SCOPUS 정보 검색 플랫폼

Physical Chemistry Chemical Physics

Volumn 13, Issue 22, 2011, Pages 10527-10537

A mesoscopic model for protein enzymatic dynamics in solution

(4) Echeverria, Carlos a Togashi, Yuichi b Mikhailov, Alexander S c Kapral, Raymond d

a UNIVERSIDAD NACIONAL EXPERIMENTAL DEL TÁCHIRA (Venezuela)

b OSAKA UNIVERSITY (Japan)

c FRITZ HABER INSTITUT DER MAX PLANCK GESELLSCHAFT (Germany)

d UNIVERSITY OF TORONTO (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ADENYLATE KINASE;

ARTICLE; BIOCATALYSIS; CHEMISTRY; MOLECULAR DYNAMICS; PROTEIN TERTIARY STRUCTURE; SOLUTION AND SOLUBILITY; THERMODYNAMICS;

ADENYLATE KINASE; BIOCATALYSIS; MOLECULAR DYNAMICS SIMULATION; PROTEIN STRUCTURE, TERTIARY; SOLUTIONS; THERMODYNAMICS;

EID: 79959742605 PISSN: 14639076 EISSN: None Source Type: Journal
DOI: 10.1039/c1cp00003a Document Type: Article

Times cited : (38)

References (68)

1
- 0003880161
- Garland, New York, 4th edn
- B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts and P. Walter, Molecular Biology of the Cell, Garland, New York, 4th edn, 1994
- (1994) Molecular Biology of the Cell
- Alberts, B.¹ Johnson, A.² Lewis, J.³ Raff, M.⁴ Roberts, K.⁵ Walter, P.⁶

2
- 79959712820
- J. A. McCammon M. Karplus Annu. Rev. Phys. Chem. Soc. 1980 131 24 45
- (1980) Annu. Rev. Phys. Chem. Soc. , vol.131 , pp. 24-45
- McCammon, J.A.¹ Karplus, M.²

3
- 33646943202
- S. A. Adcock J. A. McCammon Chem. Rev. 2006 106 1589 1615
- (2006) Chem. Rev. , vol.106 , pp. 1589-1615
- Adcock, S.A.¹ McCammon, J.A.²

4
- 77957937199
- D. E. Shaw P. Maragakis K. Lindorff-Larsen S. Piana R. O. Dror M. P. Eastwood J. A. Bank J. M. Jumper J. K. Salmon Y. Shan W. Wriggers Science 2010 330 341 346
- (2010) Science , vol.330 , pp. 341-346
- Shaw, D.E.¹ Maragakis, P.² Lindorff-Larsen, K.³ Piana, S.⁴ Dror, R.O.⁵ Eastwood, M.P.⁶ Bank, J.A.⁷ Jumper, J.M.⁸ Salmon, J.K.⁹ Shan, Y.¹⁰ Wriggers, W.¹¹

5
- 76149136021
- V. A. Voelz G. R. Bowman K. Beauchamp V. S. Pande J. Am. Chem. Soc. 2010 132 1526 1528
- (2010) J. Am. Chem. Soc. , vol.132 , pp. 1526-1528
- Voelz, V.A.¹ Bowman, G.R.² Beauchamp, K.³ Pande, V.S.⁴

6
- 25844431698
- I. Bahar A. J. Rader Curr. Opin. Struct. Biol. 2010 15 586 592
- (2010) Curr. Opin. Struct. Biol. , vol.15 , pp. 586-592
- Bahar, I.¹ Rader, A.J.²

7
- 43949106243
- CRC Press, New York, Boca Raton
- G. A. Voth, Coarse-graining of Condensed Phase and Biomolecular Systems, CRC Press, New York, Boca Raton, 2008
- (2008) Coarse-graining of Condensed Phase and Biomolecular Systems
- Voth, G.A.¹

8
- 2342473866
- S. O. Nielsen C. F. Lopez G. Srinivas M. L. Klein J. Phys.: Condens. Matter 2004 16 R481 R512
- (2004) J. Phys.: Condens. Matter , vol.16
- Nielsen, S.O.¹ Lopez, C.F.² Srinivas, G.³ Klein, M.L.⁴

9
- 33750980984
- M. Venturoli M. M. Sperotto M. Kranenburg B. Smit J. Phys: Condens. Matter 2006 437 1 54
- (2006) J. Phys: Condens. Matter , vol.437 , pp. 1-54
- Venturoli, M.¹ Sperotto, M.M.² Kranenburg, M.³ Smit, B.⁴

10
- 78650486482
- H. Flechsig A. S. Mikhailov Proc. Natl. Acad. Sci. U. S. A. 2010 107 20863 20869
- (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 20863-20869
- Flechsig, H.¹ Mikhailov, A.S.²

11
- 0001468477
- A. Malevanets R. Kapral J. Chem. Phys. 1999 110 8605 8613
- (1999) J. Chem. Phys. , vol.110 , pp. 8605-8613
- Malevanets, A.¹ Kapral, R.²

12
- 0000989411
- A. Malevanets R. Kapral J. Chem. Phys. 2000 112 7260 7269
- (2000) J. Chem. Phys. , vol.112 , pp. 7260-7269
- Malevanets, A.¹ Kapral, R.²

13
- 43949106243
- CRC Press, New York, 1st edn
- V. Tozzini and J. A. McCammon, Coarse-graining of Condensed Phase and Biomolecular Systems, CRC Press, New York, 1st edn, 2008
- (2008) Coarse-graining of Condensed Phase and Biomolecular Systems
- Tozzini, V.¹ McCammon, J.A.²

14
- 79959711454
- unpublished
- More refined models, where the diffusive, binding and unbinding dynamics of substrates and products are explicitly taken into account and explicity solvent-bead interactions are included, can be constructed. Such a model was constructed to study the enzymatic dynamics of phosphoglycerate kinase [P. Inder, J. M. Schofield and R. Kapral, unpublished]
- Inder, P.¹ Schofield, J.M.² Kapral, R.³

15
- 43449104714
- (R)
- A. Cressman Y. Togashi A. S. Mikhailov R. Kapral Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 2008 77 050901
- (2008) Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. , vol.77 , pp. 050901
- Cressman, A.¹ Togashi, Y.² Mikhailov, A.S.³ Kapral, R.⁴

16
- 24644483073
- P. Maragakis M. Karplus J. Mol. Biol. 2005 352 807 822
- (2005) J. Mol. Biol. , vol.352 , pp. 807-822
- Maragakis, P.¹ Karplus, M.²

17
- 33747065536
- K. Okazaki N. Koga S. Takada J. Onuchic P. Wolynes Proc. Natl. Acad. Sci. U. S. A. 2006 103 11844 11849
- (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , pp. 11844-11849
- Okazaki, K.¹ Koga, N.² Takada, S.³ Onuchic, J.⁴ Wolynes, P.⁵

18
- 0000197372
- M. M. Tirion Phys. Rev. Lett. 1996 77 1905 1908
- (1996) Phys. Rev. Lett. , vol.77 , pp. 1905-1908
- Tirion, M.M.¹

19
- 0000243262
- N. G Annu. Rev. Biophys. Bioeng. 1983 12 182 210
- (1983) Annu. Rev. Biophys. Bioeng. , vol.12 , pp. 182-210

20
- 0242268469
- O. Miyashita J. N. Onuchic P. G. Wolynes Proc. Natl. Acad. Sci. U. S. A. 2003 100 12570 12575
- (2003) Proc. Natl. Acad. Sci. U. S. A. , vol.100 , pp. 12570-12575
- Miyashita, O.¹ Onuchic, J.N.² Wolynes, P.G.³

21
- 36849057606
- J.-W. Chu G. A. Voth Biophys. J. 2007 93 3860 3871
- (2007) Biophys. J. , vol.93 , pp. 3860-3871
- Chu, J.-W.¹ Voth, G.A.²

22
- 63849186682
- R. Kapral Adv. Chem. Phys. 2008 140 89 146
- (2008) Adv. Chem. Phys. , vol.140 , pp. 89-146
- Kapral, R.¹

23
- 60749102237
- G. Gompper T. Ihle D. M. Kroll R. G. Winkler Adv. Polym. Sci. 2009 221 1 87
- (2009) Adv. Polym. Sci. , vol.221 , pp. 1-87
- Gompper, G.¹ Ihle, T.² Kroll, D.M.³ Winkler, R.G.⁴

24
- 0034596580
- A similar model was constructed for a nanoscale swimmer whose dynamics was described deterministically in the overdamped limit
- A. Malevanets J. M. Yeomans Europhys. Lett. 2000 52 231 237
- (2000) Europhys. Lett. , vol.52 , pp. 231-237
- Malevanets, A.¹ Yeomans, J.M.²

25
- 77954563196
- T. Sakaue R. Kapral A. S. Mikhailov Eur. Phys. J. B 2010 75 381 387
- (2010) Eur. Phys. J. B , vol.75 , pp. 381-387
- Sakaue, T.¹ Kapral, R.² Mikhailov, A.S.³

26
- 67149111580
- P. Dzeja A. Terzic Int. J. Mol. Sci. 2009 10 1729 1772
- (2009) Int. J. Mol. Sci. , vol.10 , pp. 1729-1772
- Dzeja, P.¹ Terzic, A.²

27
- 36749083505
- J. A. Hanson K. Duderstadt L. P. Watkins S. Bhattacharyya J. Brokaw J.-W. Chu H. Yang Proc. Natl. Acad. Sci. U. S. A. 2007 104 18055 18060
- (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 18055-18060
- Hanson, J.A.¹ Duderstadt, K.² Watkins, L.P.³ Bhattacharyya, S.⁴ Brokaw, J.⁵ Chu, J.-W.⁶ Yang, H.⁷

28
- 76249127905
- Y. Santosoa C. M. Joyceb O. Potapovab L. L. Restea J. Hohlbeina J. P. Torellaa N. D. F. Grindleyb A. N. Kapanidisa Proc. Natl. Acad. Sci. U. S. A. 2010 107 715 720
- (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 715-720
- Santosoa, Y.¹ Joyceb, C.M.² Potapovab, O.³ Restea, L.L.⁴ Hohlbeina, J.⁵ Torellaa, J.P.⁶ Grindleyb, N.D.F.⁷ Kapanidisa, A.N.⁸

29
- 70349462451
- A. Korkut W. A. Hendrickson Proc. Natl. Acad. Sci. U. S. A. 2009 106 15673 15678
- (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 15673-15678
- Korkut, A.¹ Hendrickson, W.A.²

30
- 36148979311
- J. Aden M. Wolf-Watz J. Am. Chem. Soc. 2007 129 14003 14012
- (2007) J. Am. Chem. Soc. , vol.129 , pp. 14003-14012
- Aden, J.¹ Wolf-Watz, M.²

31
- 33846847773
- P. Whitford O. Miyashita Y. Levy J. Onuchic J. Mol. Biol. 2007 366 1661 1671
- (2007) J. Mol. Biol. , vol.366 , pp. 1661-1671
- Whitford, P.¹ Miyashita, O.² Levy, Y.³ Onuchic, J.⁴

32
- 38349092279
- P. Whitford S. Gosavi J. Onuchic J. Biol. Chem. 2008 283 2042 2048
- (2008) J. Biol. Chem. , vol.283 , pp. 2042-2048
- Whitford, P.¹ Gosavi, S.² Onuchic, J.³

33
- 49649084492
- K. Okazaki S. Takada Proc. Natl. Acad. Sci. U. S. A. 2008 105 11182 11187
- (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 11182-11187
- Okazaki, K.¹ Takada, S.²

34
- 10844273276
- H. Krishnamurthy H. Lou A. Kimple C. Vieille R. I. Cukier Proteins: Struct., Funct., Bioinf. 2005 58 88 100
- (2005) Proteins: Struct., Funct., Bioinf. , vol.58 , pp. 88-100
- Krishnamurthy, H.¹ Lou, H.² Kimple, A.³ Vieille, C.⁴ Cukier, R.I.⁵

35
- 33846050049
- H. Lou R. I. Cukier J. Phys. Chem. B 2006 110 24121 24137
- (2006) J. Phys. Chem. B , vol.110 , pp. 24121-24137
- Lou, H.¹ Cukier, R.I.²

36
- 0028491137
- P. Kern R. M. Brunne G. Folkers J. Comput.-Aided Mol. Des. 1994 8 367 388
- (1994) J. Comput.-Aided Mol. Des. , vol.8 , pp. 367-388
- Kern, P.¹ Brunne, R.M.² Folkers, G.³

37
- 36749008588
- K. Arora C. L. Brooks Proc. Natl. Acad. Sci. U. S. A. 2007 104 18496 18501
- (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 18496-18501
- Arora, K.¹ Brooks, C.L.²

38
- 33947431555
- C. Snow G. Qi S. Hayward Proteins: Struct., Funct., Bioinf. 2007 67 325 337
- (2007) Proteins: Struct., Funct., Bioinf. , vol.67 , pp. 325-337
- Snow, C.¹ Qi, G.² Hayward, S.³

39
- 6344231648
- N. A. Temiz E. Meirovitch I. Bahar Proteins: Struct., Funct., Bioinf. 2004 57 468 480
- (2004) Proteins: Struct., Funct., Bioinf. , vol.57 , pp. 468-480
- Temiz, N.A.¹ Meirovitch, E.² Bahar, I.³

40
- 70350146298
- O. Beckstein E. J. Denning J. R. Perilla T. B. Woolf J. Mol. Biol. 2009 394 160 176
- (2009) J. Mol. Biol. , vol.394 , pp. 160-176
- Beckstein, O.¹ Denning, E.J.² Perilla, J.R.³ Woolf, T.B.⁴

41
- 0035807849
- Q. Ruan K. Ruan C. Balny M. Glaser W. W. Mantulin Biol. Chem. 2001 40 14706 14714
- (2001) Biol. Chem. , vol.40 , pp. 14706-14714
- Ruan, Q.¹ Ruan, K.² Balny, C.³ Glaser, M.⁴ Mantulin, W.W.⁵

42
- 0346497938
- D. C. Fry S. A. Kuby A. S. Mildvan Proc. Natl. Acad. Sci. U. S. A. 1986 83 907 911
- (1986) Proc. Natl. Acad. Sci. U. S. A. , vol.83 , pp. 907-911
- Fry, D.C.¹ Kuby, S.A.² Mildvan, A.S.³

43
- 33144487234
- E. Bae G. N. Phillips Proc. Natl. Acad. Sci. U. S. A. 2006 103 2132 2137
- (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , pp. 2132-2137
- Bae, E.¹ Phillips, G.N.²

44
- 0029949248
- M. A. Sinev E. V. Sineva V. Ittah E. Haas Biochemistry 1996 35 6425 6435
- (1996) Biochemistry , vol.35 , pp. 6425-6435
- Sinev, M.A.¹ Sineva, E.V.² Ittah, V.³ Haas, E.⁴

45
- 0024438829
- C. R. Sanders G. Tian M. D. Tsai Biochemistry 1989 28 9028 9043
- (1989) Biochemistry , vol.28 , pp. 9028-9043
- Sanders, C.R.¹ Tian, G.² Tsai, M.D.³

46
- 0000398122
- X. R. Sheng X. Li X. M. Pan J. Biol. Chem. 1999 274 22238 22242
- (1999) J. Biol. Chem. , vol.274 , pp. 22238-22242
- Sheng, X.R.¹ Li, X.² Pan, X.M.³

47
- 0029644728
- C. Vonrhein G. J. Schlauderer G. E. Schulz Structure (London) 1995 3 483 490
- (1995) Structure (London) , vol.3 , pp. 483-490
- Vonrhein, C.¹ Schlauderer, G.J.² Schulz, G.E.³

48
- 0029644168
- (PDB ID:
- C. W. Mueller G. J. Schlauderer J. Reinstein G. E. Schulz Structure (Cambridge, MA, U.S.) 1996 4 147 156
- (1996) Structure (Cambridge, MA, U.S.) , vol.4 , pp. 147-156
- Mueller, C.W.¹ Schlauderer, G.J.² Reinstein, J.³ Schulz, G.E.⁴

49
- 0026544877
- (PDB ID:
- C. W. Mueller G. E. Schulz J. Mol. Biol. 1992 224 159 177
- (1992) J. Mol. Biol. , vol.224 , pp. 159-177
- Mueller, C.W.¹ Schulz, G.E.²

50
- 4243710928
- T. Ihle D. M. Kroll Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 2001 63 020201
- (2001) Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. , vol.63 , pp. 020201
- Ihle, T.¹ Kroll, D.M.²

51
- 37649027179
- 5 particles takes approximately 4.4 hours on a single 2.53 GHz Intel Xeon CPU E5540
- T. Ihle D. M. Kroll Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 2003 67 066705
- (2003) Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. , vol.67 , pp. 066705
- Ihle, T.¹ Kroll, D.M.²

52
- 0036769906
- N. Kikuchi A. Gent J. M. Yeomans Eur. Phys. J. E: Soft Matter Biol. Phys. 2002 9 63 66
- (2002) Eur. Phys. J. E: Soft Matter Biol. Phys. , vol.9 , pp. 63-66
- Kikuchi, N.¹ Gent, A.² Yeomans, J.M.³

53
- 27944502464
- N. Kikuchi J. F. Ryder C. M. Pooley J. M. Yeomans Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 2005 71 061804
- (2005) Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. , vol.71 , pp. 061804
- Kikuchi, N.¹ Ryder, J.F.² Pooley, C.M.³ Yeomans, J.M.⁴

54
- 34547853743
- S. H. Lee R. Kapral J. Chem. Phys. 2006 124 214901
- (2006) J. Chem. Phys. , vol.124 , pp. 214901
- Lee, S.H.¹ Kapral, R.²

55
- 77949576043
- C. Echeverria R. Kapral J. Chem. Phys. 2010 132 104902
- (2010) J. Chem. Phys. , vol.132 , pp. 104902
- Echeverria, C.¹ Kapral, R.²

56
- 42749099367
- J. T. Padding A. A. Louis Phys. Rev. Lett. 2004 93 220601
- (2004) Phys. Rev. Lett. , vol.93 , pp. 220601
- Padding, J.T.¹ Louis, A.A.²

57
- 34548603196
- M. Ripoll R. G. Winkler G. Gompper Eur. Phys. J. E: Soft Matter Biol. Phys. 2007 23 349 354
- (2007) Eur. Phys. J. E: Soft Matter Biol. Phys. , vol.23 , pp. 349-354
- Ripoll, M.¹ Winkler, R.G.² Gompper, G.³

58
- 33645725668
- J. T. Hynes R. Kapral M. Weinberg J. Chem. Phys. 1979 70 1456 1467
- (1979) J. Chem. Phys. , vol.70 , pp. 1456-1467
- Hynes, J.T.¹ Kapral, R.² Weinberg, M.³

59
- 79959762328
- Garland, New York, 1st edn
- B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts and P. Walter, Modern Theory of Polymer Solutions, Garland, New York, 1st edn, 1994
- (1994) Modern Theory of Polymer Solutions
- Alberts, B.¹ Johnson, A.² Lewis, J.³ Raff, M.⁴ Roberts, K.⁵ Walter, P.⁶

60
- 26944436625
- The cyclic dynamics in the SB mechanism is asymmetric since the forward and reverse cycles are not equivalent. In principle, this implies that the AKE protein executing such dynamics could "swim"
- K. Mussawisade M. Ripoll R. G. Winkler G. Gompper J. Chem. Phys. 2005 123 144905
- (2005) J. Chem. Phys. , vol.123 , pp. 144905
- Mussawisade, K.¹ Ripoll, M.² Winkler, R.G.³ Gompper, G.⁴

61
- 84890506631
- E. Purcell Am. J. Phys. 1977 45 3 11
- (1977) Am. J. Phys. , vol.45 , pp. 3-11
- Purcell, E.¹

62
- 28844463979
- T. Ihle E. Tüzel D. M. Kroll Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 2005 72 046707
- (2005) Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. , vol.72 , pp. 046707
- Ihle, T.¹ Tüzel, E.² Kroll, D.M.³

63
- 0142026522
- N. Kikuchi C. M. Pooley J. F. Ryder J. M. Yeomans J. Chem. Phys. 2003 119 6388 6396
- (2003) J. Chem. Phys. , vol.119 , pp. 6388-6396
- Kikuchi, N.¹ Pooley, C.M.² Ryder, J.F.³ Yeomans, J.M.⁴

64
- 17444377191
- C. M. Pooley J. M. Yeomans J. Phys. Chem. B 2005 109 6505 6513
- (2005) J. Phys. Chem. B , vol.109 , pp. 6505-6513
- Pooley, C.M.¹ Yeomans, J.M.²

65
- 35949037024
- F. Garisto R. Kapral Phys. Rev. A: At., Mol., Opt. Phys. 1974 10 309 318
- (1974) Phys. Rev. A: At., Mol., Opt. Phys. , vol.10 , pp. 309-318
- Garisto, F.¹ Kapral, R.²

66
- 79952426683
- C. Loken et al. J. Phys.: Conf. Ser. 2010 256 012026
- (2010) J. Phys.: Conf. Ser. , vol.256 , pp. 012026
- Loken, C.¹

67
- 33847617864
- Y.-G. Chen G. Hummer J. Am. Chem. Soc. 2007 129 2414 2415
- (2007) J. Am. Chem. Soc. , vol.129 , pp. 2414-2415
- Chen, Y.-G.¹ Hummer, G.²

68
- 34548304871
- W. Zheng C. A. Brooks G. Hummer Proteins: Struct., Funct., Bioinf. 2007 69 43 57
- (2007) Proteins: Struct., Funct., Bioinf. , vol.69 , pp. 43-57
- Zheng, W.¹ Brooks, C.A.² Hummer, G.³

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