SCOPUS 정보 검색 플랫폼

Journal of Chemical Physics

Volumn 136, Issue 12, 2012, Pages

How to accelerate protein search on DNA: Location and dissociation

(2) Kolomeisky, Anatoly B a Veksler, Alex a

a RICE UNIVERSITY (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FAST SEARCH; FIRST-PASSAGE; IRREVERSIBLE DISSOCIATION; MONTE CARLO COMPUTER SIMULATIONS; ONE-DIMENSIONAL MOTIONS; PROTEIN MOLECULES; PROTEIN-DNA INTERACTIONS; SEARCHING TIME; TARGET SITES; THEORETICAL PREDICTION; TIME ANALYSIS;

COMPUTER SIMULATION; DISSOCIATION; DNA;

PROTEINS;

DNA; DNA BINDING PROTEIN; PROTEIN;

ARTICLE; BINDING SITE; CHEMISTRY; COMPUTER SIMULATION; DIFFUSION; MONTE CARLO METHOD; THEORETICAL MODEL;

BINDING SITES; COMPUTER SIMULATION; DIFFUSION; DNA; DNA-BINDING PROTEINS; MODELS, THEORETICAL; MONTE CARLO METHOD; PROTEINS;

EID: 84859520479 PISSN: 00219606 EISSN: None Source Type: Journal
DOI: 10.1063/1.3697763 Document Type: Article

Times cited : (28)

References (34)

1
- 0003880161
- (Garland Science).
- B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Molecular Biology of the Cell (Garland Science, 2002).
- (2002) Molecular Biology of the Cell
- Alberts, B.¹ Johnson, A.² Lewis, J.³ Raff, M.⁴ Roberts, K.⁵ Walter, P.⁶

2
- 0014945567
- 10.1016/0022-2836(70)90074-4
- A. Riggs, S. Bourgeois, and M. Cohn, J. Mol. Biol. 53, 401 (1970). 10.1016/0022-2836(70)90074-4
- (1970) J. Mol. Biol. , vol.53 , pp. 401
- Riggs, A.¹ Bourgeois, S.² Cohn, M.³

3
- 0019887628
- 10.1021/bi00527a028
- O. G. Berg, R. B. Winter, and P. H. von Hippel, Biochemistry 20 6929 (1981). 10.1021/bi00527a028
- (1981) Biochemistry , vol.20 , pp. 6929
- Berg, O.G.¹ Winter, R.B.² Von Hippel, P.H.³

4
- 0019816896
- 10.1021/bi00527a029
- R. B. Winter and P. H. von Hippel, Biochemistry 20 6948 (1981). 10.1021/bi00527a029
- (1981) Biochemistry , vol.20 , pp. 6948
- Winter, R.B.¹ Von Hippel, P.H.²

5
- 3042579602
- How do site-specific DNA-binding proteins find their targets?
- DOI 10.1093/nar/gkh624
- S. Halford and J. Marko, Nucleic Acids Res. 32, 3040 (2004). 10.1093/nar/gkh624 (Pubitemid 39022995)
- (2004) Nucleic Acids Research , vol.32 , Issue.10 , pp. 3040-3052
- Halford, S.E.¹ Marko, J.F.²

6
- 27644460480
- Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA
- DOI 10.1073/pnas.0505378102
- D. M. Gowers, G. G. Wilson, and S. E. Halford, Proc. Natl. Acad. Sci. U.S.A. 102, 15883 (2005). 10.1073/pnas.0505378102 (Pubitemid 41552837)
- (2005) Proceedings of the National Academy of Sciences of the United States of America , vol.102 , Issue.44 , pp. 15883-15888
- Gowers, D.M.¹ Wilson, G.G.² Halford, S.E.³

7
- 33746649820
- Single molecule measurements of repressor protein 1D diffusion on DNA
- DOI 10.1103/PhysRevLett.97.048302
- Y. M. Wang, R. H. Austin, and E. C. Cox, Phys. Rev. Lett. 97, 048302 (2006). 10.1103/PhysRevLett.97.048302 (Pubitemid 44147316)
- (2006) Physical Review Letters , vol.97 , Issue.4 , pp. 048302
- Wang, Y.M.¹ Austin, R.H.² Cox, E.C.³

8
- 34249932435
- Probing transcription factor dynamics at the single-molecule level in a living cell
- DOI 10.1126/science.1141967
- J. Elf, G.-W. Li, and X. S. Xie, Science 316, 1191 (2007). 10.1126/science.1141967 (Pubitemid 46877481)
- (2007) Science , vol.316 , Issue.5828 , pp. 1191-1194
- Elf, J.¹ Li, G.-W.² Xie, X.S.³

9
- 65549171477
- 10.1042/BST0370343
- S. E. Halford, Biochem. Soc. Trans. 37, 343 (2009). 10.1042/BST0370343
- (2009) Biochem. Soc. Trans. , vol.37 , pp. 343
- Halford, S.E.¹

10
- 72149127671
- 10.1088/1751-8113/42/43/434013
- L. Mirny, M. Slutsky, Z. Wunderlich, A. Tafvizi, J. Leith, and A. Kosmrlj, J. Phys. A: Math. Theor. 42, 434013 (2009). 10.1088/1751-8113/42/43/ 434013
- (2009) J. Phys. A: Math. Theor. , vol.42 , pp. 434013
- Mirny, L.¹ Slutsky, M.² Wunderlich, Z.³ Tafvizi, A.⁴ Leith, J.⁵ Kosmrlj, A.⁶

11
- 73149119125
- 10.1016/j.jmb.2009.10.049
- D. C. Rau and N. Y. Sidorova, J. Mol. Biol. 395, 408 (2010). 10.1016/j.jmb.2009.10.049
- (2010) J. Mol. Biol. , vol.395 , pp. 408
- Rau, D.C.¹ Sidorova, N.Y.²

12
- 79952259642
- 10.1073/pnas.1016020107
- A. Tafvizi, F. Huang, A. R. Fersht, L. A. Mirny, and A. M. van Oijen, Proc. Natl. Acad. Sci. U.S.A. 108, 563 (2011). 10.1073/pnas.1016020107
- (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , pp. 563
- Tafvizi, A.¹ Huang, F.² Fersht, A.R.³ Mirny, L.A.⁴ Van Oijen, A.M.⁵

13
- 78149469033
- 10.1007/s00018-010-0485-5
- M. L. Hegde, T. K. Hazra, and S. Mitra, Cell Mol. Life Sci. 67, 3573 (2010). 10.1007/s00018-010-0485-5
- (2010) Cell Mol. Life Sci. , vol.67 , pp. 3573
- Hegde, M.L.¹ Hazra, T.K.² Mitra, S.³

14
- 47249153641
- Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA
- DOI 10.1093/nar/gkn376
- I. Bonnetm A. Biebricher, P.-L. Porte, C. Loverdo, O. Benichou, R. Voituriez, C. Escude, W. Wende, A. Pingoud, and P. Desbiolles, Nucleic Acids Res. 36 4118 (2008). 10.1093/nar/gkn376 (Pubitemid 351984827)
- (2008) Nucleic Acids Research , vol.36 , Issue.12 , pp. 4118-4127
- Bonnet, I.¹ Biebricher, A.² Porte, P.³ Loverdo, C.⁴ Benichou, O.⁵ Voituriez, R.⁶ Escude, C.⁷ Wende, W.⁸ Pingoud, A.⁹ Desbiolles, P.¹⁰

15
- 10044223573
- Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential
- DOI 10.1529/biophysj.104.050765
- M. Slutsky and L. Mirny, Biophys. J. 87, 4021 (2004). 10.1529/biophysj.104.050765 (Pubitemid 39602906)
- (2004) Biophysical Journal , vol.87 , Issue.6 , pp. 4021-4035
- Slutsky, M.¹ Mirny, L.A.²

16
- 33645816459
- 10.1529/biophysj.105.078162
- T. Hu, A. Grosberg, and B. Shklovskii, Biophys. J. 90, 2731 (2006). 10.1529/biophysj.105.078162
- (2006) Biophys. J. , vol.90 , pp. 2731
- Hu, T.¹ Grosberg, A.² Shklovskii, B.³

17
- 45549102933
- 10.1021/jp076432e
- A. G. Cherstvy, A. B. Kolomeisky, and A. A. Kornyshev, J. Phys. Chem. B 112, 4741 (2008). 10.1021/jp076432e
- (2008) J. Phys. Chem. B , vol.112 , pp. 4741
- Cherstvy, A.G.¹ Kolomeisky, A.B.² Kornyshev, A.A.³

18
- 66649116808
- 10.1103/PhysRevLett.102.228101
- V. Dahirel, F. Paillusson, M. Jardat, M. Barbi, and J.-M. Victor, Phys. Rev. Lett. 102, 228101 (2009). 10.1103/PhysRevLett.102.228101
- (2009) Phys. Rev. Lett. , vol.102 , pp. 228101
- Dahirel, V.¹ Paillusson, F.² Jardat, M.³ Barbi, M.⁴ Victor, J.-M.⁵

19
- 82455216733
- 10.1088/1751-8113/44/50/505002
- R. Murugan, J. Phys. A: Math. Theor. 44, 505002 (2011). 10.1088/1751-8113/44/50/505002
- (2011) J. Phys. A: Math. Theor. , vol.44 , pp. 505002
- Murugan, R.¹

20
- 81255200353
- 10.1016/j.bpj.2011.10.012
- A. Afek, I. Sela, N. Musa-Lempel, and D. B. Lukatsky, Biophys. J. 101 2465 (2011). 10.1016/j.bpj.2011.10.012
- (2011) Biophys. J. , vol.101 , pp. 2465
- Afek, A.¹ Sela, I.² Musa-Lempel, N.³ Lukatsky, D.B.⁴

21
- 65549138947
- 10.1103/PhysRevLett.102.188101
- C. Loverdo, O. Benichou, R. Voituriez, A. Biebricher, I. Bonnet, and P. Desbiolles, Phys. Rev. Lett. 102, 188101 (2009). 10.1103/PhysRevLett.102.188101
- (2009) Phys. Rev. Lett. , vol.102 , pp. 188101
- Loverdo, C.¹ Benichou, O.² Voituriez, R.³ Biebricher, A.⁴ Bonnet, I.⁵ Desbiolles, P.⁶

22
- 70349507801
- 10.1103/PhysRevLett.103.138102
- O. Benichou, Y. Kafri, M. Sheinman, and R. Voituriez, Phys. Rev. Lett. 103, 138102 (2009). 10.1103/PhysRevLett.103.138102
- (2009) Phys. Rev. Lett. , vol.103 , pp. 138102
- Benichou, O.¹ Kafri, Y.² Sheinman, M.³ Voituriez, R.⁴

23
- 77958168396
- 10.1016/j.bpj.2010.06.007
- D. Vuzman, M. Polonsky, and Y. Levy, Biophys. J. 99, 1202 (2010). 10.1016/j.bpj.2010.06.007
- (2010) Biophys. J. , vol.99 , pp. 1202
- Vuzman, D.¹ Polonsky, M.² Levy, Y.³

24
- 57849085252
- 10.1063/1.3026735
- P.-W. Fok, C.-L. Guo, and T. Chou, J. Chem. Phys. 129, 235101 (2008). 10.1063/1.3026735
- (2008) J. Chem. Phys. , vol.129 , pp. 235101
- Fok, P.-W.¹ Guo, C.-L.² Chou, T.³

25
- 77954617377
- 10.1063/1.3352571
- Y. von Hansen, R. R. Netz, and M. Hinczewski, J. Chem. Phys. 132, 135103 (2010). 10.1063/1.3352571
- (2010) J. Chem. Phys. , vol.132 , pp. 135103
- Von Hansen, Y.¹ Netz, R.R.² Hinczewski, M.³

26
- 79251584676
- 10.1039/c0cp01966f
- A. B. Kolomeisky, Phys. Chem. Chem. Phys. 13, 2088 (2011). 10.1039/c0cp01966f
- (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 2088
- Kolomeisky, A.B.¹

27
- 79957788301
- 10.1073/pnas.1101555108
- H.-X. Zhou, Proc. Natl. Acad. Sci. U.S.A. 108, 8651 (2011). 10.1073/pnas.1101555108
- (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , pp. 8651
- Zhou, H.-X.¹

28
- 80051633747
- 10.1103/PhysRevE.84.020901
- J. Reingruber and D. Holcman, Phys. Rev. E 84, 02901(R) (2011). 10.1103/PhysRevE.84.020901
- (2011) Phys. Rev. e , vol.84
- Reingruber, J.¹ Holcman, D.²

29
- 65249101772
- 10.1021/jp810009s
- A. G. Cherstvy, J. Phys. Chem. B 113, 4242 (2009). 10.1021/jp810009s
- (2009) J. Phys. Chem. B , vol.113 , pp. 4242
- Cherstvy, A.G.¹

30
- 4444236055
- Kinetics of target localization of a protein on DNA: A stochastic approach
- DOI 10.1529/biophysj.104.045773
- M. Coppey, O. Benichou, R. Voituriez, and M. Moreau, Biophys. J. 87, 1640 (2004). 10.1529/biophysj.104.045773 (Pubitemid 39167021)
- (2004) Biophysical Journal , vol.87 , Issue.3 , pp. 1640-1649
- Coppey, M.¹ Benichou, O.² Voituriez, R.³ Moreau, M.⁴

31
- 0003839881
- (Cambridge University Press).
- S. Redner, A Guide to First-Passage Processes (Cambridge University Press, 2001).
- (2001) A Guide to First-Passage Processes
- Redner, S.¹

32
- 68349125112
- 10.1016/j.tig.2009.06.002
- E. Segal and J. Widom, Trends Genet. 25, 335 (2009). 10.1016/j.tig.2009. 06.002
- (2009) Trends Genet. , vol.25 , pp. 335
- Segal, E.¹ Widom, J.²

33
- 22744432660
- Molecular biology: Genome-scale identification of nucleosome positions in S. cerevisiae
- DOI 10.1126/science.1112178
- G.-C Yuan, Y.-J. Liu, M. F. Dion, M. D. Slack, L. F. Wu, S. J. Altschuler, and O. J. Rando, Science 309, 626-630 (2005). 10.1126/science. 1112178 (Pubitemid 41033649)
- (2005) Science , vol.309 , Issue.5734 , pp. 626-630
- Yuan, G.-C.¹ Liu, Y.-J.² Dion, M.F.³ Slack, M.D.⁴ Wu, L.F.⁵ Altschuler, S.J.⁶ Rando, O.J.⁷

34
- 79960180211
- 10.1021/jz2004914
- A. B. Kolomeisky, J. Phys. Chem. Lett. 2, 1502 (2011). 10.1021/jz2004914
- (2011) J. Phys. Chem. Lett. , vol.2 , pp. 1502
- Kolomeisky, A.B.¹

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.