-
1
-
-
9144257886
-
The Pfam protein families database
-
Bateman A, et al. (2004) The Pfam protein families database. Nucleic Acids Res 32: D138-D141.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Bateman, A.1
-
2
-
-
0032568655
-
SMART, a simple modular architecture research tool: Identification of signaling domains
-
Schultz J, Milpetz F, Bork P, Ponting CP (1998) SMART, a simple modular architecture research tool: Identification of signaling domains. Proc Natl Acad Sci USA 95:5857-5864.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 5857-5864
-
-
Schultz, J.1
Milpetz, F.2
Bork, P.3
Ponting, C.P.4
-
3
-
-
0035957514
-
Evolutionary conservation of the folding nucleus
-
Mirny L, Shakhnovich E (2001) Evolutionary conservation of the folding nucleus. J Mol Biol 308:123-129.
-
(2001)
J Mol Biol
, vol.308
, pp. 123-129
-
-
Mirny, L.1
Shakhnovich, E.2
-
4
-
-
0036295887
-
Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation
-
Larson SM, Ruczinski I, Davidson AR, Baker D, Plaxco KW (2002) Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation. J Mol Biol 316:225-233.
-
(2002)
J Mol Biol
, vol.316
, pp. 225-233
-
-
Larson, S.M.1
Ruczinski, I.2
Davidson, A.R.3
Baker, D.4
Plaxco, K.W.5
-
5
-
-
0035815113
-
Evolution of function in protein superfamilies, from a structural perspective
-
Todd AE, Orengo CA, Thornton JM (2001) Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 307:1113-1143.
-
(2001)
J Mol Biol
, vol.307
, pp. 1113-1143
-
-
Todd, A.E.1
Orengo, C.A.2
Thornton, J.M.3
-
6
-
-
0034923923
-
Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies
-
Gerlt JA, Babbitt PC (2001) Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu Rev Biochem 70:209-246.
-
(2001)
Annu Rev Biochem
, vol.70
, pp. 209-246
-
-
Gerlt, J.A.1
Babbitt, P.C.2
-
9
-
-
0029962946
-
Amino acid sequence determinants of â-lactamase structure and activity
-
Huang W, Petrosino J, Hirsch M, Shenkin PS, Palzkill T (1996) Amino acid sequence determinants of â-lactamase structure and activity. J Mol Biol 258:688-703.
-
(1996)
J Mol Biol
, vol.258
, pp. 688-703
-
-
Huang, W.1
Petrosino, J.2
Hirsch, M.3
Shenkin, P.S.4
Palzkill, T.5
-
11
-
-
27944474033
-
Selectionism and neutralism in molecular evolution
-
Nei M (2005) Selectionism and neutralism in molecular evolution. Mol Biol Evol 22:2318-2342.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 2318-2342
-
-
Nei, M.1
-
12
-
-
0032990441
-
PAS domains: Internal sensors of oxygen, redox potential, and light
-
Taylor BL, Zhulin IB (1999) PAS domains: Internal sensors of oxygen, redox potential, and light. Microbiol Mol Biol Rev 63:479-506.
-
(1999)
Microbiol Mol Biol Rev
, vol.63
, pp. 479-506
-
-
Taylor, B.L.1
Zhulin, I.B.2
-
13
-
-
1642274684
-
The PAS fold. A redefinition of the PAS domain based upon structural prediction
-
Hefti MH, Françoijs KJ, de Vries SC, Dixon R, Vervoort J (2004) The PAS fold. A redefinition of the PAS domain based upon structural prediction. Eur J Biochem 271:1198-1208.
-
(2004)
Eur J Biochem
, vol.271
, pp. 1198-1208
-
-
Hefti, M.H.1
Françoijs, K.J.2
De Vries, S.C.3
Dixon, R.4
Vervoort, J.5
-
14
-
-
0037468225
-
Photoactive yellow protein, a new type of photoreceptor protein: Will this "yellow lab" bring us where we want to go?
-
Hellingwerf KJ, Hendriks J, Gensch T (2003) Photoactive yellow protein, a new type of photoreceptor protein: Will this "yellow lab" bring us where we want to go? J Phys Chem A 107:1082-1094.
-
(2003)
J Phys Chem A
, vol.107
, pp. 1082-1094
-
-
Hellingwerf, K.J.1
Hendriks, J.2
Gensch, T.3
-
15
-
-
34250183058
-
Phototropin blue-light receptors
-
Christie JM (2007) Phototropin blue-light receptors. Annu Rev Plant Biol 58:21-45.
-
(2007)
Annu Rev Plant Biol
, vol.58
, pp. 21-45
-
-
Christie, J.M.1
-
16
-
-
0022430790
-
Isolation and characterization of soluble cytochromes, ferredoxins and other chromophoric proteins from the halophilic phototrophic bacterium Ectothiorhodospira halophila
-
Meyer TE (1985) Isolation and characterization of soluble cytochromes, ferredoxins and other chromophoric proteins from the halophilic phototrophic bacterium Ectothiorhodospira halophila. Biochim Biophys Acta 806:175-183.
-
(1985)
Biochim Biophys Acta
, vol.806
, pp. 175-183
-
-
Meyer, T.E.1
-
17
-
-
0023152468
-
Properties of a water-soluble, yellow protein isolated from a halophilic phototrophic bacterium that has photochemical activity analogous to sensory rhodopsin
-
Meyer TE, Yakali E, Cusanovich MA, Tollin G (1987) Properties of a water-soluble, yellow protein isolated from a halophilic phototrophic bacterium that has photochemical activity analogous to sensory rhodopsin. Biochemistry 26:418-423.
-
(1987)
Biochemistry
, vol.26
, pp. 418-423
-
-
Meyer, T.E.1
Yakali, E.2
Cusanovich, M.A.3
Tollin, G.4
-
18
-
-
0027324441
-
The Eubacterium Ectothiorhodospira halophila is negatively phototactic, with a wavelength dependence that fits the absorption spectrum of the photoactive yellow protein
-
Sprenger WW, Hoff WD, Armitage JP, Hellingwerf KJ (1993) The Eubacterium Ectothiorhodospira halophila is negatively phototactic, with a wavelength dependence that fits the absorption spectrum of the photoactive yellow protein. J Bacteriol 175:3096-3104.
-
(1993)
J Bacteriol
, vol.175
, pp. 3096-3104
-
-
Sprenger, W.W.1
Hoff, W.D.2
Armitage, J.P.3
Hellingwerf, K.J.4
-
19
-
-
0032568630
-
Photoactive yellow protein: A structural prototype for the three-dimensional fold of the PAS domain superfamily
-
Pellequer JL, Wager-Smith KA, Kay SA, Getzoff ED (1998) Photoactive yellow protein: A structural prototype for the three-dimensional fold of the PAS domain superfamily. Proc Natl Acad Sci USA 95:5884-5890.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 5884-5890
-
-
Pellequer, J.L.1
Wager-Smith, K.A.2
Kay, S.A.3
Getzoff, E.D.4
-
20
-
-
0029110488
-
1.4 å structure of photoactive yellow protein, a cytosolic photoreceptor - Unusual fold, active site, and chromophore
-
Borgstahl GEO, Williams DR, Getzoff ED (1995) 1.4 Å structure of photoactive yellow protein, a cytosolic photoreceptor - Unusual fold, active site, and chromophore. Biochemistry 34:6278-6287.
-
(1995)
Biochemistry
, vol.34
, pp. 6278-6287
-
-
Borgstahl, G.E.O.1
Williams, D.R.2
Getzoff, E.D.3
-
21
-
-
0027940414
-
Thiol ester-linked p-coumaric acid as a new photoactive prosthetic group in a protein with rhodopsin-like photochemistry
-
Hoff WD, et al. (1994) Thiol ester-linked p-coumaric acid as a new photoactive prosthetic group in a protein with rhodopsin-like photochemistry. Biochemistry 33:13959-13962.
-
(1994)
Biochemistry
, vol.33
, pp. 13959-13962
-
-
Hoff, W.D.1
-
22
-
-
0028577744
-
Complete chemical structure of photoactive yellow protein: Novel thioester-linked 4-hydroxycinnamyl chromophore and photocycle chemistry
-
Baca M, et al. (1994) Complete chemical structure of photoactive yellow protein: Novel thioester-linked 4-hydroxycinnamyl chromophore and photocycle chemistry. Biochemistry 33:14369-14377.
-
(1994)
Biochemistry
, vol.33
, pp. 14369-14377
-
-
Baca, M.1
-
23
-
-
0027271859
-
Primary structure of a photoactive yellow protein from the phototrophic bacterium Ectothiorhodospira halophila, with evidence for the mass and the binding site of the chromophore
-
van Beeumen JJ, et al. (1993) Primary structure of a photoactive yellow protein from the phototrophic bacterium Ectothiorhodospira halophila, with evidence for the mass and the binding site of the chromophore. Protein Sci 2:1114-1125.
-
(1993)
Protein Sci
, vol.2
, pp. 1114-1125
-
-
Van Beeumen, J.J.1
-
24
-
-
52149122066
-
Identification of six new photoactive yellow proteins: Diversity and structure-function relationships in a bacterial blue light photoreceptor
-
Kumauchi M, Hara M, Stalcup P, Xie A, Hoff WD (2008) Identification of six new photoactive yellow proteins: Diversity and structure-function relationships in a bacterial blue light photoreceptor. Photochem Photobiol 84:956-969.
-
(2008)
Photochem Photobiol
, vol.84
, pp. 956-969
-
-
Kumauchi, M.1
Hara, M.2
Stalcup, P.3
Xie, A.4
Hoff, W.D.5
-
26
-
-
21744460380
-
The solution structure of a transient photoreceptor intermediate: Delta 25 photoactive yellow protein
-
DOI 10.1016/j.str.2005.04.017, PII S0969212605001826
-
Bernard C, et al. (2005) The solution structure of a transient photoreceptor intermediate: Delta 25 photoactive yellow protein. Structure 13:953-962. (Pubitemid 40943327)
-
(2005)
Structure
, vol.13
, Issue.7
, pp. 953-962
-
-
Bernard, C.1
Houben, K.2
Derix, N.M.3
Marks, D.4
Van Der Horst, M.A.5
Hellingwerf, K.J.6
Boelens, R.7
Kaptein, R.8
Van Nuland, N.A.J.9
-
27
-
-
0029950952
-
Protein folding thermodynamics applied to the photocycle of the photoactive yellow protein
-
van Brederode ME, Hoff WD, van Stokkum IHM, Groot ML, Hellingwerf KJ (1996) Protein folding thermodynamics applied to the photocycle of the photoactive yellow protein. Biophys J 71:365-380.
-
(1996)
Biophys J
, vol.71
, pp. 365-380
-
-
Van Brederode, M.E.1
Hoff, W.D.2
Van Stokkum, I.H.M.3
Groot, M.L.4
Hellingwerf, K.J.5
-
28
-
-
0033579823
-
Global conformational changes upon receptor stimulation in photoactive yellow protein
-
Hoff WD, et al. (1999) Global conformational changes upon receptor stimulation in photoactive yellow protein. Biochemistry 38:1009-1017.
-
(1999)
Biochemistry
, vol.38
, pp. 1009-1017
-
-
Hoff, W.D.1
-
29
-
-
33746804669
-
Single-molecule detection of structural changes during Per-Arnt- Sim (PAS) domain activation
-
Zhao JM, et al. (2006) Single-molecule detection of structural changes during Per-Arnt- Sim (PAS) domain activation. Proc Natl Acad Sci USA 103:11561-11666.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 11561-11666
-
-
Zhao, J.M.1
-
30
-
-
0035906913
-
The role of the N-terminal domain of photoactive yellow protein in the transient partial unfolding during signalling state formation
-
DOI 10.1016/S0014-5793(01)02427-9, PII S0014579301024279
-
van der Horst MA, van Stokkum IH, Crielaard W, Hellingwerf KJ (2001) The role of the N-terminal domain of photoactive yellow protein in the transient partial unfolding during signalling state formation. FEBS Lett 497:26-30. (Pubitemid 32480175)
-
(2001)
FEBS Letters
, vol.497
, Issue.1
, pp. 26-30
-
-
Van Der Horst, M.A.1
Van Stokkum, I.H.2
Crielaard, W.3
Hellingwerf, K.J.4
-
31
-
-
0037137227
-
Light-induced global conformational change of photoactive yellow protein in solution
-
DOI 10.1021/bi0264768
-
Imamoto Y, Kamikubo H, Harigai M, Shimizu N, Kataoka M (2002) Light-induced global conformational change of photoactive yellow protein in solution. Biochemistry 41:13595-13601. (Pubitemid 35332695)
-
(2002)
Biochemistry
, vol.41
, Issue.46
, pp. 13595-13601
-
-
Imamoto, Y.1
Kamikubo, H.2
Harigai, M.3
Shimizu, N.4
Kataoka, M.5
-
33
-
-
34249848425
-
Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila
-
DOI 10.1073/pnas.0701572104
-
Sawyer SA, Parsch J, Zhang Z, Hartl DL (2007) Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. Proc Natl Acad Sci USA 104:6504-6510. (Pubitemid 47175532)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.16
, pp. 6504-6510
-
-
Sawyer, S.A.1
Parsch, J.2
Zhang, Z.3
Hartl, D.L.4
-
34
-
-
0005876924
-
Bacteriophage λ cro mutations: Effects on activity and intracellular degradation
-
Pakula AA, Young VB, Sauer RT (1986) Bacteriophage λ cro mutations: Effects on activity and intracellular degradation. Proc Natl Acad Sci USA 83:8829-8833.
-
(1986)
Proc Natl Acad Sci USA
, vol.83
, pp. 8829-8833
-
-
Pakula, A.A.1
Young, V.B.2
Sauer, R.T.3
-
35
-
-
0034911722
-
Amino acids in the N-terminal region regulate the photocycle of photoactive yellow protein
-
Harigai M, et al. (2001) Amino acids in the N-terminal region regulate the photocycle of photoactive yellow protein. J Biochem 130:51-56. (Pubitemid 32674564)
-
(2001)
Journal of Biochemistry
, vol.130
, Issue.1
, pp. 51-56
-
-
Harigai, M.1
Yasuda, S.2
Imamoto, Y.3
Yoshihara, K.4
Tokunaga, F.5
Kataoka, M.6
-
36
-
-
0037596438
-
Solution structure and backbone dynamics of the photoactive yellow protein
-
Düx P, et al. (1998) Solution structure and backbone dynamics of the photoactive yellow protein. Biochemistry 37:12689-12699.
-
(1998)
Biochemistry
, vol.37
, pp. 12689-12699
-
-
Düx, P.1
-
37
-
-
0035877707
-
PAS domain receptor photoactive yellow protein is converted to a molten globule state upon activation
-
Lee B-C, Croonquist PA, Sosnick TR, Hoff WD (2001) PAS domain receptor photoactive yellow protein is converted to a molten globule state upon activation. J Biol Chem 276:20821-20823.
-
(2001)
J Biol Chem
, vol.276
, pp. 20821-20823
-
-
Lee, B.-C.1
Croonquist, P.A.2
Sosnick, T.R.3
Hoff, W.D.4
-
38
-
-
0036199841
-
Transient exposure of hydrophobic surface in the photoactive yellow protein monitored with Nile red
-
Hendriks J, et al. (2002) Transient exposure of hydrophobic surface in the photoactive yellow protein monitored with Nile red. Biophys J 82:1632-1643.
-
(2002)
Biophys J
, vol.82
, pp. 1632-1643
-
-
Hendriks, J.1
-
39
-
-
0035852878
-
Formation of a new buried charge drives a large-amplitude protein quake in photoreceptor activation
-
DOI 10.1021/bi002449a
-
Xie A, et al. (2001) Formation of a new buried charge drives a large-amplitude protein quake in photoreceptor activation. Biochemistry 40:1510-1517. (Pubitemid 32144019)
-
(2001)
Biochemistry
, vol.40
, Issue.6
, pp. 1510-1517
-
-
Xie, A.1
Kelemen, L.2
Hendriks, J.3
White, B.J.4
Hellingwerf, K.J.5
Hoff, W.D.6
-
40
-
-
0141707094
-
Structural basis of a phototropin light switch
-
Harper SM, Neil LC, Garner KH (2003) Structural basis of a phototropin light switch. Science 301:1541-1544.
-
(2003)
Science
, vol.301
, pp. 1541-1544
-
-
Harper, S.M.1
Neil, L.C.2
Garner, K.H.3
-
41
-
-
19944426818
-
Crystal structure and interactions of the PAS repeat region of the Drosophila clock protein PERIOD
-
DOI 10.1016/j.molcel.2004.11.022, PII S1097276504007130
-
Yildiz O, et al. (2005) Crystal structure and interactions of the PAS repeat region of the Drosophila clock protein PERIOD. Mol Cell 17:69-82. (Pubitemid 40075366)
-
(2005)
Molecular Cell
, vol.17
, Issue.1
, pp. 69-82
-
-
Yildiz, O.1
Doi, M.2
Yujnovsky, I.3
Cardone, L.4
Berndt, A.5
Hennig, S.6
Schulze, S.7
Urbanke, C.8
Sassone-Corsi, P.9
Wolf, E.10
-
42
-
-
34249080375
-
Conformational switching in the fungal light sensor vivid
-
Zoltowski BD, et al. (2007) Conformational switching in the fungal light sensor vivid. Science 316:1054-1057.
-
(2007)
Science
, vol.316
, pp. 1054-1057
-
-
Zoltowski, B.D.1
-
43
-
-
0346734132
-
Structural basis for PAS domain heterodimerization in the basic helix-loop-helix-PAS transcription factor hypoxia-inducible factor
-
DOI 10.1073/pnas.2533374100
-
Erbel PJA, Card PB, Karakuzu O, Bruick RK, Gardner KH (2003) Structural basis for PAS domain heterodimerization in the basic helix-loop-helix-PAS transcription factor hypoxia-inducible factor. Proc Natl Acad Sci USA 100:15504-15509. (Pubitemid 38021019)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.26
, pp. 15504-15509
-
-
Erbel, P.J.A.1
Card, P.B.2
Karakuzu, O.3
Bruick, R.K.4
Gardner, K.H.5
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