SCOPUS 정보 검색 플랫폼

Volumn 149, Issue 22, 2018, Pages

An efficient strategy to estimate thermodynamics and kinetics of G protein-coupled receptor activation using metadynamics and maximum caliber

(3) Meral, Derya a Provasi, Davide a Filizola, Marta a

a MOUNT SINAI SCHOOL OF MEDICINE (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATION THEORY; COMPUTATIONAL CHEMISTRY; FREE ENERGY; INFORMATION THEORY; KINETICS; MOLECULAR DYNAMICS; PROTEINS;

ALLOSTERIC COMMUNICATION; COLLECTIVE VARIABLES; COMPUTATIONAL STRATEGY; CONFORMATIONAL SPACE; FREE ENERGY LANDSCAPE; G PROTEIN COUPLED RECEPTORS; MOLECULAR DYNAMICS SIMULATIONS; THERMODYNAMICS AND KINETICS;

CHEMICAL ACTIVATION;

MORPHINE; MU OPIATE RECEPTOR;

CHEMISTRY; KINETICS; MOLECULAR DYNAMICS; THERMODYNAMICS;

KINETICS; MOLECULAR DYNAMICS SIMULATION; MORPHINE; RECEPTORS, OPIOID, MU; THERMODYNAMICS;

EID: 85058454913 PISSN: 00219606 EISSN: None Source Type: Journal
DOI: 10.1063/1.5060960 Document Type: Article

Times cited : (32)

References (44)

1
- 66249144426
- D. M. Rosenbaum, S. G. Rasmussen, and B. K. Kobilka, Nature 459 (7245), 356 (2009). 10.1038/nature08144
- (2009) Nature , vol.459 , Issue.7245 , pp. 356
- Rosenbaum, D.M.¹ Rasmussen, S.G.² Kobilka, B.K.³

2
- 0038024615
- R. Fredriksson, M. C. Lagerström, L.-G. Lundin, and H. B. Schiöth, Mol. Pharmacol. 63 (6), 1256-1272 (2003). 10.1124/mol.63.6.1256
- (2003) Mol. Pharmacol. , vol.63 , Issue.6 , pp. 1256-1272
- Fredriksson, R.¹ Lagerström, M.C.² Lundin, L.-G.³ Schiöth, H.B.⁴

3
- 85039034321
- e19
- A. S. Hauser, S. Chavali, I. Masuho, L. J. Jahn, K. A. Martemyanov, D. E. Gloriam and M. M. Babu, Cell 172 (1-2), 41-54.e19 (2018). 10.1016/j.cell.2017.11.033
- (2018) Cell , vol.172 , Issue.1-2 , pp. 41-54
- Hauser, A.S.¹ Chavali, S.² Masuho, I.³ Jahn, L.J.⁴ Martemyanov, K.A.⁵ Gloriam, D.E.⁶ Babu, M.M.⁷

4
- 84939832832
- R. Sounier, C. Mas, J. Steyaert, T. Laeremans, A. Manglik, W. Huang, B. K. Kobilka, H. Déméné, and S. Granier, Nature 524 (7565), 375-378 (2015). 10.1038/nature14680
- (2015) Nature , vol.524 , Issue.7565 , pp. 375-378
- Sounier, R.¹ Mas, C.² Steyaert, J.³ Laeremans, T.⁴ Manglik, A.⁵ Huang, W.⁶ Kobilka, B.K.⁷ Déméné, H.⁸ Granier, S.⁹

5
- 38349091489
- A. Barducci, G. Bussi, and M. Parrinello, Phys. Rev. Lett. 100 (2), 020603 (2008). 10.1103/physrevlett.100.020603
- (2008) Phys. Rev. Lett. , vol.100 , Issue.2
- Barducci, A.¹ Bussi, G.² Parrinello, M.³

6
- 33846946504
- D. Branduardi, F. L. Gervasio, and M. Parrinello, J. Chem. Phys. 126 (5), 054103 (2007). 10.1063/1.2432340
- (2007) J. Chem. Phys. , vol.126 , Issue.5
- Branduardi, D.¹ Gervasio, F.L.² Parrinello, M.³

7
- 77956638608
- D. Provasi and M. Filizola, Biophys. J. 98 (10), 2347-2355 (2010). 10.1016/j.bpj.2010.01.047
- (2010) Biophys. J. , vol.98 , Issue.10 , pp. 2347-2355
- Provasi, D.¹ Filizola, M.²

8
- 80055099699
- D. Provasi, M. C. Artacho, A. Negri, J. C. Mobarec, and M. Filizola, PLoS Comput. Biol. 7 (10), e1002193 (2011). 10.1371/journal.pcbi.1002193
- (2011) PLoS Comput. Biol. , vol.7 , Issue.10 , pp. e1002193
- Provasi, D.¹ Artacho, M.C.² Negri, A.³ Mobarec, J.C.⁴ Filizola, M.⁵

9
- 84964649164
- S. Doerr, M. J. Harvey, F. Noé, and G. De Fabritiis, J. Chem. Theory Comput. 12 (4), 1845-1852 (2016). 10.1021/acs.jctc.6b00049
- (2016) J. Chem. Theory Comput. , vol.12 , Issue.4 , pp. 1845-1852
- Doerr, S.¹ Harvey, M.J.² Noé, F.³ De Fabritiis, G.⁴

10
- 67650099787
- M. J. Harvey, G. Giupponi, and G. D. Fabritiis, J. Chem. Theory Comput. 5 (6), 1632-1639 (2009). 10.1021/ct9000685
- (2009) J. Chem. Theory Comput. , vol.5 , Issue.6 , pp. 1632-1639
- Harvey, M.J.¹ Giupponi, G.² Fabritiis, G.D.³

11
- 85029306197
- A. Kapoor, G. Martinez-Rosell, D. Provasi, G. de Fabritiis, and M. Filizola, Sci. Rep. 7 (1), 11255 (2017). 10.1038/s41598-017-11483-8
- (2017) Sci. Rep. , vol.7 , Issue.1 , pp. 11255
- Kapoor, A.¹ Martinez-Rosell, G.² Provasi, D.³ De Fabritiis, G.⁴ Filizola, M.⁵

12
- 84937351341
- W. McGill, Trans. IRE Prof. Group Inf. Theory 4 (4), 93-111 (1954). 10.1109/tit.1954.1057469
- (1954) Trans. IRE Prof. Group Inf. Theory , vol.4 , Issue.4 , pp. 93-111
- McGill, W.¹

13
- 84901660019
- M. V. LeVine and H. Weinstein, PLoS Comput. Biol. 10 (5), e1003603 (2014). 10.1371/journal.pcbi.1003603
- (2014) PLoS Comput. Biol. , vol.10 , Issue.5 , pp. e1003603
- Levine, M.V.¹ Weinstein, H.²

14
- 84946924995
- P. D. Dixit, A. Jain, G. Stock, and K. A. Dill, J. Chem. Theory Comput. 11 (11), 5464-5472 (2015). 10.1021/acs.jctc.5b00537
- (2015) J. Chem. Theory Comput. , vol.11 , Issue.11 , pp. 5464-5472
- Dixit, P.D.¹ Jain, A.² Stock, G.³ Dill, K.A.⁴

15
- 84857354366
- H. Ge, S. Pressé, K. Ghosh, and K. A. Dill, J. Chem. Phys. 136 (6), 064108 (2012). 10.1063/1.3681941
- (2012) J. Chem. Phys. , vol.136 , Issue.6
- Ge, H.¹ Pressé, S.² Ghosh, K.³ Dill, K.A.⁴

16
- 84882279791
- S. Pressé, K. Ghosh, J. Lee, and K. A. Dill, Rev. Mod. Phys. 85 (3), 1115 (2013). 10.1103/revmodphys.85.1115
- (2013) Rev. Mod. Phys. , vol.85 , Issue.3 , pp. 1115
- Pressé, S.¹ Ghosh, K.² Lee, J.³ Dill, K.A.⁴

17
- 84861096654
- A. Manglik, A. C. Kruse, T. S. Kobilka, F. S. Thian, J. M. Mathiesen, R. K. Sunahara, L. Pardo, W. I. Weis, B. K. Kobilka, and S. Granier, Nature 485 (7398), 321-326 (2012). 10.1038/nature10954
- (2012) Nature , vol.485 , Issue.7398 , pp. 321-326
- Manglik, A.¹ Kruse, A.C.² Kobilka, T.S.³ Thian, F.S.⁴ Mathiesen, J.M.⁵ Sunahara, R.K.⁶ Pardo, L.⁷ Weis, W.I.⁸ Kobilka, B.K.⁹ Granier, S.¹⁰

18
- 84939795137
- W. Huang, A. Manglik, A. J. Venkatakrishnan, T. Laeremans, E. N. Feinberg, A. L. Sanborn, H. E. Kato, K. E. Livingston, T. S. Thorsen, R. C. Kling, S. Granier, P. Gmeiner, S. M. Husbands, J. R. Traynor, W. I. Weis, J. Steyaert, R. O. Dror, and B. K. Kobilka, Nature 524 (7565), 315-321 (2015). 10.1038/nature14886
- (2015) Nature , vol.524 , Issue.7565 , pp. 315-321
- Huang, W.¹ Manglik, A.² Venkatakrishnan, A.J.³ Laeremans, T.⁴ Feinberg, E.N.⁵ Sanborn, A.L.⁶ Kato, H.E.⁷ Livingston, K.E.⁸ Thorsen, T.S.⁹ Kling, R.C.¹⁰ Granier, S.¹¹ Gmeiner, P.¹² Husbands, S.M.¹³ Traynor, J.R.¹⁴ Weis, W.I.¹⁵ Steyaert, J.¹⁶ Dror, R.O.¹⁷ Kobilka, B.K.¹⁸

19
- 47149096704
- S. Jo, T. Kim, V. G. Iyer, and W. Im, J. Comput. Chem. 29 (11), 1859-1865 (2008). 10.1002/jcc.20945
- (2008) J. Comput. Chem. , vol.29 , Issue.11 , pp. 1859-1865
- Jo, S.¹ Kim, T.² Iyer, V.G.³ Im, W.⁴

20
- 33947139278
- C. Kandt, W. L. Ash, and D. P. Tieleman, Methods 41 (4), 475-488 (2007). 10.1016/j.ymeth.2006.08.006
- (2007) Methods , vol.41 , Issue.4 , pp. 475-488
- Kandt, C.¹ Ash, W.L.² Tieleman, D.P.³

21
- 84865723813
- R. B. Best, X. Zhu, J. Shim, P. E. Lopes, J. Mittal, M. Feig, and A. D. Mackerell, Jr., J. Chem. Theory Comput. 8 (9), 3257-3273 (2012). 10.1021/ct300400x
- (2012) J. Chem. Theory Comput. , vol.8 , Issue.9 , pp. 3257-3273
- Best, R.B.¹ Zhu, X.² Shim, J.³ Lopes, P.E.⁴ Mittal, J.⁵ Feig, M.⁶ Mackerell, A.D.⁷

22
- 77953377650
- J. B. Klauda, R. M. Venable, J. A. Freites, J. W. O'Connor, D. J. Tobias, C. Mondragon-Ramirez, I. Vorobyov, A. D. MacKerell, Jr., and R. W. Pastor, J. Phys. Chem. B 114 (23), 7830-7843 (2010). 10.1021/jp101759q
- (2010) J. Phys. Chem. B , vol.114 , Issue.23 , pp. 7830-7843
- Klauda, J.B.¹ Venable, R.M.² Freites, J.A.³ O'Connor, J.W.⁴ Tobias, D.J.⁵ Mondragon-Ramirez, C.⁶ Vorobyov, I.⁷ Mackerell, A.D.⁸ Pastor, R.W.⁹

23
- 84946416234
- M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, and E. Lindahl, SoftwareX 1-2, 19-25 (2015). 10.1016/j.softx.2015.06.001
- (2015) SoftwareX , vol.1-2 , pp. 19-25
- Abraham, M.J.¹ Murtola, T.² Schulz, R.³ Páll, S.⁴ Smith, J.C.⁵ Hess, B.⁶ Lindahl, E.⁷

24
- 76249087938
- K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov, and A. D. Mackerell, Jr., J. Comput. Chem. 31 (4), 671-690 (2010). 10.1002/jcc.21367
- (2010) J. Comput. Chem. , vol.31 , Issue.4 , pp. 671-690
- Vanommeslaeghe, K.¹ Hatcher, E.² Acharya, C.³ Kundu, S.⁴ Zhong, S.⁵ Shim, J.⁶ Darian, E.⁷ Guvench, O.⁸ Lopes, P.⁹ Vorobyov, I.¹⁰ Mackerell, A.D.¹¹

25
- 84997830677
- S. Schneider, D. Provasi, and M. Filizola, Biochemistry 55 (46), 6456-6466 (2016). 10.1021/acs.biochem.6b00948
- (2016) Biochemistry , vol.55 , Issue.46 , pp. 6456-6466
- Schneider, S.¹ Provasi, D.² Filizola, M.³

26
- 33750587438
- H. J. Berendsen, J. v. Postma, W. F. van Gunsteren, A. DiNola, and J. Haak, J. Chem. Phys. 81 (8), 3684-3690 (1984). 10.1063/1.448118
- (1984) J. Chem. Phys. , vol.81 , Issue.8 , pp. 3684-3690
- Berendsen, H.J.¹ Postma, J.V.² Van Gunsteren, W.F.³ Dinola, A.⁴ Haak, J.⁵

27
- 33846086933
- G. Bussi, D. Donadio, and M. Parrinello, J. Chem. Phys. 126 (1), 014101 (2007). 10.1063/1.2408420
- (2007) J. Chem. Phys. , vol.126 , Issue.1
- Bussi, G.¹ Donadio, D.² Parrinello, M.³

28
- 84943200457
- W. F. Van Gunsteren and H. Berendsen, Mol. Simul. 1 (3), 173-185 (1988). 10.1080/08927028808080941
- (1988) Mol. Simul. , vol.1 , Issue.3 , pp. 173-185
- Van Gunsteren, W.F.¹ Berendsen, H.²

29
- 0000388705
- B. Hess, H. Bekker, H. J. Berendsen, and J. G. Fraaije, J. Comput. Chem. 18 (12), 1463-1472 (1997). 10.1002/(sici)1096-987x(199709)18:12<1463::aid-jcc4>3.3.co;2-l
- (1997) J. Comput. Chem. , vol.18 , Issue.12 , pp. 1463-1472
- Hess, B.¹ Bekker, H.² Berendsen, H.J.³ Fraaije, J.G.⁴

30
- 33645961739
- U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys. 103 (19), 8577-8593 (1995). 10.1063/1.470117
- (1995) J. Chem. Phys. , vol.103 , Issue.19 , pp. 8577-8593
- Essmann, U.¹ Perera, L.² Berkowitz, M.L.³ Darden, T.⁴ Lee, H.⁵ Pedersen, L.G.⁶

31
- 84888294449
- S. Páll and B. Hess, Comput. Phys. Commun. 184 (12), 2641-2650 (2013). 10.1016/j.cpc.2013.06.003
- (2013) Comput. Phys. Commun. , vol.184 , Issue.12 , pp. 2641-2650
- Páll, S.¹ Hess, B.²

32
- 84882349032
- C. L. Wennberg, T. Murtola, B. Hess, and E. Lindahl, J. Chem. Theory Comput. 9 (8), 3527-3537 (2013). 10.1021/ct400140n
- (2013) J. Chem. Theory Comput. , vol.9 , Issue.8 , pp. 3527-3537
- Wennberg, C.L.¹ Murtola, T.² Hess, B.³ Lindahl, E.⁴

33
- 84949640540
- C. L. Wennberg, T. Murtola, S. Pavll, M. J. Abraham, B. Hess, and E. Lindahl, J. Chem. Theory Comput. 11 (12), 5737-5746 (2015). 10.1021/acs.jctc.5b00726
- (2015) J. Chem. Theory Comput. , vol.11 , Issue.12 , pp. 5737-5746
- Wennberg, C.L.¹ Murtola, T.² Pavll, S.³ Abraham, M.J.⁴ Hess, B.⁵ Lindahl, E.⁶

34
- 0001160648
- M. Marchi and P. Ballone, J. Chem. Phys. 110 (8), 3697-3702 (1999). 10.1063/1.478259
- (1999) J. Chem. Phys. , vol.110 , Issue.8 , pp. 3697-3702
- Marchi, M.¹ Ballone, P.²

35
- 84888642158
- G. A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, and G. Bussi, Comput. Phys. Commun. 185 (2), 604-613 (2014). 10.1016/j.cpc.2013.09.018
- (2014) Comput. Phys. Commun. , vol.185 , Issue.2 , pp. 604-613
- Tribello, G.A.¹ Bonomi, M.² Branduardi, D.³ Camilloni, C.⁴ Bussi, G.⁵

36
- 84907327659
- P. Tiwary and M. Parrinello, J. Phys. Chem. B 119 (3), 736-742 (2015). 10.1021/jp504920s
- (2015) J. Phys. Chem. B , vol.119 , Issue.3 , pp. 736-742
- Tiwary, P.¹ Parrinello, M.²

37
- 85036670087
- J. McCarty and M. Parrinello, J. Chem. Phys. 147 (20), 204109 (2017). 10.1063/1.4998598
- (2017) J. Chem. Phys. , vol.147 , Issue.20
- McCarty, J.¹ Parrinello, M.²

38
- 84902817448
- J. F. Dama, M. Parrinello, and G. A. Voth, Phys. Rev. Lett. 112 (24), 240602 (2014). 10.1103/physrevlett.112.240602
- (2014) Phys. Rev. Lett. , vol.112 , Issue.24
- Dama, J.F.¹ Parrinello, M.² Voth, G.A.³

39
- 84946887423
- M. K. Scherer, B. Trendelkamp-Schroer, F. Paul, G. Pérez-Hernández, M. Hoffmann, N. Plattner, C. Wehmeyer, J. H. Prinz, and F. Noé, J. Chem. Theory Comput. 11 (11), 5525-5542 (2015). 10.1021/acs.jctc.5b00743
- (2015) J. Chem. Theory Comput. , vol.11 , Issue.11 , pp. 5525-5542
- Scherer, M.K.¹ Trendelkamp-Schroer, B.² Paul, F.³ Pérez-Hernández, G.⁴ Hoffmann, M.⁵ Plattner, N.⁶ Wehmeyer, C.⁷ Prinz, J.H.⁸ Noé, F.⁹

40
- 84889779905
- P. Tiwary and M. Parrinello, Phys. Rev. Lett. 111 (23), 230602 (2013). 10.1103/physrevlett.111.230602
- (2013) Phys. Rev. Lett. , vol.111 , Issue.23
- Tiwary, P.¹ Parrinello, M.²

41
- 84898429568
- M. Salvalaglio, P. Tiwary, and M. Parrinello, J. Chem. Theory Comput. 10 (4), 1420-1425 (2014). 10.1021/ct500040r
- (2014) J. Chem. Theory Comput. , vol.10 , Issue.4 , pp. 1420-1425
- Salvalaglio, M.¹ Tiwary, P.² Parrinello, M.³

42
- 85051070390
- L. Donati and B. G. Keller, J. Chem. Phys. 149 (7), 072335 (2018). 10.1063/1.5027728
- (2018) J. Chem. Phys. , vol.149 , Issue.7
- Donati, L.¹ Keller, B.G.²

43
- 84906240969
- P. D. Dixit and K. A. Dill, J. Chem. Theory Comput. 10 (8), 3002-3005 (2014). 10.1021/ct5001389
- (2014) J. Chem. Theory Comput. , vol.10 , Issue.8 , pp. 3002-3005
- Dixit, P.D.¹ Dill, K.A.²

44
- 84962482196
- P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. U. S. A. 113 (11), 2839-2844 (2016). 10.1073/pnas.1600917113
- (2016) Proc. Natl. Acad. Sci. U. S. A. , vol.113 , Issue.11 , pp. 2839-2844
- Tiwary, P.¹ Berne, B.J.²

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.