-
1
-
-
0029093864
-
AppA a novel gene encoding a transacting factor involved in the regulation of photosynthesis geneexpression in rhodobacter-sphaeroides-2.4.1
-
M. Gomelsky and S. Kaplan, AppA, a novel gene encoding a transacting factor involved in the regulation of photosynthesis geneexpression in rhodobacter-sphaeroides-2.4.1, J. Bacteriol. 177 (1995), pp. 4609-4618.
-
(1995)
J. Bacteriol.
, vol.177
, pp. 4609-4618
-
-
Gomelsky, M.1
Kaplan, S.2
-
2
-
-
0031026315
-
Molecular genetic analysis suggesting interactions between AppA and PpsR in regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1
-
M. Gomelsky and S. Kaplan, Molecular genetic analysis suggesting interactions between AppA and PpsR in regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1, J. Bacteriol. 179 (1997), pp. 128-134.
-
(1997)
J. Bacteriol.
, vol.179
, pp. 128-134
-
-
Gomelsky, M.1
Kaplan, S.2
-
3
-
-
0036371637
-
A single flavoprotein AppA, integrates both redox and light signals in Rhodobacter sphaeroides
-
S. Braatsch, M. Gomelsky, S. Kuphal, and G. Klug, A single flavoprotein, AppA, integrates both redox and light signals in Rhodobacter sphaeroides, Mol. Microbiol. 45 (2002), pp. 827-836.
-
(2002)
Mol. Microbiol.
, vol.45
, pp. 827-836
-
-
Braatsch, S.1
Gomelsky, M.2
Kuphal, S.3
Klug, G.4
-
4
-
-
0036804709
-
BLUF: A novel FAD-binding domain involved in sensory transduction in microorganisms
-
M. Gomelsky and G. Klug, BLUF: A novel FAD-binding domain involved in sensory transduction in microorganisms, Trends Biochem. Sci. 27 (2002), pp. 497-500.
-
(2002)
Trends Biochem. Sci.
, vol.27
, pp. 497-500
-
-
Gomelsky, M.1
Klug, G.2
-
5
-
-
36249024090
-
Flavin-based blue-light photosensors: A photobiophysics update
-
A. Losi, Flavin-based blue-light photosensors: A photobiophysics update, Photochem. Photobiol. 83 (2007), pp. 1283-1300.
-
(2007)
Photochem. Photobiol.
, vol.83
, pp. 1283-1300
-
-
Losi, A.1
-
6
-
-
0037186598
-
A blue-light-activated adenylyl cyclase mediates photoavoidance in Euglena gracilis
-
M. Iseki, S. Matsunaga, A. Murakami, K. Ohno, K. Shiga, K. Yoshida, M. Sugai, T. Takahashi, T. Hori, and M. Watanabe, A blue-light-activated adenylyl cyclase mediates photoavoidance in Euglena gracilis, Nature 415 (2002), pp. 1047-1051.
-
(2002)
Nature
, vol.415
, pp. 1047-1051
-
-
Iseki, M.1
Matsunaga, S.2
Murakami, A.3
Ohno, K.4
Shiga, K.5
Yoshida, K.6
Sugai, M.7
Takahashi, T.8
Hori, T.9
Watanabe, M.10
-
7
-
-
2442454713
-
Structural and functional analysis of a novel flavoprotein in cyanobacteria
-
K. Okajima, S. Yoshihara, X.X. Geng, M. Katayama, and M. Ikeuchi, Structural and functional analysis of a novel flavoprotein in cyanobacteria, Plant Cell Physiol. 44 (2003), p. S162.
-
(2003)
Plant Cell Physiol.
, vol.44
-
-
Okajima, K.1
Yoshihara, S.2
Geng, X.X.3
Katayama, M.4
Ikeuchi, M.5
-
8
-
-
2442559284
-
Light-induced structural changes in a putative blue-light receptor with a novel FAD binding fold sensor of blue-light using FAD (BLUF); Slr1694 of Synechocystis sp PCC6803
-
S. Masuda, K. Hasegawa, A. Ishii, and T. Ono, Light-induced structural changes in a putative blue-light receptor with a novel FAD binding fold sensor of blue-light using FAD (BLUF); Slr1694 of Synechocystis sp PCC6803, Biochemistry 43 (2004), pp. 5304-5313.
-
(2004)
Biochemistry
, vol.43
, pp. 5304-5313
-
-
Masuda, S.1
Hasegawa, K.2
Ishii, A.3
Ono, T.4
-
9
-
-
9744258714
-
Structural intermediate in the photocycle of a BLUF (sensor of blue light using FAD) protein Slr1694 in a cyanobacterium Synechocystis sp PCC6803
-
K. Hasegawa, S. Masuda, and T. Ono, Structural intermediate in the photocycle of a BLUF (sensor of blue light using FAD) protein Slr1694 in a cyanobacterium Synechocystis sp PCC6803, Biochemistry 43 (2004), pp. 14979-14986.
-
(2004)
Biochemistry
, vol.43
, pp. 14979-14986
-
-
Hasegawa, K.1
Masuda, S.2
Ono, T.3
-
10
-
-
7544245885
-
Biochemical characterization of the major adenylyl cyclase
-
S. Masuda and T. Ono, Biochemical characterization of the major adenylyl cyclase, Cya1, in the cyanobacterium Synechocystis sp PCC 6803, FEBS Lett. 577 (2004), pp. 255-258.
-
(2004)
Cya1, in the Cyanobacterium Synechocystis Sp PCC 6803, FEBS Lett.
, vol.577
, pp. 255-258
-
-
Masuda, S.1
Ono, T.2
-
11
-
-
0032567446
-
AppA a redox regulator of photosystem formation in Rhodobacter sphaeroides 2.4.1, is a flavoprotein-Identification of a novel FAD binding domain
-
M. Gomelsky and S. Kaplan, AppA, a redox regulator of photosystem formation in Rhodobacter sphaeroides 2.4.1, is a flavoprotein-Identification of a novel FAD binding domain, J. Biol. Chem. 273 (1998), pp. 35319-35325.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 35319-35325
-
-
Gomelsky, M.1
Kaplan, S.2
-
12
-
-
65249090230
-
Structure and insight into blue lightinduced changes in the BlrP1 BLUF domain
-
Q. Wu and K.H. Gardner, Structure and insight into blue lightinduced changes in the BlrP1 BLUF domain, Biochemistry 48 (2009), pp. 2620-2629.
-
(2009)
Biochemistry
, vol.48
, pp. 2620-2629
-
-
Wu, Q.1
Gardner, K.H.2
-
13
-
-
0037031561
-
AppA is a blue light photoreceptor that antirepresses photosynthesis gene expression in Rhodobacter sphaeroides
-
S. Masuda and C.E. Bauer, AppA is a blue light photoreceptor that antirepresses photosynthesis gene expression in Rhodobacter sphaeroides, Cell 110 (2002), pp. 613-623.
-
(2002)
Cell
, vol.110
, pp. 613-623
-
-
Masuda, S.1
Bauer, C.E.2
-
14
-
-
20144368776
-
Structure of a novel photoreceptor the BLUF domain of AppA from Rhodobacter sphaeroides
-
S. Anderson, V. Dragnea, S. Masuda, J. Ybe, K. Moffat, and C. Bauer, Structure of a novel photoreceptor, the BLUF domain of AppA from Rhodobacter sphaeroides, Biochemistry 44 (2005), pp. 7998-8005.
-
(2005)
Biochemistry
, vol.44
, pp. 7998-8005
-
-
Anderson, S.1
Dragnea, V.2
Masuda, S.3
Ybe, J.4
Moffat, K.5
Bauer, C.6
-
15
-
-
30444432981
-
The solution structure of the AppA BLUF domain: Insight into the mechanism of lightinduced signaling
-
J.S. Grinstead, S.T.D. Hsu, W. Laan, A.M.J.J. Bonvin, K.J. Hellingwerf, R. Boelens, and R. Kaptein, The solution structure of the AppA BLUF domain: Insight into the mechanism of lightinduced signaling, ChemBioChem 7 (2006), pp. 187-193.
-
(2006)
ChemBioChem
, vol.7
, pp. 187-193
-
-
Grinstead, J.S.1
Hsu, S.T.D.2
Laan, W.3
Bonvin, A.M.J.J.4
Hellingwerf, K.J.5
Boelens, R.6
Kaptein, R.7
-
16
-
-
33748300578
-
Crystal structures of the AppA BLUF domainphotoreceptor provide insights into blue light-mediated signal transduction
-
A. Jung, J. Reinstein, T. Domratcheva, R.L. Shoeman, and I. Schlichting, Crystal structures of the AppA BLUF domainphotoreceptor provide insights into blue light-mediated signal transduction, J. Mol. Biol. 362 (2006), pp. 717-732.
-
(2006)
J. Mol. Biol.
, vol.362
, pp. 717-732
-
-
Jung, A.1
Reinstein, J.2
Domratcheva, T.3
Shoeman, R.L.4
Schlichting, I.5
-
17
-
-
0141844456
-
Initial characterization of the primary photochemistry of AppA a blue-light-using flavin adenine dinucleotide-domain containing transcriptional antirepressor protein from Rhodobacter sphaeroides: A key role for reversible intramolecular proton transfer from the flavin adenine dinucleotide chromophore to a conserved tyrosine
-
W. Laan, M.A. Horstvan der, I.H. Stokkumvan, and K.J. Hellingwerf, Initial characterization of the primary photochemistry of AppA, a blue-light-using flavin adenine dinucleotide-domain containing transcriptional antirepressor protein from Rhodobacter sphaeroides: A key role for reversible intramolecular proton transfer from the flavin adenine dinucleotide chromophore to a conserved tyrosine? Photochem. Photobiol. 78 (2003), pp. 290-297.
-
(2003)
Photochem. Photobiol.
, vol.78
, pp. 290-297
-
-
Laan, W.1
Horstvan Der, M.A.2
Stokkumvan, I.H.3
Hellingwerf, K.J.4
-
18
-
-
0037984816
-
Spectroscopic and mutational analysis of the blue-light photoreceptor AppA: A novel photocycle involving flavin stacking with an aromatic amino acid
-
B.J. Kraft, S. Masuda, J. Kikuchi, V. Dragnea, G. Tollin, J.M. Zaleski, and C.E. Bauer, Spectroscopic and mutational analysis of the blue-light photoreceptor AppA: A novel photocycle involving flavin stacking with an aromatic amino acid, Biochemistry 42 (2003), pp. 6726-6734.
-
(2003)
Biochemistry
, vol.42
, pp. 6726-6734
-
-
Kraft, B.J.1
Masuda, S.2
Kikuchi, J.3
Dragnea, V.4
Tollin, G.5
Zaleski, J.M.6
Bauer, C.E.7
-
19
-
-
22744445702
-
Lightinduced structural changes in the active site of the BLUF domain in AppA by Raman spectroscopy
-
M. Unno, R. Sano, S. Masuda, T.A. Ono, and S. Yamauchi, Lightinduced structural changes in the active site of the BLUF domain in AppA by Raman spectroscopy, J. Phys. Chem. B 109 (2005), pp. 12620-12626.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 12620-12626
-
-
Unno, M.1
Sano, R.2
Masuda, S.3
Ono, T.A.4
Yamauchi, S.5
-
20
-
-
14844365385
-
Photocycle of the flavin-binding photoreceptor AppA
-
M. Gauden, S. Yeremenko, W. Laan, I.H.M. Stokkumvan, J.A. Ihalainen, R. Grondellevan, K.J. Hellingwerf, and J.T.M. Kennis, Photocycle of the flavin-binding photoreceptor AppA, a bacterial transcriptional antirepressor of photosynthesis genes, Biochemistry 44 (2005), pp. 3653-3662.
-
(2005)
A Bacterial Transcriptional Antirepressor of Photosynthesis Genes, Biochemistry
, vol.44
, pp. 3653-3662
-
-
Gauden, M.1
Yeremenko, S.2
Laan, W.3
Stokkumvan, I.H.M.4
Ihalainen, J.A.5
Grondellevan, R.6
Hellingwerf, K.J.7
Kennis, J.T.M.8
-
21
-
-
23044447414
-
Absorption and fluorescence spectroscopic characterization of BLUF domain of AppA from Rhodobacter sphaeroides
-
P. Zirak, A. Penzkofer, T. Schiereis, P. Hegemann, A. Jung, and I. Schlichting, Absorption and fluorescence spectroscopic characterization of BLUF domain of AppA from Rhodobacter sphaeroides, Chem. Phys. 315 (2005), pp. 142-154.
-
(2005)
Chem. Phys.
, vol.315
, pp. 142-154
-
-
Zirak, P.1
Penzkofer, A.2
Schiereis, T.3
Hegemann, P.4
Jung, A.5
Schlichting, I.6
-
22
-
-
30344475204
-
Tryptophan at position 104 is involved in transforming light signal into changes of beta-sheet structure for the signaling state in the BLUF domain of AppA
-
S. Masuda, K. Hasegawa, and T.A. Ono, Tryptophan at position 104 is involved in transforming light signal into changes of beta-sheet structure for the signaling state in the BLUF domain of AppA, Plant Cell Physiol. 46 (2005), pp. 1894-1901.
-
(2005)
Plant Cell Physiol.
, vol.46
, pp. 1894-1901
-
-
Masuda, S.1
Hasegawa, K.2
Ono, T.A.3
-
23
-
-
13444291923
-
Light-induced structural changes of apoprotein and chromophore in the sensor of blue light using FAD (BLUF) domain of AppA for a signaling state
-
S. Masuda, K. Hasegawa, and T. Ono, Light-induced structural changes of apoprotein and chromophore in the sensor of blue light using FAD (BLUF) domain of AppA for a signaling state, Biochemistry 44 (2005), pp. 1215-1224.
-
(2005)
Biochemistry
, vol.44
, pp. 1215-1224
-
-
Masuda, S.1
Hasegawa, K.2
Ono, T.3
-
24
-
-
28944448536
-
Time-resolved spectroscopic studies of the AppA blue-light receptor BLUF domain from Rhodobacter sphaeroides
-
V. Dragnea, M. Waegele, S. Balascuta, C. Bauer, and B. Dragnea, Time-resolved spectroscopic studies of the AppA blue-light receptor BLUF domain from Rhodobacter sphaeroides, Biochemistry 44 (2005), pp. 15978-15985.
-
(2005)
Biochemistry
, vol.44
, pp. 15978-15985
-
-
Dragnea, V.1
Waegele, M.2
Balascuta, S.3
Bauer, C.4
Dragnea, B.5
-
25
-
-
30144431572
-
On the mechanism of activation of the BLUF domain of AppA
-
W. Laan, M. Gauden, S. Yeremenko, R. Grondellevan, J.T.M. Kennis, and K.J. Hellingwerf, On the mechanism of activation of the BLUF domain of AppA, Biochemistry 45 (2006), pp. 51-60.
-
(2006)
Biochemistry
, vol.45
, pp. 51-60
-
-
Laan, W.1
Gauden, M.2
Yeremenko, S.3
Grondellevan, R.4
Kennis, J.T.M.5
Hellingwerf, K.J.6
-
26
-
-
33646549579
-
Orientation of a key glutamine residue in the BLUF domain from AppA revealed by mutagenesis spectroscopy, and quantum chemical calculations
-
M. Unno, S. Masuda, T.A. Ono, and S. Yamauchi, Orientation of a key glutamine residue in the BLUF domain from AppA revealed by mutagenesis, spectroscopy, and quantum chemical calculations, J. Am. Chem. Soc. 128 (2006), pp. 5638-5639.
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 5638-5639
-
-
Unno, M.1
Masuda, S.2
Ono, T.A.3
Yamauchi, S.4
-
27
-
-
33845188381
-
Light-induced flipping of a conserved glutamine side chain and its orientation in the AppA BLUF domain
-
J.S. Grinstead, M. Avila-Perez, K.J. Hellingwerf, R. Boelens, and R. Kaptein, Light-induced flipping of a conserved glutamine side chain and its orientation in the AppA BLUF domain, J. Am. Chem. Soc. 128 (2006), pp. 15066-15067.
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 15066-15067
-
-
Grinstead, J.S.1
Avila-Perez, M.2
Hellingwerf, K.J.3
Boelens, R.4
Kaptein, R.5
-
28
-
-
34250890102
-
On the role of aromatic side chains in the photoactivation of BLUF domains
-
M. Gauden, J.S. Grinstead, W. Laan, H.M. Stokkumvan, M. Avila-Perez, K.C. Toh, R. Boelens, R. Kaptein, R. Grondellevan, K.J. Hellingwerf, and J.T.M. Kennis, On the role of aromatic side chains in the photoactivation of BLUF domains, Biochemistry 46 (2007), pp. 7405-7415.
-
(2007)
Biochemistry
, vol.46
, pp. 7405-7415
-
-
Gauden, M.1
Grinstead, J.S.2
Laan, W.3
Stokkumvan, H.M.4
Avila-Perez, M.5
Toh, K.C.6
Boelens, R.7
Kaptein, R.8
Grondellevan, R.9
Hellingwerf, K.J.10
Kennis, J.T.M.11
-
29
-
-
34248168172
-
Photo dynamics of BLUF domain mutant H44R of AppA from Rhodobacter sphaeroides
-
P. Zirak, A. Penzkofer, P. Hegemann, and T. Mathes, Photo dynamics of BLUF domain mutant H44R of AppA from Rhodobacter sphaeroides, Chem. Phys. 335 (2007), pp. 15-27.
-
(2007)
Chem. Phys.
, vol.335
, pp. 15-27
-
-
Zirak, P.1
Penzkofer, A.2
Hegemann, P.3
Mathes, T.4
-
30
-
-
34247263900
-
The critical role of a hydrogen bond between Gln63 and Trp104 in the blue-light sensing BLUF domain that controls AppA activity
-
S. Masuda, Y. Tomida, H. Ohta, and K.I. Takamiya, The critical role of a hydrogen bond between Gln63 and Trp104 in the blue-light sensing BLUF domain that controls AppA activity, J. Mol. Biol. 368 (2007), pp. 1223-1230.
-
(2007)
J. Mol. Biol.
, vol.368
, pp. 1223-1230
-
-
Masuda, S.1
Tomida, Y.2
Ohta, H.3
Takamiya, K.I.4
-
31
-
-
37849021588
-
Ultrafast structural dynamics in BLUF domains: Transient infrared spectroscopy of AppA and its mutants
-
A.L. Stelling, K.L. Ronayne, J. Nappa, P.J. Tonge, and S.R. Meech, Ultrafast structural dynamics in BLUF domains: Transient infrared spectroscopy of AppA and its mutants, J. Am. Chem. Soc. 129 (2007), pp. 15556-15564.
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 15556-15564
-
-
Stelling, A.L.1
Ronayne, K.L.2
Nappa, J.3
Tonge, P.J.4
Meech, S.R.5
-
32
-
-
46749090030
-
On the signaling mechanism and the absence of photoreversibility in the AppA BLUF domain
-
K.C. Toh, I.H.M. Stokkumvan, J. Hendriks, M.T.A. Alexandre, J.C. Arents, M.A. Perez, R. Grondellevan, K.J. Hellingwerf, and J.T.M. Kennis, On the signaling mechanism and the absence of photoreversibility in the AppA BLUF domain, Biophys. J. 95 (2008), pp. 312-321.
-
(2008)
Biophys. J.
, vol.95
, pp. 312-321
-
-
Toh, K.C.1
Stokkumvan, I.H.M.2
Hendriks, J.3
Alexandre, M.T.A.4
Arents, J.C.5
Perez, M.A.6
Grondellevan, R.7
Hellingwerf, K.J.8
Kennis, J.T.M.9
-
33
-
-
70350703393
-
Spectroscopic studies of the AppA BLUF domain from Rhodobacter sphaeroides: Addressing movement of tryptophan 104 in the signaling state
-
V. Dragnea, A.I. Arunkumar, H. Yuan, D.P. Giedroc, and C.E. Bauer, Spectroscopic studies of the AppA BLUF domain from Rhodobacter sphaeroides: Addressing movement of tryptophan 104 in the signaling state, Biochemistry 48 (2009), pp. 9969-9979.
-
(2009)
Biochemistry
, vol.48
, pp. 9969-9979
-
-
Dragnea, V.1
Arunkumar, A.I.2
Yuan, H.3
Giedroc, D.P.4
Bauer, C.E.5
-
34
-
-
77952259197
-
Structural refinement of a key tryptophan residue in the BLUF photoreceptor AppA by ultraviolet resonance Raman spectroscopy
-
M. Unno, S. Kikuchi, and S. Masuda, Structural refinement of a key tryptophan residue in the BLUF photoreceptor AppA by ultraviolet resonance Raman spectroscopy, Biophys. J. 98 (2010), pp. 1949-1956.
-
(2010)
Biophys. J.
, vol.98
, pp. 1949-1956
-
-
Unno, M.1
Kikuchi, S.2
Masuda, S.3
-
35
-
-
79955917653
-
Strong donation of the hydrogen bond of tyrosine during photoactivation of the BLUF domain
-
T. Iwata, A. Watanabe, M. Iseki, M. Watanabe, and H. Kandori, Strong donation of the hydrogen bond of tyrosine during photoactivation of the BLUF domain, J. Phys. Chem. Lett. 2 (2011), pp. 1015-1019.
-
(2011)
J. Phys. Chem. Lett.
, vol.2
, pp. 1015-1019
-
-
Iwata, T.1
Watanabe, A.2
Iseki, M.3
Watanabe, M.4
Kandori, H.5
-
36
-
-
78650345258
-
A Q63E Rhodobacter sphaeroides AppA BLUF domain mutant is locked in a pseudo-light-excited signaling state
-
V. Dragnea, A.I. Arunkumar, C.W. Lee, D.P. Giedroc, and C.E. Bauer, A Q63E Rhodobacter sphaeroides AppA BLUF domain mutant is locked in a pseudo-light-excited signaling state, Biochemistry 49 (2010), pp. 10682-10690.
-
(2010)
Biochemistry
, vol.49
, pp. 10682-10690
-
-
Dragnea, V.1
Arunkumar, A.I.2
Lee, C.W.3
Giedroc, D.P.4
Bauer, C.E.5
-
37
-
-
58149280493
-
Hydrogen bond switching among Flavin and amino acid side chains in the BLUF photoreceptor observed by ultrafast infrared spectroscopy
-
C. Bonetti, T. Mathes, I.H.M. Stokkumvan, K.M. Mullen, M.L. Groot, R. Grondellevan, P. Hegemann, and J.T.M. Kennis, Hydrogen bond switching among Flavin and amino acid side chains in the BLUF photoreceptor observed by ultrafast infrared spectroscopy, Biophys. J. 95 (2008), pp. 4790-4802.
-
(2008)
Biophys. J.
, vol.95
, pp. 4790-4802
-
-
Bonetti, C.1
Mathes, T.2
Stokkumvan, I.H.M.3
Mullen, K.M.4
Groot, M.L.5
Grondellevan, R.6
Hegemann, P.7
Kennis, J.T.M.8
-
38
-
-
24644477536
-
Structure of a bacterial BLUF photoreceptor: Insights into blue light-mediated signal transduction
-
A. Jung, T. Domratcheva, M. Tarutina, Q. Wu, W.H. Ko, R.L. Shoeman, M. Gomelsky, K.H. Gardner, and L. Schlichting, Structure of a bacterial BLUF photoreceptor: Insights into blue light-mediated signal transduction, Proc. Natl. Acad. Sci. U.S.A. 102 (2005), pp. 12350-12355.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 12350-12355
-
-
Jung, A.1
Domratcheva, T.2
Tarutina, M.3
Wu, Q.4
Ko, W.H.5
Shoeman, R.L.6
Gomelsky, M.7
Gardner, K.H.8
Schlichting, L.9
-
39
-
-
33750317872
-
Crystal structures of the Synechocystis photoreceptor Slr1694 reveal distinct structural states related to signaling
-
H. Yuan, S. Anderson, S. Masuda, V. Dragnea, K. Moffat, and C. Bauer, Crystal structures of the Synechocystis photoreceptor Slr1694 reveal distinct structural states related to signaling, Biochemistry 45 (2006), pp. 12687-12694.
-
(2006)
Biochemistry
, vol.45
, pp. 12687-12694
-
-
Yuan, H.1
Anderson, S.2
Masuda, S.3
Dragnea, V.4
Moffat, K.5
Bauer, C.6
-
40
-
-
52149124133
-
Structures of the chromophore binding sites in BLUF domains as studied by molecular dynamics and quantum chemical calculations
-
K. Obanayama, H. Kobayashi, K. Fukushima, and M. Sakurai, Structures of the chromophore binding sites in BLUF domains as studied by molecular dynamics and quantum chemical calculations, Photochem. Photobiol. 84 (2008), pp. 1003-1010.
-
(2008)
Photochem. Photobiol.
, vol.84
, pp. 1003-1010
-
-
Obanayama, K.1
Kobayashi, H.2
Fukushima, K.3
Sakurai, M.4
-
41
-
-
43849105414
-
Molecular models predict light-induced glutamine tautomerization in BLUF photoreceptors
-
T. Domratcheva, B.L. Grigorenko, I. Schlichting, and A.V. Nemukhin, Molecular models predict light-induced glutamine tautomerization in BLUF photoreceptors, Biophys. J. 94 (2008), pp. 3872-3879.
-
(2008)
Biophys. J.
, vol.94
, pp. 3872-3879
-
-
Domratcheva, T.1
Grigorenko, B.L.2
Schlichting, I.3
Nemukhin, A.V.4
-
42
-
-
77955564849
-
Quantum chemistry calculations provide support to the mechanism of the light-induced structural changes in the flavin-binding photoreceptor proteins
-
M.G. Khrenova, A.V. Nemukhin, B.L. Grigorenko, A.I. Krylov, and T.M. Domratcheva, Quantum chemistry calculations provide support to the mechanism of the light-induced structural changes in the flavin-binding photoreceptor proteins, J. Chem. Theory Comput. 6 (2010), pp. 2293-2302.
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 2293-2302
-
-
Khrenova, M.G.1
Nemukhin, A.V.2
Grigorenko, B.L.3
Krylov, A.I.4
Domratcheva, T.M.5
-
43
-
-
79955438204
-
Computational characterization of reaction intermediates in the photocycle of the sensory domain of the AppA blue light photoreceptor
-
M.G. Khrenova, T. Domratcheva, I. Schlichting, B.L. Grigorenko, and A.V. Nemukhin, Computational characterization of reaction intermediates in the photocycle of the sensory domain of the AppA blue light photoreceptor, Photochem. Photobiol. 87 (2011), pp. 564-573.
-
(2011)
Photochem. Photobiol.
, vol.87
, pp. 564-573
-
-
Khrenova, M.G.1
Domratcheva, T.2
Schlichting, I.3
Grigorenko, B.L.4
Nemukhin, A.V.5
-
44
-
-
51949088672
-
A conclusive mechanism of the photoinduced reaction cascade in blue light using flavin photoreceptors
-
K. Sadeghian, M. Bocola, and M. Schutz, A conclusive mechanism of the photoinduced reaction cascade in blue light using flavin photoreceptors, J. Am. Chem. Soc. 130 (2008), pp. 12501-12513.
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 12501-12513
-
-
Sadeghian, K.1
Bocola, M.2
Schutz, M.3
-
45
-
-
80053116136
-
DFT/MM description of Flavin IR spectra in BLUF domains
-
B. Rieff, S. Bauer, G. Mathias, and P. Tavan, DFT/MM description of Flavin IR spectra in BLUF domains, J. Phys. Chem. B 115 (2011), pp. 11239-11253.
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 11239-11253
-
-
Rieff, B.1
Bauer, S.2
Mathias, G.3
Tavan, P.4
-
46
-
-
84855667383
-
On the effect of a variation of the force field spatial boundary condition and size of the QM region in QM/MM MD simulations
-
K. Meier, W. Thiel, and W.F. van Gunsteren, On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations, J. Comput. Chem. 33 (2012), pp. 363-378.
-
(2012)
J. Comput. Chem.
, vol.33
, pp. 363-378
-
-
Meier, K.1
Thiel, W.2
Van Gunsteren, W.F.3
-
47
-
-
0028710015
-
Local elevation-A method for improving the searching properties of moleculardynamics simulation
-
T. Huber, A.E. Torda, and W.F. van Gunsteren, Local elevation-A method for improving the searching properties of moleculardynamics simulation, J. Comput. Aided Mol. Des. 8 (1994), pp. 695-708.
-
(1994)
J. Comput. Aided Mol. Des.
, vol.8
, pp. 695-708
-
-
Huber, T.1
Torda, A.E.2
Van Gunsteren, W.F.3
-
48
-
-
0030589439
-
A method to calculate the probability distribution for systems with large energy barriers
-
O. Engkvist and G. Karlstrom, A method to calculate the probability distribution for systems with large energy barriers, Chem. Phys. 213 (1996), pp. 63-76.
-
(1996)
Chem. Phys.
, vol.213
, pp. 63-76
-
-
Engkvist, O.1
Karlstrom, G.2
-
50
-
-
72449125773
-
Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water
-
H.S. Hansen and P.H. Hunenberger, Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water, J. Comput. Chem. 31 (2010), pp. 1-23.
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 1-23
-
-
Hansen, H.S.1
Hunenberger, P.H.2
-
51
-
-
0342929614
-
Non-physical sampling distributions in Monte-Carlo free-energy estimation-Umbrella sampling
-
G.M. Torrie and J.P. Valleau, Non-physical sampling distributions in Monte-Carlo free-energy estimation-Umbrella sampling, J. Comput. Phys. 23 (1977), pp. 187-199.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
52
-
-
0000249851
-
Avoiding singularities and numerical instabilities in free-energy calculations based on molecular simulations
-
T.C. Beutler, A.E. Mark, R.C. Schaikvan, P.R. Gerber, and W.F. van Gunsteren, Avoiding singularities and numerical instabilities in free-energy calculations based on molecular simulations, Chem. Phys. Lett. 222 (1994), pp. 529-539.
-
(1994)
Chem. Phys. Lett.
, vol.222
, pp. 529-539
-
-
Beutler, T.C.1
Mark, A.E.2
Schaikvan, R.C.3
Gerber, P.R.4
Van Gunsteren, W.F.5
-
54
-
-
2342607286
-
Intermolecular forces
-
H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans, Intermolecular forces, Reidel, Dordrecht, 1981.
-
(1981)
Reidel, Dordrecht
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Hermans, J.4
-
55
-
-
84866264966
-
Architecture implementation and parallelization of the GROMOS software for biomolecular simulation
-
N. Schmid, C.D. Christ, M. Christen, A.P. Eichenberger, and W.F. van Gunsteren, Architecture, implementation and parallelization of the GROMOS software for biomolecular simulation, Comp. Phys. Comm. 33 (2011), pp. 340-353.
-
(2011)
Comp. Phys. Comm.
, vol.33
, pp. 340-353
-
-
Schmid, N.1
Christ, C.D.2
Christen, M.3
Eichenberger, A.P.4
Van Gunsteren, W.F.5
-
56
-
-
17844363454
-
An improved nucleic acid parameter set for the GROMOS force field
-
T.A. Soares, P.H. Hunenberger, M.A. Kastenholz, V. Krautler, T. Lenz, R.D. Lins, C. Oostenbrink, and W.F. van Gunsteren, An improved nucleic acid parameter set for the GROMOS force field, J. Comput. Chem. 26 (2005), pp. 725-737.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 725-737
-
-
Soares, T.A.1
Hunenberger, P.H.2
Kastenholz, M.A.3
Krautler, V.4
Lenz, T.5
Lins, R.D.6
Oostenbrink, C.7
Van Gunsteren, W.F.8
-
57
-
-
4544369164
-
A generalized reaction field method for molecular-dynamics simulations
-
I.G. Tironi, R. Sperb, P.E. Smith, and W.F. van Gunsteren, A generalized reaction field method for molecular-dynamics simulations, J. Chem. Phys. 102 (1995), pp. 5451-5459.
-
(1995)
J. Chem. Phys.
, vol.102
, pp. 5451-5459
-
-
Tironi, I.G.1
Sperb, R.2
Smith, P.E.3
Van Gunsteren, W.F.4
-
58
-
-
0001158363
-
Monte-Carlo studies of dielectric properties of water-like models
-
J.A. Barker and R.O. Watts, Monte-Carlo studies of dielectric properties of water-like models, Mol. Phys. 26 (1973), pp. 789-792.
-
(1973)
Mol. Phys.
, vol.26
, pp. 789-792
-
-
Barker, J.A.1
Watts, R.O.2
-
59
-
-
0035878765
-
Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations
-
T.N. Heinz, W.F. van Gunsteren, and P.H. Hunenberger, Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations, J. Chem. Phys. 115 (2001), pp. 1125-1136.
-
(2001)
J. Chem. Phys.
, vol.115
, pp. 1125-1136
-
-
Heinz, T.N.1
Van Gunsteren, W.F.2
Hunenberger, P.H.3
-
60
-
-
80054003196
-
The GROMOS software for the analysis of biomolecular simulation trajectories
-
A.P. Eichenberger, J.R. Allison, J. Dolenc, D.P. Geerke, B.A.C. Horta, K. Meier, C. Oostenbrink, N. Schmid, D. Steiner, D. Wang, and W.F. van Gunsteren, The GROMOS software for the analysis of biomolecular simulation trajectories, J. Chem. Theory Comput. 7 (2011), pp. 3379-3390.
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 3379-3390
-
-
Eichenberger, A.P.1
Allison, J.R.2
Dolenc, J.3
Geerke, D.P.4
Horta, B.A.C.5
Meier, K.6
Oostenbrink, C.7
Schmid, N.8
Steiner, D.9
Wang, D.10
Van Gunsteren, W.F.11
-
62
-
-
33646940952
-
Numericalintegration of Cartesian equations of motion of a system with constraints-Molecular-dynamics of N-alkanes
-
J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen, Numericalintegration of Cartesian equations of motion of a system with constraints-Molecular-dynamics of N-alkanes, J. Comput. Phys. 23 (1977), pp. 327-341.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
63
-
-
33750587438
-
Molecular-dynamics with coupling to an external bath
-
H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. Dinola, and J.R. Haak, Molecular-dynamics with coupling to an external bath, J. Chem. Phys. 81 (1984), pp. 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.R.5
-
64
-
-
0029878720
-
VMD: Visual molecular dynamics
-
W. Humphrey, A. Dalke, and K. Schulten, VMD: Visual molecular dynamics, J. Mol. Graph. 14 (1996), p. 33.
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 33
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
65
-
-
77955659423
-
Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling
-
L. Peric-Hassler, H.S. Hansen, R. Baron, and P.H. Hunenberger, Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling, Carbohydr. Res. 345 (2010), pp. 1781-1801.
-
(2010)
Carbohydr. Res.
, vol.345
, pp. 1781-1801
-
-
Peric-Hassler, L.1
Hansen, H.S.2
Baron, R.3
Hunenberger, P.H.4
-
66
-
-
77954388093
-
In vivo effects on photosynthesis gene expression of base pair exchanges in the gene encoding the light-responsive BLUF domain of AppA in Rhodobacter Sphaeroides
-
S. Metz, J. Hendriks, A. Jager, K. Hellingwerf, and G. Klug, In vivo effects on photosynthesis gene expression of base pair exchanges in the gene encoding the light-responsive BLUF domain of AppA in Rhodobacter Sphaeroides, Photochem. Photobiol. 86 (2010), pp. 882-889.
-
(2010)
Photochem. Photobiol.
, vol.86
, pp. 882-889
-
-
Metz, S.1
Hendriks, J.2
Jager, A.3
Hellingwerf, K.4
Klug, G.5
-
67
-
-
80054992434
-
Photoexcitation of the blue light using FAD photoreceptor AppA results in ultrafast changes to the protein matrix
-
A. Lukacs, A. Haigney, R. Brust, R.K. Zhao, A.L. Stelling, I.P. Clark, M. Towrie, G.M. Greetham, S.R. Meech, and P.J. Tonge, Photoexcitation of the blue light using FAD photoreceptor AppA results in ultrafast changes to the protein matrix, J. Am. Chem. Soc. 133 (2011), pp. 16893-16900.
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 16893-16900
-
-
Lukacs, A.1
Haigney, A.2
Brust, R.3
Zhao, R.K.4
Stelling, A.L.5
Clark, I.P.6
Towrie, M.7
Greetham, G.M.8
Meech, S.R.9
Tonge, P.J.10
-
68
-
-
58749098215
-
Serine in BLUF domains displays spectral importance in computational models
-
J. Gotze and P. Saalfrank, Serine in BLUF domains displays spectral importance in computational models, J. Photochem. Photobiol. B Biol. 94 (2009), pp. 87-95.
-
(2009)
J. Photochem. Photobiol. B Biol.
, vol.94
, pp. 87-95
-
-
Gotze, J.1
Saalfrank, P.2
-
69
-
-
70349163360
-
Analysis of photoinduced electron transfer in AppA
-
N. Nunthaboot, F. Tanaka, and S. Kokpol, Analysis of photoinduced electron transfer in AppA, J. Photochem. Photobiol. A-Chem. 207 (2009), pp. 274-281.
-
(2009)
J. Photochem. Photobiol. A-Chem.
, vol.207
, pp. 274-281
-
-
Nunthaboot, N.1
Tanaka, F.2
Kokpol, S.3
-
70
-
-
72249107764
-
Simultaneous analysis of photoinduced electron transfer in wild type and mutated AppAs
-
N. Nunthaboot, F. Tanaka, and S. Kokpol, Simultaneous analysis of photoinduced electron transfer in wild type and mutated AppAs, J. Photochem. Photobiol. A Chem. 209 (2010), pp. 79-87.
-
(2010)
J. Photochem. Photobiol. A Chem.
, vol.209
, pp. 79-87
-
-
Nunthaboot, N.1
Tanaka, F.2
Kokpol, S.3
-
71
-
-
77955104039
-
A QM/MM study on the fast photocycle of blue light using flavin photoreceptors in their light-adapted/active form
-
K. Sadeghian, M. Bocola, and M. Schutz, A QM/MM study on the fast photocycle of blue light using flavin photoreceptors in their light-adapted/active form, Phys. Chem. Chem. Phys. 12 (2010), pp. 8840-8846.
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 8840-8846
-
-
Sadeghian, K.1
Bocola, M.2
Schutz, M.3
-
72
-
-
79955480100
-
Photoreaction in BLUF receptors: Proton-coupled electron transfer in the flavin-Gln-Tyr system
-
A. Udvarhelyi and T. Domratcheva, Photoreaction in BLUF receptors: Proton-coupled electron transfer in the flavin-Gln-Tyr system, Photochem. Photobiol. 87 (2011), pp. 554-563.
-
(2011)
Photochem. Photobiol.
, vol.87
, pp. 554-563
-
-
Udvarhelyi, A.1
Domratcheva, T.2
-
73
-
-
0020997912
-
Dictionary of protein secondary structure-Pattern-recognition of hydrogen-bonded and geometrical features
-
W. Kabsch and C. Sander, Dictionary of protein secondary structure-Pattern-recognition of hydrogen-bonded and geometrical features, Biopolymers 22 (1983), pp. 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
|