-
1
-
-
33746363486
-
Domains, motifs, and scaffolds: The role of modular interactions in the evolution and wiring of cell signaling circuits
-
Bhattacharyya RP, Remenyi A, Yeh BJ, Lim WA (2006) Domains, motifs, and scaffolds: The role of modular interactions in the evolution and wiring of cell signaling circuits. Annu Rev Biochem 75:655-680.
-
(2006)
Annu Rev Biochem
, vol.75
, pp. 655-680
-
-
Bhattacharyya, R.P.1
Remenyi, A.2
Yeh, B.J.3
Lim, W.A.4
-
2
-
-
14844321287
-
Synthetic modular systems - Reverse engineering of signal transduction
-
Pawson T, Linding R (2005) Synthetic modular systems - Reverse engineering of signal transduction. FEBS Lett 579:1808-1814.
-
(2005)
FEBS Lett
, vol.579
, pp. 1808-1814
-
-
Pawson, T.1
Linding, R.2
-
3
-
-
0037453510
-
Assembly of cell regulatory systems through protein interaction domains
-
Pawson T, Nash P (2003) Assembly of cell regulatory systems through protein interaction domains. Science 300:445-452.
-
(2003)
Science
, vol.300
, pp. 445-452
-
-
Pawson, T.1
Nash, P.2
-
5
-
-
23944444109
-
Engineering allosteric protein switches by domain insertion
-
Ostermeier M (2005) Engineering allosteric protein switches by domain insertion. Protein Eng Des Sel 18:359-364.
-
(2005)
Protein Eng Des Sel
, vol.18
, pp. 359-364
-
-
Ostermeier, M.1
-
6
-
-
0028588070
-
Domain insertion
-
Russell RB (1994) Domain insertion. Protein Eng 7:1407-1410.
-
(1994)
Protein Eng
, vol.7
, pp. 1407-1410
-
-
Russell, R.B.1
-
7
-
-
0033613235
-
Circular permutation and receptor insertion within green fluorescent proteins
-
Baird GS, Zacharias DA, Tsien RY (1999) Circular permutation and receptor insertion within green fluorescent proteins. Proc Natl Acad Sci USA 96:11241-11246.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 11241-11246
-
-
Baird, G.S.1
Zacharias, D.A.2
Tsien, R.Y.3
-
8
-
-
23844465160
-
Directed evolution of protein switches and their application to the creation of ligand-binding proteins
-
Guntas G, Mansell TJ, Kim JR, Ostermeier M (2005) Directed evolution of protein switches and their application to the creation of ligand-binding proteins. Proc Natl Acad Sci USA 102:11224-11229.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 11224-11229
-
-
Guntas, G.1
Mansell, T.J.2
Kim, J.R.3
Ostermeier, M.4
-
9
-
-
0042736856
-
Allosteric switching by mutually exclusive folding of protein domains
-
Radley TL, Markowska AI, Bettinger BT, Ha JH, Loh SN (2003) Allosteric switching by mutually exclusive folding of protein domains. J Mol Biol 332:529-536.
-
(2003)
J Mol Biol
, vol.332
, pp. 529-536
-
-
Radley, T.L.1
Markowska, A.I.2
Bettinger, B.T.3
Ha, J.H.4
Loh, S.N.5
-
10
-
-
35448990907
-
A modular and extensible RNA-based gene-regulatory platform for engineering cellular function
-
Win MN, Smolke CD (2007) A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc Natl Acad Sci USA 104:14283-14288.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 14283-14288
-
-
Win, M.N.1
Smolke, C.D.2
-
11
-
-
6344219895
-
Is allostery an intrinsic property of all dynamic proteins?
-
Gunasekaran K, Ma B, Nussinov R (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins 57:433-443.
-
(2004)
Proteins
, vol.57
, pp. 433-443
-
-
Gunasekaran, K.1
Ma, B.2
Nussinov, R.3
-
12
-
-
0033621118
-
The propagation of binding interactions to remote sites in proteins: Analysis of the binding of the monoclonal antibody D1.3 to lysozyme
-
Freire E (1999) The propagation of binding interactions to remote sites in proteins: Analysis of the binding of the monoclonal antibody D1.3 to lysozyme. Proc Natl Acad Sci USA 96:10118-10122.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 10118-10122
-
-
Freire, E.1
-
13
-
-
34347235156
-
Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins
-
Hilser VJ, Thompson EB (2007) Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins. Proc Natl Acad Sci USA 104:8311-8315.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 8311-8315
-
-
Hilser, V.J.1
Thompson, E.B.2
-
14
-
-
0035937443
-
Two-state allosteric behavior in a single-domain signaling protein
-
Volkman BF, Lipson D, Wemmer DE, Kern D (2001) Two-state allosteric behavior in a single-domain signaling protein. Science 291:2429-2433.
-
(2001)
Science
, vol.291
, pp. 2429-2433
-
-
Volkman, B.F.1
Lipson, D.2
Wemmer, D.E.3
Kern, D.4
-
15
-
-
0037013143
-
The conformational plasticity of protein kinases
-
Huse M, Kuriyan J (2002) The conformational plasticity of protein kinases. Cell 109:275-282.
-
(2002)
Cell
, vol.109
, pp. 275-282
-
-
Huse, M.1
Kuriyan, J.2
-
16
-
-
0141757323
-
Reprogramming control of an allosteric signaling switch through modular recombination
-
Dueber JE, Yeh BJ, Chak K, Lim WA (2003) Reprogramming control of an allosteric signaling switch through modular recombination. Science 301:1904-1908.
-
(2003)
Science
, vol.301
, pp. 1904-1908
-
-
Dueber, J.E.1
Yeh, B.J.2
Chak, K.3
Lim, W.A.4
-
17
-
-
34247465989
-
Engineering modular protein interaction switches by sequence overlap
-
Sallee NA, Yeh BJ, Lim WA (2007) Engineering modular protein interaction switches by sequence overlap. J Am Chem Soc 129:4606-4611.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 4606-4611
-
-
Sallee, N.A.1
Yeh, B.J.2
Lim, W.A.3
-
18
-
-
0346500466
-
Creation of an allosteric enzyme by domain insertion
-
Guntas G, Ostermeier M (2004) Creation of an allosteric enzyme by domain insertion. J Mol Biol 336:263-273.
-
(2004)
J Mol Biol
, vol.336
, pp. 263-273
-
-
Guntas, G.1
Ostermeier, M.2
-
19
-
-
24644523298
-
Design and folding of a multidomain protein
-
Zhou Z, Feng H, Zhou H, Zhou Y, Bai Y (2005) Design and folding of a multidomain protein. Biochemistry 44:12107-12112.
-
(2005)
Biochemistry
, vol.44
, pp. 12107-12112
-
-
Zhou, Z.1
Feng, H.2
Zhou, H.3
Zhou, Y.4
Bai, Y.5
-
20
-
-
22244458915
-
Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library
-
Jha AK, et al. (2005) Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. Biochemistry 44:9691-9702.
-
(2005)
Biochemistry
, vol.44
, pp. 9691-9702
-
-
Jha, A.K.1
-
21
-
-
0033642945
-
Structural stability of binding sites: Consequences for binding affinity and allosteric effects
-
Luque I, Freire E (2000) Structural stability of binding sites: Consequences for binding affinity and allosteric effects. Proteins Suppl 4:63-71.
-
(2000)
Proteins Suppl
, vol.4
, pp. 63-71
-
-
Luque, I.1
Freire, E.2
-
22
-
-
15444362906
-
Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins
-
Whitten ST, Garcia-Moreno EB, Hilser VJ (2005) Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins. Proc Natl Acad Sci USA 102:4282-4287.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 4282-4287
-
-
Whitten, S.T.1
Garcia-Moreno, E.B.2
Hilser, V.J.3
-
23
-
-
0031470701
-
Arabidopsis NPH1: A protein kinase with a putative redox-sensing domain
-
Huala E, et al. (1997) Arabidopsis NPH1: A protein kinase with a putative redox-sensing domain. Science 278:2120-2123.
-
(1997)
Science
, vol.278
, pp. 2120-2123
-
-
Huala, E.1
-
24
-
-
33947412138
-
Structure of the redox sensor domain of Azotobacter vinelandii NifL at atomic resolution: Signaling, dimerization, and mechanism
-
Key J, Hefti M, Purcell EB, Moffat K (2007) Structure of the redox sensor domain of Azotobacter vinelandii NifL at atomic resolution: Signaling, dimerization, and mechanism. Biochemistry 46:3614-3623.
-
(2007)
Biochemistry
, vol.46
, pp. 3614-3623
-
-
Key, J.1
Hefti, M.2
Purcell, E.B.3
Moffat, K.4
-
25
-
-
0037435618
-
The LOV domain family: Photoresponsive signaling modules coupled to diverse output domains
-
Crosson S, Rajagopal S, Moffat K (2003) The LOV domain family: Photoresponsive signaling modules coupled to diverse output domains. Biochemistry 42:2-10.
-
(2003)
Biochemistry
, vol.42
, pp. 2-10
-
-
Crosson, S.1
Rajagopal, S.2
Moffat, K.3
-
26
-
-
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
-
27
-
-
0035965307
-
The photocycle of a flavin-binding domain of the blue light photoreceptor phototropin
-
Swartz TE, et al. (2001) The photocycle of a flavin-binding domain of the blue light photoreceptor phototropin. J Biol Chem 276:36493-36500.
-
(2001)
J Biol Chem
, vol.276
, pp. 36493-36500
-
-
Swartz, T.E.1
-
28
-
-
11144344967
-
Disruption of the LOV-Jalpha helix interaction activates phototropin kinase activity
-
Harper SM, Christie JM, Gardner KH (2004) Disruption of the LOV-Jalpha helix interaction activates phototropin kinase activity. Biochemistry 43:16184-16192.
-
(2004)
Biochemistry
, vol.43
, pp. 16184-16192
-
-
Harper, S.M.1
Christie, J.M.2
Gardner, K.H.3
-
29
-
-
0141707094
-
Structural basis of a phototropin light switch
-
Harper SM, Neil LC, Gardner 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
Gardner, K.H.3
-
30
-
-
0011023559
-
Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor
-
Gunsalus RP, Yanofsky C (1980) Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor. Proc Natl Acad Sci USA 77:7117-7121.
-
(1980)
Proc Natl Acad Sci USA
, vol.77
, pp. 7117-7121
-
-
Gunsalus, R.P.1
Yanofsky, C.2
-
31
-
-
0029131681
-
Engineering proteins without primary sequence tryptophan residues: Mutant trp repressors with aliphatic substitutions for tryptophan side chains
-
Chapman D, Hochstrasser R, Millar D, Youderian P (1995) Engineering proteins without primary sequence tryptophan residues: Mutant trp repressors with aliphatic substitutions for tryptophan side chains. Gene 163:1-11.
-
(1995)
Gene
, vol.163
, pp. 1-11
-
-
Chapman, D.1
Hochstrasser, R.2
Millar, D.3
Youderian, P.4
-
32
-
-
0033534367
-
Long-range effects on dynamics in a temperature-sensitive mutant of trp repressor
-
Jin L, Fukayama JW, Pelczer I, Carey J (1999) Long-range effects on dynamics in a temperature-sensitive mutant of trp repressor. J Mol Biol 285:361-378.
-
(1999)
J Mol Biol
, vol.285
, pp. 361-378
-
-
Jin, L.1
Fukayama, J.W.2
Pelczer, I.3
Carey, J.4
-
33
-
-
0031596571
-
Mutational analysis of the NH2-terminal arms of the trp repressor indicates a multifunctional domain
-
Mackintosh SG, McDermott PF, Hurlburt BK (1998) Mutational analysis of the NH2-terminal arms of the trp repressor indicates a multifunctional domain. Mol Microbiol 27:1119-1127.
-
(1998)
Mol Microbiol
, vol.27
, pp. 1119-1127
-
-
Mackintosh, S.G.1
McDermott, P.F.2
Hurlburt, B.K.3
-
34
-
-
0030598345
-
Characterization of charge change super-repressor mutants of trp repressor: Effects on oligomerization conformation, ligation and stability
-
Reedstrom RJ, et al. (1996) Characterization of charge change super-repressor mutants of trp repressor: Effects on oligomerization conformation, ligation and stability. J Mol Biol 264:32-45.
-
(1996)
J Mol Biol
, vol.264
, pp. 32-45
-
-
Reedstrom, R.J.1
-
35
-
-
0027372621
-
Tandem binding in crystals of a trp repressor/operator half-site complex
-
Lawson CL, Carey J (1993) Tandem binding in crystals of a trp repressor/operator half-site complex. Nature 366:178-182.
-
(1993)
Nature
, vol.366
, pp. 178-182
-
-
Lawson, C.L.1
Carey, J.2
-
36
-
-
0345677967
-
Purification and characterization of trp aporepressor
-
Joachimiak A, Kelley RL, Gunsalus RP, Yanofsky C, Sigler PB (1983) Purification and characterization of trp aporepressor. Proc Natl Acad Sci USA 80:668-672.
-
(1983)
Proc Natl Acad Sci USA
, vol.80
, pp. 668-672
-
-
Joachimiak, A.1
Kelley, R.L.2
Gunsalus, R.P.3
Yanofsky, C.4
Sigler, P.B.5
-
37
-
-
0037428497
-
Intramolecular proton transfers and structural changes during the photocycle of the LOV2 domain of phototropin 1
-
Corchnoy SB, et al. (2003) Intramolecular proton transfers and structural changes during the photocycle of the LOV2 domain of phototropin 1. J Biol Chem 278:724-731.
-
(2003)
J Biol Chem
, vol.278
, pp. 724-731
-
-
Corchnoy, S.B.1
-
38
-
-
0030792524
-
Construction and characterization of monomeric tryptophan repressor: A model for an early intermediate in the folding of a dimeric protein
-
Shao X, Hensley P, Matthews CR (1997) Construction and characterization of monomeric tryptophan repressor: A model for an early intermediate in the folding of a dimeric protein. Biochemistry 36:9941-9949.
-
(1997)
Biochemistry
, vol.36
, pp. 9941-9949
-
-
Shao, X.1
Hensley, P.2
Matthews, C.R.3
-
39
-
-
0026910457
-
Determination of the regularization parameter in indirect-transform methods using perceptual criteria
-
Svergun DI (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Cryst 25:495-503.
-
(1992)
J Appl Cryst
, vol.25
, pp. 495-503
-
-
Svergun, D.I.1
-
40
-
-
0029643911
-
Solution structures of GroEL and its complex with rhodanese from small-angle neutron scattering
-
Thiyagarajan P, Henderson SJ, Joachimiak A (1996) Solution structures of GroEL and its complex with rhodanese from small-angle neutron scattering. Structure (London) 4:79-88.
-
(1996)
Structure (London)
, vol.4
, pp. 79-88
-
-
Thiyagarajan, P.1
Henderson, S.J.2
Joachimiak, A.3
-
41
-
-
0033001996
-
Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing
-
Svergun DI (1999) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J 76:2879-2886.
-
(1999)
Biophys J
, vol.76
, pp. 2879-2886
-
-
Svergun, D.I.1
-
42
-
-
0033522219
-
Structure of the amino-terminal domain of Cbl complexed to its binding site on ZAP-70 kinase
-
Meng W, Sawasdikosol S, Burakoff SJ, Eck MJ (1999) Structure of the amino-terminal domain of Cbl complexed to its binding site on ZAP-70 kinase. Nature 398:84-90.
-
(1999)
Nature
, vol.398
, pp. 84-90
-
-
Meng, W.1
Sawasdikosol, S.2
Burakoff, S.J.3
Eck, M.J.4
-
43
-
-
0036427580
-
The molecular basis of sensing and responding to light in microorganisms
-
Hellingwerf KJ (2002) The molecular basis of sensing and responding to light in microorganisms. Ant V Leeuwenhoek 81:51-59.
-
(2002)
Ant V Leeuwenhoek
, vol.81
, pp. 51-59
-
-
Hellingwerf, K.J.1
-
44
-
-
0031473847
-
SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
-
Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18:2714-2723.
-
(1997)
Electrophoresis
, vol.18
, pp. 2714-2723
-
-
Guex, N.1
Peitsch, M.C.2
-
45
-
-
0037701585
-
Uniqueness of ab initio shape determination in small-angle scattering
-
Volkov VV, Svergun DI (2003) Uniqueness of ab initio shape determination in small-angle scattering. J Appl Cryst 36:860-864.
-
(2003)
J Appl Cryst
, vol.36
, pp. 860-864
-
-
Volkov, V.V.1
Svergun, D.I.2
-
46
-
-
37049002915
-
N- and C-terminal flanking regions modulate light-induced signal transduction in the LOV2 domain of the blue light sensor phototropin 1 from Avena sativa
-
Halavaty AS, Moffat K (2007) N- and C-terminal flanking regions modulate light-induced signal transduction in the LOV2 domain of the blue light sensor phototropin 1 from Avena sativa. Biochemistry 46:14001-14009.
-
(2007)
Biochemistry
, vol.46
, pp. 14001-14009
-
-
Halavaty, A.S.1
Moffat, K.2
|