.1
Berne, B.J.2
Germain, R.3
-
25
-
-
0036467163
-
Structure of Met-Enkephalin in explicit aqueous solution using replica exchange molecular dynamics
-
Sanbonmatsu K.Y., Garcia A.E. Structure of Met-Enkephalin in explicit aqueous solution using replica exchange molecular dynamics. Proteins: Struct. Funct. Genet. 46:2002;225-234.
-
(2002)
Proteins: Struct. Funct. Genet.
, vol.46
, pp. 225-234
-
-
Sanbonmatsu, K.Y.1
Garcia, A.E.2
-
26
-
-
0025734125
-
Filamentous phage assembly
-
Russel M. Filamentous phage assembly. Mol. Microbiol. 5:1991;1607-1616.
-
(1991)
Mol. Microbiol.
, vol.5
, pp. 1607-1616
-
-
Russel, M.1
-
27
-
-
0031577283
-
Fd coat protein structure in membrane environments: Structural dynamics of the loop between the hydrophobic transmembrane helix and the amphipathic in-plane helix
-
Almeida F.C.L., Opella S.J. fd coat protein structure in membrane environments: structural dynamics of the loop between the hydrophobic transmembrane helix and the amphipathic in-plane helix. J. Mol. Biol. 270:1997;481-495.
-
(1997)
J. Mol. Biol.
, vol.270
, pp. 481-495
-
-
Almeida, F.C.L.1
Opella, S.J.2
-
28
-
-
0037372352
-
Simultaneous assignment and structure determination of a membrane protein from nmr orientational restraints
-
Almeida F.C.L., Opella S.J. Simultaneous assignment and structure determination of a membrane protein from nmr orientational restraints. Protein Sci. 12:2003;403-411.
-
(2003)
Protein Sci.
, vol.12
, pp. 403-411
-
-
Almeida, F.C.L.1
Opella, S.J.2
-
29
-
-
0038652081
-
Structure of the coat protein in fd filamentous bacteriophage particles determined by solid-state nmr spectroscopy
-
Zeri A.C., Mesleh M.F., Nevzorov A.A., Opella S.J. Structure of the coat protein in fd filamentous bacteriophage particles determined by solid-state nmr spectroscopy. Proc. Natl Acad. Sci. USA. 100:2003;6458-6463.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 6458-6463
-
-
Zeri, A.C.1
Mesleh, M.F.2
Nevzorov, A.A.3
Opella, S.J.4
-
30
-
-
84986512474
-
CHARMM: A program for macromolecular energy minimization and dynamics calculations
-
Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Comput. Chem. 4:1983;187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
32
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell A.D. Jr, Bashford D., Bellot M., Dunbrack R.L., Evanseck J.D., Field M.J., et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:1998;3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
Mackerell Jr., A.D.1
Bashford, D.2
Bellot, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
-
33
-
-
0038054912
-
Force field influence on the observation of π-helical protein structures in molecular dynamics simulations
-
Feig M., MacKerell A.D. Jr, Brooks C.L. III. Force field influence on the observation of π-helical protein structures in molecular dynamics simulations. J. Phys. Chem. B. 107:2003;2831-2836.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 2831-2836
-
-
Feig, M.1
Mackerell Jr., A.D.2
Brooks III, C.L.3
-
34
-
-
34547809547
-
A unified formulation of the constant temperature molecular dynamics methods
-
Nosé S. A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys. 81:1984;511-519.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 511-519
-
-
Nosé, S.1
-
35
-
-
0001538909
-
Canonical dynamics: Equilibrium phase-space distributions
-
Hoover W.G. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A. 31:1985;1695-1697.
-
(1985)
Phys. Rev. a
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
36
-
-
0031167555
-
Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations
-
Nina M., Beglov D., Roux B. Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations. J. Phys. Chem. B. 101:1997;5239-5248.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 5239-5248
-
-
Nina, M.1
Beglov, D.2
Roux, B.3
-
37
-
-
0032968444
-
Optimized atomic radii for protein continuum electrostatics solvation forces
-
Nina M., Im W., Roux B. Optimized atomic radii for protein continuum electrostatics solvation forces. Biophys. Chem. 78:1999;89-96.
-
(1999)
Biophys. Chem.
, vol.78
, pp. 89-96
-
-
Nina, M.1
Im, W.2
Roux, B.3
-
38
-
-
0028020035
-
Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer
-
Woolf T.B., Roux B. Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. Proc. Natl Acad. Sci. USA. 91:1994;11631-11635.
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 11631-11635
-
-
Woolf, T.B.1
Roux, B.2
-
39
-
-
0001125152
-
15N chemical shift interaction tensors in a peptide bond by three-dimensional solid-state NMR spectroscopy
-
15N chemical shift interaction tensors in a peptide bond by three-dimensional solid-state NMR spectroscopy. J. Am. Chem. Soc. 117:1995;6148-6149.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 6148-6149
-
-
Wu, C.H.1
Ramamoorthy, A.2
Gierasch, L.M.3
Opella, S.J.4
|