-
1
-
-
77957055780
-
Integrated methods for the construction of three dimensional models and computational probing of structure function relations in G protein-coupled receptors
-
C. P. Sealfon, editor. Academic Press, San Diego, CA
-
Ballesteros, J., and H. Weinstein. 1995. Integrated methods for the construction of three dimensional models and computational probing of structure function relations in G protein-coupled receptors. In Methods in Neurosciences. C. P. Sealfon, editor. Academic Press, San Diego, CA.
-
(1995)
Methods in Neurosciences
-
-
Ballesteros, J.1
Weinstein, H.2
-
2
-
-
71749103741
-
Progress in elucidating the structural and dynamic character of G protein-coupled receptor oligomers for use in drug discovery
-
Bortolato, A., J. C. Mobarec, ..., M. Filizola. 2009. Progress in elucidating the structural and dynamic character of G protein-coupled receptor oligomers for use in drug discovery. Curr. Pharm. Des. 15:4017-4025.
-
(2009)
Curr. Pharm. Des.
, vol.15
, pp. 4017-4025
-
-
Bortolato, A.1
Mobarec, J.C.2
Filizola, M.3
-
3
-
-
34248215318
-
Visual rhodopsin sees the light: Structure and mechanism of G protein, signaling
-
Ridge, K. D., and K. Palczewski. 2007. Visual rhodopsin sees the light: structure and mechanism of G protein, signaling. J. Biol. Chem. 282:9297-9301.
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 9297-9301
-
-
Ridge, K.D.1
Palczewski, K.2
-
4
-
-
22744435933
-
Direct observation of the complex formation of GDP-bound transducin with the rhodopsin intermediate having a visible absorption maximum in rod outer segment membranes
-
DOI 10.1021/bi0504512
-
4. Morizumi, T., H. Imai, and Y. Shichida. 2005. Direct observation of the complex formation of GDP-bound transducin with the rhodopsin intermediate having a visible absorption maximum in rod outer segment membranes. Biochemistry. 44:9936-9943. (Pubitemid 41033460)
-
(2005)
Biochemistry
, vol.44
, Issue.29
, pp. 9936-9943
-
-
Morizumi, T.1
Imai, H.2
Shichida, Y.3
-
5
-
-
0027317273
-
Two different forms of metarhodopsin II: Schiff base deprotonation precedes proton uptake and signaling state
-
Amis, S., and K. P. Hofmann. 1993. Two different forms of metarhodopsin II: Schiff base deprotonation precedes proton uptake and signaling state. Proc. Natl. Acad. Sci. USA. 90:7849-7853.
-
(1993)
Proc. Natl. Acad. Sci. USA.
, vol.90
, pp. 7849-7853
-
-
Amis, S.1
Hofmann, K.P.2
-
6
-
-
60849127906
-
Rhodopsin activation switches in a native membrane environment
-
Lüdeke, S., M. Mahalingam, and R. Vogel. 2009. Rhodopsin activation switches in a native membrane environment. Photochem. Photobiol. 85:437-441.
-
(2009)
Photochem. Photobiol.
, vol.85
, pp. 437-441
-
-
Lüdeke, S.1
Mahalingam, M.2
Vogel, R.3
-
7
-
-
38049100706
-
Sequence of late molecular events in the activation of rhodopsin
-
Knierim, B., K. P. Hofmann, ..., W. L. Hubbell. 2007. Sequence of late molecular events in the activation of rhodopsin. Proc. Natl. Acad. Sci. USA. 104:20290-20295.
-
(2007)
Proc. Natl. Acad. Sci. USA.
, vol.104
, pp. 20290-20295
-
-
Knierim, B.1
Hofmann, K.P.2
Hubbell, W.L.3
-
8
-
-
34447633368
-
Conformational complexity of G-protein-coupled receptors
-
Kobilka, B. K., and X. Deupi. 2007. Conformational complexity of G-protein-coupled receptors. Trends Pharmacol, Sci. 28:397-406.
-
(2007)
Trends Pharmacol, Sci.
, vol.28
, pp. 397-406
-
-
Kobilka, B.K.1
Deupi, X.2
-
9
-
-
14844307607
-
Dynamics of ar-restin-rhodopsin interactions: Arrestin and retinal release are directly linked events
-
Sommer, M. E., W. C. Smith, and D. L. Farrens. 2005. Dynamics of ar-restin-rhodopsin interactions: arrestin and retinal release are directly linked events. Z Biol. Chem. 280:6861-6871.
-
(2005)
Z Biol. Chem.
, vol.280
, pp. 6861-6871
-
-
Sommer, M.E.1
Smith, W.C.2
Farrens, D.L.3
-
10
-
-
33746321096
-
Crystallographic analysis of primary visual photochemistry
-
DOI 10.1002/anie.200600595
-
10. Nakamichi, H., and T. Okada. 2006. Crystallography analysis of primary visual photochemistry. Angew. Chem. Int. Ed. Engl. 45:4270-4273. (Pubitemid 44105630)
-
(2006)
Angewandte Chemie - International Edition
, vol.45
, Issue.26
, pp. 4270-4273
-
-
Nakamichi, H.1
Okada, T.2
-
12
-
-
5044235587
-
Electron crystallography reveals the structure of metarhodopsin I
-
Ruprecht, J. J., T. Mielke, ..., G. F. Scheitlet 2004. Electron crystallography reveals the structure of metarhodopsin I. EMBO J. 23:3609-3620.
-
(2004)
EMBO J.
, vol.23
, pp. 3609-3620
-
-
Ruprecht, J.J.1
Mielke, T.2
Scheitlet, G.F.3
-
13
-
-
33750836895
-
Crystal structure of a photoactivated deprotonated intermediate of rhodopsin
-
DOI 10.1073/pnas.0608022103
-
13. Salom, D., D. T. Lodowski, ..., K. Palczewski. 2006. Crystal structure of a photoactivated deprotonated intermediate of rhodopsin. Prot: Natl. Acad. Sci. USA. 103:16123-16128. (Pubitemid 44715162)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.44
, pp. 16123-16128
-
-
Salom, D.1
Lodowski, D.T.2
Stenkamp, R.E.3
Le Trong, I.4
Golczak, M.5
Jastrzebska, B.6
Harris, T.7
Ballesteros, J.A.8
Palczewski, K.9
-
14
-
-
44949236117
-
High-resolution distance mapping in rhodopsin reveals the pattern of helix movement due to activation
-
DOI 10.1073/pnas.0802515105
-
14. Altenbach, C., A. K. Kusnetzow, ..., W. L. Hubbell. 2008. High-resolution, distance mapping in rhodopsin reveals the pattern of helix movement due to activation. Prot: Natl, Acad. Sci. USA. 105: 7439-7444. (Pubitemid 351830036)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.21
, pp. 7439-7444
-
-
Altenbach, C.1
Kusnetzow, A.K.2
Ernst, O.P.3
Hofmann, K.P.4
Hubbell, W.L.5
-
15
-
-
47049130668
-
Crystal structure of the ligand-free G-protein-coupled receptor opsin
-
Park, J. H., P. Scheerer, ..., O. P. Ernst. 2008. Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature. 454:183-187.
-
(2008)
Nature
, vol.454
, pp. 183-187
-
-
Park, J.H.1
Scheerer, P.2
Ernst, O.P.3
-
16
-
-
47049130668
-
Crystal structure of the ligand-free G-protein-coupled receptor opsin
-
DOI 10.1038/nature07063, PII NATURE07063
-
16. Scheerer, P., J. H. Park, ...,O. P. Ernst. 2008. Crystal structure of opsin in its G-protein-interacting conformation. Nature. 455:497-502. (Pubitemid 351969893)
-
(2008)
Nature
, vol.454
, Issue.7201
, pp. 183-187
-
-
Park, J.H.1
Scheerer, P.2
Hofmann, K.P.3
Choe, H.-W.4
Ernst, O.P.5
-
18
-
-
66749144240
-
Observation of "ionic lock" formation in molecular dynamics simulations of wild-type β1 and 32 adrenergic receptors
-
Vanni, S., M. Neri, ..., U. Rothlisberger. 2009. Observation of "ionic lock" formation in molecular dynamics simulations of wild-type β1 and (32 adrenergic receptors. Biochemistry. 48:4789-4797.
-
(2009)
Biochemistry
, Issue.48
, pp. 4789-4797
-
-
Vanni, S.1
Neri, M.2
Rothlisberger, U.3
-
19
-
-
63849294621
-
Identification of two distinct inactive conformations of the β 2-adrenergic receptor reconciles structural and biochemical observations
-
Dror, R. O., D. H. Arlow, ..., D. E. Shaw. 2009. Identification of two distinct inactive conformations of the β 2-adrenergic receptor reconciles structural and biochemical observations. Prot: Natl. Acad. Sci. USA. 106:4689-4694.
-
(2009)
Prot: Natl. Acad. Sci. USA
, vol.106
, pp. 4689-4694
-
-
Dror, R.O.1
Arlow, D.H.2
Shaw, D.E.3
-
20
-
-
74049108724
-
Concerted interconversion between ionic lock substates of the β2 adrenergic receptor revealed by microsecond timescale molecular dynamics
-
Romo, T. D., A. Grossfield, and M. C. Pitman. 2010. Concerted interconversion between ionic lock substates of the β2 adrenergic receptor revealed by microsecond timescale molecular dynamics. Biophys. J. 98:76-84.
-
(2010)
Biophys. J.
, vol.98
, pp. 76-84
-
-
Romo, T.D.1
Grossfield, A.2
Pitman, M.C.3
-
22
-
-
41149173662
-
Advances in the development and application of computational methodologies for structural modeling of G-protein-coupled receptors
-
Mobarec, J. C., and M. Filizola. 2008. Advances in the development and application of computational methodologies for structural modeling of G-protein-coupled receptors. Expert Opin. Drug Discov. 3:343-355.
-
(2008)
Expert Opin. Drug Discov.
, vol.3
, pp. 343-355
-
-
Mobarec, J.C.1
Filizola, M.2
-
23
-
-
0027757062
-
Effects of temperature on rhodopsin photointermediates from lumirhodopsin to metarhodopsin II
-
Thorgeirsson, T. E., J. W. Lewis, ..., D. S. Kliger. 1993. Effects of temperature on rhodopsin photointermediates from lumirhodopsin to metarhodopsin II. Biochemistry. 32:13861-13872.
-
(1993)
Biochemistry
, vol.32
, pp. 13861-13872
-
-
Thorgeirsson, T.E.1
Lewis, J.W.2
Kliger, D.S.3
-
24
-
-
77952769056
-
Light activation of rhodopsin: Insights from molecular dynamics simulations guided by solid-state NMR distance restraints
-
2009 Dec 11 [Epub ahead of print]
-
Hornak, V., S. Ahuja, ..., S. O. Smith. 2009. Light activation of rhodopsin: insights from molecular dynamics simulations guided by solid-state NMR distance restraints. J. Mol, Biol. 2009 Dec 11 [Epub ahead of print].
-
(2009)
J. Mol, Biol.
-
-
Hornak, V.1
Ahuja, S.2
Smith, S.O.3
-
25
-
-
0001160648
-
Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems
-
Marchi, M., and P. Ballone. .1999. Adiabatic bias molecular dynamics: a method to navigate the conformational space of complex molecular systems. J. Chem. Phys. 110:3697-3702.
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 3697-3702
-
-
Marchi, M.1
Ballone, P.2
-
26
-
-
0033531973
-
Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations
-
DOI 10.1006/jmbi.1999.2670
-
26. Paci, E., and M. Karplus. 1999. Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations. J. Mol. Biol. 288:441-459. (Pubitemid 29221813)
-
(1999)
Journal of Molecular Biology
, vol.288
, Issue.3
, pp. 441-459
-
-
Paci, E.1
Karplus, M.2
-
27
-
-
38349091489
-
Well-tempered metadynamics: A smoothly converging and tunable free-energy method
-
Barducci, A., G. Bussi, and M. Parrinello. 2008. Well-tempered metadynamics: a smoothly converging and tunable free-energy method. Phys. Rev. Lett. 100:020603.
-
(2008)
Phys. Rev. Lett.
, vol.100
, pp. 020603
-
-
Barducci, A.1
Bussi, G.2
Parrinello, M.3
-
28
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
Van Der Spoel, D., E. Lindahl, ..., H. J. Berendsen. 2005. GROMACS: fast, flexible, and free. J. Comput. Chem. 26:1701-1718.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Berendsen, H.J.3
-
29
-
-
69349100797
-
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
-
Bonomi, M., D. Branduardi, ..., M. Parrinello. 2009. PLUMED: a portable plugin for free-energy calculations with molecular dynamics. Comput. Phys. Commun. 180:1961-1972.
-
(2009)
Comput. Phys. Commun.
, vol.180
, pp. 1961-1972
-
-
Bonomi, M.1
Branduardi, D.2
Parrinello, M.3
-
30
-
-
34548861782
-
Protein-protein docking with backbone flexibility
-
Wang, C., P. Bradley, and D. Baker. 2007. Protein-protein docking with backbone flexibility. J.. Mol. Biol. 373:503-519.
-
(2007)
J.. Mol. Biol.
, vol.373
, pp. 503-519
-
-
Wang, C.1
Bradley, P.2
Baker, D.3
-
32
-
-
33745630723
-
Membrane protein simulations with a united-atom lipid and all-atom protein model: Lipid-protein interactions, side chain, transfer free energies and model proteins
-
Tieleman, D. P., J. L. MacCallum, ..., L. Monticelli. 2006. Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid-protein interactions, side chain, transfer free energies and model proteins. J. Phys. Condens. Matter. 18:1221-1234.
-
(2006)
J. Phys. Condens. Matter.
, vol.18
, pp. 1221-1234
-
-
Tieleman, D.P.1
MacCallum, J.L.2
Monticelli, L.3
-
33
-
-
0030999097
-
Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature
-
33. Berger, O., O. Edholm, and F. Jähnig. 1997. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys. J. 72:2002-2013. (Pubitemid 27184429)
-
(1997)
Biophysical Journal
, vol.72
, Issue.5
, pp. 2002-2013
-
-
Berger, O.1
Edholm, O.2
Jahnig, F.3
-
34
-
-
33645941402
-
The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin
-
Jorgensen, W. L., and J. Tirado-Rives. 1988. The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1657-1666.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
35
-
-
33947139278
-
Setting up and running molecular dynamics simulations of membrane proteins
-
DOI 10.1016/j.ymeth.2006.08.006, PII S1046202306001873
-
35. Kandt, C., W. L. Ash, and D. P. Tieleman. 2007. Setting up and running molecular dynamics simulations of membrane proteins. Methods. 41:475-488. (Pubitemid 46400527)
-
(2007)
Methods
, vol.41
, Issue.4
, pp. 475-488
-
-
Kandt, C.1
Ash, W.L.2
Peter Tieleman, D.3
-
36
-
-
0017617172
-
Effect of a single cis double bond on the structure of a phospholipid bilayer
-
DOI 10.1021/bi00620a008
-
36. Seelig, A., and J. Seelig. 1977. Effect of a single cis double bond on the structures of a phospholipid bilayer. Biochemistry. 16:45-50. (Pubitemid 8030063)
-
(1977)
Biochemistry
, vol.16
, Issue.1
, pp. 45-50
-
-
Seelig, A.1
Seelig, J.2
-
38
-
-
26144434487
-
Crystal, structure and pair potentials: A molecular-dynamics study
-
Parrinello, M., and A. Rahman.. 1980. Crystal, structure and pair potentials: a molecular-dynamics study. Phys. Rev. Lett. 45:11.96-1199.
-
(1980)
Phys. Rev. Lett.
, vol.45
, pp. 1196-1199
-
-
Parrinello, M.1
Rahman, A.2
-
39
-
-
84926811618
-
Constant pressure molecular dynamics for molecular systems
-
Nose, S., and M. L. Klein. 1983. Constant pressure molecular dynamics for molecular systems. Mol. Phys. 50:1055-1076.
-
(1983)
Mol. Phys.
, vol.50
, pp. 1055-1076
-
-
Nose, S.1
Klein, M.L.2
-
40
-
-
0000388705
-
LINCS: A Linear Constraint Solver for molecular simulations
-
40. Hess, B., H. Bekker,..., J. G. E. M. Fraaije. 1997. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18:1463-1472. (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
-
41
-
-
84986440341
-
SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
-
4.1, Miyamoto, S., and P. A. Kollman. 1992. SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. 13:952-962.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
42
-
-
33846823909
-
Particle mesh Ewald. (PME): An N log(N) method for Ewald sums in large systems
-
Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald. (PME): 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
-
43
-
-
0028455053
-
Targeted molecular dynamics: A new approach for searching pathways of conformational transitions
-
DOI 10.1016/0263-7855(94)80072-3
-
43. Schlitter, J., M. Engels, and P. Krüger. 1994. Targeted molecular dynamics: a new approach for searching pathways of conformational transitions. J. Mol. Graph. 12:84-89. (Pubitemid 24219247)
-
(1994)
Journal of Molecular Graphics
, vol.12
, Issue.2
, pp. 84-89
-
-
Schlitter, J.1
Engels, M.2
Kruger, P.3
-
44
-
-
18644374892
-
Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method
-
van der Vaart, A., and M. Karplus. 2005. Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method. J.. Chem, Phys. 122:114903.
-
(2005)
J.. Chem, Phys.
, vol.122
, pp. 114903
-
-
Van Der Vaart, A.1
Karplus, M.2
-
47
-
-
54249091171
-
The unfolded ensemble and folding mechanism of the C-terminal GB1 β-hairpin
-
Bonomi, M., D. Branduardi, ..., M. Parrinello. 2008. The unfolded ensemble and folding mechanism of the C-terminal GB1 β-hairpin. J. Am. Chem. Soc. 130:13938-13944.
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 13938-13944
-
-
Bonomi, M.1
Branduardi, D.2
Parrinello, M.3
-
48
-
-
1842786894
-
Rhodopsin photoproducts in 2D crystals
-
Vogel, R., J. Ruprecht, ...,F. Siebert. 2004. Rhodopsin photoproducts in 2D crystals. J. Mol. Biol. 338:597-609.
-
(2004)
J. Mol. Biol.
, vol.338
, pp. 597-609
-
-
Vogel, R.1
Ruprecht, J.2
Siebert, F.3
-
49
-
-
0037036457
-
Manipulation of cholesterol levels in rod disk membranes by methyl-β-cyclodextrin: Effects on receptor activation
-
Niu, S. L., D. C Mitchell, and B. J. Litman. 2002. Manipulation of cholesterol levels in rod disk membranes by methyl-β-cyclodextrin: effects on receptor activation. J. Biol. Chem, 277:20139-20145.
-
(2002)
J. Biol. Chem
, vol.277
, pp. 20139-20145
-
-
Niu, S.L.1
Mitchell, D.C.2
Litman, B.J.3
-
50
-
-
67650266997
-
Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from, microsecond length molecular dynamics simulations
-
Khelashvili, G., A. Grossfield, ..., H. Weinstein. 2008. Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from, microsecond length molecular dynamics simulations. Proteins. 76:403-417.
-
(2008)
Proteins
, vol.76
, pp. 403-417
-
-
Khelashvili, G.1
Grossfield, A.2
Weinstein, H.3
-
51
-
-
59649112109
-
Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activation
-
Ahuja, S., V. Hornak, ..., M. Eilers. 2009. Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activation. Nat. Struct. Mol. Biol. 16:168-175.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 168-175
-
-
Ahuja, S.1
Hornak, V.2
Eilers, M.3
|