-
1
-
-
34347262391
-
Bilayer thickness and membrane protein function: An energetic perspective
-
DOI 10.1146/annurev.biophys.36.040306.132643
-
Andersen, O. S., and R. E. Koeppe, 2nd. 2007. Bilayer thickness and membrane protein function: an energetic perspective. Annu. Rev. Biophys. Biomol. Struct. 36:107-130. (Pubitemid 46998112)
-
(2007)
Annual Review of Biophysics and Biomolecular Structure
, vol.36
, pp. 107-130
-
-
Andersen, O.S.1
Koeppe II, R.E.2
-
2
-
-
0031740415
-
Hydrophobic mismatch between proteins and lipids in membranes
-
Killian, J. A, 1998. Hydrophobic mismatch between proteins and lipids in membranes. Biochim, Biophys. Acta. 1376:401-415.
-
(1998)
Biochim, Biophys. Acta.
, vol.1376
, pp. 401-415
-
-
Killian, J.A.1
-
3
-
-
0027489133
-
Sorting of membrane proteins in the secretory pathway
-
Pelham, H. R. B., and S. Munro. 1993. Sorting of membrane proteins in the secretory pathway. Cell. 75:603-605.
-
(1993)
Cell.
, vol.75
, pp. 603-605
-
-
Pelham, H.R.B.1
Munro, S.2
-
6
-
-
0030837927
-
Are there dominant membrane protein, families with, a given number of helices?
-
Arkin, I. T., A. T. Brünger, and D. M. Engelman. 1997. Are there dominant membrane protein, families with, a given number of helices? Proteins: Struct. Funct. Gen. 28:465-466.
-
(1997)
Proteins: Struct. Funct. Gen.
, vol.28
, pp. 465-466
-
-
Arkin, I.T.1
Brünger, A.T.2
Engelman, D.M.3
-
7
-
-
38549107447
-
New insights into growth hormone receptor function and clinical, implications
-
Lichanska, A. M., and M. J. Waters. 2008. New insights into growth hormone receptor function and clinical, implications. Hormone Res Paed. 69:138-145.
-
(2008)
Hormone Res Paed.
, vol.69
, pp. 138-145
-
-
Lichanska, A.M.1
Waters, M.J.2
-
9
-
-
20444366208
-
Tilt angle of a trans-membrane helix is determined by hydrophobic mismatch
-
Park, S. H., and S. J. Opella. 2005. Tilt angle of a trans-membrane helix is determined by hydrophobic mismatch. J. Mol. Biol. 350:310-318.
-
(2005)
J. Mol. Biol.
, vol.350
, pp. 310-318
-
-
Park, S.H.1
Opella, S.J.2
-
10
-
-
0242659352
-
Protein-lipid interactions studied with designed transmembrane peptides: Role of hydrophobic matching and interfacial anchoring
-
de Planque, M. R. R., and J. A. Killian. 2003. Protein-lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring. Mol. Membr. Biol. 20:271-284, (Review).
-
(2003)
Mol. Membr. Biol.
, vol.20
, pp. 271-284
-
-
De Planque, M.R.R.1
Killian, J.A.2
-
11
-
-
33746647787
-
Peptides in lipid bilayers: The power of simple models
-
DOI 10.1016/j.sbi.2006.06.007, PII S0959440X06001114
-
Killian, J. A., and T. K. Nyholm. 2006. Peptides in lipid bilayers: the power of simple models. Curr. Opin. Struct. Biol, 16:473-479. (Pubitemid 44149068)
-
(2006)
Current Opinion in Structural Biology
, vol.16
, Issue.4
, pp. 473-479
-
-
Killian, J.A.1
Nyholm, T.K.2
-
14
-
-
33646198955
-
Molecular dynamics simulations of model, trans-membrane peptides in lipid bilayers: A systematic investigation of hydrophobic mismatch
-
Kandasamy, S. K., and R. G. Larson. 2006. Molecular dynamics simulations of model, trans-membrane peptides in lipid bilayers: a systematic investigation of hydrophobic mismatch. Biophys. J. 90:2326-2343.
-
(2006)
Biophys. J.
, vol.90
, pp. 2326-2343
-
-
Kandasamy, S.K.1
Larson, R.G.2
-
15
-
-
0037133485
-
Hydrophobic matching mechanism investigated by molecular dynamics simulations
-
DOI 10.1021/la011338p
-
Petrache, H. I., D. M. Zuckerman, ..., T. B. Woolf. 2002. Hydrophobic matching mechanism investigated by molecular dynamics simulations. Langmuir. 18:1340-1351 (Pubitemid 35384066)
-
(2002)
Langmuir
, vol.18
, Issue.4
, pp. 1340-1351
-
-
Petrache, H.I.1
Zuckerman, D.M.2
Sachs, J.N.3
Antoinette, K.J.4
Koeppe II, R.E.5
Woolf, T.B.6
-
16
-
-
37049023237
-
On the orientation of a designed transmembrane peptide: Toward the right tilt angle?
-
DOI 10.1021/ja073784q
-
Ozdirekcan, S., C. Etchebest, ..., P. F. Fuchs. 2007. On the orientation of a designed transmembrane peptide: toward the right tilt angle? J. Am. Chem. Soc. 129:15.174-15181 (Pubitemid 350247801)
-
(2007)
Journal of the American Chemical Society
, vol.129
, Issue.49
, pp. 15174-15181
-
-
Ozdirekcan, S.1
Etchebest, C.2
Killian, J.A.3
Fuchs, P.F.J.4
-
17
-
-
37349011230
-
The dynamic orientation of membrane-bound peptides: Bridging simulations and experiments
-
Esteban-Martín, S., and J. Salgado. 2007. The dynamic orientation of membrane-bound peptides: bridging simulations and experiments. Biophys. J. 93:4278-4288.
-
(2007)
Biophys. J.
, vol.93
, pp. 4278-4288
-
-
Esteban-Martín, S.1
Salgado, J.2
-
18
-
-
40749090459
-
Transmembrane helix tilting: Insights from calculating the potential of mean, force
-
Lee, J., and W. Im. 2008. Transmembrane helix tilting: insights from calculating the potential of mean, force. Phys. Rev. Lett. 100:018103.
-
(2008)
Phys. Rev. Lett.
, vol.100
, pp. 018103
-
-
Lee, J.1
Im, W.2
-
19
-
-
18744403982
-
Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations
-
Im, W., and C. L. Brooks, 3rd. 2005. Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proc. Natl. Acad. Sci. USA. 102:6771-6776.
-
(2005)
Proc. Natl. Acad. Sci. USA.
, vol.102
, pp. 6771-6776
-
-
Im, W.1
Brooks III, C.L.2
-
20
-
-
70449125771
-
Tilt and rotation angles of a transmembrane model peptide as studied by fluorescence spectroscopy
-
Holt, A., R. B. M. Koehorst, ..., J. A. Killian. 2009. Tilt and rotation angles of a transmembrane model peptide as studied by fluorescence spectroscopy. Biophys. J. 97:2258-2266.
-
(2009)
Biophys. J.
, vol.97
, pp. 2258-2266
-
-
Holt, A.1
Koehorst, R.B.M.2
Killian, J.A.3
-
21
-
-
0342929614
-
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
-
Torrie, G. M., and J. P. Valleau. 1977. Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J. Comp. Phys. 23:187-199.
-
(1977)
J. Comp. Phys.
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
22
-
-
34249737504
-
Restraint potential and free energy decomposition formalism for helical tilting
-
Lee, J., and W. Im, 2007. Restraint potential and free energy decomposition formalism for helical tilting. Chem. Phys. Lett. 441:132-135.
-
(2007)
Chem. Phys. Lett.
, vol.441
, pp. 132-135
-
-
Lee, J.1
Im, W.2
-
23
-
-
33847678434
-
Implementation and application of helix-helix distance and crossing angle restraint potentials
-
Lee, J., and W. Im. 2007. Implementation and application of helix-helix distance and crossing angle restraint potentials. J. Comput. Chem. 28:669-680.
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 669-680
-
-
Lee, J.1
Im, W.2
-
24
-
-
67650480197
-
Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function
-
Im, W., J. Lee, ..., H. Rui. 2009. Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function. J. Comput. Chem. 30:1622-1633.
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 1622-1633
-
-
Im, W.1
Lee, J.2
Rui, H.3
-
25
-
-
68949149548
-
CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes
-
Jo, S., J. B. Lim, ..., W. Im. 2009. CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys. J. 97:50-58.
-
(2009)
Biophys. J.
, vol.97
, pp. 50-58
-
-
Jo, S.1
Lim, J.B.2
Im, W.3
-
26
-
-
41149134824
-
Automated builder and database of protein/membrane complexes for molecular dynamics simulations
-
Jo, S., T. Kim, and W. Im. 2007. Automated builder and database of protein/membrane complexes for molecular dynamics simulations. PLoS One. 2:e880.
-
(2007)
PLoS One.
, vol.2
-
-
Jo, S.1
Kim, T.2
Im, W.3
-
27
-
-
47149096704
-
CHARMM-GUI: A web-based graphical user interface for CHARMM
-
Jo, S., T. Kim, ..., W. Im. 2008. CHARMM-GUI: a web-based graphical user interface for CHARMM. J. Comput. Chem. 29:1859-1865.
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 1859-1865
-
-
Jo, S.1
Kim, T.2
Im, W.3
-
28
-
-
67650500988
-
CHARMM: The biomolecular simulation program
-
Brooks, B. R., C. L. Brooks, 3rd, ..., M. Karplus. 2009. CHARMM: the biomolecular simulation program. J. Comput. Chem. 30:1545-1614.
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks III, C.L.2
Karplus, M.3
-
29
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, Jr., A. D., D. Bashford, ..., M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. .102:3586-3616.
-
(1998)
J. Phys. Chem. B..
, vol.102
, pp. 3586-3616
-
-
Bashford, D.1
Karplus, M.2
-
30
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
Mackerell Jr., A. D., M. Feig, and C. L. Brooks, 3rd. 2004. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 25:1400-1415.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1400-1415
-
-
Mackerell Jr., A.D.1
Feig, M.2
Brooks III, C.L.3
-
31
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W.L., J.Chandrasekhar, ..., M.L.Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Klein, M.L.3
-
32
-
-
15744368593
-
An ab initio study on the torsional, surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer
-
Klauda, J. B., B. R. Brooks, ..., R. W. Pastor. 2005. An ab initio study on the torsional, surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. J. Phys. Chem. B. 109:5300-5311
-
(2005)
J. Phys. Chem. B.
, vol.109
, pp. 5300-5311
-
-
Klauda, J.B.1
Brooks, B.R.2
Pastor, R.W.3
-
34
-
-
33646940952
-
Numerical. integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J.-.P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical. integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341
-
(1977)
J. Comp. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
35
-
-
0001538909
-
Canonical dynamics: Equilibrium, phase-space distributions
-
Hoover, W. G. 1985. Canonical dynamics: equilibrium, phase-space distributions. Phys. Rev. A: At. Mol. Opt. Phys. 31:1695-1697.
-
(1985)
Phys. Rev. A: At. Mol. Opt. Phys.
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
36
-
-
36449007836
-
Constant pressure molecular dynamics simulation: The Langevin piston, method
-
Feller, S. E., Y. Zhang, ..., B. R. Brooks. 1995. Constant pressure molecular dynamics simulation: the Langevin piston, method. J. Chem. Phys. 103:4613-4621.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.2
Brooks, B.R.3
-
37
-
-
12244255728
-
Hydrophobic mismatch between helices and lipid bilayers
-
Weiss, T. M., P. C. A. van der Wel, ..., H. W. Huang. 2003. Hydrophobic mismatch between helices and lipid bilayers. Biophys. J. 84:379-385.
-
(2003)
Biophys. J.
, vol.84
, pp. 379-385
-
-
Weiss, T.M.1
Van Der Wel, P.C.A.2
Huang, H.W.3
-
38
-
-
0026704101
-
Combined influence of cholesterol, and synthetic amphiphilic peptides upon bilayer thickness in model membranes
-
Nezil, F. A., and M. Bloom. 1992. Combined influence of cholesterol, and synthetic amphiphilic peptides upon bilayer thickness in model membranes. Biophys. J. 61:1176-1183.
-
(1992)
Biophys. J.
, vol.61
, pp. 1176-1183
-
-
Nezil, F.A.1
Bloom, M.2
-
39
-
-
10744228856
-
Effects of phospholipid unsaturation on the bilayer nonpolar region: A molecular simulation study
-
DOI 10.1194/jlr.M300187-JLR200
-
Róg, T., K. Murzyn, ..., M. Pasenkiewicz-Gierula. 2004. Effects of phospholipid unsaturation on the bilayer nonpolar region: a molecular simulation study. J. Lipid Res. 45:326-336. (Pubitemid 38228831)
-
(2004)
Journal of Lipid Research
, vol.45
, Issue.2
, pp. 326-336
-
-
Rog, T.1
Murzyn, K.2
Gurbiel, R.3
Takaoka, Y.4
Kusumi, A.5
Pasenkiewicz-Gierula, M.6
-
40
-
-
0037008040
-
The effects of hydrophobic mismatch between phosphatidylcholine bilayers and transmembrane a-helical peptides depend on the nature of interfacially exposed aromatic and charged residues
-
de Planque, M. R. R., J.-W. P. Boots, ..., J. A. Killian. 2002. The effects of hydrophobic mismatch between phosphatidylcholine bilayers and transmembrane a-helical peptides depend on the nature of interfacially exposed aromatic and charged residues. Biochemistry. 41:8396-8404.
-
(2002)
Biochemistry.
, vol.41
, pp. 8396-8404
-
-
De Planque, M.R.R.1
Boots, J.-W.P.2
Killian, J.A.3
-
41
-
-
0029738872
-
Experimentally determined hydrophobicity scale for proteins at membrane interfaces
-
Wimley, W. C, and S. H. White. 1996. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat. Struct. Mol Biol. 3:842-848.
-
(1996)
Nat. Struct. Mol Biol.
, vol.3
, pp. 842-848
-
-
Wimley, W.C.1
White, S.H.2
-
42
-
-
0038694994
-
Snorkeling of lysine side chains in transmembrane helices: How easy can it get?
-
DOI 10.1016/S0014-5793(03)00475-7
-
Strandberg, E., and J. A. Killian. 2003. Snorkeling of lysine side chains in transmembrane helices: how easy can it get? FEBS Lett. 544:69-73. (Pubitemid 36628038)
-
(2003)
FEBS Letters
, vol.544
, Issue.1-3
, pp. 69-73
-
-
Strandberg, E.1
Killian, J.A.2
|