-
1
-
-
0034621834
-
Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution
-
DOI 10.1038/35015017
-
C. Toyoshima, M. Nakasako, H. Nomura, and H. Ogawa Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution Nature 405 2000 647 655 (Pubitemid 30428644)
-
(2000)
Nature
, vol.405
, Issue.6787
, pp. 647-655
-
-
Toyoshima, C.1
Nakasako, M.2
Nomura, H.3
Ogawa, H.4
-
2
-
-
0037043709
-
Structural changes in the calcium pump accompanying the dissociation of calcium
-
C. Toyoshima, and H. Nomura Structural changes in the calcium pump accompanying the dissociation of calcium Nature 418 2002 605 611
-
(2002)
Nature
, vol.418
, pp. 605-611
-
-
Toyoshima, C.1
Nomura, H.2
-
3
-
-
3242888769
-
Crystal structure of the calcium pump with a bound ATP analogue
-
DOI 10.1038/nature02680
-
C. Toyoshima, and T. Mizutani Crystal structure of the calcium pump with a bound ATP analogue Nature 430 2004 529 535 (Pubitemid 38998620)
-
(2004)
Nature
, vol.430
, Issue.6999
, pp. 529-535
-
-
Toyoshima, C.1
Mizutani, T.2
-
4
-
-
3943055518
-
2+-ATPase of the sarcoplasmic reticulum
-
DOI 10.1146/annurev.biochem.73.011303.073700
-
2 +-ATPase of the sarcoplasmic reticulum Annu. Rev. Biochem. 73 2004 269 292 (Pubitemid 39050370)
-
(2004)
Annual Review of Biochemistry
, vol.73
, pp. 269-292
-
-
Toyoshima, C.1
Inesi, G.2
-
6
-
-
11144330054
-
Dephosphorylation of the calcium pump coupled to counterion occlusion
-
DOI 10.1126/science.1106289
-
C. Olesen, T.L. Sorensen, R.C. Nielsen, J.V. Moller, and P. Nissen Dephosphorylation of the calcium pump coupled to counterion occlusion Science 306 2004 2251 2255 (Pubitemid 40024461)
-
(2004)
Science
, vol.306
, Issue.5705
, pp. 2251-2255
-
-
Olesen, C.1
Sorensen, T.L.-M.2
Nielsen, R.C.3
Moller, J.V.4
Nissen, P.5
-
7
-
-
37249043376
-
The structural basis of calcium transport by the calcium pump
-
C. Olesen, M. Picard, A.M.L. Winther, C. Gyrup, J.P. Morth, and C. Oxvig The structural basis of calcium transport by the calcium pump Nature 450 2007 1036
-
(2007)
Nature
, vol.450
, pp. 1036
-
-
Olesen, C.1
Picard, M.2
Winther, A.M.L.3
Gyrup, C.4
Morth, J.P.5
Oxvig, C.6
-
8
-
-
9244232176
-
Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues
-
DOI 10.1038/nature02981
-
C. Toyoshima, H. Nomura, and T. Tsuda Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues Nature 432 2004 361 368 (Pubitemid 39555518)
-
(2004)
Nature
, vol.432
, Issue.7015
, pp. 361-368
-
-
Toyoshima, C.1
Nomura, H.2
Tsuda, T.3
-
9
-
-
47049101464
-
2 +-ATPase of sarcoplasmic reticulum
-
2 +-ATPase of sarcoplasmic reticulum Arch. Biochem. Biophys. 476 2008 3 11
-
(2008)
Arch. Biochem. Biophys.
, vol.476
, pp. 3-11
-
-
Toyoshima, C.1
-
10
-
-
0029565489
-
2+-ATPase by site-directed mutagenesis
-
DOI 10.1007/BF01788358
-
2 +-ATPase by site-directed mutagenesis Biosci. Rep. 15 1995 243 261 (Pubitemid 26050845)
-
(1995)
Bioscience Reports
, vol.15
, Issue.5
, pp. 243-261
-
-
Andersen, J.P.1
-
12
-
-
77954238208
-
Glutamate 90 at the luminal ion gate of sarcoplasmic reticulum Ca(2 +)-ATPase is critical for Ca(2 +) binding on both sides of the membrane
-
J.D. Clausen, and J.P. Andersen Glutamate 90 at the luminal ion gate of sarcoplasmic reticulum Ca(2 +)-ATPase is critical for Ca(2 +) binding on both sides of the membrane J. Biol. Chem. 285 2010 20780 20792
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 20780-20792
-
-
Clausen, J.D.1
Andersen, J.P.2
-
13
-
-
0037064017
-
2+-ATPase: Role of the a domain and its C-terminal link with the transmembrane region
-
DOI 10.1074/jbc.M204603200
-
2 +-ATPase-role of the A domain and its C-terminal link with the transmembrane region J. Biol. Chem. 277 2002 38647 38659 (Pubitemid 35154725)
-
(2002)
Journal of Biological Chemistry
, vol.277
, Issue.41
, pp. 38647-38659
-
-
Moller, J.V.1
Lenoir, G.2
Marchand, C.3
Montigny, C.4
Le Maire, M.5
Toyoshima, C.6
Juul, B.S.7
Champeil, P.8
-
17
-
-
84863785264
-
The role of domain:domain interactions vs domain:water interactions in the coarse-grained simulations of the E1P to E2P transitions in Ca-ATPase (SERCA)
-
A. Nagarajan, J.P. Andersen, and T.B. Woolf The role of domain:domain interactions vs domain:water interactions in the coarse-grained simulations of the E1P to E2P transitions in Ca-ATPase (SERCA) Proteins: Struct. Funct. Bioinform. 80 2012 1929 1947
-
(2012)
Proteins: Struct. Funct. Bioinform.
, vol.80
, pp. 1929-1947
-
-
Nagarajan, A.1
Andersen, J.P.2
Woolf, T.B.3
-
18
-
-
0021191208
-
Fluctuations in protein structure from X-ray diffraction
-
G.A. Petsko, and D. Ringe Fluctuations in protein structure from X-ray diffraction Annu. Rev. Biophys. Bioeng. 13 1984 331 371
-
(1984)
Annu. Rev. Biophys. Bioeng.
, vol.13
, pp. 331-371
-
-
Petsko, G.A.1
Ringe, D.2
-
20
-
-
0038241788
-
Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments RID A-9558-2010 RID A-6222-2010
-
Y. Mu, D. Kosov, and G. Stock Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments RID A-9558-2010 RID A-6222-2010 J. Phys. Chem. B 107 2003 5064 5073
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 5064-5073
-
-
Mu, Y.1
Kosov, D.2
Stock, G.3
-
21
-
-
77957937199
-
Atomic-level characterization of the structural dynamics of proteins
-
D.E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R.O. Dror, and M.P. Eastwood Atomic-level characterization of the structural dynamics of proteins Science 330 2010 341 346
-
(2010)
Science
, vol.330
, pp. 341-346
-
-
Shaw, D.E.1
Maragakis, P.2
Lindorff-Larsen, K.3
Piana, S.4
Dror, R.O.5
Eastwood, M.P.6
-
23
-
-
0027794972
-
Targeted molecular dynamics simulation of conformational change-application to the TR transition in insulin
-
J. Schlitter, M. Engels, P. Kruger, E. Jacoby, and A. Wollmer Targeted molecular dynamics simulation of conformational change-application to the TR transition in insulin Mol. Simul. 10 1993 291 308
-
(1993)
Mol. Simul.
, vol.10
, pp. 291-308
-
-
Schlitter, J.1
Engels, M.2
Kruger, P.3
Jacoby, E.4
Wollmer, A.5
-
24
-
-
44849124493
-
End-point targeted molecular dynamics: Large-scale conformational changes in potassium channels
-
R.J. Mashl, and E. Jakobsson End-point targeted molecular dynamics: large-scale conformational changes in potassium channels Biophys. J. 94 2008 4307 4319
-
(2008)
Biophys. J.
, vol.94
, pp. 4307-4319
-
-
Mashl, R.J.1
Jakobsson, E.2
-
25
-
-
34247210226
-
Extending molecular dynamics time scales with milestoning: Example of complex kinetics in a solvated peptide
-
A.M.A. West, R. Elber, and D. Shalloway Extending molecular dynamics time scales with milestoning: example of complex kinetics in a solvated peptide J. Chem. Phys. 126 2007 145104
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 145104
-
-
West, A.M.A.1
Elber, R.2
Shalloway, D.3
-
26
-
-
0030070532
-
Weighted-ensemble Brownian dynamics simulations for protein association reactions
-
G.A. Huber, and S. Kim Weighted-ensemble Brownian dynamics simulations for protein association reactions Biophys. J. 70 1996 97 110 (Pubitemid 26021452)
-
(1996)
Biophysical Journal
, vol.70
, Issue.1
, pp. 97-110
-
-
Huber, G.A.1
Kim, S.2
-
28
-
-
0032546697
-
Path corrected functionals of stochastic trajectories: Towards relative free energy and reaction coordinate calculations
-
PII S0009261498004278
-
T.B. Woolf Path corrected functionals of stochastic trajectories: towards relative free energy and reaction coordinate calculations Chem. Phys. Lett. 289 1998 433 441 (Pubitemid 128185994)
-
(1998)
Chemical Physics Letters
, vol.289
, Issue.5-6
, pp. 433-441
-
-
Woolf, T.B.1
-
29
-
-
0000801009
-
Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements
-
C. Dellago, P.G. Bolhuis, and D. Chandler Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements J. Chem. Phys. 108 1998 9236 9245 (Pubitemid 128571335)
-
(1998)
Journal of Chemical Physics
, vol.108
, Issue.22
, pp. 9236-9245
-
-
Dellago, C.1
Bolhuis, P.G.2
Chandler, D.3
-
30
-
-
78650127789
-
Computing ensembles of transitions from stable states: Dynamic importance sampling
-
J.R. Perilla, O. Beckstein, E.J. Denning, and T.B. Woolf Computing ensembles of transitions from stable states: dynamic importance sampling J. Comput. Chem. 32 2011 196 209
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 196-209
-
-
Perilla, J.R.1
Beckstein, O.2
Denning, E.J.3
Woolf, T.B.4
-
31
-
-
36549043024
-
Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
-
DOI 10.1016/j.sbi.2007.09.011, PII S0959440X07001534, Catalysis and Regulation /Protein
-
I. Bahar, C. Chennubhotla, and D. Tobi Intrinsic dynamics of enzymes in the unbound state and, relation to allosteric regulation Curr. Opin. Struct. Biol. 17 2007 633 640 (Pubitemid 350180409)
-
(2007)
Current Opinion in Structural Biology
, vol.17
, Issue.6
, pp. 633-640
-
-
Bahar, I.1
Chennubhotla, C.2
Tobi, D.3
-
32
-
-
84986512474
-
CHARMM-a program for macromolecular energy, minimization, and dynamics calculations
-
B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus 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
-
33
-
-
49449113010
-
The MARTINI coarse-grained force field: Extension to proteins
-
L. Monticelli, S.K. Kandasamy, X. Periole, R.G. Larson, D.P. Tieleman, and S.J. Marrink The MARTINI coarse-grained force field: extension to proteins J. Chem. Theory Comput. 4 2008 819 834
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 819-834
-
-
Monticelli, L.1
Kandasamy, S.K.2
Periole, X.3
Larson, R.G.4
Tieleman, D.P.5
Marrink, S.J.6
-
34
-
-
34547474332
-
MARTINI force field: Coarse grained model for biomolecular simulations
-
Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P. & de Vries,A. H. (2007). The MARTINI force field: Coarse grained model for biomolecular simulations. J. Phys. Chem.
-
(2007)
J. Phys. Chem
-
-
Marrink, S.J.1
Risselada, H.J.2
Yefimov, S.3
Tieleman, D.P.4
De Vries, A.H.5
-
35
-
-
0026076090
-
Collective motions in proteins-a covariance analysis of atomic fluctuations in molecular-dynamics and normal mode simulations
-
T. Ichiye, and M. Karplus Collective motions in proteins-a covariance analysis of atomic fluctuations in molecular-dynamics and normal mode simulations Proteins 11 1991 205 217
-
(1991)
Proteins
, vol.11
, pp. 205-217
-
-
Ichiye, T.1
Karplus, M.2
-
37
-
-
0033955055
-
Protein dynamics in enzymatic catalysis: Exploration of dihydrofolate reductase
-
DOI 10.1021/ja9913838
-
J.L. Radkiewicz, and C.L. Brooks Protein dynamics in enzymatic catalysis: exploration of dihydrofolate reductase J. Am. Chem. Soc. 122 2000 225 231 (Pubitemid 30061051)
-
(2000)
Journal of the American Chemical Society
, vol.122
, Issue.2
, pp. 225-231
-
-
Radkiewicz, J.L.1
Brooks III, C.L.2
-
38
-
-
33845184202
-
Theory of enthalpy-entropy compensation
-
H.M.J. Boots, and P.K. Debokx Theory of enthalpy-entropy compensation J. Phys. Chem. 93 1989 8240 8243
-
(1989)
J. Phys. Chem.
, vol.93
, pp. 8240-8243
-
-
Boots, H.M.J.1
Debokx, P.K.2
-
39
-
-
0001594721
-
Entropy-enthalpy compensation in solvation and ligand binding revisited
-
E. Gallicchio, M.M. Kubo, and R.M. Levy Entropy-enthalpy compensation in solvation and ligand binding revisited J. Am. Chem. Soc. 120 1998 4526 4527
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 4526-4527
-
-
Gallicchio, E.1
Kubo, M.M.2
Levy, R.M.3
-
40
-
-
0030757235
-
Mutants of rat intestinal fatty acid-binding protein illustrate the critical role played by enthalpy-entropy compensation in ligand binding
-
DOI 10.1074/jbc.272.27.16737
-
G.V. Richieri, P.J. Low, R.T. Ogata, and A.M. Kleinfeld Mutants of rat intestinal fatty acid-binding protein illustrate the critical role played by enthalpy-entropy compensation in ligand binding J. Biol. Chem. 272 1997 16737 16740 (Pubitemid 27289767)
-
(1997)
Journal of Biological Chemistry
, vol.272
, Issue.27
, pp. 16737-16740
-
-
Richieri, G.V.1
Low, P.J.2
Ogata, R.T.3
Kleinfeld, A.M.4
-
41
-
-
0842333152
-
Implicit solvation based on generalized Born theory in different dielectric environments
-
M. Feig, W. Im, and C.L. Brooks Implicit solvation based on generalized Born theory in different dielectric environments J. Chem. Phys. 120 2004 903 911
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 903-911
-
-
Feig, M.1
Im, W.2
Brooks, C.L.3
-
42
-
-
0346971105
-
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
-
M. Feig, A. Onufriev, M.S. Lee, W. Im, D.A. Case, and C.L. Brooks Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures J. Comput. Chem. 25 2004 265 284
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 265-284
-
-
Feig, M.1
Onufriev, A.2
Lee, M.S.3
Im, W.4
Case, D.A.5
Brooks, C.L.6
-
43
-
-
0242322528
-
An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins
-
W. Im, M. Feig, and C.L. Brooks An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins Biophys. J. 85 2003 2900 2918 (Pubitemid 37345782)
-
(2003)
Biophysical Journal
, vol.85
, Issue.5
, pp. 2900-2918
-
-
Im, W.1
Feig, M.2
Brooks III, C.L.3
-
44
-
-
0141956090
-
Generalized Born model with a simple smoothing function
-
W.P. Im, M.S. Lee, and C.L. Brooks 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.P.1
Lee, M.S.2
Brooks, C.L.3
-
45
-
-
0000778360
-
Dynamic reaction paths and rates through importance-sampled stochastic dynamics
-
D.M. Zuckerman, and T.B. Woolf Dynamic reaction paths and rates through importance-sampled stochastic dynamics J. Chem. Phys. 111 1999 9475 9484 (Pubitemid 129579891)
-
(1999)
Journal of Chemical Physics
, vol.111
, Issue.21
, pp. 9475-9484
-
-
Zuckerman, D.M.1
Woolf, T.B.2
-
46
-
-
20444367704
-
Efficient dynamic importance sampling of rare events in one dimension
-
D.M. Zuckerman, and T.B. Woolf Efficient dynamic importance sampling of rare events in one dimension Phys. Rev. E 63 2001 016702
-
(2001)
Phys. Rev. e
, vol.63
, pp. 016702
-
-
Zuckerman, D.M.1
Woolf, T.B.2
-
47
-
-
33745911151
-
Multiple pathways in conformational transitions of the alanine dipeptide: An Application of dynamic importance sampling
-
DOI 10.1002/jcc.20444
-
H. Jang, and T.B. Woolf Multiple pathways in conformational transitions of the alanine dipeptide: an application of dynamic importance sampling J. Comput. Chem. 27 2006 1136 1141 (Pubitemid 44049056)
-
(2006)
Journal of Computational Chemistry
, vol.27
, Issue.11
, pp. 1136-1141
-
-
Jang, H.1
Woolf, T.B.2
-
48
-
-
0037039980
-
Transition events in butane simulations: Similarities across models
-
DOI 10.1063/1.1433501
-
D.M. Zuckerman, and T.B. Woolf Transition events in butane simulations: similarities across models J. Chem. Phys. 116 2002 2586 2591 (Pubitemid 34167996)
-
(2002)
Journal of Chemical Physics
, vol.116
, Issue.6
, pp. 2586-2591
-
-
Zuckerman, D.M.1
Woolf, T.B.2
-
50
-
-
0028360307
-
The contribution of vibrational entropy to molecular association-the dimerization of insulin
-
B. Tidor, and M. Karplus The contribution of vibrational entropy to molecular association-the dimerization of insulin J. Mol. Biol. 238 1994 405 414
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 405-414
-
-
Tidor, B.1
Karplus, M.2
|