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Journal of Physical Chemistry B

Volumn 116, Issue 30, 2012, Pages 8733-8740

Polarizable molecular dynamics simulations of aqueous dipeptides

(2) Kucukkal, Tugba G a Stuart, Steven J a

a CLEMSON UNIVERSITY (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DYNAMICS; EXPERIMENTS; MOLECULAR DYNAMICS; NEUTRON DIFFRACTION;

AGGREGATION BEHAVIOR; BIOMOLECULAR SYSTEM; DI-PEPTIDES; DIPEPTIDE; ELECTROSTATIC ENVIRONMENTS; FORCE FIELDS; MOLECULAR DYNAMICS SIMULATIONS; NEUTRON DIFFRACTION MEASUREMENTS; PEPTIDE AGGREGATION; PEPTIDE SOLUTIONS; STRUCTURE AND DYNAMICS;

PEPTIDES;

EID: 84864751487 PISSN: 15206106 EISSN: 15205207 Source Type: Journal
DOI: 10.1021/jp300528m Document Type: Article

Times cited : (8)

References (67)

1
- 70349087354
- Cieplak, P.; Dupradeau, F.-Y.; Duan, Y.; Wang, J. J. Phys.: Cond. Matt. 2009, 21, 333102
- (2009) J. Phys.: Cond. Matt. , vol.21 , pp. 333102
- Cieplak, P.¹ Dupradeau, F.-Y.² Duan, Y.³ Wang, J.⁴

2
- 36148946078
- Vorobyov, I.; Anisimov, V. M.; Greene, S.; Venable, R. M.; Moser, A.; Pastor, R. W.; MacKerell, A. D., Jr. J. Chem. Theory Comput. 2007, 3, 1120-1133
- (2007) J. Chem. Theory Comput. , vol.3 , pp. 1120-1133
- Vorobyov, I.¹ Anisimov, V.M.² Greene, S.³ Venable, R.M.⁴ Moser, A.⁵ Pastor, R.W.⁶ Mackerell Jr., A.D.⁷

3
- 67149131694
- Illingworth, C. J.; Domene, C. Proc. R. Soc. A 2009, 465, 1701-1716
- (2009) Proc. R. Soc. A , vol.465 , pp. 1701-1716
- Illingworth, C.J.¹ Domene, C.²

4
- 0037380854
- Allen, T. W.; Bastug, T.; Kuyucak, S.; Chung, S. H. Biophys. J. 2003, 84, 2159-2168
- (2003) Biophys. J. , vol.84 , pp. 2159-2168
- Allen, T.W.¹ Bastug, T.² Kuyucak, S.³ Chung, S.H.⁴

5
- 33646844088
- Bastug, T.; Kuyucak, S. Chem. Phys. Lett. 2006, 424, 82-85
- (2006) Chem. Phys. Lett. , vol.424 , pp. 82-85
- Bastug, T.¹ Kuyucak, S.²

6
- 33744944511
- Bastug, T.; Kuyucak, S. Biophys. J. 2006, 90, 3941-3950
- (2006) Biophys. J. , vol.90 , pp. 3941-3950
- Bastug, T.¹ Kuyucak, S.²

7
- 78651298607
- Illingworth, C. J. R.; Furini, S.; Domene, C. J. Chem. Theory Comput. 2010, 6, 3780-3792
- (2010) J. Chem. Theory Comput. , vol.6 , pp. 3780-3792
- Illingworth, C.J.R.¹ Furini, S.² Domene, C.³

8
- 0030197443
- Stuart, S. J.; Berne, B. J. J. Phys. Chem. 1996, 100, 11934-11943
- (1996) J. Phys. Chem. , vol.100 , pp. 11934-11943
- Stuart, S.J.¹ Berne, B.J.²

9
- 0000153331
- Stuart, S. J.; Berne, B. J. J. Phys. Chem. A 1999, 103, 10300-10307
- (1999) J. Phys. Chem. A , vol.103 , pp. 10300-10307
- Stuart, S.J.¹ Berne, B.J.²

10
- 0035312821
- Halgren, T. A.; Damm, W. Curr. Opin. Struct. Biol. 2001, 11, 236-242
- (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 236-242
- Halgren, T.A.¹ Damm, W.²

11
- 79957510489
- Wei, C.; Tung, D.; Yip, Y. M.; Mei, Y.; Zhang, D. J. Chem. Phys. 2011, 134, 171101
- (2011) J. Chem. Phys. , vol.134 , pp. 171101
- Wei, C.¹ Tung, D.² Yip, Y.M.³ Mei, Y.⁴ Zhang, D.⁵

12
- 77949975511
- Rick, S. W.; Stuart, S. J. Rev. Comput. Chem. 2002, 18, 89-146
- (2002) Rev. Comput. Chem. , vol.18 , pp. 89-146
- Rick, S.W.¹ Stuart, S.J.²

13
- 58149211457
- Rick, S. W.; Stuart, S. J.; Bader, J. S.; Berne, B. J. J. Mol. Liq. 1995, 65-6, 31-40
- (1995) J. Mol. Liq. , vol.656 , pp. 31-40
- Rick, S.W.¹ Stuart, S.J.² Bader, J.S.³ Berne, B.J.⁴

14
- 36448999850
- Rick, S. W.; Stuart, S. J.; Berne, B. J. J. Chem. Phys. 1994, 101, 6141-6156
- (1994) J. Chem. Phys. , vol.101 , pp. 6141-6156
- Rick, S.W.¹ Stuart, S.J.² Berne, B.J.³

15
- 67650079292
- Davis, J. E.; Patel, S. J. Phys. Chem. B 2009, 113, 9183-9196
- (2009) J. Phys. Chem. B , vol.113 , pp. 9183-9196
- Davis, J.E.¹ Patel, S.²

16
- 58849129143
- Davis, J. E.; Raharnan, O.; Patel, S. Biophys. J. 2009, 96, 385-402
- (2009) Biophys. J. , vol.96 , pp. 385-402
- Davis, J.E.¹ Raharnan, O.² Patel, S.³

17
- 33746597823
- Patel, S.; Brooks, C. L. Mol. Simul. 2006, 32, 231-249
- (2006) Mol. Simul. , vol.32 , pp. 231-249
- Patel, S.¹ Brooks, C.L.²

18
- 0347655649
- Patel, S.; Brooks, C. L. J. Comput. Chem. 2004, 25, 1-15
- (2004) J. Comput. Chem. , vol.25 , pp. 1-15
- Patel, S.¹ Brooks, C.L.²

19
- 4043057278
- Patel, S.; Mackerell, A. D.; Brooks, C. L. J. Comput. Chem. 2004, 25, 1504-1514
- (2004) J. Comput. Chem. , vol.25 , pp. 1504-1514
- Patel, S.¹ MacKerell, A.D.² Brooks, C.L.³

20
- 0037899660
- Ren, P. Y.; Ponder, J. W. J. Phys. Chem. B 2003, 107, 5933-5947
- (2003) J. Phys. Chem. B , vol.107 , pp. 5933-5947
- Ren, P.Y.¹ Ponder, J.W.²

21
- 0036890275
- Ren, P. Y.; Ponder, J. W. J. Comput. Chem. 2002, 23, 1497-1506
- (2002) J. Comput. Chem. , vol.23 , pp. 1497-1506
- Ren, P.Y.¹ Ponder, J.W.²

22
- 30344482264
- Lamoureux, G.; Harder, E.; Vorobyov, I. V.; Roux, B.; MacKerell, A. D. Chem. Phys. Lett. 2006, 418, 245-249
- (2006) Chem. Phys. Lett. , vol.418 , pp. 245-249
- Lamoureux, G.¹ Harder, E.² Vorobyov, I.V.³ Roux, B.⁴ MacKerell, A.D.⁵

23
- 0041878923
- Lamoureux, G.; Roux, B. J. Chem. Phys. 2003, 119, 3025-3039
- (2003) J. Chem. Phys. , vol.119 , pp. 3025-3039
- Lamoureux, G.¹ Roux, B.²

24
- 68549085135
- Lopes, P. E. M.; Lamoureux, G.; Mackerell, A. D., Jr. J. Comput. Chem. 2009, 30, 1821-1838
- (2009) J. Comput. Chem. , vol.30 , pp. 1821-1838
- Lopes, P.E.M.¹ Lamoureux, G.² Mackerell Jr., A.D.³

25
- 34047226258
- Lopes, P. E. M.; Lamoureux, G.; Roux, B.; MacKerell, A. D., Jr. J. Phys. Chem. B 2007, 111, 2873-2885
- (2007) J. Phys. Chem. B , vol.111 , pp. 2873-2885
- Lopes, P.E.M.¹ Lamoureux, G.² Roux, B.³ Mackerell Jr., A.D.⁴

26
- 77950132714
- Yu, H.; Whitfield, T. W.; Harder, E.; Lamoureux, G.; Vorobyov, I.; Anisimov, V. M.; MacKerell, A. D., Jr.; Roux, B. J. Chem. Theory Comput. 2010, 6, 774-786
- (2010) J. Chem. Theory Comput. , vol.6 , pp. 774-786
- Yu, H.¹ Whitfield, T.W.² Harder, E.³ Lamoureux, G.⁴ Vorobyov, I.⁵ Anisimov, V.M.⁶ Mackerell Jr., A.D.⁷ Roux, B.⁸

27
- 0346850017
- Grossfield, A.; Ren, P. Y.; Ponder, J. W. J. Am. Chem. Soc. 2003, 125, 15671-15682
- (2003) J. Am. Chem. Soc. , vol.125 , pp. 15671-15682
- Grossfield, A.¹ Ren, P.Y.² Ponder, J.W.³

28
- 0037328221
- Kaminski, G. A.; Friesner, R. A.; Zhou, R. H. J. Comput. Chem. 2003, 24, 267-276
- (2003) J. Comput. Chem. , vol.24 , pp. 267-276
- Kaminski, G.A.¹ Friesner, R.A.² Zhou, R.H.³

29
- 0036882094
- Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A.; Cao, Y. X. X.; Murphy, R. B.; Zhou, R. H.; Halgren, T. A. J. Comput. Chem. 2002, 23, 1515-1531
- (2002) J. Comput. Chem. , vol.23 , pp. 1515-1531
- Kaminski, G.A.¹ Stern, H.A.² Berne, B.J.³ Friesner, R.A.⁴ Cao, Y.X.X.⁵ Murphy, R.B.⁶ Zhou, R.H.⁷ Halgren, T.A.⁸

30
- 36749024620
- Warshel, A.; Kato, M.; Pisliakov, A. V. J. Chem. Theory Comput. 2007, 3, 2034-2045
- (2007) J. Chem. Theory Comput. , vol.3 , pp. 2034-2045
- Warshel, A.¹ Kato, M.² Pisliakov, A.V.³

31
- 70449529413
- Lopes, P. E.; Roux, B.; Mackerell, A. D. Theor. Chem. Acc. 2009, 124, 11-28
- (2009) Theor. Chem. Acc. , vol.124 , pp. 11-28
- Lopes, P.E.¹ Roux, B.² MacKerell, A.D.³

32
- 77749298172
- Ponder, J. W.; Wu, C.; Ren, P.; Pande, V. S.; Chodera, J. D.; Schnieders, M. J.; Haque, I.; Mobley, D. L.; Lambrecht, D. S.; DiStasio, R. A., Jr. J. Phys. Chem. B 2010, 114, 2549-2564
- (2010) J. Phys. Chem. B , vol.114 , pp. 2549-2564
- Ponder, J.W.¹ Wu, C.² Ren, P.³ Pande, V.S.⁴ Chodera, J.D.⁵ Schnieders, M.J.⁶ Haque, I.⁷ Mobley, D.L.⁸ Lambrecht, D.S.⁹ Distasio Jr., R.A.¹⁰

33
- 36649022649
- Geerke, D. P.; van Gunsteren, W. F. J. Chem. Theory Comput. 2007, 3, 2128-2137
- (2007) J. Chem. Theory Comput. , vol.3 , pp. 2128-2137
- Geerke, D.P.¹ Van Gunsteren, W.F.²

34
- 33645716062
- Wang, Z. X.; Zhang, W.; Wu, C.; Lei, H. X.; Cieplak, P.; Duan, Y. J. Comput. Chem. 2006, 27, 781-790
- (2006) J. Comput. Chem. , vol.27 , pp. 781-790
- Wang, Z.X.¹ Zhang, W.² Wu, C.³ Lei, H.X.⁴ Cieplak, P.⁵ Duan, Y.⁶

35
- 49349103357
- Malardier-Jugroot, C.; Johnson, M. E.; Murarka, R. K.; Head-Gordon, T. Phys. Chem. Chem. Phys. 2008, 10, 4903-4908
- (2008) Phys. Chem. Chem. Phys. , vol.10 , pp. 4903-4908
- Malardier-Jugroot, C.¹ Johnson, M.E.² Murarka, R.K.³ Head-Gordon, T.⁴

36
- 65249149750
- Johnson, M. E.; Malardier-Jugroot, C.; Murarka, R. K.; Head-Gordon, T. J. Phys. Chem. B 2008, 113, 4082-4092
- (2008) J. Phys. Chem. B , vol.113 , pp. 4082-4092
- Johnson, M.E.¹ Malardier-Jugroot, C.² Murarka, R.K.³ Head-Gordon, T.⁴

37
- 56249149240
- McLain, S. E.; Soper, A. K.; Daidone, I.; Smith, J. C.; Watts, A. Angew. Chem., Int. Ed. 2008, 47, 9059-9062
- (2008) Angew. Chem., Int. Ed. , vol.47 , pp. 9059-9062
- McLain, S.E.¹ Soper, A.K.² Daidone, I.³ Smith, J.C.⁴ Watts, A.⁵

38
- 49349114751
- Russo, D.; Ollivier, J.; Teixeira, J. Phys. Chem. Chem. Phys. 2008, 10, 4968-4974
- (2008) Phys. Chem. Chem. Phys. , vol.10 , pp. 4968-4974
- Russo, D.¹ Ollivier, J.² Teixeira, J.³

39
- 22344440932
- Russo, D.; Murarka, R. K.; Copley, J. R. D.; Head-Gordon, T. J. Phys. Chem. B 2005, 109, 12966-12975
- (2005) J. Phys. Chem. B , vol.109 , pp. 12966-12975
- Russo, D.¹ Murarka, R.K.² Copley, J.R.D.³ Head-Gordon, T.⁴

40
- 38849196324
- Ball, P. Chem. Rev. 2008, 108, 74-108
- (2008) Chem. Rev. , vol.108 , pp. 74-108
- Ball, P.¹

41
- 71649107610
- Nakagawa, H.; Kamikubo, H.; Kataoka, M. Biochim. Biophys. Acta, Proteins Proteomics 2010, 1804, 27-33
- (2010) Biochim. Biophys. Acta, Proteins Proteomics , vol.1804 , pp. 27-33
- Nakagawa, H.¹ Kamikubo, H.² Kataoka, M.³

42
- 45449108973
- McLain, S. E.; Soper, A. K.; Watts, A. Eur. Biophys. J. 2008, 37, 647-655
- (2008) Eur. Biophys. J. , vol.37 , pp. 647-655
- McLain, S.E.¹ Soper, A.K.² Watts, A.³

43
- 67650418242
- Tulip, P. R.; Bates, S. P. J. Chem. Phys. 2009, 131, 015103
- (2009) J. Chem. Phys. , vol.131 , pp. 015103
- Tulip, P.R.¹ Bates, S.P.²

44
- 0041784950
- MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S. J. Phys. Chem. B 1998, 102, 3586-3616
- (1998) J. Phys. Chem. B , vol.102 , pp. 3586-3616
- Mackerell Jr., A.D.¹ Bashford, D.² Bellott, M.³ Dunbrack, R.L.⁴ Evanseck, J.D.⁵ Field, M.J.⁶ Fischer, S.⁷ Gao, J.⁸ Guo, H.⁹ Ha, S.¹⁰

45
- 0004016501
- Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
- (1983) J. Chem. Phys. , vol.79 , pp. 926-935
- Jorgensen, W.L.¹ Chandrasekhar, J.² Madura, J.D.³ Impey, R.W.⁴ Klein, M.L.⁵

46
- 36749117884
- Jorgensen, W. L. J. Chem. Phys. 1982, 77, 4156-4163
- (1982) J. Chem. Phys. , vol.77 , pp. 4156-4163
- Jorgensen, W.L.¹

47
- 67650500988
- Brooks, B. R.; Brooks, C. L., III; MacKerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S. J. Comput. Chem. 2009, 30, 1545-1614
- (2009) J. Comput. Chem. , vol.30 , pp. 1545-1614
- Brooks, B.R.¹ Brooks III, C.L.² Mackerell Jr., A.D.³ Nilsson, L.⁴ Petrella, R.J.⁵ Roux, B.⁶ Won, Y.⁷ Archontis, G.⁸ Bartels, C.⁹ Boresch, S.¹⁰

48
- 1642576012
- MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III. J. Am. Chem. Soc. 2004, 126, 698-699
- (2004) J. Am. Chem. Soc. , vol.126 , pp. 698-699
- Mackerell Jr., A.D.¹ Feig, M.² Brooks III, C.L.³

49
- 3142714765
- MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III. J. Comput. Chem. 2004, 25, 1400-1415
- (2004) J. Comput. Chem. , vol.25 , pp. 1400-1415
- Mackerell Jr., A.D.¹ Feig, M.² Brooks III, C.L.³

50
- 84943502952
- Nose, S. Mol. Phys. 1984, 52, 255-268
- (1984) Mol. Phys. , vol.52 , pp. 255-268
- Nose, S.¹

51
- 84926811618
- Nose, S.; Klein, M. L. Mol. Phys. 1983, 50, 1055-1076
- (1983) Mol. Phys. , vol.50 , pp. 1055-1076
- Nose, S.¹ Klein, M.L.²

52
- 36449007836
- Feller, S. E.; Zhang, Y. H.; Pastor, R. W.; Brooks, B. R. J. Chem. Phys. 1995, 103, 4613-4621
- (1995) J. Chem. Phys. , vol.103 , pp. 4613-4621
- Feller, S.E.¹ Zhang, Y.H.² Pastor, R.W.³ Brooks, B.R.⁴

53
- 33646940952
- Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341
- (1977) J. Comput. Phys. , vol.23 , pp. 327-341
- Ryckaert, J.P.¹ Ciccotti, G.² Berendsen, H.J.C.³

54
- 33846823909
- Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092
- (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
- Darden, T.¹ York, D.² Pedersen, L.³

55
- 0031338986
- Nandi, N.; Bagchi, B. J. Phys. Chem. B 1997, 101, 10954-10961
- (1997) J. Phys. Chem. B , vol.101 , pp. 10954-10961
- Nandi, N.¹ Bagchi, B.²

56
- 0037028161
- Pal, S. K.; Peon, J.; Bagchi, B.; Zewail, A. H. J. Phys. Chem. B 2002, 106, 12376-12395
- (2002) J. Phys. Chem. B , vol.106 , pp. 12376-12395
- Pal, S.K.¹ Peon, J.² Bagchi, B.³ Zewail, A.H.⁴

57
- 0027016652
- Pethig, R. Annu. Rev. Phys. Chem. 1992, 43, 177-205
- (1992) Annu. Rev. Phys. Chem. , vol.43 , pp. 177-205
- Pethig, R.¹

58
- 33947425139
- Li, T.; Hassanali, A. A.; Kao, Y.-T.; Zhong, D.; Singer, S. J. J. Am. Chem. Soc. 2007, 129, 3376-3382
- (2007) J. Am. Chem. Soc. , vol.129 , pp. 3376-3382
- Li, T.¹ Hassanali, A.A.² Kao, Y.-T.³ Zhong, D.⁴ Singer, S.J.⁵

59
- 37049095962
- Krynicki, K.; Green, C.; Sawyer, D. Faraday Discuss. 1978, 66, 199-208
- (1978) Faraday Discuss. , vol.66 , pp. 199-208
- Krynicki, K.¹ Green, C.² Sawyer, D.³

60
- 0347760067
- Modig, K.; Liepinsh, E.; Otting, G.; Halle, B. J. Am. Chem. Soc. 2004, 126, 102-114
- (2004) J. Am. Chem. Soc. , vol.126 , pp. 102-114
- Modig, K.¹ Liepinsh, E.² Otting, G.³ Halle, B.⁴

61
- 0006755755
- Ludwig, R.; Weinhold, F.; Farrar, T. C. J. Chem. Phys. 1995, 103, 6941-6950
- (1995) J. Chem. Phys. , vol.103 , pp. 6941-6950
- Ludwig, R.¹ Weinhold, F.² Farrar, T.C.³

62
- 77949975511
- Rick, S. W.; Stuart, S. J. Rev. Comput. Chem. 2002, 18, 89-146
- (2002) Rev. Comput. Chem. , vol.18 , pp. 89-146
- Rick, S.W.¹ Stuart, S.J.²

63
- 0037067120
- Yeh, I.-C.; Hummer, G. J. Am. Chem. Soc. 2002, 124, 6563-6568
- (2002) J. Am. Chem. Soc. , vol.124 , pp. 6563-6568
- Yeh, I.-C.¹ Hummer, G.²

64
- 44949166524
- Kent, A.; Jha, A. K.; Fitzgerald, J. E.; Freed, K. F. J. Phys. Chem. B 2008, 112, 6175-6186
- (2008) J. Phys. Chem. B , vol.112 , pp. 6175-6186
- Kent, A.¹ Jha, A.K.² Fitzgerald, J.E.³ Freed, K.F.⁴

65
- 84864108285
- Collier, G.; Vellore, N. A.; Yancey, J. A.; Stuart, S. J.; Latour, R. A. Biointerphases 2012, 7, 24
- (2012) Biointerphases , vol.7 , pp. 24
- Collier, G.¹ Vellore, N.A.² Yancey, J.A.³ Stuart, S.J.⁴ Latour, R.A.⁵

66
- 67650359927
- Freddolino, P. L.; Park, S.; Roux, B.; Schulten, K. Biophys. J. 2009, 96, 3772-3780
- (2009) Biophys. J. , vol.96 , pp. 3772-3780
- Freddolino, P.L.¹ Park, S.² Roux, B.³ Schulten, K.⁴

67
- 77957572546
- Freddolino, P. L.; Harrison, C. B.; Liu, Y.; Schulten, K. Nat. Phys. 2010, 10, 751-758
- (2010) Nat. Phys. , vol.10 , pp. 751-758
- Freddolino, P.L.¹ Harrison, C.B.² Liu, Y.³ Schulten, K.⁴

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