-
1
-
-
84878941023
-
Signal recognition particle: An essential protein-targeting machine
-
Akopian, D., Shen, K., Zhang, X., and Shan, S. O. (2013) Signal recognition particle: an essential protein-targeting machine. Annu. Rev. Biochem. 82, 693-721
-
(2013)
Annu. Rev. Biochem.
, vol.82
, pp. 693-721
-
-
Akopian, D.1
Shen, K.2
Zhang, X.3
Shan, S.O.4
-
2
-
-
0038415649
-
Protein translocation in the three domains of life: Variations on a theme
-
Pohlschröder, M., Prinz, W. A., Hartmann, E., and Beckwith, J. (1997) Protein translocation in the three domains of life: variations on a theme. Cell 91, 563-566
-
(1997)
Cell
, vol.91
, pp. 563-566
-
-
Pohlschröder, M.1
Prinz, W.A.2
Hartmann, E.3
Beckwith, J.4
-
3
-
-
0019849075
-
Translocation of proteins across the endoplasmic reticulum. 1. Signal recognition protein (SRP) binds to in vitro-assembled polysomes synthesizing secretory protein
-
Walter, P., Ibrahimi, I., and Blobel, G. (1981) Translocation of proteins across the endoplasmic reticulum. 1. Signal recognition protein (SRP) binds to in vitro-assembled polysomes synthesizing secretory protein. J. Cell Biol. 91, 545-550
-
(1981)
J. Cell Biol.
, vol.91
, pp. 545-550
-
-
Walter, P.1
Ibrahimi, I.2
Blobel, G.3
-
4
-
-
0029952518
-
Protein transport across the eukaryotic endoplasmic reticulum and bacterial inner membranes
-
Rapoport, T. A., Jungnickel, B., and Kutay, U. (1996) Protein transport across the eukaryotic endoplasmic reticulum and bacterial inner membranes. Annu. Rev. Biochem. 65, 271-303
-
(1996)
Annu. Rev. Biochem.
, vol.65
, pp. 271-303
-
-
Rapoport, T.A.1
Jungnickel, B.2
Kutay, U.3
-
5
-
-
0030832397
-
Co-translational protein targeting catalyzed by the Escherichia coli signal recognition particle and its receptor
-
Powers, T., and Walter, P. (1997) Co-translational protein targeting catalyzed by the Escherichia coli signal recognition particle and its receptor. EMBO J. 16, 4880-4886
-
(1997)
EMBO J.
, vol.16
, pp. 4880-4886
-
-
Powers, T.1
Walter, P.2
-
6
-
-
36749001066
-
Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes
-
Rapoport, T. A. (2007) Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes. Nature 450, 663-669
-
(2007)
Nature
, vol.450
, pp. 663-669
-
-
Rapoport, T.A.1
-
7
-
-
50649104037
-
Protein translocation across the bacterial cytoplasmic membrane
-
Driessen, A. J., and Nouwen, N. (2008) Protein translocation across the bacterial cytoplasmic membrane. Annu. Rev. Biochem. 77, 643-667
-
(2008)
Annu. Rev. Biochem.
, vol.77
, pp. 643-667
-
-
Driessen, A.J.1
Nouwen, N.2
-
8
-
-
84865443871
-
Direct simulation of early-stage Sec-facilitated protein translocation
-
Zhang, B., and Miller, T. F., 3rd (2012) Direct simulation of early-stage Sec-facilitated protein translocation. J. Am. Chem. Soc. 134, 13700-13707
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 13700-13707
-
-
Zhang, B.1
Miller, T.F.2
-
9
-
-
84868136627
-
Long-timescale dynamics and regulation of Sec-facilitated protein translocation
-
Zhang, B., and Miller, T. F., 3rd (2012) Long-timescale dynamics and regulation of Sec-facilitated protein translocation. Cell Rep. 2, 927-937
-
(2012)
Cell Rep.
, vol.2
, pp. 927-937
-
-
Zhang, B.1
Miller, T.F.2
-
10
-
-
0024963567
-
Signal sequences
-
Gierasch, L. M. (1989) Signal sequences. Biochemistry 28, 923-930
-
(1989)
Biochemistry
, vol.28
, pp. 923-930
-
-
Gierasch, L.M.1
-
11
-
-
0021856417
-
Signal sequences-the limits of variation
-
von Heijne, G. (1985) Signal sequences-the limits of variation. J. Mol. Biol. 184, 99-105
-
(1985)
J. Mol. Biol.
, vol.184
, pp. 99-105
-
-
Von Heijne, G.1
-
12
-
-
33751325296
-
Following the signal sequence from ribosomal tunnel exit to signal recognition particle
-
Halic, M., Blau, M., Becker, T., Mielke, T., Pool, M. R., Wild, K., Sinning, I., and Beckmann, R. (2006) Following the signal sequence from ribosomal tunnel exit to signal recognition particle. Nature 444, 507-511
-
(2006)
Nature
, vol.444
, pp. 507-511
-
-
Halic, M.1
Blau, M.2
Becker, T.3
Mielke, T.4
Pool, M.R.5
Wild, K.6
Sinning, I.7
Beckmann, R.8
-
13
-
-
33751325833
-
Structure of the E-coli signal recognition particle bound to a translating ribosome
-
Schaffitzel, C., Oswald, M., Berger, I., Ishikawa, T., Abrahams, J. P., Koerten, H. K., Koning, R. I., and Ban, N. (2006) Structure of the E-coli signal recognition particle bound to a translating ribosome. Nature 444, 503-506
-
(2006)
Nature
, vol.444
, pp. 503-506
-
-
Schaffitzel, C.1
Oswald, M.2
Berger, I.3
Ishikawa, T.4
Abrahams, J.P.5
Koerten, H.K.6
Koning, R.I.7
Ban, N.8
-
14
-
-
78650974443
-
Cryo-EM structure of the E. Coli translating ribosome in complex with SRP and its receptor
-
Estrozi, L. F., Boehringer, D., Shan, S. O., Ban, N., and Schaffitzel, C. (2011) Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor. Nat. Struct. Mol. Biol. 18, 88-90
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 88-90
-
-
Estrozi, L.F.1
Boehringer, D.2
Shan, S.O.3
Ban, N.4
Schaffitzel, C.5
-
15
-
-
84870817496
-
Dynamic switch of the signal recognition particle from scanning to targeting
-
Holtkamp, W., Lee, S., Bornemann, T., Senyushkina, T., Rodnina, M. V., and Wintermeyer, W. (2012) Dynamic switch of the signal recognition particle from scanning to targeting. Nat. Struct. Mol. Biol. 19, 1332-1337
-
(2012)
Nat. Struct. Mol. Biol.
, vol.19
, pp. 1332-1337
-
-
Holtkamp, W.1
Lee, S.2
Bornemann, T.3
Senyushkina, T.4
Rodnina, M.V.5
Wintermeyer, W.6
-
16
-
-
84870979537
-
Activated GTPase movement on an RNA scaffold drives co-translational protein targeting
-
Shen, K., Arslan, S., Akopian, D., Ha, T., and Shan, S. O. (2012) Activated GTPase movement on an RNA scaffold drives co-translational protein targeting. Nature 492, 271-275
-
(2012)
Nature
, vol.492
, pp. 271-275
-
-
Shen, K.1
Arslan, S.2
Akopian, D.3
Ha, T.4
Shan, S.O.5
-
17
-
-
77953025666
-
Recognition of a signal peptide by the signal recognition particle
-
Janda, C. Y., Li, J., Oubridge, C., Hernández, H., Robinson, C. V., and Nagai, K. (2010) Recognition of a signal peptide by the signal recognition particle. Nature 465, 507-510
-
(2010)
Nature
, vol.465
, pp. 507-510
-
-
Janda, C.Y.1
Li, J.2
Oubridge, C.3
Hernández, H.4
Robinson, C.V.5
Nagai, K.6
-
18
-
-
35448950462
-
Interaction of signalrecognition particle 54 GTPase domain and signal-recognition particleRNAin the free signal-recognition particle
-
Hainzl, T., Huang, S., and Sauer-Eriksson, A. E. (2007) Interaction of signalrecognition particle 54 GTPase domain and signal-recognition particleRNAin the free signal-recognition particle. Proc. Natl. Acad. Sci. U. S. A. 104, 14911-14916
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 14911-14916
-
-
Hainzl, T.1
Huang, S.2
Sauer-Eriksson, A.E.3
-
19
-
-
79952363483
-
Structural basis of signal-sequence recognition by the signal recognition particle
-
Hainzl, T., Huang, S., Meriläinen, G., Brännström, K., and Sauer-Eriksson, A. E. (2011) Structural basis of signal-sequence recognition by the signal recognition particle. Nat. Struct. Mol. Biol. 18, 389-391
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 389-391
-
-
Hainzl, T.1
Huang, S.2
Meriläinen, G.3
Brännström, K.4
Sauer-Eriksson, A.E.5
-
20
-
-
0344304454
-
Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication
-
Rosendal, K. R., Wild, K., Montoya, G., and Sinning, I. (2003) Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication. Proc. Natl. Acad. Sci. U. S. A. 100, 14701-14706
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 14701-14706
-
-
Rosendal, K.R.1
Wild, K.2
Montoya, G.3
Sinning, I.4
-
21
-
-
79951826865
-
The crystal structure of the signal recognition particle in complex with its receptor
-
Ataide, S. F., Schmitz, N., Shen, K., Ke, A., Shan, S. O., Doudna, J. A., and Ban, N. (2011) The crystal structure of the signal recognition particle in complex with its receptor. Science 331, 881-886
-
(2011)
Science
, vol.331
, pp. 881-886
-
-
Ataide, S.F.1
Schmitz, N.2
Shen, K.3
Ke, A.4
Shan, S.O.5
Doudna, J.A.6
Ban, N.7
-
22
-
-
3242876011
-
A structural step into the SRP cycle
-
Wild, K., Rosendal, K. R., and Sinning, I. (2004) A structural step into the SRP cycle. Mol. Microbiol. 53, 357-363
-
(2004)
Mol. Microbiol.
, vol.53
, pp. 357-363
-
-
Wild, K.1
Rosendal, K.R.2
Sinning, I.3
-
23
-
-
77649165415
-
Structural insights into the assembly of the human and archaeal signal recognition particles
-
Wild, K., Bange, G., Bozkurt, G., Segnitz, B., Hendricks, A., and Sinning, I. (2010) Structural insights into the assembly of the human and archaeal signal recognition particles. Acta Crystallogr. D Biol. Crystallogr. 66, 295-303
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 295-303
-
-
Wild, K.1
Bange, G.2
Bozkurt, G.3
Segnitz, B.4
Hendricks, A.5
Sinning, I.6
-
24
-
-
84904208463
-
Signal recognition particleribosome binding is sensitive to nascent-chain length
-
Noriega, T. R., Tsai, A., Elvekrog, M. M., Petrov, A., Neher, S. B., Chen, J., Bradshaw, N., Puglisi, J. D., and Walter, P. (2014) Signal recognition particleribosome binding is sensitive to nascent-chain length. J. Biol. Chem. 289, 19294-19305
-
(2014)
J. Biol. Chem.
, vol.289
, pp. 19294-19305
-
-
Noriega, T.R.1
Tsai, A.2
Elvekrog, M.M.3
Petrov, A.4
Neher, S.B.5
Chen, J.6
Bradshaw, N.7
Puglisi, J.D.8
Walter, P.9
-
25
-
-
0022527444
-
The signal sequence of nascent preprolactin interacts with the 54K polypeptide of the signal recognition particle
-
Kurzchalia, T. V., Wiedmann, M., Girshovich, A. S., Bochkareva, E. S., Bielka, H., and Rapoport, T. A. (1986) The signal sequence of nascent preprolactin interacts with the 54K polypeptide of the signal recognition particle. Nature 320, 634-636
-
(1986)
Nature
, vol.320
, pp. 634-636
-
-
Kurzchalia, T.V.1
Wiedmann, M.2
Girshovich, A.S.3
Bochkareva, E.S.4
Bielka, H.5
Rapoport, T.A.6
-
26
-
-
0025605808
-
An E. Coli ribonucleoprotein containing 4.5 SRNAresembles mammalian signal recognition particle
-
Poritz, M. A., Bernstein, H. D., Strub, K., Zopf, D., Wilhelm, H., and Walter, P. (1990) An E. coli ribonucleoprotein containing 4.5 SRNAresembles mammalian signal recognition particle. Science 250, 1111-1117
-
(1990)
Science
, vol.250
, pp. 1111-1117
-
-
Poritz, M.A.1
Bernstein, H.D.2
Strub, K.3
Zopf, D.4
Wilhelm, H.5
Walter, P.6
-
27
-
-
0031017523
-
Structure of the conserved GTPase domain of the signal recognition particle
-
Freymann, D. M., Keenan, R. J., Stroud, R. M., and Walter, P. (1997) Structure of the conserved GTPase domain of the signal recognition particle. Nature 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
-
28
-
-
0032563163
-
Crystal structure of the signal sequence binding subunit of the signal recognition particle
-
Keenan, R. J., Freymann, D. M., Walter, P., and Stroud, R. M. (1998) Crystal structure of the signal sequence binding subunit of the signal recognition particle. Cell 94, 181-191
-
(1998)
Cell
, vol.94
, pp. 181-191
-
-
Keenan, R.J.1
Freymann, D.M.2
Walter, P.3
Stroud, R.M.4
-
29
-
-
0034681490
-
Crystal structure of the ribonucleoprotein core of the signal recognition particle
-
Batey, R. T., Rambo, R. P., Lucast, L., Rha, B., and Doudna, J. A. (2000) Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science 287, 1232-1239
-
(2000)
Science
, vol.287
, pp. 1232-1239
-
-
Batey, R.T.1
Rambo, R.P.2
Lucast, L.3
Rha, B.4
Doudna, J.A.5
-
30
-
-
77952127782
-
Sequential checkpoints govern substrate selection during cotranslational protein targeting
-
Zhang, X., Rashid, R., Wang, K., and Shan, S. O. (2010) Sequential checkpoints govern substrate selection during cotranslational protein targeting. Science 328, 757-760
-
(2010)
Science
, vol.328
, pp. 757-760
-
-
Zhang, X.1
Rashid, R.2
Wang, K.3
Shan, S.O.4
-
31
-
-
17044419154
-
Targeting proteins to membranes: Structure of the signal recognition particle
-
Egea, P. F., Stroud, R. M., and Walter, P. (2005) Targeting proteins to membranes: structure of the signal recognition particle. Curr. Opin. Struct. Biol. 15, 213-220
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 213-220
-
-
Egea, P.F.1
Stroud, R.M.2
Walter, P.3
-
32
-
-
0346373753
-
Heterodimeric GTPase core of the SRP targeting complex
-
Focia, P. J., Shepotinovskaya, I. V., Seidler, J. A., and Freymann, D. M. (2004) Heterodimeric GTPase core of the SRP targeting complex. Science 303, 373-377
-
(2004)
Science
, vol.303
, pp. 373-377
-
-
Focia, P.J.1
Shepotinovskaya, I.V.2
Seidler, J.A.3
Freymann, D.M.4
-
33
-
-
0035909810
-
Role of SRP RNA in the GTPase cycles of Ffh and FtsY
-
Peluso, P., Shan, S. O., Nock, S., Herschlag, D., and Walter, P. (2001) Role of SRP RNA in the GTPase cycles of Ffh and FtsY. Biochemistry 40, 15224-15233
-
(2001)
Biochemistry
, vol.40
, pp. 15224-15233
-
-
Peluso, P.1
Shan, S.O.2
Nock, S.3
Herschlag, D.4
Walter, P.5
-
34
-
-
33846456974
-
SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting
-
Siu, F. Y., Spanggord, R. J., and Doudna, J. A. (2007) SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting. RNA 13, 240-250
-
(2007)
RNA
, vol.13
, pp. 240-250
-
-
Siu, F.Y.1
Spanggord, R.J.2
Doudna, J.A.3
-
35
-
-
58149264965
-
Signal sequences activate the catalytic switch of SRP RNA
-
Bradshaw, N., Neher, S. B., Booth, D. S., and Walter, P. (2009) Signal sequences activate the catalytic switch of SRP RNA. Science 323, 127-130
-
(2009)
Science
, vol.323
, pp. 127-130
-
-
Bradshaw, N.1
Neher, S.B.2
Booth, D.S.3
Walter, P.4
-
36
-
-
60549083291
-
Multiple conformational switches in a GTPase complex control co-translational protein targeting
-
Zhang, X., Schaffitzel, C., Ban, N., and Shan, S. O. (2009) Multiple conformational switches in a GTPase complex control co-translational protein targeting. Proc. Natl. Acad. Sci. U. S. A. 106, 1754-1759
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 1754-1759
-
-
Zhang, X.1
Schaffitzel, C.2
Ban, N.3
Shan, S.O.4
-
37
-
-
79955585362
-
Direct visualization reveals dynamics of a transient intermediate during protein assembly
-
Zhang, X., Lam, V. Q., Mou, Y., Kimura, T., Chung, J., Chandrasekar, S., Winkler, J. R., Mayo, S. L., and Shan, S. O. (2011) Direct visualization reveals dynamics of a transient intermediate during protein assembly. Proc. Natl. Acad. Sci. U. S. A. 108, 6450-6455
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. 6450-6455
-
-
Zhang, X.1
Lam, V.Q.2
Mou, Y.3
Kimura, T.4
Chung, J.5
Chandrasekar, S.6
Winkler, J.R.7
Mayo, S.L.8
Shan, S.O.9
-
38
-
-
79955005771
-
Synergistic actions between the SRP RNA and translating ribosome allow efficient delivery of the correct cargos during cotranslational protein targeting
-
Shen, K., Zhang, X., and Shan, S. O. (2011) Synergistic actions between the SRP RNA and translating ribosome allow efficient delivery of the correct cargos during cotranslational protein targeting. RNA 17, 892-902
-
(2011)
RNA
, vol.17
, pp. 892-902
-
-
Shen, K.1
Zhang, X.2
Shan, S.O.3
-
39
-
-
85027954333
-
Structural basis of signal sequence surveillance and selection by the SRPFtsY complex
-
von Loeffelholz, O., Knoops, K., Ariosa, A., Zhang, X., Karuppasamy, M., Huard, K., Schoehn, G., Berger, I., Shan, S. O., and Schaffitzel, C. (2013) Structural basis of signal sequence surveillance and selection by the SRPFtsY complex. Nat. Struct. Mol. Biol. 20, 604-610
-
(2013)
Nat. Struct. Mol. Biol.
, vol.20
, pp. 604-610
-
-
Von Loeffelholz, O.1
Knoops, K.2
Ariosa, A.3
Zhang, X.4
Karuppasamy, M.5
Huard, K.6
Schoehn, G.7
Berger, I.8
Shan, S.O.9
Schaffitzel, C.10
-
40
-
-
84872339013
-
Fingerloop activates cargo delivery and unloading during cotranslational protein targeting
-
Ariosa, A. R., Duncan, S. S., Saraogi, I., Lu, X., Brown, A., Phillips, G. J., and Shan, S. O. (2013) Fingerloop activates cargo delivery and unloading during cotranslational protein targeting. Mol. Biol. Cell 24, 63-73
-
(2013)
Mol. Biol. Cell
, vol.24
, pp. 63-73
-
-
Ariosa, A.R.1
Duncan, S.S.2
Saraogi, I.3
Lu, X.4
Brown, A.5
Phillips, G.J.6
Shan, S.O.7
-
41
-
-
84902330606
-
Regulation of cargo recognition, commitment, and unloading drives cotranslational protein targeting
-
Saraogi, I., Akopian, D., and Shan, S. O. (2014) Regulation of cargo recognition, commitment, and unloading drives cotranslational protein targeting. J. Cell Biol. 205, 693-706
-
(2014)
J. Cell Biol.
, vol.205
, pp. 693-706
-
-
Saraogi, I.1
Akopian, D.2
Shan, S.O.3
-
42
-
-
0004504539
-
Monte Carlo simulation of differences in free energies of hydration
-
Jorgensen, W. L., and Ravimohan, C. (1985) Monte Carlo simulation of differences in free energies of hydration. J. Chem. Phys. 83, 3050-3054
-
(1985)
J. Chem. Phys.
, vol.83
, pp. 3050-3054
-
-
Jorgensen, W.L.1
Ravimohan, C.2
-
43
-
-
0023346161
-
Free energy calculations by computer simulation
-
Bash, P. A., Singh, U. C., Langridge, R., and Kollman, P. A. (1987) Free energy calculations by computer simulation. Science 236, 564-568
-
(1987)
Science
, vol.236
, pp. 564-568
-
-
Bash, P.A.1
Singh, U.C.2
Langridge, R.3
Kollman, P.A.4
-
44
-
-
0023262075
-
Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin
-
Rao, S. N., Singh, U. C., Bash, P. A., and Kollman, P. A. (1987) Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin. Nature 328, 551-554
-
(1987)
Nature
, vol.328
, pp. 551-554
-
-
Rao, S.N.1
Singh, U.C.2
Bash, P.A.3
Kollman, P.A.4
-
45
-
-
0029757992
-
Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: A molecular dynamics free energy perturbation study
-
Roux, B., Nina, M., Pomès, R., and Smith, J. (1996) Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. Biophys. J. 71, 670-681
-
(1996)
Biophys. J.
, vol.71
, pp. 670-681
-
-
Roux, B.1
Nina, M.2
Pomès, R.3
Smith, J.4
-
46
-
-
0031275544
-
Monte Carlo simulations for proteins: Binding affinities for trypsin-benzamidine complexes via free-energy perturbations
-
Essex, J. W., Severance, D. L., Tirado-Rives, J., and Jorgensen, W. L. (1997) Monte Carlo simulations for proteins: binding affinities for trypsin-benzamidine complexes via free-energy perturbations. J. Phys. Chem. B 101, 9663-9669
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 9663-9669
-
-
Essex, J.W.1
Severance, D.L.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
47
-
-
18744372751
-
Calculation of absolute protein-ligand binding free energy from computer simulations
-
Woo, H.-J., and Roux, B. (2005) Calculation of absolute protein-ligand binding free energy from computer simulations. Proc. Natl. Acad. Sci. U. S. A. 102, 6825-6830
-
(2005)
Proc. Natl. Acad. Sci. U. S. A.
, vol.102
, pp. 6825-6830
-
-
Woo, H.-J.1
Roux, B.2
-
48
-
-
0032556243
-
Free energy analysis of the conformational preferences of A and B forms of DNA in solution
-
Jayaram, B., Sprous, D., Young, M. A., and Beveridge, D. L. (1998) Free energy analysis of the conformational preferences of A and B forms of DNA in solution. J. Am. Chem. Soc. 120, 10629-10633
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 10629-10633
-
-
Jayaram, B.1
Sprous, D.2
Young, M.A.3
Beveridge, D.L.4
-
49
-
-
79958158111
-
Free energy Simulations of a GTPase: GTP and GDP binding to archaeal initiation factor 2
-
Satpati, P., Clavaguéra, C., Ohanessian, G., and Simonson, T. (2011) Free energy Simulations of a GTPase: GTP and GDP binding to archaeal initiation factor 2. J. Phys. Chem. B 115, 6749-6763
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 6749-6763
-
-
Satpati, P.1
Clavaguéra, C.2
Ohanessian, G.3
Simonson, T.4
-
50
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., and Higgins, D. G. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
Thompson, J.D.11
Gibson, T.J.12
Higgins, D.G.13
-
51
-
-
43749107283
-
Comparative protein structure modeling using modeller
-
Chapter 5, Unit 5.6, 2006
-
Eswar, N., Webb, B., Marti-Renom, M. A., Madhusudhan, M., Eramian, D., Shen, M.-Y., Pieper, U., and Sali, A. (2006) Comparative protein structure modeling using modeller. Curr. Protoc. Bioinformatics. 2006 Chapter 5, Unit 5.6
-
(2006)
Curr. Protoc. Bioinformatics.
-
-
Eswar, N.1
Webb, B.2
Marti-Renom, M.A.3
Madhusudhan, M.4
Eramian, D.5
Shen, M.-Y.6
Pieper, U.7
Sali, A.8
-
52
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiórkiewicz-Kuczera, J., Yin, D., and Karplus, M. (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
-
-
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.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
Wiórkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
53
-
-
0029952547
-
Signal sequences specify the targeting route to the endoplasmic reticulum membrane
-
Ng, D. T., Brown, J. D., and Walter, P. (1996) Signal sequences specify the targeting route to the endoplasmic reticulum membrane. J. Cell Biol. 134, 269-278
-
(1996)
J. Cell Biol.
, vol.134
, pp. 269-278
-
-
Ng, D.T.1
Brown, J.D.2
Walter, P.3
-
54
-
-
17644386832
-
Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation
-
Huber, D., Boyd, D., Xia, Y., Olma, M. H., Gerstein, M., and Beckwith, J. (2005) Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation. J. Bacteriol. 187, 2983-2991
-
(2005)
J. Bacteriol.
, vol.187
, pp. 2983-2991
-
-
Huber, D.1
Boyd, D.2
Xia, Y.3
Olma, M.H.4
Gerstein, M.5
Beckwith, J.6
-
55
-
-
0000387235
-
A rapidly convergent descent method for minimization
-
Fletcher, R., and Powell, M. J. D. (1963) A rapidly convergent descent method for minimization. Comput. J. 6, 163-168
-
(1963)
Comput. J.
, vol.6
, pp. 163-168
-
-
Fletcher, R.1
Powell, M.J.D.2
-
56
-
-
0000249851
-
Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations
-
Beutler, T. C., Mark, A. E., van Schaik, R. C., Gerber, P. R., and van Gunsteren, W. F. (1994) Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chem. Phys. Lett. 222, 529-539
-
(1994)
Chem. Phys. Lett.
, vol.222
, pp. 529-539
-
-
Beutler, T.C.1
Mark, A.E.2
Van Schaik, R.C.3
Gerber, P.R.4
Van Gunsteren, W.F.5
-
57
-
-
36849077550
-
Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations
-
Steinbrecher, T., Mobley, D. L., and Case, D. A. (2007) Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. J. Chem. Phys. 127, 214108
-
(2007)
J. Chem. Phys.
, vol.127
, pp. 214108
-
-
Steinbrecher, T.1
Mobley, D.L.2
Case, D.A.3
-
58
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess, B., Kutzner, C., van der Spoel, D., and Lindahl, E. (2008) GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4, 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
-
59
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., and Kollman, P. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24, 1999-2012
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.12
Kollman, P.13
-
60
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (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
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
61
-
-
69349100797
-
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
-
Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, D., Raiteri, P., Donadio, D., Marinelli, F., Pietrucci, F., Broglia, R. A., and Parrinello, M. (2009) PLUMED: A portable plugin for free-energy calculations with molecular dynamics. Comput. Phys. Comm. 180, 1961-1972
-
(2009)
Comput. Phys. Comm.
, vol.180
, pp. 1961-1972
-
-
Bonomi, M.1
Branduardi, D.2
Bussi, G.3
Camilloni, C.4
Provasi, D.5
Raiteri, P.6
Donadio, D.7
Marinelli, F.8
Pietrucci, F.9
Broglia, R.A.10
Parrinello, M.11
-
62
-
-
0019707626
-
Polymorphic transitions in single crystals: A new molecular dynamics method
-
Parrinello, M., and Rahman, A. (1981) Polymorphic transitions in single crystals: A new molecular dynamics method. J. Appl. Phys. 52, 7182-7190
-
(1981)
J. Appl. Phys.
, vol.52
, pp. 7182-7190
-
-
Parrinello, M.1
Rahman, A.2
-
63
-
-
33846823909
-
Particle mesh Ewald: An N log (N) method for Ewald sums in large systems
-
Darden, T., York, D., and Pedersen, L. (1993) Particle mesh Ewald: 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
-
64
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. (1995) A smooth particle mesh Ewald method. J. Chem. Phys. 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
-
65
-
-
2142813682
-
Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry
-
van Gunsteren, W. F., and Berendsen, H. J. (1990) Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry. Angew. Chem. Int. Ed. Engl. 29, 992-1023
-
(1990)
Angew. Chem. Int. Ed. Engl.
, vol.29
, pp. 992-1023
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.2
-
66
-
-
5244304444
-
Efficient estimation of free-energy differences from Monte-Carlo data
-
Bennett, C. H. (1976) Efficient estimation of free-energy differences from Monte-Carlo data. J. Comput. Phys. 22, 245-268
-
(1976)
J. Comput. Phys.
, vol.22
, pp. 245-268
-
-
Bennett, C.H.1
-
67
-
-
77955577540
-
Good practices in freeenergy calculations
-
Pohorille, A., Jarzynski, C., and Chipot, C. (2010) Good practices in freeenergy calculations. J. Phys. Chem. B 114, 10235-10253
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 10235-10253
-
-
Pohorille, A.1
Jarzynski, C.2
Chipot, C.3
-
68
-
-
84904131114
-
An overview of electrostatic free energy computations for solutions and proteins
-
Lin, Y.-L., Aleksandrov, A., Simonson, T., and Roux, B. (2014) An overview of electrostatic free energy computations for solutions and proteins. J. Chem. Theory Comput. 10, 2690-2709
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 2690-2709
-
-
Lin, Y.-L.1
Aleksandrov, A.2
Simonson, T.3
Roux, B.4
-
69
-
-
0035913537
-
Extending the applicability of the nonlinear Poisson Boltzmann equation: Multiple dielectric constants and multivalent ions
-
Rocchia, W., Alexov, E., and Honig, B. (2001) Extending the applicability of the nonlinear Poisson Boltzmann equation: multiple dielectric constants and multivalent ions. J. Phys. Chem. B 105, 6507-6514
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6507-6514
-
-
Rocchia, W.1
Alexov, E.2
Honig, B.3
-
70
-
-
35348886062
-
Anton, a special-purpose machine for molecular dynamics simulation
-
Shaw, D. E., Deneroff, M. M., Dror, R. O., Kuskin, J. S., Larson, R. H., Salmon, J. K., Young, C., Batson, B., Bowers, K. J., Chao, J. C., Eastwood, M. P., Gagliardo, J., Grossman, J. P., Ho, C. R., Ierardi, D. J., Klepeis, J. L., Layman, T., McLeavey, C., Moraes, M. A., Mueller, R., Priest, E. C., Shan, Y., Spengler, J., Theobald, M., Towles, B., and Wang, S. C. (2007) Anton, a special-purpose machine for molecular dynamics simulation. SIGARCH Comput. Archit. News 35, 1-12
-
(2007)
SIGARCH Comput. Archit. News
, vol.35
, pp. 1-12
-
-
Shaw, D.E.1
Deneroff, M.M.2
Dror, R.O.3
Kuskin, J.S.4
Larson, R.H.5
Salmon, J.K.6
Young, C.7
Batson, B.8
Bowers, K.J.9
Chao, J.C.10
Eastwood, M.P.11
Gagliardo, J.12
Grossman, J.P.13
Ho, C.R.14
Ierardi, D.J.15
Klepeis, J.L.16
Layman, T.17
McLeavey, C.18
Moraes, M.A.19
Mueller, R.20
Priest, E.C.21
Shan, Y.22
Spengler, J.23
Theobald, M.24
Towles, B.25
Wang, S.C.26
more..
-
71
-
-
84856878089
-
-
New York, Association of Computer Machinery, New York, 2009
-
Shaw, D., Dror, R., Salmon, J., Grossman, J., Mackenzie, K., Bank, J., Young, C., Deneroff, M., Batson, B., Bowers, K., Chow, E., Eastwood, M., Ierardi, D., Klepeis, J., Kuskin, J., Larson, R., Lindorff-Larsen, K., Maragakis, P., Moraes, M., Piana, S., Shan, Y., and Towles, B. (2009) in Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis, New York 2009, pp. 1-11, Association of Computer Machinery, New York
-
(2009)
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
, pp. 1-11
-
-
Shaw, D.1
Dror, R.2
Salmon, J.3
Grossman, J.4
Mackenzie, K.5
Bank, J.6
Young, C.7
Deneroff, M.8
Batson, B.9
Bowers, K.10
Chow, E.11
Eastwood, M.12
Ierardi, D.13
Klepeis, J.14
Kuskin, J.15
Larson, R.16
Lindorff-Larsen, K.17
Maragakis, P.18
Moraes, M.19
Piana, S.20
Shan, Y.21
Towles, B.22
more..
-
72
-
-
0348244547
-
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
-
Foloppe, N., and MacKerell, A. D., Jr. (2000) All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 21, 86-104
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerell, A.D.2
-
73
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., and Schulten, K. (2005) Scalable molecular dynamics with NAMD. J. Comput. Chem. 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
-
74
-
-
36449007836
-
Constant pressure molecular dynamics simulation-the Langevin piston method
-
Feller, S. E., Zhang, Y., Pastor, R. W., and Brooks, B. R. (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
Pastor, R.W.3
Brooks, B.R.4
-
75
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J.-P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
76
-
-
33646650705
-
Reversible multiple timescale molecular dynamics
-
Tuckerman, M., Berne, B. J., and Martyna, G. J. (1992) Reversible multiple timescale molecular dynamics. J. Chem. Phys. 97, 1990-2001
-
(1992)
J. Chem. Phys.
, vol.97
, pp. 1990-2001
-
-
Tuckerman, M.1
Berne, B.J.2
Martyna, G.J.3
-
77
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., and Haak, J. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
DiNola, A.4
Haak, J.5
-
78
-
-
22944460220
-
Gaussian split Ewald: A fast Ewald mesh method for molecular simulation
-
Shan, Y., Klepeis, J. L., Eastwood, M. P., Dror, R. O., and Shaw, D. E. (2005) Gaussian split Ewald: A fast Ewald mesh method for molecular simulation. J. Chem. Phys. 122, 054101
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 054101
-
-
Shan, Y.1
Klepeis, J.L.2
Eastwood, M.P.3
Dror, R.O.4
Shaw, D.E.5
-
79
-
-
0035871686
-
A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations
-
Kraütler, V., van Gunsteren, W. F., and Hünenberger, P. H. (2001) A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. J. Comput. Chem. 22, 501-508
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 501-508
-
-
Kraütler, V.1
Van Gunsteren, W.F.2
Hünenberger, P.H.3
-
80
-
-
0031045695
-
The hydrophobic region of signal peptides is a determinant for SRP recognition and protein translocation across the ER membrane
-
Hatsuzawa, K., Tagaya, M., and Mizushima, S. (1997) The hydrophobic region of signal peptides is a determinant for SRP recognition and protein translocation across the ER membrane. J. Biochem. 121, 270-277
-
(1997)
J. Biochem.
, vol.121
, pp. 270-277
-
-
Hatsuzawa, K.1
Tagaya, M.2
Mizushima, S.3
-
81
-
-
0347584006
-
Substrate twinning activates the signal recognition particle and its receptor
-
Egea, P. F., Shan, S. O., Napetschnig, J., Savage, D. F., Walter, P., and Stroud, R. M. (2004) Substrate twinning activates the signal recognition particle and its receptor. Nature 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
-
82
-
-
0029878720
-
VMD: Visual molecular dynamics
-
Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: Visual molecular dynamics. J. Mol. Graphics 14, 33-38
-
(1996)
J. Mol. Graphics
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
|