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Physical Review Letters

Volumn 110, Issue 10, 2013, Pages

Efficient numerical reconstruction of protein folding kinetics with partial path sampling and pathlike variables

(4) Juraszek, J a Saladino, G a Van Erp, T S b,c Gervasio, F L a

a Centro Nacional de Investigaciones Oncológicas (Spain)

b NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY (Norway)

c UNIVERSITY COLLEGE LONDON (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL APPLICATIONS; COLLECTIVE VARIABLES; NUMERICAL RECONSTRUCTION; PATH SAMPLING; PROTEIN FOLDING KINETICS; TRANSITION PATH SAMPLING;

PROTEIN FOLDING;

RATE CONSTANTS;

PEPTIDE; TRP CAGE PEPTIDE; TRP-CAGE PEPTIDE;

ARTICLE; CHEMICAL MODEL; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; KINETICS; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS;

HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS;

EID: 84874844718 PISSN: 00319007 EISSN: 10797114 Source Type: Journal
DOI: 10.1103/PhysRevLett.110.108106 Document Type: Article

Times cited : (43)

References (35)

1
- 80055081145
- SCIEAS 0036-8075 10.1126/science.1208351
- K. Lindorff-Larsen, S. Piana, R. O. Dror, and D. E. Shaw, Science 334, 517 (2011). SCIEAS 0036-8075 10.1126/science.1208351
- (2011) Science , vol.334 , pp. 517
- Lindorff-Larsen, K.¹ Piana, S.² Dror, R.O.³ Shaw, D.E.⁴

2
- 0037065310
- The Trp cage: Folding kinetics and unfolded state topology via molecular dynamics simulations
- DOI 10.1021/ja028604l
- C. D. Snow, B. Zagrovic, and V. Pande, J. Am. Chem. Soc. 124, 14548 (2002). JACSAT 0002-7863 10.1021/ja028604l (Pubitemid 35425023)
- (2002) Journal of the American Chemical Society , vol.124 , Issue.49 , pp. 14548-14549
- Snow, C.D.¹ Zagrovic, B.² Pande, V.S.³

3
- 0003399724
- Academic, San Diego, 2nd ed.
- D. Frenkel and B. Smit, Understanding Molecular Simulation (Academic, San Diego, 2002), 2nd ed.
- (2002) Understanding Molecular Simulation
- Frenkel, D.¹ Smit, B.²

4
- 0000729781
- JCPSA6 0021-9606 10.1063/1.475562
- C. Dellago, P. G. Bolhuis, F. S. Csajka, and D. Chandler, J. Chem. Phys. 108, 1964 (1998). JCPSA6 0021-9606 10.1063/1.475562
- (1998) J. Chem. Phys. , vol.108 , pp. 1964
- Dellago, C.¹ Bolhuis, P.G.² Csajka, F.S.³ Chandler, D.⁴

5
- 66749099419
- ADCPAA 0065-2385 10.1002/0471231509
- C. Dellago, P. G. Bolhuis, and P. L. Geissler, Adv. Chem. Phys. 123, 1 (2002). ADCPAA 0065-2385 10.1002/0471231509
- (2002) Adv. Chem. Phys. , vol.123 , pp. 1
- Dellago, C.¹ Bolhuis, P.G.² Geissler, P.L.³

6
- 3042660129
- JCPSA6 0021-9606 10.1063/1.451695
- L. R. Pratt, J. Chem. Phys. 85, 5045 (1986). JCPSA6 0021-9606 10.1063/1.451695
- (1986) J. Chem. Phys. , vol.85 , pp. 5045
- Pratt, L.R.¹

7
- 0038515443
- JCPSA6 0021-9606 10.1063/1.1562614
- T. S. van Erp, D. Moroni, and P. G. Bolhuis, J. Chem. Phys. 118, 7762 (2003). JCPSA6 0021-9606 10.1063/1.1562614
- (2003) J. Chem. Phys. , vol.118 , pp. 7762
- Van Erp, T.S.¹ Moroni, D.² Bolhuis, P.G.³

8
- 72749105901
- JCOMEL 0953-8984 10.1088/0953-8984/21/46/463102
- R. Allen, C. Valeriani, and P. ten Wolde, J. Phys. Condens. Matter 21, 463102 (2009). JCOMEL 0953-8984 10.1088/0953-8984/21/46/463102
- (2009) J. Phys. Condens. Matter , vol.21 , pp. 463102
- Allen, R.¹ Valeriani, C.² Ten Wolde, P.³

9
- 1842581318
- JCPSA6 0021-9606 10.1063/1.1644537
- D. Moroni, P. G. Bolhuis, and T. S. van Erp, J. Chem. Phys. 120, 4055 (2004). JCPSA6 0021-9606 10.1063/1.1644537
- (2004) J. Chem. Phys. , vol.120 , pp. 4055
- Moroni, D.¹ Bolhuis, P.G.² Van Erp, T.S.³

10
- 16844362197
- JCTPAH 0021-9991 10.1016/j.jcp.2004.11.003
- T. van Erp and P. Bolhuis, J. Comput. Phys. 205, 157 (2005). JCTPAH 0021-9991 10.1016/j.jcp.2004.11.003
- (2005) J. Comput. Phys. , vol.205 , pp. 157
- Van Erp, T.¹ Bolhuis, P.²

11
- 3042545299
- JCPSA6 0021-9606 10.1063/1.1738640
- A. K. Faradjian and R. Elber, J. Chem. Phys. 120, 10880 (2004). JCPSA6 0021-9606 10.1063/1.1738640
- (2004) J. Chem. Phys. , vol.120 , pp. 10880
- Faradjian, A.K.¹ Elber, R.²

12
- 73349135352
- JPCBFK 1520-6106 10.1021/jp9074898
- D. R. Glowacki, E. Paci, and D. V. Shalashilin, J. Phys. Chem. B 113, 16603 (2009). JPCBFK 1520-6106 10.1021/jp9074898
- (2009) J. Phys. Chem. B , vol.113 , pp. 16603
- Glowacki, D.R.¹ Paci, E.² Shalashilin, D.V.³

13
- 84897584803
- ADCPAA 0065-2385 10.1002/9781118309513.ch2
- T. S. van Erp, Adv. Chem. Phys. 151, 27 (2012). ADCPAA 0065-2385 10.1002/9781118309513.ch2
- (2012) Adv. Chem. Phys. , vol.151 , pp. 27
- Van Erp, T.S.¹

14
- 84874820370
- See Supplemental Material http://link.aps.org/supplemental/10.1103/ PhysRevLett.110.108106 for full derivation of the TS-PPTIS method, application to a realistic protein ligand binding example, and tests of the memory loss assumption.

15
- 33846946504
- JCPSA6 0021-9606 10.1063/1.2432340
- D. Branduardi, F. Gervasio, and M. Parrinello, J. Chem. Phys. 126, 054103 (2007). JCPSA6 0021-9606 10.1063/1.2432340
- (2007) J. Chem. Phys. , vol.126 , pp. 054103
- Branduardi, D.¹ Gervasio, F.² Parrinello, M.³

16
- 33750816009
- Efficiency analysis of reaction rate calculation methods using analytical models I: The two-dimensional sharp barrier
- DOI 10.1063/1.2363996
- T. S. van Erp, J. Chem. Phys. 125, 174106 (2006). JCPSA6 0021-9606 10.1063/1.2363996 (Pubitemid 44711864)
- (2006) Journal of Chemical Physics , vol.125 , Issue.17 , pp. 174106
- Van Erp, T.S.¹

17
- 0036264492
- Designing a 20-residue protein
- DOI 10.1038/nsb798
- J. Neidigh, R. Fesinmeyer, and H. Andersen, Nat. Struct. Biol. 9, 425 (2002). NSBIEW 1072-8368 10.1038/nsb798 (Pubitemid 34568786)
- (2002) Nature Structural Biology , vol.9 , Issue.6 , pp. 425-430
- Neidigh, J.W.¹ Fesinmeyer, R.M.² Andersen, N.H.³

18
- 0037032225
- Smaller and faster: The 20-residue Trp-cage protein folds in 4 μs
- DOI 10.1021/ja0279141
- L. Qiu, S. Pabit, A. Roitberg, and S. Hagen, J. Am. Chem. Soc. 124, 12952 (2002). JACSAT 0002-7863 10.1021/ja0279141 (Pubitemid 35247099)
- (2002) Journal of the American Chemical Society , vol.124 , Issue.44 , pp. 12952-12953
- Qiu, L.¹ Pabit, S.A.² Roitberg, A.E.³ Hagen, S.J.⁴

19
- 0037174385
- JACSAT 0002-7863 10.1021/ja0273851
- C. Simmerling, B. Strockbine, and A. Roitberg, J. Am. Chem. Soc. 124, 11258 (2002). JACSAT 0002-7863 10.1021/ja0273851
- (2002) J. Am. Chem. Soc. , vol.124 , pp. 11258
- Simmerling, C.¹ Strockbine, B.² Roitberg, A.³

20
- 11144226928
- Phylogeny of protein-folding trajectories reveals a unique pathway to native structure
- DOI 10.1073/pnas.0407015102
- M. Ota, M. Ikeguchi, and A. Kidera, Proc. Natl. Acad. Sci. U.S.A. 101, 17658 (2004). PNASA6 0027-8424 10.1073/pnas.0407015102 (Pubitemid 40051942)
- (2004) Proceedings of the National Academy of Sciences of the United States of America , vol.101 , Issue.51 , pp. 17658-17663
- Ota, M.¹ Ikeguchi, M.² Kidera, A.³

21
- 0037934616
- Understanding folding and design: Replica-exchange simulations of "Trp-cage" miniproteins
- DOI 10.1073/pnas.1330954100
- J. Pitera and W. Swope, Proc. Natl. Acad. Sci. U.S.A. 100, 7587 (2003). PNASA6 0027-8424 10.1073/pnas.1330954100 (Pubitemid 36760013)
- (2003) Proceedings of the National Academy of Sciences of the United States of America , vol.100 , Issue.13 , pp. 7587-7592
- Pitera, J.W.¹ Swope, W.²

22
- 4544223597
- JPCBFK 1520-6106 10.1021/jp0478920
- S. Chowdhury, M. Lee, and Y. Duan, J. Phys. Chem. B 108, 13855 (2004). JPCBFK 1520-6106 10.1021/jp0478920
- (2004) J. Phys. Chem. B , vol.108 , pp. 13855
- Chowdhury, S.¹ Lee, M.² Duan, Y.³

23
- 79951523268
- JPCBFK 1520-6106 10.1021/jp1089596
- W. Zheng, E. Gallicchio, N. Deng, M. Andrec, and R. Levy, J. Phys. Chem. B 115, 1512 (2011). JPCBFK 1520-6106 10.1021/jp1089596
- (2011) J. Phys. Chem. B , vol.115 , pp. 1512
- Zheng, W.¹ Gallicchio, E.² Deng, N.³ Andrec, M.⁴ Levy, R.⁵

24
- 0344824394
- Trp-cage: Folding free energy landscape in explicit water
- DOI 10.1073/pnas.2233312100
- R. Zhou, Proc. Natl. Acad. Sci. U.S.A. 100, 13280 (2003). PNASA6 0027-8424 10.1073/pnas.2233312100 (Pubitemid 37444733)
- (2003) Proceedings of the National Academy of Sciences of the United States of America , vol.100 , Issue.23 , pp. 13280-13285
- Zhou, R.¹

25
- 33750468665
- Sampling the multiple folding mechanisms of Trp-cage in explicit solvent
- DOI 10.1073/pnas.0606692103
- J. Juraszek and P. G. Bolhuis, Proc. Natl. Acad. Sci. U.S.A. 103, 15859 (2006). PNASA6 0027-8424 10.1073/pnas.0606692103 (Pubitemid 44657557)
- (2006) Proceedings of the National Academy of Sciences of the United States of America , vol.103 , Issue.43 , pp. 15859-15864
- Juraszek, J.¹ Bolhuis, P.G.²

26
- 58149146888
- BIOJAU 0006-3495 10.1529/biophysj.108.136267
- J. Juraszek and P. G. Bolhuis, Biophys. J. 95, 4246 (2008). BIOJAU 0006-3495 10.1529/biophysj.108.136267
- (2008) Biophys. J. , vol.95 , pp. 4246
- Juraszek, J.¹ Bolhuis, P.G.²

27
- 33847254549
- Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: On the structure and possible role of internal water
- DOI 10.1016/j.jsb.2006.10.031, PII S1047847706003297, Advanced in Molecular Dynamics Simulations
- D. Paschek, H. Nymeyer, and A. Garcia, J. Struct. Biol. 157, 524 (2007). JSBIEM 1047-8477 10.1016/j.jsb.2006.10.031 (Pubitemid 46321518)
- (2007) Journal of Structural Biology , vol.157 , Issue.3 , pp. 524-533
- Paschek, D.¹ Nymeyer, H.² Garcia, A.E.³

28
- 80053253228
- PPCPFQ 1463-9076 10.1039/c1cp21193e
- C. Jimenez-Cruz, G. Makhatadze, and A. Garcia, Phys. Chem. Chem. Phys. 13, 17056 (2011). PPCPFQ 1463-9076 10.1039/c1cp21193e
- (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 17056
- Jimenez-Cruz, C.¹ Makhatadze, G.² Garcia, A.³

29
- 77953508894
- PSFGEY 0887-3585 10.1002/prot.22702
- R. Day, D. Paschek, and A. E. Garcia, Proteins 78, 1889 (2010). PSFGEY 0887-3585 10.1002/prot.22702
- (2010) Proteins , vol.78 , pp. 1889
- Day, R.¹ Paschek, D.² Garcia, A.E.³

30
- 34249071886
- JPCBFK 1520-6106 10.1021/jp067873l
- S. Piana and A. Laio, J. Phys. Chem. B 111, 4553 (2007). JPCBFK 1520-6106 10.1021/jp067873l
- (2007) J. Phys. Chem. B , vol.111 , pp. 4553
- Piana, S.¹ Laio, A.²

31
- 80855133540
- ACIEAY 0570-0833 10.1002/anie.v50.46
- R. Culik, A. Serrano, M. Bunagan, and F. Gai, Angew. Chem., Int. Ed. Engl. 50, 10884 (2011). ACIEAY 0570-0833 10.1002/anie.v50.46
- (2011) Angew. Chem., Int. Ed. Engl. , vol.50 , pp. 10884
- Culik, R.¹ Serrano, A.² Bunagan, M.³ Gai, F.⁴

32
- 46249092554
- 1549-9618 10.1021/ct700301q
- B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, J. Chem. Theory Comput. 4, 435 (2008). 1549-9618 10.1021/ct700301q
- (2008) J. Chem. Theory Comput. , vol.4 , pp. 435
- Hess, B.¹ Kutzner, C.² Van Der Spoel, D.³ Lindahl, E.⁴

33
- 69349100797
- CPHCBZ 0010-4655 10.1016/j.cpc.2009.05.011
- M. Bonomi, Comput. Phys. Commun. 180, 1961 (2009). CPHCBZ 0010-4655 10.1016/j.cpc.2009.05.011
- (2009) Comput. Phys. Commun. , vol.180 , pp. 1961
- Bonomi, M.¹

34
- 67650477115
- JCCHDD 0192-8651 10.1002/jcc.v30:11
- M. Bonomi, A. Barducci, and M. Parrinello, J. Comput. Chem. 30, 1615 (2009). JCCHDD 0192-8651 10.1002/jcc.v30:11
- (2009) J. Comput. Chem. , vol.30 , pp. 1615
- Bonomi, M.¹ Barducci, A.² Parrinello, M.³

35
- 77956929951
- JCPSA6 0021-9606 10.1063/1.3474803
- F. E. C. Velez-Vega and E. E. Borrero, J. Chem. Phys. 133, 105103 (2010). JCPSA6 0021-9606 10.1063/1.3474803
- (2010) J. Chem. Phys. , vol.133 , pp. 105103
- Velez-Vega, F.E.C.¹ Borrero, E.E.²

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