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Volumn 110, Issue 51, 2013, Pages 20545-20550

Protein recognition and selection through conformational and mutually induced fit

Author keywords

Calmodulin binding target; Coarse grained molecular simulations; Conformational flexibility; Hydrophobic motif; Stopped flow fluorescence techniques

Indexed keywords

CALMODULIN; CALMODULIN BINDING PROTEIN;

EID: 84890843915     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1312788110     Document Type: Article
Times cited : (45)

References (44)
  • 1
    • 84886098705 scopus 로고    scopus 로고
    • Structural diversity of calmodulin binding to its target sites
    • 101111/febs12296
    • Tidow H, Nissen P (2013) Structural diversity of calmodulin binding to its target sites. FEBS J 280(21):5551-5565, 10.1111/febs.12296.
    • (2013) FEBS J , vol.280 , Issue.21 , pp. 5551-5565
    • Tidow, H.1    Nissen, P.2
  • 2
    • 1942496481 scopus 로고    scopus 로고
    • Calmodulin's flexibility allows for promiscuity in its interactions with target proteins and peptides
    • Yamniuk AP, Vogel HJ (2004) Calmodulin's flexibility allows for promiscuity in its interactions with target proteins and peptides. Mol Biotechnol 27(1):33-57.
    • (2004) Mol Biotechnol , vol.27 , Issue.1 , pp. 33-57
    • Yamniuk, A.P.1    Vogel, H.J.2
  • 3
    • 22344451979 scopus 로고    scopus 로고
    • Single-Molecule tracking of submillisecond domain motion in calmodulin
    • Slaughter BD, Bieber-Urbauer RJ, Johnson CK (2005) Single-Molecule tracking of submillisecond domain motion in calmodulin. J Phys Chem B 109(26):12658-12662.
    • (2005) J Phys Chem B , vol.109 , Issue.26 , pp. 12658-12662
    • Slaughter, B.D.1    Bieber-Urbauer, R.J.2    Johnson, C.K.3
  • 4
    • 68349084565 scopus 로고    scopus 로고
    • Modulation of calmodulin plasticity by the effect of macromolecular crowding
    • Homouz D, Sanabria H, Waxham MN, Cheung MS (2009) Modulation of calmodulin plasticity by the effect of macromolecular crowding. J Mol Biol 391(5):933-943.
    • (2009) J Mol Biol , vol.391 , Issue.5 , pp. 933-943
    • Homouz, D.1    Sanabria, H.2    Waxham, M.N.3    Cheung, M.S.4
  • 5
    • 79960962805 scopus 로고    scopus 로고
    • The effect of macromolecular crowding, ionic strength and calcium binding on calmodulin dynamics
    • Wang Q, Liang KC, Czader A, Waxham MN, Cheung MS (2011) The effect of macromolecular crowding, ionic strength and calcium binding on calmodulin dynamics. PLOS Comput Biol 7(7):e1002114.
    • (2011) PLOS Comput Biol , vol.7 , Issue.7
    • Wang, Q.1    Liang, K.C.2    Czader, A.3    Waxham, M.N.4    Cheung, M.S.5
  • 6
    • 83055186781 scopus 로고    scopus 로고
    • Transient, sparsely populated compact states of apo and calcium-Loaded calmodulin probed by paramagnetic relaxation enhancement: Interplay of conformational selection and induced fit
    • Anthis NJ, Doucleff M, Clore GM (2011) Transient, sparsely populated compact states of apo and calcium-Loaded calmodulin probed by paramagnetic relaxation enhancement: Interplay of conformational selection and induced fit. J Am Chem Soc 133(46):18966-18974.
    • (2011) J Am Chem Soc , vol.133 , Issue.46 , pp. 18966-18974
    • Anthis, N.J.1    Doucleff, M.2    Clore, G.M.3
  • 7
    • 0001289724 scopus 로고    scopus 로고
    • Einfluss der Configuration auf die Wirkung der Enzyme [Configuration of the influence on the action of enzymes]
    • 1894 German
    • Fischer E (1894) Einfluss der Configuration auf die Wirkung der Enzyme [Configuration of the influence on the action of enzymes]. Ber Dtsch Chem Ges 27:2984-2993. German.
    • Ber Dtsch Chem Ges , vol.27 , pp. 2984-2993
    • Fischer, E.1
  • 8
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity of protein synthesis
    • Koshland DEJ (1958) Application of a theory of enzyme specificity of protein synthesis. Proc Natl Acad Sci USA 44(2):98-104.
    • (1958) Proc Natl Acad Sci USA , vol.44 , Issue.2 , pp. 98-104
    • Koshland, D.E.J.1
  • 9
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: A plausible model
    • Monod J, Wyman J, Changeux JP (1965) On the nature of allosteric transitions: A plausible model. J Mol Biol 12:88-118.
    • (1965) J Mol Biol , vol.12 , pp. 88-118
    • Monod, J.1    Wyman, J.2    Changeux, J.P.3
  • 10
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels, and protein function
    • Tsai CJ, Kumar S, Ma BY, Nussinov R (1999) Folding funnels, binding funnels, and protein function. Protein Sci 8(6):1181-1190.
    • (1999) Protein Sci , vol.8 , Issue.6 , pp. 1181-1190
    • Tsai, C.J.1    Kumar, S.2    Ma, B.Y.3    Nussinov, R.4
  • 11
    • 0033784534 scopus 로고    scopus 로고
    • Induced fit in RNA-Protein recognition
    • Williamson JR (2000) Induced fit in RNA-Protein recognition. Nat Struct Biol 7(10): 834-837.
    • (2000) Nat Struct Biol , vol.7 , Issue.10 , pp. 834-837
    • Williamson, J.R.1
  • 12
    • 0034255123 scopus 로고    scopus 로고
    • Speeding molecular recognition by using the folding funnel: The fly-Casting mechanism
    • Shoemaker BA, Portman JJ, Wolynes PG (2000) Speeding molecular recognition by using the folding funnel: The fly-Casting mechanism. Proc Natl Acad Sci USA 97(16): 8868-8873.
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.16 , pp. 8868-8873
    • Shoemaker, B.A.1    Portman, J.J.2    Wolynes, P.G.3
  • 13
  • 14
    • 84879543236 scopus 로고    scopus 로고
    • Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition
    • Chu X, Gan L, Wang E, Wang J (2013) Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition. Proc Natl Acad Sci USA 110(26):E2342-E2351.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.26 , pp. 2342-2351
    • Chu, X.1    Gan, L.2    Wang, E.3    Wang, J.4
  • 15
    • 0032749078 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins: Re-Assessing the protein structure-Function paradigm
    • Wright PE, Dyson HJ (1999) Intrinsically unstructured proteins: Re-Assessing the protein structure-Function paradigm. J Mol Biol 293(2):321-331.
    • (1999) J Mol Biol , vol.293 , Issue.2 , pp. 321-331
    • Wright, P.E.1    Dyson, H.J.2
  • 16
    • 0035022941 scopus 로고    scopus 로고
    • Intrinsically disordered protein
    • Dunker AK, et al. (2001) Intrinsically disordered protein. J Mol Graph Model 19(1): 26-59.
    • (2001) J Mol Graph Model , vol.19 , Issue.1 , pp. 26-59
    • Dunker, A.K.1
  • 17
    • 0036128797 scopus 로고    scopus 로고
    • Natively unfolded proteins: A point where biology waits for physics
    • Uversky VN (2002) Natively unfolded proteins: A point where biology waits for physics. Protein Sci 11(4):739-756.
    • (2002) Protein Sci , vol.11 , Issue.4 , pp. 739-756
    • Uversky, V.N.1
  • 18
    • 0032504199 scopus 로고    scopus 로고
    • A mechanism for calmodulin (CaM) trapping by CaM-Kinase II defined by a family of CaM-Binding peptides
    • Waxham MN, Tsai AL, Putkey JA (1998) A mechanism for calmodulin (CaM) trapping by CaM-Kinase II defined by a family of CaM-Binding peptides. J Biol Chem 273(28): 17579-17584.
    • (1998) J Biol Chem , vol.273 , Issue.28 , pp. 17579-17584
    • Waxham, M.N.1    Tsai, A.L.2    Putkey, J.A.3
  • 19
    • 80051664755 scopus 로고    scopus 로고
    • Fast methionine-Based solution structure determination of calcium-Calmodulin complexes
    • Gifford JL, Ishida H, Vogel HJ (2011) Fast methionine-Based solution structure determination of calcium-Calmodulin complexes. J Biomol NMR 50(1):71-81.
    • (2011) J Biomol NMR , vol.50 , Issue.1 , pp. 71-81
    • Gifford, J.L.1    Ishida, H.2    Vogel, H.J.3
  • 20
    • 0027759276 scopus 로고
    • Modulation of calmodulin plasticity in molecular recognition on the basis of x-Ray structures
    • Meador WE, Means AR, Quiocho FA (1993) Modulation of calmodulin plasticity in molecular recognition on the basis of x-Ray structures. Science 262(5140):1718-1721.
    • (1993) Science , vol.262 , Issue.5140 , pp. 1718-1721
    • Meador, W.E.1    Means, A.R.2    Quiocho, F.A.3
  • 21
    • 0035830963 scopus 로고    scopus 로고
    • Protein-Protein association: Investigation of factors influencing association rates by Brownian dynamics simulations
    • Gabdoulline RR, Wade RC (2001) Protein-Protein association: Investigation of factors influencing association rates by Brownian dynamics simulations. J Mol Biol 306(5): 1139-1155.
    • (2001) J Mol Biol , vol.306 , Issue.5 , pp. 1139-1155
    • Gabdoulline, R.R.1    Wade, R.C.2
  • 22
    • 33846847968 scopus 로고    scopus 로고
    • Prediction of protein-Protein association rates from a transition-State theory
    • Alsallaq R, Zhou HX (2007) Prediction of protein-Protein association rates from a transition-State theory. Structure 15(2):215-224.
    • (2007) Structure , vol.15 , Issue.2 , pp. 215-224
    • Alsallaq, R.1    Zhou, H.X.2
  • 23
    • 0344500752 scopus 로고    scopus 로고
    • Computer simulation of protein-Protein association kinetics: Acetylcholinesterase-Fasciculin
    • Elcock AH, Gabdoulline RR, Wade RC, McCammon JA (1999) Computer simulation of protein-Protein association kinetics: Acetylcholinesterase- Fasciculin. J Mol Biol 291(1): 149-162.
    • (1999) J Mol Biol , vol.291 , Issue.1 , pp. 149-162
    • Elcock, A.H.1    Gabdoulline, R.R.2    Wade, R.C.3    McCammon, J.A.4
  • 24
    • 42949161558 scopus 로고    scopus 로고
    • Binding-Induced folding of a natively unstructured transcription factor
    • Turjanski AG, Gutkind JS, Best RB, Hummer G (2008) Binding-Induced folding of a natively unstructured transcription factor. PLOS Comput Biol 4(4):e1000060.
    • (2008) PLOS Comput Biol , vol.4 , Issue.4
    • Turjanski, A.G.1    Gutkind, J.S.2    Best, R.B.3    Hummer, G.4
  • 25
    • 79955570145 scopus 로고    scopus 로고
    • Multi-Scaled explorations of binding-Induced folding of intrinsically disordered protein inhibitor IA3 to its target enzyme
    • Wang J, et al. (2011) Multi-Scaled explorations of binding-Induced folding of intrinsically disordered protein inhibitor IA3 to its target enzyme. PLOS Comput Biol 7(4):e1001118.
    • (2011) PLOS Comput Biol , vol.7 , Issue.4
    • Wang, J.1
  • 26
    • 84864578471 scopus 로고    scopus 로고
    • Importance of electrostatic interactions in the association of intrinsically disordered histone chaperone Chz1 and histone H2A.Z-H2B
    • Chu X, et al. (2012) Importance of electrostatic interactions in the association of intrinsically disordered histone chaperone Chz1 and histone H2A.Z-H2B. PLOS Comput Biol 8(7):e1002608.
    • (2012) PLOS Comput Biol , vol.8 , Issue.7
    • Chu, X.1
  • 27
    • 28844466824 scopus 로고    scopus 로고
    • Slow protein conformational dynamics from multiple experimental structures: The helix/sheet transition of arc repressor
    • Best RB, Chen YG, Hummer G (2005) Slow protein conformational dynamics from multiple experimental structures: The helix/sheet transition of arc repressor. Structure 13(12):1755-1763.
    • (2005) Structure , vol.13 , Issue.12 , pp. 1755-1763
    • Best, R.B.1    Chen, Y.G.2    Hummer, G.3
  • 28
    • 33747065536 scopus 로고    scopus 로고
    • Multiple-Basin energy landscapes for large-Amplitude conformational motions of proteins: Structure-Based molecular dynamics simulations
    • Okazaki K, Koga N, Takada S, Onuchic JN, Wolynes PG (2006) Multiple-Basin energy landscapes for large-Amplitude conformational motions of proteins: Structure-Based molecular dynamics simulations. Proc Natl Acad Sci USA 103(32):11844-11849.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.32 , pp. 11844-11849
    • Okazaki, K.1    Koga, N.2    Takada, S.3    Onuchic, J.N.4    Wolynes, P.G.5
  • 29
    • 49649084492 scopus 로고    scopus 로고
    • Dynamic energy landscape view of coupled binding and protein conformational change: Induced-Fit versus population-Shift mechanisms
    • Okazaki KI, Takada S (2008) Dynamic energy landscape view of coupled binding and protein conformational change: Induced-Fit versus population-Shift mechanisms. Proc Natl Acad Sci USA 105(32):11182-11187.
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.32 , pp. 11182-11187
    • Okazaki, K.I.1    Takada, S.2
  • 30
    • 84859455527 scopus 로고    scopus 로고
    • Structure-Based model of allostery predicts coupling between distant sites
    • Weinkam P, Pons J, Sali A (2012) Structure-Based model of allostery predicts coupling between distant sites. Proc Natl Acad Sci USA 109(13):4875-4880.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.13 , pp. 4875-4880
    • Weinkam, P.1    Pons, J.2    Sali, A.3
  • 31
    • 33846847773 scopus 로고    scopus 로고
    • Conformational transitions of adenylate kinase: Switching by cracking
    • Whitford PC, Miyashita O, Levy Y, Onuchic JN (2007) Conformational transitions of adenylate kinase: Switching by cracking. J Mol Biol 366(5):1661-1671.
    • (2007) J Mol Biol , vol.366 , Issue.5 , pp. 1661-1671
    • Whitford, P.C.1    Miyashita, O.2    Levy, Y.3    Onuchic, J.N.4
  • 32
    • 41849107614 scopus 로고    scopus 로고
    • Single molecule conformational dynamics of adenylate kinase: Energy landscape, structural correlations, and transition state ensembles
    • Lu Q, Wang J (2008) Single molecule conformational dynamics of adenylate kinase: Energy landscape, structural correlations, and transition state ensembles. J Am Chem Soc 130(14):4772-4783.
    • (2008) J Am Chem Soc , vol.130 , Issue.14 , pp. 4772-4783
    • Lu, Q.1    Wang, J.2
  • 33
    • 84865350201 scopus 로고    scopus 로고
    • Coarse-Grained simulations of protein-Protein association: An energy landscape perspective
    • Ravikumar KM, Huang W, Yang S (2012) Coarse-Grained simulations of protein-Protein association: An energy landscape perspective. Biophys J 103(4):837-845.
    • (2012) Biophys J , vol.103 , Issue.4 , pp. 837-845
    • Ravikumar, K.M.1    Huang, W.2    Yang, S.3
  • 34
    • 60549089572 scopus 로고    scopus 로고
    • Inherent flexibility determines the transition mechanisms of the EF-Hands of calmodulin
    • Tripathi S, Portman JJ (2009) Inherent flexibility determines the transition mechanisms of the EF-Hands of calmodulin. Proc Natl Acad Sci USA 106(7):2104-2109.
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.7 , pp. 2104-2109
    • Tripathi, S.1    Portman, J.J.2
  • 35
    • 2342471328 scopus 로고    scopus 로고
    • Simulation of an ensemble of conformational transitions in a united-Residue model of calmodulin
    • Zuckerman DM (2004) Simulation of an ensemble of conformational transitions in a united-Residue model of calmodulin. J Phys Chem B 108(16):5127-5137.
    • (2004) J Phys Chem B , vol.108 , Issue.16 , pp. 5127-5137
    • Zuckerman, D.M.1
  • 36
    • 0242368163 scopus 로고    scopus 로고
    • Exploring the interplay between topology and secondary structural formation in the protein folding problem
    • Cheung MS, Finke JM, Callahan B, Onuchic JN (2003) Exploring the interplay between topology and secondary structural formation in the protein folding problem. J Phys Chem B 107(40):11193-11200.
    • (2003) J Phys Chem B , vol.107 , Issue.40 , pp. 11193-11200
    • Cheung, M.S.1    Finke, J.M.2    Callahan, B.3    Onuchic, J.N.4
  • 37
    • 0001166734 scopus 로고
    • The theory of electrolytes. I. Lowering of freezing point and related phenomena
    • Debye P, Hückel E (1923) The theory of electrolytes. I. Lowering of freezing point and related phenomena. Phys Z 24:185-206.
    • (1923) Phys Z , vol.24 , pp. 185-206
    • Debye, P.1    Hückel, E.2
  • 39
    • 0024334344 scopus 로고
    • Changes in the structure of calmodulin induced by a peptide based on the calmodulin-Binding domain of myosin light chain kinase
    • Heidorn DB, et al. (1989) Changes in the structure of calmodulin induced by a peptide based on the calmodulin-Binding domain of myosin light chain kinase. Biochemistry 28(16):6757-6764.
    • (1989) Biochemistry , vol.28 , Issue.16 , pp. 6757-6764
    • Heidorn, D.B.1
  • 40
    • 30344440627 scopus 로고    scopus 로고
    • University of California San Francisco)
    • Case D, et al. (2008) AMBER 10 (University of California, San Francisco).
    • (2008) AMBER , vol.10
    • Case, D.1
  • 41
    • 36549102274 scopus 로고
    • Brownian dynamics simulation of diffusion-Influenced bimolecular reactions
    • Northrup SH, Allison SA, McCammon JA (1984) Brownian dynamics simulation of diffusion-Influenced bimolecular reactions. J Chem Phys 80(4):1517-1526.
    • (1984) J Chem Phys , vol.80 , Issue.4 , pp. 1517-1526
    • Northrup, S.H.1    Allison, S.A.2    McCammon, J.A.3
  • 42
    • 3442896792 scopus 로고    scopus 로고
    • Single-Molecule resonance energy transfer and fluorescence correlation spectroscopy of calmodulin in solution
    • Slaughter BD, Allen MW, Unruh JR, Urbauer RJB, Johnson CK (2004) Single-Molecule resonance energy transfer and fluorescence correlation spectroscopy of calmodulin in solution. J Phys Chem B 108(29):10388-10397.
    • (2004) J Phys Chem B , vol.108 , Issue.29 , pp. 10388-10397
    • Slaughter, B.D.1    Allen, M.W.2    Unruh, J.R.3    Urbauer, R.J.B.4    Johnson, C.K.5
  • 43
    • 0024040620 scopus 로고
    • Brownian dynamics of cytochrome c and cytochrome c peroxidase association
    • Northrup SH, Boles JO, Reynolds JCL (1988) Brownian dynamics of cytochrome c and cytochrome c peroxidase association. Science 241(4861):67-70.
    • (1988) Science , vol.241 , Issue.4861 , pp. 67-70
    • Northrup, S.H.1    Boles, J.O.2    Reynolds, J.C.L.3
  • 44
    • 0030891436 scopus 로고    scopus 로고
    • Simulation of the diffusional association of barnase and barstar
    • Gabdoulline RR, Wade RC (1997) Simulation of the diffusional association of barnase and barstar. Biophys J 72(5):1917-1929.
    • (1997) Biophys J , vol.72 , Issue.5 , pp. 1917-1929
    • Gabdoulline, R.R.1    Wade, R.C.2


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