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Volumn 2014, Issue 3, 2014, Pages

Encounter complexes and dimensionality reduction in protein-protein association

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; RETINOID X RECEPTOR ALPHA; PROTEIN; PROTEIN BINDING;

EID: 84898410458     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.01370     Document Type: Article
Times cited : (54)

References (52)
  • 1
    • 74849106907 scopus 로고    scopus 로고
    • Visualization of the encounter ensemble of the transient electron transfer complex of cytochrome c and cytochrome c peroxidase
    • doi: 10.1021/Ja9064574
    • Bashir Q, Volkov AN, Ullmann GM, Ubbink M. 2010. Visualization of the encounter ensemble of the transient electron transfer complex of cytochrome c and cytochrome c peroxidase. Journal of the American Chemical Society 132:241-247. doi: 10.1021/Ja9064574.
    • (2010) Journal of the American Chemical Society , vol.132 , pp. 241-247
    • Bashir, Q.1    Volkov, A.N.2    Ullmann, G.M.3    Ubbink, M.4
  • 3
  • 4
    • 0034049350 scopus 로고    scopus 로고
    • Kinetics of desolvation-mediated protein-protein binding
    • doi: 10.1016/S0006-3495(00)76668-9
    • Camacho CJ, Kimura SR, DeLisi C, Vajda S. 2000. Kinetics of desolvation-mediated protein-protein binding. Biophysical Journal 78:1094-1105. doi: 10.1016/S0006-3495(00)76668-9.
    • (2000) Biophysical Journal , vol.78 , pp. 1094-1105
    • Camacho, C.J.1    Kimura, S.R.2    Delisi, C.3    Vajda, S.4
  • 5
    • 0032981961 scopus 로고    scopus 로고
    • Free energy landscapes of encounter complexes in protein-protein association
    • doi: 10.1016/S0006-3495(99)77281-4
    • Camacho CJ, Weng Z, Vajda S, DeLisi C. 1999. Free energy landscapes of encounter complexes in protein-protein association. Biophysical Journal 76:1166-1178. doi: 10.1016/S0006-3495(99)77281-4.
    • (1999) Biophysical Journal , vol.76 , pp. 1166-1178
    • Camacho, C.J.1    Weng, Z.2    Vajda, S.3    Delisi, C.4
  • 6
    • 75449096571 scopus 로고    scopus 로고
    • Cross-talk between PPARs and the partners of RXR: A molecular perspective
    • doi: 10.1155/2009/925309
    • Chan LSA, Wells RA. 2009. Cross-talk between PPARs and the partners of RXR: a molecular perspective. PPAR Research 2009:925309. doi: 10.1155/2009/925309.
    • (2009) PPAR Research , pp. 925309
    • Chan, L.S.A.1    Wells, R.A.2
  • 7
    • 0038187615 scopus 로고    scopus 로고
    • A protein-protein docking benchmark
    • doi: 10.1002/prot.10390
    • Chen R, Mintseris J, Janin J, Weng Z. 2003. A protein-protein docking benchmark. Proteins 52:88-91. doi: 10.1002/prot.10390.
    • (2003) Proteins , vol.52 , pp. 88-91
    • Chen, R.1    Mintseris, J.2    Janin, J.3    Weng, Z.4
  • 8
    • 58149152509 scopus 로고    scopus 로고
    • DARS (Decoys as the reference state) potentials for protein-protein docking
    • doi: 10.1529/biophysj.108.135814
    • Chuang GY, Kozakov D, Brenke R, Comeau SR, Vajda S. 2008. DARS (Decoys as the reference state) potentials for protein-protein docking. Biophysical Journal 95:4217-4227. doi: 10.1529/biophysj.108.135814.
    • (2008) Biophysical Journal , vol.95 , pp. 4217-4227
    • Chuang, G.Y.1    Kozakov, D.2    Brenke, R.3    Comeau, S.R.4    Vajda, S.5
  • 9
    • 58149354711 scopus 로고    scopus 로고
    • Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement
    • doi: 10.1039/B810232e
    • Clore GM. 2008. Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement. Molecular Biosystems 4:1058-1069. doi: 10.1039/B810232e.
    • (2008) Molecular Biosystems , vol.4 , pp. 1058-1069
    • Clore, G.M.1
  • 10
    • 70349093561 scopus 로고    scopus 로고
    • Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes
    • doi: 10.1021/cr900033p
    • Clore GM, Iwahara J. 2009. Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. Chemical Reviews 109:4108-4139. doi: 10.1021/cr900033p.
    • (2009) Chemical Reviews , vol.109 , pp. 4108-4139
    • Clore, G.M.1    Iwahara, J.2
  • 11
    • 36749031065 scopus 로고    scopus 로고
    • ClusPro: Performance in CAPRI rounds 6-11 and the new server
    • doi: 10.1002/prot.21795
    • Comeau SR, Kozakov D, Brenke R, Shen Y, Beglov D, Vajda S. 2007. ClusPro: performance in CAPRI rounds 6-11 and the new server. Proteins 69:781-785. doi: 10.1002/prot.21795.
    • (2007) Proteins , vol.69 , pp. 781-785
    • Comeau, S.R.1    Kozakov, D.2    Brenke, R.3    Shen, Y.4    Beglov, D.5    Vajda, S.6
  • 12
    • 0036829797 scopus 로고    scopus 로고
    • Solution structure of the phosphoryl transfer complex between the cytoplasmic A domain of the mannitol transporter IIMannitol and HPr of the Escherichia coli phoshotransferase system
    • doi: 10.1074/Jbc.M207314200
    • Cornilescu G, Lee BR, Cornilescu CC, Wang GS, Peterkofsky A, Clore GM. 2002. Solution structure of the phosphoryl transfer complex between the cytoplasmic A domain of the mannitol transporter IIMannitol and HPr of the Escherichia coli phoshotransferase system. The Journal Biological Chemistry 277:42289-42298. doi: 10.1074/Jbc.M207314200.
    • (2002) The Journal Biological Chemistry , vol.277 , pp. 42289-42298
    • Cornilescu, G.1    Lee, B.R.2    Cornilescu, C.C.3    Wang, G.S.4    Peterkofsky, A.5    Clore, G.M.6
  • 13
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to Pathways to Funnels
    • doi: 10.1038/ nsb0197-10
    • Dill KA, Chan HS. 1997. From Levinthal to pathways to funnels. Nat Struct Biol 4:10-19. doi: 10.1038/ nsb0197-10.
    • (1997) Nat Struct Biol , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 14
    • 76549128494 scopus 로고    scopus 로고
    • Mechanistic details of a protein-protein association pathway revealed by paramagnetic relaxation enhancement titration measurements
    • doi: 10.1073/pnas.0909370107
    • Fawzi NL, Doucleff M, Suh JY, Clore GM. 2010. Mechanistic details of a protein-protein association pathway revealed by paramagnetic relaxation enhancement titration measurements. Proceedings of the National Academy of Sciences of the United States of America 107:1379-1384. doi: 10.1073/pnas.0909370107.
    • (2010) Proceedings of the National Academy of Sciences of the United States of America , vol.107 , pp. 1379-1384
    • Fawzi, N.L.1    Doucleff, M.2    Suh, J.Y.3    Clore, G.M.4
  • 16
    • 0032939176 scopus 로고    scopus 로고
    • Solution structure of the 40,000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr
    • doi: 10.1038/5854
    • Garrett DS, Seok YJ, Peterkofsky A, Gronenborn AM, Clore GM. 1999. Solution structure of the 40,000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr. Nature Structural Biology 6:166-173. doi: 10.1038/5854.
    • (1999) Nature Structural Biology , vol.6 , pp. 166-173
    • Garrett, D.S.1    Seok, Y.J.2    Peterkofsky, A.3    Gronenborn, A.M.4    Clore, G.M.5
  • 17
    • 49449107340 scopus 로고    scopus 로고
    • Visualizing one-dimensional diffusion of proteins along DNA
    • doi: 10.1038/Nsmb.1441
    • Gorman J, Greene EC. 2008. Visualizing one-dimensional diffusion of proteins along DNA. Nature Structural & Molecular Biology 15:768-774. doi: 10.1038/Nsmb.1441.
    • (2008) Nature Structural & Molecular Biology , vol.15 , pp. 768-774
    • Gorman, J.1    Greene, E.C.2
  • 18
    • 0002321764 scopus 로고    scopus 로고
    • Practical parameterization of rotations using the exponential map
    • doi: 10.1080/10867651.1998.10487493
    • Grassia SF. 1998. Practical parameterization of rotations using the exponential map. Journal of Graphics Tools 3:29-48. doi: 10.1080/10867651.1998.10487493.
    • (1998) Journal of Graphics Tools , vol.3 , pp. 29-48
    • Grassia, S.F.1
  • 19
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • doi: 10.1016/S0022-2836(03)00670-3
    • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. 2003. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. Journal of Molecular Biology 331:281-299. doi: 10.1016/S0022-2836(03)00670-3.
    • (2003) Journal of Molecular Biology , vol.331 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 20
    • 33646356250 scopus 로고    scopus 로고
    • Detecting transient intermediates in macromolecular binding by paramagnetic NMR
    • doi: 10.1038/nature04673
    • Iwahara J, Clore GM. 2006. Detecting transient intermediates in macromolecular binding by paramagnetic NMR. Nature 440:1227-1230. doi: 10.1038/nature04673.
    • (2006) Nature , vol.440 , pp. 1227-1230
    • Iwahara, J.1    Clore, G.M.2
  • 21
    • 5644226078 scopus 로고    scopus 로고
    • Characterization of nonspecific protein-DNA interactions by H-1 paramagnetic relaxation enhancement
    • doi: 10.1021/Ja046246b
    • Iwahara J, Schwieters CD, Clore GM. 2004. Characterization of nonspecific protein-DNA interactions by H-1 paramagnetic relaxation enhancement. Journal of the American Chemical Society 126:12800-12808. doi: 10.1021/Ja046246b.
    • (2004) Journal of the American Chemical Society , vol.126 , pp. 12800-12808
    • Iwahara, J.1    Schwieters, C.D.2    Clore, G.M.3
  • 25
    • 33749020839 scopus 로고    scopus 로고
    • PIPER: An FFT-based protein docking program with pairwise potentials
    • doi: 10.1002/prot.21117
    • Kozakov D, Brenke R, Comeau SR, Vajda S. 2006. PIPER: an FFT-based protein docking program with pairwise potentials. Proteins 65:392-406. doi: 10.1002/prot.21117.
    • (2006) Proteins , vol.65 , pp. 392-406
    • Kozakov, D.1    Brenke, R.2    Comeau, S.R.3    Vajda, S.4
  • 26
    • 77957963055 scopus 로고    scopus 로고
    • Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19
    • doi: 10.1002/prot.22835
    • Kozakov D, Hall DR, Beglov D, Brenke R, Comeau SR, Shen Y, Li K, Zheng J, Vakili P, Paschalidis ICH, Vajda S. 2010. Achieving reliability and high accuracy in automated protein docking: clusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19. Proteins 78:3124-3130. doi: 10.1002/prot.22835.
    • (2010) Proteins , vol.78 , pp. 3124-3130
    • Kozakov, D.1    Hall, D.R.2    Beglov, D.3    Brenke, R.4    Comeau, S.R.5    Shen, Y.6    Li, K.7    Zheng, J.8    Vakili, P.9    Paschalidis, I.C.H.10    Vajda, S.11
  • 29
    • 84888289172 scopus 로고    scopus 로고
    • Docking, scoring, and affinity prediction in CAPRI
    • doi: 10.1002/prot.24428
    • Lensink MF, Wodak SJ. 2013. Docking, scoring, and affinity prediction in CAPRI. Proteins 81:2082-2095. doi: 10.1002/prot.24428.
    • (2013) Proteins , vol.81 , pp. 2082-2095
    • Lensink, M.F.1    Wodak, S.J.2
  • 30
    • 0032054612 scopus 로고    scopus 로고
    • Theory of biomolecular recognition
    • doi: 10.1016/S0959-440X(98)80046-8
    • McCammon JA. 1998. Theory of biomolecular recognition. Current Opinion In Structural Biology 8:245-249. doi: 10.1016/S0959-440X(98)80046-8.
    • (1998) Current Opinion In Structural Biology , vol.8 , pp. 245-249
    • McCammon, J.A.1
  • 33
    • 0029272466 scopus 로고
    • Distance metrics on the rigid-body motions with applications to mechanism design
    • doi: 10.1115/1.2826116
    • Park FC. 1995. Distance metrics on the rigid-body motions with applications to mechanism design. Journal of Mechanical Design 117:48-54. doi: 10.1115/1.2826116.
    • (1995) Journal of Mechanical Design , vol.117 , pp. 48-54
    • Park, F.C.1
  • 34
    • 0031189315 scopus 로고    scopus 로고
    • Smooth invariant interpolation of rotations
    • doi: 10.1145/256157.256160
    • Park FC, Ravani B. 1997. Smooth invariant interpolation of rotations. ACM Transactions on Graphic 16:277-295. doi: 10.1145/256157.256160.
    • (1997) ACM Transactions On Graphic , vol.16 , pp. 277-295
    • Park, F.C.1    Ravani, B.2
  • 35
    • 0014945567 scopus 로고
    • Lac repressor-operator interaction. 3. Kinetic studies
    • doi: 10.1016/0022-2836(70)90074-4
    • Riggs AD, Bourgeoi S, Cohn M. 1970. Lac repressor-operator interaction. 3. Kinetic studies. Journal of Molecular Biology 53:401-417. doi: 10.1016/0022-2836(70)90074-4.
    • (1970) Journal of Molecular Biology , vol.53 , pp. 401-417
    • Riggs, A.D.1    Bourgeoi, S.2    Cohn, M.3
  • 36
    • 65249099497 scopus 로고    scopus 로고
    • Fundamental aspects of protein-protein association kinetics
    • doi: 10.1021/Cr800373w
    • Schreiber G, Haran G, Zhou HX. 2009. Fundamental aspects of protein-protein association kinetics. Chemical Reviews 109:839-860. doi: 10.1021/Cr800373w.
    • (2009) Chemical Reviews , vol.109 , pp. 839-860
    • Schreiber, G.1    Haran, G.2    Zhou, H.X.3
  • 37
    • 0035889692 scopus 로고    scopus 로고
    • New insights into the mechanism of protein-protein association
    • doi: 10.1002/Prot.1139
    • Selzer T, Schreiber G. 2001. New insights into the mechanism of protein-protein association. Proteins Structure Function and Genetics 45:190-198. doi: 10.1002/Prot.1139.
    • (2001) Proteins Structure Function and Genetics , vol.45 , pp. 190-198
    • Selzer, T.1    Schreiber, G.2
  • 38
    • 55449101982 scopus 로고    scopus 로고
    • Protein docking by the underestimation of free energy funnels in the space of encounter complexes
    • doi: 10.1371/journal.pcbi.1000191
    • Shen Y, Paschalidis I, Vakili P, Vajda S. 2008. Protein docking by the underestimation of free energy funnels in the space of encounter complexes. PLOS Computational Biology 4:e1000191. doi: 10.1371/journal.pcbi.1000191.
    • (2008) PLOS Computational Biology , vol.4
    • Shen, Y.1    Paschalidis, I.2    Vakili, P.3    Vajda, S.4
  • 40
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • doi: 10.1016/S0959-440X(02)00285-3
    • Smith GR, Sternberg MJ. 2002. Prediction of protein-protein interactions by docking methods. Current Opinion In Structural Biology 12:28-35. doi: 10.1016/S0959-440X(02)00285-3.
    • (2002) Current Opinion In Structural Biology , vol.12 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.2
  • 41
    • 33646200644 scopus 로고    scopus 로고
    • Free energy landscape of protein-protein encounter resulting from Brownian dynamics simulations of Barnase: Barstar
    • doi: 10.1021/Ct050036n
    • Spaar A, Helms V. 2005. Free energy landscape of protein-protein encounter resulting from Brownian dynamics simulations of Barnase: Barstar. Journal of Chemical Theory and Computation 1:723-736. doi: 10.1021/Ct050036n.
    • (2005) Journal of Chemical Theory and Computation , vol.1 , pp. 723-736
    • Spaar, A.1    Helms, V.2
  • 42
    • 49649105539 scopus 로고    scopus 로고
    • Impact of phosphorylation on structure and thermodynamics of the interaction between the N-terminal domain of enzyme I and the histidine phosphocarrier protein of the bacterial phosphotransferase system
    • doi: 10.1074/Jbc.M802211200
    • Suh JY, Cai ML, Clore GM. 2008. Impact of phosphorylation on structure and thermodynamics of the interaction between the N-terminal domain of enzyme I and the histidine phosphocarrier protein of the bacterial phosphotransferase system. The Journal of Biological Chemistry 283:18980-18989. doi: 10.1074/Jbc.M802211200.
    • (2008) The Journal of Biological Chemistry , vol.283 , pp. 18980-18989
    • Suh, J.Y.1    Cai, M.L.2    Clore, G.M.3
  • 43
    • 35848929057 scopus 로고    scopus 로고
    • Role of electrostatic interactions in transient encounter complexes in protein-protein association investigated by paramagnetic relaxation enhancement
    • doi: 10.1021/Ja0760978
    • Suh JY, Tang C, Clore GM. 2007. Role of electrostatic interactions in transient encounter complexes in protein-protein association investigated by paramagnetic relaxation enhancement. Journal of the American Chemical Society 129:12954-12960. doi: 10.1021/Ja0760978.
    • (2007) Journal of the American Chemical Society , vol.129 , pp. 12954-12960
    • Suh, J.Y.1    Tang, C.2    Clore, G.M.3
  • 44
    • 41149167049 scopus 로고    scopus 로고
    • Visualization of transient ultra-weak protein self-association in solution using paramagnetic relaxation enhancement
    • doi: 10.1021/Ja710493m
    • Tang C, Ghirlando R, Clore GM. 2008. Visualization of transient ultra-weak protein self-association in solution using paramagnetic relaxation enhancement. Journal of the American Chemical Society 130:4048-4056. doi: 10.1021/Ja710493m.
    • (2008) Journal of the American Chemical Society , vol.130 , pp. 4048-4056
    • Tang, C.1    Ghirlando, R.2    Clore, G.M.3
  • 45
    • 33751086423 scopus 로고    scopus 로고
    • Visualization of transient encounter complexes in protein-protein association
    • doi: 10.1038/Nature05201
    • Tang C, Iwahara J, Clore GM. 2006. Visualization of transient encounter complexes in protein-protein association. Nature 444:383-386. doi: 10.1038/Nature05201.
    • (2006) Nature , vol.444 , pp. 383-386
    • Tang, C.1    Iwahara, J.2    Clore, G.M.3
  • 46
    • 0034916879 scopus 로고    scopus 로고
    • How common is the funnel-like energy landscape in protein-protein interactions?
    • doi: 10.1110/Ps.8701
    • Tovchigrechko A, Vakser IA. 2001. How common is the funnel-like energy landscape in protein-protein interactions? Protein Science 10:1572-1583. doi: 10.1110/Ps.8701.
    • (2001) Protein Science , vol.10 , pp. 1572-1583
    • Tovchigrechko, A.1    Vakser, I.A.2
  • 47
    • 62849090890 scopus 로고    scopus 로고
    • The courtship of proteins: Understanding the encounter complex
    • doi: 10.1016/j.febslet.2009.02.046
    • Ubbink M. 2009. The courtship of proteins: understanding the encounter complex. FEBS Letters 583:1060-1066. doi: 10.1016/j.febslet.2009.02.046.
    • (2009) FEBS Letters , vol.583 , pp. 1060-1066
    • Ubbink, M.1
  • 48
    • 64549106038 scopus 로고    scopus 로고
    • Convergence and combination of methods in protein-protein docking
    • doi: 10.1016/j.sbi.2009.02.008
    • Vajda S, Kozakov D. 2009. Convergence and combination of methods in protein-protein docking. Current Opinion In Structural Biology 19:164-170. doi: 10.1016/j.sbi.2009.02.008.
    • (2009) Current Opinion In Structural Biology , vol.19 , pp. 164-170
    • Vajda, S.1    Kozakov, D.2
  • 50
    • 0037230970 scopus 로고    scopus 로고
    • Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation
    • doi: 10.1002/prot.10248
    • Wang T, Wade RC. 2003. Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation. Proteins 50:158-169. doi: 10.1002/prot.10248.
    • (2003) Proteins , vol.50 , pp. 158-169
    • Wang, T.1    Wade, R.C.2
  • 51
    • 0033081069 scopus 로고    scopus 로고
    • Protein-protein Recognition: Exploring the Energy Funnels Near the Binding Sites
    • doi: 10.1002/(SICI)1097-0134(19990201)34:2<255::AID-PROT10>3.0.CO;2-O
    • Zhang C, Chen J, DeLisi C. 1999. Protein-protein recognition: exploring the energy funnels near the binding sites. Proteins 34:255-267. doi: 10.1002/(SICI)1097-0134(19990201)34:2<255::AID-PROT10>3.0.CO;2-O.
    • (1999) Proteins , vol.34 , pp. 255-267
    • Zhang, C.1    Chen, J.2    Delisi, C.3


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