메뉴 건너뛰기




Volumn 366, Issue 5, 2007, Pages 1661-1671

Conformational Transitions of Adenylate Kinase: Switching by Cracking

Author keywords

conformational change; cracking; energy landscape theory; strain

Indexed keywords

ADENYLATE KINASE;

EID: 33846847773     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.11.085     Document Type: Article
Times cited : (264)

References (43)
  • 1
    • 32344434479 scopus 로고    scopus 로고
    • The changing landscape of protein allostery
    • Swain J., and Gierasch L. The changing landscape of protein allostery. Curr. Opin. Struct. Biol. 16 (2006) 102-108
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 102-108
    • Swain, J.1    Gierasch, L.2
  • 5
    • 0026544877 scopus 로고
    • 5A refined at 1.9 A resolution. A model for a catalytic transition state
    • 5A refined at 1.9 A resolution. A model for a catalytic transition state. J. Mol. Biol. 224 (1992) 159-177
    • (1992) J. Mol. Biol. , vol.224 , pp. 159-177
    • Muller, C.W.1    Schulz, G.E.2
  • 7
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels, and protein function
    • Tsai C.J., Kumar S., Ma B., and Nussinov R. Folding funnels, binding funnels, and protein function. Prot. Sci. 8 (1999) 1181-1190
    • (1999) Prot. Sci. , vol.8 , pp. 1181-1190
    • Tsai, C.J.1    Kumar, S.2    Ma, B.3    Nussinov, R.4
  • 9
    • 0346220393 scopus 로고    scopus 로고
    • The role of dynamics in allosteric regulation
    • Kern D., and Zuiderweg E.R.P. The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13 (2003) 748-757
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 748-757
    • Kern, D.1    Zuiderweg, E.R.P.2
  • 10
    • 0242268469 scopus 로고    scopus 로고
    • Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
    • Miyashita O., Onuchic J.N., and Wolynes P.G. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc. Nat. Acad. Sci. USA 100 (2003) 12570-12575
    • (2003) Proc. Nat. Acad. Sci. USA , vol.100 , pp. 12570-12575
    • Miyashita, O.1    Onuchic, J.N.2    Wolynes, P.G.3
  • 11
    • 13444305369 scopus 로고    scopus 로고
    • Simple energy landscape model for kinetics of functional transitions in proteins
    • Miyashita O., Wolynes P.G., and Onuchic J.N. Simple energy landscape model for kinetics of functional transitions in proteins. J. Phys. Chem. B 109 (2005) 1959-1969
    • (2005) J. Phys. Chem. B , vol.109 , pp. 1959-1969
    • Miyashita, O.1    Wolynes, P.G.2    Onuchic, J.N.3
  • 12
    • 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 J.N., and Wolynes P.G. Multiple-basin energy landscapes for large amplitude conformational motions of proteins: structure-based molecular dynamics simulations. Proc. Nat. Acad. Sci. USA 103 (2006) 11844-11849
    • (2006) Proc. Nat. Acad. Sci. USA , vol.103 , pp. 11844-11849
    • Okazaki, K.1    Koga, N.2    Takada, S.3    Onuchic, J.N.4    Wolynes, P.G.5
  • 13
    • 2342471328 scopus 로고    scopus 로고
    • Simulation of an ensemble of conformational transitions in a united-residue model of calmodulin
    • Zuckerman D.M. Simulation of an ensemble of conformational transitions in a united-residue model of calmodulin. J. Phys. Chem. B 108 (2004) 5127-5137
    • (2004) J. Phys. Chem. B , vol.108 , pp. 5127-5137
    • Zuckerman, D.M.1
  • 14
    • 28844466824 scopus 로고    scopus 로고
    • Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of Arc repressor
    • Best R.B., Chen Y., and Hummer G. Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of Arc repressor. Structure 13 (2005) 1755-1763
    • (2005) Structure , vol.13 , pp. 1755-1763
    • Best, R.B.1    Chen, Y.2    Hummer, G.3
  • 15
    • 24644483073 scopus 로고    scopus 로고
    • Large amplitude conformational change in proteins explored with a plastic network model: adenylate Kinase
    • Maragakis P., and Karplus M. Large amplitude conformational change in proteins explored with a plastic network model: adenylate Kinase. J. Mol. Biol. 352 (2005) 807-822
    • (2005) J. Mol. Biol. , vol.352 , pp. 807-822
    • Maragakis, P.1    Karplus, M.2
  • 16
    • 0016696599 scopus 로고
    • Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effects of specific amino acid sequence represented by specific inter-unit interactions
    • Ueda Y., Taketomi H., and Go N. Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effects of specific amino acid sequence represented by specific inter-unit interactions. Int. J. Pept. Res. 7 (1975) 445-459
    • (1975) Int. J. Pept. Res. , vol.7 , pp. 445-459
    • Ueda, Y.1    Taketomi, H.2    Go, N.3
  • 18
    • 0032568599 scopus 로고    scopus 로고
    • Folding funnels and frustration in off-lattice minimalist protein landscapes
    • Nymeyer H., Garcia A.E., and Onuchic J.N. Folding funnels and frustration in off-lattice minimalist protein landscapes. Proc. Nat. Acad. Sci. USA 95 (1998) 5921-5928
    • (1998) Proc. Nat. Acad. Sci. USA , vol.95 , pp. 5921-5928
    • Nymeyer, H.1    Garcia, A.E.2    Onuchic, J.N.3
  • 19
    • 3142782241 scopus 로고    scopus 로고
    • Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates
    • Chavez L.L., Onuchic J.N., and Clementi C. Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates. J. Am. Chem. Soc. 126 (2004) 8426-8432
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 8426-8432
    • Chavez, L.L.1    Onuchic, J.N.2    Clementi, C.3
  • 20
    • 0035943433 scopus 로고    scopus 로고
    • Prediction of folding mechanism for circular-permuted proteins
    • Clementi C., Jennings P.A., and Onuchic J.N. Prediction of folding mechanism for circular-permuted proteins. J. Mol. Biol. 311 (2001) 879-890
    • (2001) J. Mol. Biol. , vol.311 , pp. 879-890
    • Clementi, C.1    Jennings, P.A.2    Onuchic, J.N.3
  • 21
    • 0034685604 scopus 로고    scopus 로고
    • Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
    • Clementi C., Nymeyer H., and Onuchic J.N. Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J. Mol. Biol. 298 (2000) 937-953
    • (2000) J. Mol. Biol. , vol.298 , pp. 937-953
    • Clementi, C.1    Nymeyer, H.2    Onuchic, J.N.3
  • 22
    • 33645030244 scopus 로고    scopus 로고
    • Topological frustration and the folding of interleukin-1 beta
    • Gosavi S., Chavez L.L., Jennings P.A., and Onuchic J.N. Topological frustration and the folding of interleukin-1 beta. J. Mol. Biol. 357 (2006) 986-996
    • (2006) J. Mol. Biol. , vol.357 , pp. 986-996
    • Gosavi, S.1    Chavez, L.L.2    Jennings, P.A.3    Onuchic, J.N.4
  • 23
    • 33644986099 scopus 로고    scopus 로고
    • Mechanisms of protein assembly: lessons from minimalist models
    • Levy Y., and Onuchic J.N. Mechanisms of protein assembly: lessons from minimalist models. Acc. Chem. Res. 39 (2006) 135-142
    • (2006) Acc. Chem. Res. , vol.39 , pp. 135-142
    • Levy, Y.1    Onuchic, J.N.2
  • 24
    • 14044275168 scopus 로고    scopus 로고
    • Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery
    • Levy Y., Cho S.S., Shen T., Onuchic J.N., and Wolynes P.G. Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery. Proc. Nat. Acad. Sci. USA 102 (2005) 2373-2378
    • (2005) Proc. Nat. Acad. Sci. USA , vol.102 , pp. 2373-2378
    • Levy, Y.1    Cho, S.S.2    Shen, T.3    Onuchic, J.N.4    Wolynes, P.G.5
  • 25
    • 13444301037 scopus 로고    scopus 로고
    • A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes
    • Levy Y., Cho S.S., Onuchic J.N., and Wolynes P.G. A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. J. Mol. Biol. 346 (2005) 1121-1145
    • (2005) J. Mol. Biol. , vol.346 , pp. 1121-1145
    • Levy, Y.1    Cho, S.S.2    Onuchic, J.N.3    Wolynes, P.G.4
  • 27
    • 0026723063 scopus 로고
    • Protein folding funnels- a kinetic approach to the sequence structure relationship
    • Leopold P.E., Montal M., and Onuchic J.N. Protein folding funnels- a kinetic approach to the sequence structure relationship. Proc. Nat. Acad. Sci. USA 18 (1992) 8721-8725
    • (1992) Proc. Nat. Acad. Sci. USA , vol.18 , pp. 8721-8725
    • Leopold, P.E.1    Montal, M.2    Onuchic, J.N.3
  • 28
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein-folding- a synthesis
    • Bryngelson J.D., Onuchic J.N., Socci N.D., and Wolynes P.G. Funnels, pathways, and the energy landscape of protein-folding- a synthesis. Proteins 21 (1995) 167-195
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 33
    • 10844273276 scopus 로고    scopus 로고
    • Associative mechanism for phosphoryl transfer: a molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates
    • Krishnamurthy H., Lou H., Kimple A., Vieille C., and Cukier R. Associative mechanism for phosphoryl transfer: a molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates. Proteins: Struct. Funct. Bioinfo. 58 (2005) 88-100
    • (2005) Proteins: Struct. Funct. Bioinfo. , vol.58 , pp. 88-100
    • Krishnamurthy, H.1    Lou, H.2    Kimple, A.3    Vieille, C.4    Cukier, R.5
  • 37
    • 0023449962 scopus 로고
    • Spin-glasses and the statistical mechanics of protein folding
    • Bryngelson J.D., and Wolynes P.G. Spin-glasses and the statistical mechanics of protein folding. Proc. Nat. Acad. Sci. USA 84 (1987) 7524-7528
    • (1987) Proc. Nat. Acad. Sci. USA , vol.84 , pp. 7524-7528
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 39
    • 4243819810 scopus 로고
    • New Monte Carlo technique for studying phase transitions
    • Ferrenberg A.M., and Swendsen R.H. New Monte Carlo technique for studying phase transitions. Phys. Rev. Letters. 61 (1988) 2635-2638
    • (1988) Phys. Rev. Letters. , vol.61 , pp. 2635-2638
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 41
    • 0000009443 scopus 로고
    • Rapid comparison of protein structures
    • McLachlan A.D. Rapid comparison of protein structures. Acta. Cryst. A. 38 (1982) 871-873
    • (1982) Acta. Cryst. A. , vol.38 , pp. 871-873
    • McLachlan, A.D.1
  • 42
    • 0029644168 scopus 로고    scopus 로고
    • Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding
    • Mueller C.W., Schlauderer G.J., Reinstein J., and Schulz G.E. Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding. Structure 4 (1996) 147-156
    • (1996) Structure , vol.4 , pp. 147-156
    • Mueller, C.W.1    Schlauderer, G.J.2    Reinstein, J.3    Schulz, G.E.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.