-
1
-
-
0035846819
-
Does functional photosytem II complex have an oxygen channel?
-
DOI 10.1016/S0014-5793(00)02358-9, PII S0014579300023589
-
J.M. Anderson, Does functional photosystem II complex have an oxygen channel? FEBS Lett. 488 (2001) 1-4. (Pubitemid 32332795)
-
(2001)
FEBS Letters
, vol.488
, Issue.1-2
, pp. 1-4
-
-
Anderson, J.M.1
-
2
-
-
0037295369
-
Photosystem II: The engine of life
-
DOI 10.1017/S0033583502003839
-
J. Barber, Photosystem II: the engine of life, Q. Rev. Biophys. 36 (2003) 71-89. (Pubitemid 36313960)
-
(2003)
Quarterly Reviews of Biophysics
, vol.36
, Issue.1
, pp. 71-89
-
-
Barber, J.1
-
3
-
-
67649819680
-
Multiple pathways guide oxygen diffusion into flavoenzyme active sites
-
R. Baron, C. Riley, P. Chenprakhon, K. Thotsaporn, R.T. Winter, A. Alfieri, F. Forneris, W.J.H. van Berkel, P. Chaiyen, M.W. Fraaije, A. Mattevi, J.A. McCammon, Multiple pathways guide oxygen diffusion into flavoenzyme active sites, Proc. Natl. Acad. Sci. U. S. A. 106 (2009) 10603-10608.
-
(2009)
Proc. Natl. Acad. Sci. U. S. A
, vol.106
, pp. 10603-10608
-
-
Baron, R.1
Riley, C.2
Chenprakhon, P.3
Thotsaporn, K.4
Winter, R.T.5
Alfieri, A.6
Forneris, F.7
Van Berkel, W.J.H.8
Chaiyen, P.9
Fraaije, M.W.10
Mattevi, A.11
McCammon, J.A.12
-
4
-
-
0035425778
-
Solvated ensemble averaging in the calculation of partial atomic charges
-
DOI 10.1002/jcc.1072
-
M. Basma, S. Sundara, D. Calgan, T. Vernali, R.J.Woods, Solvated ensemble averaging in the calculation of partial atomic charges, J. Comput. Chem. 22 (2001) 1125-1137. (Pubitemid 32662792)
-
(2001)
Journal of Computational Chemistry
, vol.22
, Issue.11
, pp. 1125-1137
-
-
Basma, M.1
Sundara, S.2
Calgan, D.3
Vernali, T.4
Woods, R.J.5
-
5
-
-
85031136416
-
-
Tenth Workshop on Graphics Hardware
-
M. Bosma, J. Smit, J. Terwisscha, J. van Scheltinga, Super resolution volume rendering hardware, Tenth Workshop on Graphics Hardware, 1995.
-
(1995)
Super Resolution Volume Rendering Hardware
-
-
Bosma, M.1
Smit, J.2
Terwisscha, J.3
Van Scheltinga, J.4
-
6
-
-
0021114712
-
Penetration of dioxygen into proteins studied by quenching of phosphorescence and fluorescence
-
D.B. Calhoun, J.M. Vanderkooi, G.V. Woodrow, S.W. Englander, Penetration of dioxygen into proteins studied by quenching of phosphorescence and fluorescence, Biochemistry 22 (1983) 1526-1532.
-
(1983)
Biochemistry
, vol.22
, pp. 1526-1532
-
-
Calhoun, D.B.1
Vanderkooi, J.M.2
Woodrow, G.V.3
Englander, S.W.4
-
7
-
-
84555218287
-
Fluorescent protein barrel fluctuations and oxygen diffusion pathways in mCherry
-
P.P. Chapagain, C.K. Regmi, W. Castillo, Fluorescent protein barrel fluctuations and oxygen diffusion pathways in mCherry, J. Chem. Phys. 135 (2011).
-
(2011)
J. Chem. Phys
, vol.135
-
-
Chapagain, P.P.1
Regmi, C.K.2
Castillo, W.3
-
8
-
-
33748460871
-
Imaging the migration pathways for O-2
-
J. Cohen, A. Arkhipov, R. Braun, K. Schulten, Imaging the migration pathways for O-2, CO, NO, and Xe inside myoglobin, Biophys. J. 91 (2006) 1844-1857.
-
(2006)
CO, NO, and Xe Inside Myoglobin, Biophys. J
, vol.91
, pp. 1844-1857
-
-
Cohen, J.1
Arkhipov, A.2
Braun, R.3
Schulten, K.4
-
9
-
-
24344440880
-
2 transport in CpI [FeFe]-hydrogenase and the role of packing defects
-
DOI 10.1016/j.str.2005.05.013, PII S096921260500239X
-
J. Cohen, K. Kim, P. King, M. Seibert, K. Schulten, Finding gas diffusion pathways in proteins: application to O-2 and H-2 transport in CplFe-hydrogenase and the role of packing defects, Structure 13 (2005) 1321-1329. (Pubitemid 41262099)
-
(2005)
Structure
, vol.13
, Issue.9
, pp. 1321-1329
-
-
Cohen, J.1
Kim, K.2
King, P.3
Seibert, M.4
Schulten, K.5
-
10
-
-
84861367246
-
Biomolecular simulation: A computational microscope for molecular biology
-
R.O. Dror, R.M. Dirks, J.P. Grossman, H.F. Xu, D.E. Shaw, Biomolecular simulation: a computational microscope for molecular biology, Annu. Rev. Biophys. 41 (2012) 429-452.
-
(2012)
Annu. Rev. Biophys
, vol.41
, pp. 429-452
-
-
Dror, R.O.1
Dirks, R.M.2
Grossman, J.P.3
Xu, H.F.4
Shaw, D.E.5
-
11
-
-
48949103837
-
Tryptophan quenching as linear sensor for oxygen binding of arthropod hemocyanins
-
W. Erker, R. Hubler, H. Decker, Tryptophan quenching as linear sensor for oxygen binding of arthropod hemocyanins, Biochim. Biophys. Acta, Gen. Subj. 1780 (2008) 1143-1147.
-
(2008)
Biochim. Biophys. Acta, Gen. Subj
, vol.1780
, pp. 1143-1147
-
-
Erker, W.1
Hubler, R.2
Decker, H.3
-
12
-
-
1642331709
-
Architecture of the photosynthetic oxygen-evolving center
-
DOI 10.1126/science.1093087
-
K.N. Ferreira, T.M. Iverson, K. Maghlaoui, J. Barber, S. Iwata, Architecture of the photosynthetic oxygen-evolving center, Science 303 (2004) 1831-1838. (Pubitemid 38374869)
-
(2004)
Science
, vol.303
, Issue.5665
, pp. 1831-1838
-
-
Ferreira, K.N.1
Iverson, T.M.2
Maghlaoui, K.3
Barber, J.4
Iwata, S.5
-
13
-
-
69849088750
-
Probing the accessibility of the Mn4Ca cluster in photosystem II: Channels calculation, noble gas derivatization, and cocrystallization with DMSO
-
A. Gabdulkhakov, A. Guskov, M. Broser, J. Kern, F. Muh, W. Saenger, A. Zouni, Probing the accessibility of the Mn4Ca cluster in photosystem II: channels calculation, noble gas derivatization, and cocrystallization with DMSO, Structure 17 (2009) 1223-1234.
-
(2009)
Structure
, vol.17
, pp. 1223-1234
-
-
Gabdulkhakov, A.1
Guskov, A.2
Broser, M.3
Kern, J.4
Muh, F.5
Saenger, W.6
Zouni, A.7
-
14
-
-
45749150851
-
Photosystem II: The light-driven water: Plastoquinone oxidoreductase
-
Thomas J. Wydrzynski, Kimiyuki Satoh (Eds.) 87, Springer, Dordrecht, The Netherlands
-
Govindjee, Photosystem II: the light-driven water: plastoquinone oxidoreductase, in: Thomas J. Wydrzynski, Kimiyuki Satoh (Eds.), Volume 22, Advances in Photosynthesis and Respiration, Photosynth. Res., 87, Springer, Dordrecht, The Netherlands, 2006, pp. 331-335.
-
(2006)
Advances in Photosynthesis and Respiration, Photosynth. Res
, vol.22
, pp. 331-335
-
-
Govindjee1
-
16
-
-
34548029736
-
New force fields for nitrous oxide and oxygen and their application to phase equilibria simulations
-
DOI 10.1016/j.fluid.2007.07.014, PII S0378381207003822
-
N. Hansen, F.A.B. Agbor, F.J. Keil, New force fields for nitrous oxide and oxygen and their application to phase equilibria simulations, Fluid Phase Equilib. 259 (2007) 180-188. (Pubitemid 47285592)
-
(2007)
Fluid Phase Equilibria
, vol.259
, Issue.2
, pp. 180-188
-
-
Hansen, N.1
Agbor, F.A.B.2
Keil, F.J.3
-
18
-
-
38849188029
-
4 cluster in Photosystem II based on solvent accessibility simulations, with implications for substrate water access
-
DOI 10.1016/j.bbabio.2007.08.009, PII S0005272807002009
-
F.M. Ho, S. Styring, Access channels and methanol binding site to the CaMn4 cluster in Photosystem II based on solvent accessibility simulations, with implications for substrate water access, Biochim. Biophys. Acta Bioenerg. 1777 (2008) 140-153. (Pubitemid 351187745)
-
(2008)
Biochimica et Biophysica Acta - Bioenergetics
, vol.1777
, Issue.2
, pp. 140-153
-
-
Ho, F.M.1
Styring, S.2
-
19
-
-
39549085136
-
Mechanismof selectivity in aquaporins and aquaglyceroporins
-
J.S. Hub, B.L. de Groot,Mechanismof selectivity in aquaporins and aquaglyceroporins, Proc. Natl. Acad. Sci. U. S. A. 105 (2008) 1198-1203.
-
(2008)
Proc. Natl. Acad. Sci. U. S. A
, vol.105
, pp. 1198-1203
-
-
Hub, J.S.1
De Groot, B.L.2
-
21
-
-
34547101240
-
Exploring molecular oxygen pathways in Hansenula polymorpha copper-containing amine oxidase
-
DOI 10.1074/jbc.M701308200
-
B.J. Johnson, J. Cohen, R.W. Welford, A.R. Pearson, K. Schulten, J.P. Klinman, C.M. Wilmot, Exploring molecular oxygen pathways in Hansenula polymorpha coppercontaining amine oxidase, J. Biol. Chem. 282 (2007) 17767-17776. (Pubitemid 47100291)
-
(2007)
Journal of Biological Chemistry
, vol.282
, Issue.24
, pp. 17767-17776
-
-
Johnson, B.J.1
Cohen, J.2
Welford, R.W.3
Pearson, A.R.4
Schulten, K.5
Klinman, J.P.6
Wilmot, C.M.7
-
22
-
-
0042415783
-
NAMD2: Greater scalability for parallel molecular dynamics
-
L. Kale, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, K. Schulten, NAMD2: greater scalability for parallel molecular dynamics, J. Comput. Phys. 151 (1999) 283-312.
-
(1999)
J. Comput. Phys
, vol.151
, pp. 283-312
-
-
Kale, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.4
Gursoy, A.5
Krawetz, N.6
Phillips, J.7
Shinozaki, A.8
Varadarajan, K.9
Schulten, K.10
-
23
-
-
23444460717
-
Cyanobacterial Photosystem II at 3.2 Akappa resolution - The plastoquinone binding pockets
-
DOI 10.1007/s11120-004-7077-x
-
J. Kern, B. Loll, A. Zouni, W. Saenger, K.D. Irrgang, J. Biesiadka, Cyanobacterial photosystem II at 3.2 angstrom resolution-the plastoquinone binding pockets, Photosynth. Res. 84 (2005) 153-159. (Pubitemid 41110641)
-
(2005)
Photosynthesis Research
, vol.84
, Issue.1-3
, pp. 153-159
-
-
Kern, J.1
Loll, B.2
Zouni, A.3
Saenger, W.4
Irrgang, K.-D.5
Biesiadka, J.6
-
24
-
-
84862181022
-
Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase
-
V.M. Luna, J.A. Fee, A.A. Deniz, C.D. Stout, Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase, Biochemistry 51 (2012) 4669-4676.
-
(2012)
Biochemistry
, vol.51
, pp. 4669-4676
-
-
Luna, V.M.1
Fee, J.A.2
Deniz, A.A.3
Stout, C.D.4
-
25
-
-
34547116864
-
Structural characteristics of channels and pathways in photosystem II including the identification of an oxygen channel
-
DOI 10.1016/j.jsb.2007.01.016, PII S1047847707000238
-
J.W. Murray, J. Barber, Structural characteristics of channels and pathways in photosystem II including the identification of an oxygen channel, J. Struct. Biol. 159 (2007) 228-237. (Pubitemid 47096868)
-
(2007)
Journal of Structural Biology
, vol.159
, Issue.2 SPEC. ISSUE
, pp. 228-237
-
-
Murray, J.W.1
Barber, J.2
-
26
-
-
0026053222
-
Finite-difference computation of traveltimes in very contrasted velocity models-A massively parallel approach and its associated tools
-
P. Podvin, I. Lecomte, Finite-difference computation of traveltimes in very contrasted velocity models-a massively parallel approach and its associated tools, Geophys. J. Int. 105 (1991) 271-284.
-
(1991)
Geophys. J. Int
, vol.105
, pp. 271-284
-
-
Podvin, P.1
Lecomte, I.2
-
27
-
-
78651455171
-
Diffusion pathways of oxygen species in the phototoxic fluorescent protein KillerRed
-
A. Roy, P. Carpentier, D. Bourgeois, M. Field, Diffusion pathways of oxygen species in the phototoxic fluorescent protein KillerRed, Photochem. Photobiol. Sci. 9 (2010) 1342-1350.
-
(2010)
Photochem. Photobiol. Sci
, vol.9
, pp. 1342-1350
-
-
Roy, A.1
Carpentier, P.2
Bourgeois, D.3
Field, M.4
-
28
-
-
34548060346
-
Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels
-
DOI 10.1073/pnas.0702401104
-
J. Saam, I. Ivanov, M. Walther, H.G. Holzhutter, H. Kuhn, Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels, Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 13319-13324. (Pubitemid 47293943)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.33
, pp. 13319-13324
-
-
Saam, J.1
Ivanov, I.2
Walther, M.3
Holzhutter, H.-G.4
Kuhn, H.5
-
29
-
-
77955288875
-
O-2 reactivity of flavoproteins dynamic access of dioxygen to the active site and role of a H+ relay system in D-amino acid oxidase
-
J. Saam, E. Rosini, G. Molla, K. Schulten, L. Pollegioni, S. Ghisla, O-2 reactivity of flavoproteins dynamic access of dioxygen to the active site and role of a H+ relay system in D-amino acid oxidase, J. Biol. Chem. 285 (2010) 24439-24446.
-
(2010)
J. Biol. Chem
, vol.285
, pp. 24439-24446
-
-
Saam, J.1
Rosini, E.2
Molla, G.3
Schulten, K.4
Pollegioni, L.5
Ghisla, S.6
-
30
-
-
0037174385
-
All-atomstructure prediction and folding simulations of a stable protein
-
C. Simmerling, B. Strockbine, A.E. Roitberg, All-atomstructure prediction and folding simulations of a stable protein, J. Am. Chem. Soc. 124 (2002) 11258-11259.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 11258-11259
-
-
Simmerling, C.1
Strockbine, B.2
Roitberg, A.E.3
-
31
-
-
62749167980
-
MCCE2: Improving protein pK(a) calculations with extensive side chain rotamer sampling
-
Y.F. Song, J.J. Mao, M.R. Gunner, MCCE2: improving protein pK(a) calculations with extensive side chain rotamer sampling, J. Comput. Chem. 30 (2009) 2231-2247.
-
(2009)
J. Comput. Chem
, vol.30
, pp. 2231-2247
-
-
Song, Y.F.1
Mao, J.J.2
Gunner, M.R.3
-
32
-
-
48549102241
-
Computational insights into the O-2-evolving complex of photosystem II
-
E.M. Sproviero, J.P. McEvoy, J.A. Gascon, G.W. Brudvig, V.S. Batista, Computational insights into the O-2-evolving complex of photosystem II, Photosynth. Res. 97 (2008) 91-114.
-
(2008)
Photosynth. Res
, vol.97
, pp. 91-114
-
-
Sproviero, E.M.1
McEvoy, J.P.2
Gascon, J.A.3
Brudvig, G.W.4
Batista, V.S.5
-
33
-
-
0021766921
-
Cavities in proteins-structure of ametmyoglobinxenon complex solved to 1.9-A
-
R.F. Tilton, I.D. Kuntz, G.A. Petsko, Cavities in proteins-structure of ametmyoglobinxenon complex solved to 1.9-A, Biochemistry 23 (1984) 2849-2857.
-
(1984)
Biochemistry
, vol.23
, pp. 2849-2857
-
-
Tilton, R.F.1
Kuntz, I.D.2
Petsko, G.A.3
-
34
-
-
0342929614
-
Non-physical sampling distributions in Monte-Carlo free-energy estimation-umbrella sampling
-
G.M. Torrie, J.P. Valleau, Non-physical sampling distributions in Monte-Carlo free-energy estimation-umbrella sampling, J. Comput. Phys. 23 (1977) 187-199.
-
(1977)
J. Comput. Phys
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
35
-
-
85028099698
-
Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 angstrom
-
Y. Umena, K. Kawakami, J.R. Shen, N. Kamiya, Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 angstrom, Nature 473 (2011) 55-60.
-
(2011)
Nature
, vol.473
, pp. 55-60
-
-
Umena, Y.1
Kawakami, K.2
Shen, J.R.3
Kamiya, N.4
-
36
-
-
33646154454
-
A protein dynamics study of photosystem II: The effects of protein conformation on reaction center function
-
S. Vasil'ev, D. Bruce, A protein dynamics study of photosystem II: the effects of protein conformation on reaction center function, Biophys. J. 90 (2006) 3062-3073.
-
(2006)
Biophys. J
, vol.90
, pp. 3062-3073
-
-
Vasil'ev, S.1
Bruce, D.2
-
37
-
-
77749255459
-
Tracking the flow of water through photosystem II using molecular dynamics and streamline tracing
-
S. Vassiliev, P. Comte, A. Mahboob, D. Bruce, Tracking the flow of water through photosystem II using molecular dynamics and streamline tracing, Biochemistry 49 (2010) 1873-1881.
-
(2010)
Biochemistry
, vol.49
, pp. 1873-1881
-
-
Vassiliev, S.1
Comte, P.2
Mahboob, A.3
Bruce, D.4
-
38
-
-
84862318595
-
Exploring the energetics of water permeation in photosystem II by multiple steered molecular dynamics simulations
-
S. Vassiliev, T. Zaraiskaya, D. Bruce, Exploring the energetics of water permeation in photosystem II by multiple steered molecular dynamics simulations, Biochim. Biophys. Acta Bioenerg. 1817 (2013) 1671-1678.
-
(2013)
Biochim. Biophys. Acta Bioenerg
, vol.1817
, pp. 1671-1678
-
-
Vassiliev, S.1
Zaraiskaya, T.2
Bruce, D.3
-
39
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
-
J.M. Wang, P. Cieplak, P.A. Kollman, How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21 (2000) 1049-1074.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 1049-1074
-
-
Wang, J.M.1
Cieplak, P.2
Kollman, P.A.3
-
40
-
-
33847313314
-
Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics
-
DOI 10.1016/j.jsb.2006.11.008, PII S1047847706003789, Advanced in Molecular Dynamics Simulations
-
Y. Wang, J. Cohen, W.F. Boron, K. Schulten, E. Tajkhorshid, Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics, J. Struct. Biol. 157 (2007) 534-544. (Pubitemid 46321519)
-
(2007)
Journal of Structural Biology
, vol.157
, Issue.3
, pp. 534-544
-
-
Wang, Y.1
Cohen, J.2
Boron, W.F.3
Schulten, K.4
Tajkhorshid, E.5
-
41
-
-
80055093132
-
Tunnels modulate ligand flux in a heme nitric oxide/oxygen binding (H-NOX) domain
-
M.B. Winter, M.A. Herzik, J. Kuriyan, M.A. Marletta, Tunnels modulate ligand flux in a heme nitric oxide/oxygen binding (H-NOX) domain, Proc. Natl. Acad. Sci. U. S. A. 108 (2011) E881-E889.
-
(2011)
Proc. Natl. Acad. Sci. U. S. A
, vol.108
-
-
Winter, M.B.1
Herzik, M.A.2
Kuriyan, J.3
Marletta, M.A.4
-
42
-
-
0030042115
-
On the functional significance of substrate accessibility in the photosynthetic water oxidation mechanism
-
T. Wydrzynski, W. Hillier, J. Messinger, On the functional significance of substrate accessibility in the photosynthetic water oxidation mechanism, Physiol. Plant. 96 (1996) 342-350.
-
(1996)
Physiol. Plant
, vol.96
, pp. 342-350
-
-
Wydrzynski, T.1
Hillier, W.2
Messinger, J.3
-
43
-
-
84884881413
-
Revealing molecular oxygen migration pathways in photosystem II using implicit ligand sampling and wavefront propagation
-
press)
-
T. Zaraiskaya, S. Vassiliev, D. Bruce, Revealing molecular oxygen migration pathways in photosystem II using implicit ligand sampling and wavefront propagation, J. Comput. Sci. 4 (2013), (in press).
-
(2013)
J. Comput. Sci
, vol.4
-
-
Zaraiskaya, T.1
Vassiliev, S.2
Bruce, D.3
-
44
-
-
0029937870
-
Hydrophilicity of cavities in proteins
-
DOI 10.1002/(SICI)1097-0134(199604)24:4 <433::AID-PROT3>3.0.CO;2-F
-
L. Zhang, J. Hermans, Hydrophilicity of cavities in proteins, Proteins Struct. Funct. Genet. 24 (1996) 433-438. (Pubitemid 26122057)
-
(1996)
Proteins: Structure, Function and Genetics
, vol.24
, Issue.4
, pp. 433-438
-
-
Zhang, L.1
Hermans, J.2
-
45
-
-
77951978029
-
H-NOX domains display different tunnel systems for ligand migration
-
Y.B. Zhang, M. Lu, Y.K. Cheng, Z.Q. Li, H-NOX domains display different tunnel systems for ligand migration, J. Mol. Graph. Model. 28 (2010) 814-819.
-
(2010)
J. Mol. Graph. Model
, vol.28
, pp. 814-819
-
-
Zhang, Y.B.1
Lu, M.2
Cheng, Y.K.3
Li, Z.Q.4
|