-
1
-
-
36749001066
-
Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes
-
Rapoport TA. Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes. Nature 2007; 450: 663-669.
-
(2007)
Nature
, vol.450
, pp. 663-669
-
-
Rapoport, T.A.1
-
2
-
-
18844387083
-
Signal recognition particles in chloroplasts, bacteria, yeast and mammals (Review)
-
Pool MR. Signal recognition particles in chloroplasts, bacteria, yeast and mammals (Review). Mol Membr Biol 2005; 22: 3-15.
-
(2005)
Mol Membr Biol
, vol.22
, pp. 3-15
-
-
Pool, M.R.1
-
3
-
-
0028170807
-
Signal sequence recognition and protein targeting to the endoplasmic-reticulum membrane
-
Walter P, Johnson AE. Signal sequence recognition and protein targeting to the endoplasmic-reticulum membrane. Annu Rev Cell Biol 1994; 10: 87-119.
-
(1994)
Annu Rev Cell Biol
, vol.10
, pp. 87-119
-
-
Walter, P.1
Johnson, A.E.2
-
4
-
-
0031030085
-
Crystal structure of the NG domain from the signal-recognition particle receptor FtsY
-
Montoya G, Svensson C, Luirink J, Sinning I. Crystal structure of the NG domain from the signal-recognition particle receptor FtsY. Nature 1997; 385: 365-368.
-
(1997)
Nature
, vol.385
, pp. 365-368
-
-
Montoya, G.1
Svensson, C.2
Luirink, J.3
Sinning, I.4
-
5
-
-
0031017523
-
Structure of the conserved GTPase domain of the signal recognition particle
-
Freymann DM, Keenan RJ, Stroud RM, Walter P. Structure of the conserved GTPase domain of the signal recognition particle. Nature 1997; 385: 361-364.
-
(1997)
Nature
, vol.385
, pp. 361-364
-
-
Freymann, D.M.1
Keenan, R.J.2
Stroud, R.M.3
Walter, P.4
-
6
-
-
8844253060
-
Mechanism of association and reciprocal activation of two GTPases
-
Shan SO, Stroud RM, Walter P. Mechanism of association and reciprocal activation of two GTPases. PLOS Biol 2004; 2: 1572-1581.
-
(2004)
PLOS Biol
, vol.2
, pp. 1572-1581
-
-
Shan, S.O.1
Stroud, R.M.2
Walter, P.3
-
7
-
-
0029097359
-
Reciprocal stimulation of GTP hydrolysis by 2 directly interacting GTPases
-
Powers T, Walter P. Reciprocal stimulation of GTP hydrolysis by 2 directly interacting GTPases. Science 1995; 269: 1422-1424.
-
(1995)
Science
, vol.269
, pp. 1422-1424
-
-
Powers, T.1
Walter, P.2
-
8
-
-
33947320768
-
Structure of the GMPPNP-stabilized NG domain complex of the SRP GTPases Ffh and FtsY
-
Gawronski-Salerno J, Freymann DM. Structure of the GMPPNP-stabilized NG domain complex of the SRP GTPases Ffh and FtsY. J Struct Biol 2007; 158: 122-128.
-
(2007)
J Struct Biol
, vol.158
, pp. 122-128
-
-
Gawronski-Salerno, J.1
Freymann, D.M.2
-
9
-
-
33745644462
-
Structure of a GDP:AlF4 complex of the SRP GTPases Ffh and FtsY, and identification of a peripheral nucleotide interaction site
-
Focia PJ, Gawronski-Salerno J, Coon VJS, Freymann DM. Structure of a GDP:AlF4 complex of the SRP GTPases Ffh and FtsY, and identification of a peripheral nucleotide interaction site. J Mol Biol 2006; 360: 631-643.
-
(2006)
J Mol Biol
, vol.360
, pp. 631-643
-
-
Focia, P.J.1
Gawronski-Salerno, J.2
Coon, V.J.S.3
Freymann, D.M.4
-
11
-
-
0347584006
-
Substrate twinning activates the signal recognition particle and its receptor
-
Egea PF, Shan SO, Napetschnig J, Savage DF, Walter P, Stroud RM. Substrate twinning activates the signal recognition particle and its receptor. Nature 2004; 427: 215-221.
-
(2004)
Nature
, vol.427
, pp. 215-221
-
-
Egea, P.F.1
Shan, S.O.2
Napetschnig, J.3
Savage, D.F.4
Walter, P.5
Stroud, R.M.6
-
12
-
-
34547929138
-
Conformational changes in the GTPase modules of the signal reception particle and its initiation of protein translocation
-
Shan SO, Chandrasekar S, Walter P. Conformational changes in the GTPase modules of the signal reception particle and its initiation of protein translocation. J Cell Biol 2007; 178: 611-620.
-
(2007)
J Cell Biol
, vol.178
, pp. 611-620
-
-
Shan, S.O.1
Chandrasekar, S.2
Walter, P.3
-
13
-
-
60549083291
-
Multiple conformational switches in a GTPase complex control co-translational protein targeting
-
Zhang X, Schaffitzel C, Ban N, Shan SO. Multiple conformational switches in a GTPase complex control co-translational protein targeting. Proc Natl Acad Sci USA 2009; 106: 1754-1759.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 1754-1759
-
-
Zhang, X.1
Schaffitzel, C.2
Ban, N.3
Shan, S.O.4
-
14
-
-
67651230544
-
Signal recognition particle (SRP) and SRP receptor: a new paradigm for multistate regulatory GTPases
-
Shan SO, Schmid SL, Zhang X. Signal recognition particle (SRP) and SRP receptor: a new paradigm for multistate regulatory GTPases. Biochemistry 2009; 48: 6696-6704.
-
(2009)
Biochemistry
, vol.48
, pp. 6696-6704
-
-
Shan, S.O.1
Schmid, S.L.2
Zhang, X.3
-
15
-
-
58149264965
-
Signal sequences activate the catalytic switch of SRP RNA
-
Bradshaw N, Neher SB, Booth DS, Walter P. Signal sequences activate the catalytic switch of SRP RNA. Science 2009; 323: 127-130.
-
(2009)
Science
, vol.323
, pp. 127-130
-
-
Bradshaw, N.1
Neher, S.B.2
Booth, D.S.3
Walter, P.4
-
16
-
-
0029963973
-
Regulation by the ribosome of the GTPase of the signal-recognition particle during protein targeting
-
Bacher G, Lutcke H, Jungnickel B, Rapoport TA, Dobberstein B. Regulation by the ribosome of the GTPase of the signal-recognition particle during protein targeting. Nature 1996; 381: 248-251.
-
(1996)
Nature
, vol.381
, pp. 248-251
-
-
Bacher, G.1
Lutcke, H.2
Jungnickel, B.3
Rapoport, T.A.4
Dobberstein, B.5
-
17
-
-
77952127782
-
Sequential checkpoints govern substrate selection during cotranslational protein targeting
-
Zhang X, Rashid R, Wang K, Shan SO. Sequential checkpoints govern substrate selection during cotranslational protein targeting. Science 2010; 328: 757-760.
-
(2010)
Science
, vol.328
, pp. 757-760
-
-
Zhang, X.1
Rashid, R.2
Wang, K.3
Shan, S.O.4
-
18
-
-
77955839666
-
Molecular dynamics simulation of SRP GTPases: towards an understanding of the complex formation from equilibrium fluctuations
-
Yang MJ, Zhang X, Han KL. Molecular dynamics simulation of SRP GTPases: towards an understanding of the complex formation from equilibrium fluctuations. Proteins Struct Funct Bioinform 2010; 78: 2222-2237.
-
(2010)
Proteins Struct Funct Bioinform
, vol.78
, pp. 2222-2237
-
-
Yang, M.J.1
Zhang, X.2
Han, K.L.3
-
19
-
-
78649905953
-
Molecular dynamics simulation reveals preorganization of the chloroplast FtsY towards complex formation induced by GTP binding
-
Yang MJ, Pang XQ, Zhang X, Han KL. Molecular dynamics simulation reveals preorganization of the chloroplast FtsY towards complex formation induced by GTP binding. J Struct Biol 2010; 173: 57-66.
-
(2010)
J Struct Biol
, vol.173
, pp. 57-66
-
-
Yang, M.J.1
Pang, X.Q.2
Zhang, X.3
Han, K.L.4
-
20
-
-
55549094402
-
A molecular modeling study of the interaction between SRP-receptor complex and peptide translocon
-
Chen SF, Fan Y, Shen XL, Sun P, Jiang GS, Shen Y, Xue WF, Li YQ, Chen X. A molecular modeling study of the interaction between SRP-receptor complex and peptide translocon. Biochem Biophys Res Commun 2008; 377: 346-350.
-
(2008)
Biochem Biophys Res Commun
, vol.377
, pp. 346-350
-
-
Chen, S.F.1
Fan, Y.2
Shen, X.L.3
Sun, P.4
Jiang, G.S.5
Shen, Y.6
Xue, W.F.7
Li, Y.Q.8
Chen, X.9
-
21
-
-
0348244547
-
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
-
Foloppe N, MacKerell AD. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem 2000; 21: 86-104.
-
(2000)
J Comput Chem
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerell, A.D.2
-
22
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998; 102: 3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
23
-
-
3242886771
-
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
-
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucl Acids Res 2004; 32 (suppl 2): W665-W667.
-
(2004)
Nucl Acids Res
, vol.32
, Issue.SUPPL. 2
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
-
24
-
-
84986512474
-
CHARMM: a program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983; 4: 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
-
25
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem 2005; 26: 1781-1802.
-
(2005)
J Comput Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kalé, L.9
Schulten, K.10
-
26
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys 1995; 103: 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
-
27
-
-
33846823909
-
Particle mesh Ewald-an N·log(N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L. Particle mesh Ewald-an N·log(N) method for Ewald sums in large systems. J Chem Phys 1993; 98: 10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
28
-
-
33646940952
-
Numerical-integration of Cartesian equations of motion of a system with constraints-molecular-dynamics of n-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical-integration of Cartesian equations of motion of a system with constraints-molecular-dynamics of n-alkanes. J Computat Phys 1977; 23: 327-341.
-
(1977)
J Computat Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
29
-
-
36449007836
-
Constant-pressure molecular-dynamics simulation-the Langevin piston method
-
Feller SE, Zhang YH, Pastor RW, Brooks BR. Constant-pressure molecular-dynamics simulation-the Langevin piston method. J Chem Phys 1995; 103: 4613-4621.
-
(1995)
J Chem Phys
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.H.2
Pastor, R.W.3
Brooks, B.R.4
-
30
-
-
0001538909
-
Canonical dynamics-equilibrium phase-space distributions
-
Hoover WG. Canonical dynamics-equilibrium phase-space distributions. Phys Rev A 1985; 31: 1695-1697.
-
(1985)
Phys Rev A
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
31
-
-
36449003554
-
Constant-pressure molecular-dynamics algorithms
-
Martyna GJ, Tobias DJ, Klein ML. Constant-pressure molecular-dynamics algorithms. J Chem Phys 1994; 101: 4177-4189.
-
(1994)
J Chem Phys
, vol.101
, pp. 4177-4189
-
-
Martyna, G.J.1
Tobias, D.J.2
Klein, M.L.3
-
32
-
-
0004014257
-
-
Department of Biochemistry and Molecular Biology, University College London.
-
Hubbard SJ, Thornton JM. NACCESS. Department of Biochemistry and Molecular Biology, University College London; 1993.
-
(1993)
NACCESS
-
-
Hubbard, S.J.1
Thornton, J.M.2
-
33
-
-
14544302354
-
Co-translational protein targeting by the signal recognition particle
-
Shan SO, Walter P. Co-translational protein targeting by the signal recognition particle. FEBS Lett 2005; 579: 921-926.
-
(2005)
FEBS Lett
, vol.579
, pp. 921-926
-
-
Shan, S.O.1
Walter, P.2
-
34
-
-
0035834388
-
Signal transduction-the guanine nucleotide-binding switch in three dimensions
-
Vetter IR, Wittinghofer A. Signal transduction-the guanine nucleotide-binding switch in three dimensions. Science 2001; 294: 1299-1304.
-
(2001)
Science
, vol.294
, pp. 1299-1304
-
-
Vetter, I.R.1
Wittinghofer, A.2
-
35
-
-
0025010979
-
The GTPase superfamily-a conserved switch for diverse cell functions
-
Bourne HR, Sanders DA, McCormick F. The GTPase superfamily-a conserved switch for diverse cell functions. Nature 1990; 348: 125-132.
-
(1990)
Nature
, vol.348
, pp. 125-132
-
-
Bourne, H.R.1
Sanders, D.A.2
McCormick, F.3
-
36
-
-
23044445638
-
QM/MM modeling the Ras-GAP catalyzed hydrolysis of guanosine triphosphate
-
Grigorenko BL, Nemukhin AV, Topol IA, Cachau RE, Burt SK. QM/MM modeling the Ras-GAP catalyzed hydrolysis of guanosine triphosphate. Proteins Struct Funct Bioinform 2005; 60: 495-503.
-
(2005)
Proteins Struct Funct Bioinform
, vol.60
, pp. 495-503
-
-
Grigorenko, B.L.1
Nemukhin, A.V.2
Topol, I.A.3
Cachau, R.E.4
Burt, S.K.5
-
37
-
-
0035933139
-
The arginine finger of RasGAP helps Gln-61 align the nucleophilic water in GAP-stimulated hydrolysis of GTP
-
Resat H, Straatsma TP, Dixon DA, Miller JH. The arginine finger of RasGAP helps Gln-61 align the nucleophilic water in GAP-stimulated hydrolysis of GTP. Proc Natl Acad Sci USA 2001; 98: 6033-6038.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 6033-6038
-
-
Resat, H.1
Straatsma, T.P.2
Dixon, D.A.3
Miller, J.H.4
-
38
-
-
67349250817
-
It takes two to tango: regulation of G proteins by dimerization
-
Gasper R, Meyer S, Gotthardt K, Sirajuddin M, Wittinghofer A. It takes two to tango: regulation of G proteins by dimerization. Nat Rev Mol Cell Biol 2009; 10: 423-429.
-
(2009)
Nat Rev Mol Cell Biol
, vol.10
, pp. 423-429
-
-
Gasper, R.1
Meyer, S.2
Gotthardt, K.3
Sirajuddin, M.4
Wittinghofer, A.5
-
39
-
-
70349632843
-
The influence of protein dynamics on the success of computational enzyme design
-
Ruscio JZ, Kohn JE, Ball KA, Head-Gordon T. The influence of protein dynamics on the success of computational enzyme design. J Am Chem Soc 2009; 131: 14111-14115.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 14111-14115
-
-
Ruscio, J.Z.1
Kohn, J.E.2
Ball, K.A.3
Head-Gordon, T.4
-
40
-
-
53849113368
-
Selectivity of neutral/weakly basic P1 group inhibitors of thrombin and trypsin by a molecular dynamics study
-
Wu EL, Han KL, Zhang JZH. Selectivity of neutral/weakly basic P1 group inhibitors of thrombin and trypsin by a molecular dynamics study. Chem Eur J 2008; 14: 8704-8714.
-
(2008)
Chem Eur J
, vol.14
, pp. 8704-8714
-
-
Wu, E.L.1
Han, K.L.2
Zhang, J.Z.H.3
-
41
-
-
36549031819
-
How dopamine transporter interacts with dopamine: insights from molecular modeling and simulation
-
Huang X, Zhan CG. How dopamine transporter interacts with dopamine: insights from molecular modeling and simulation. Biophys J 2007; 93: 3627-3639.
-
(2007)
Biophys J
, vol.93
, pp. 3627-3639
-
-
Huang, X.1
Zhan, C.G.2
|