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Volumn 133, Issue 13, 2010, Pages

An off-lattice frustrated model protein with a six-stranded β -barrel structure

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL SPACE ANNEALING; FRUSTRATED MODELS; GLOBAL MINIMA; GLOBAL OPTIMIZATION METHOD; HIGH-ENERGY BARRIERS; LINUX PC; LOCAL MINIMUMS; PROTEIN FOLDS;

EID: 79952116602     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3494038     Document Type: Article
Times cited : (12)

References (41)
  • 1
    • 0015859467 scopus 로고
    • 0036-8075, 10.1126/science.181.4096.223
    • C. B. Anfinsen, Science 0036-8075 181, 223 (1973). 10.1126/science.181. 4096.223
    • (1973) Science , vol.181 , pp. 223
    • Anfinsen, C.B.1
  • 3
  • 5
    • 0001083082 scopus 로고
    • 0022-3654, 10.1021/j100040a039
    • P. Amara and J. E. Straub, J. Phys. Chem. 0022-3654 99, 14840 (1995). 10.1021/j100040a039
    • (1995) J. Phys. Chem. , vol.99 , pp. 14840
    • Amara, P.1    Straub, J.E.2
  • 6
    • 0002304341 scopus 로고    scopus 로고
    • 1089-5639, 10.1021/jp991868i
    • Y. -H. Lee and B. J. Berne, J. Phys. Chem. A 1089-5639 104, 86 (2000). 10.1021/jp991868i
    • (2000) J. Phys. Chem. A , vol.104 , pp. 86
    • Lee, Y.-H.1    Berne, B.J.2
  • 8
    • 0028835443 scopus 로고
    • 0006-3525, 10.1002/bi360350114
    • D. Thirumalai and Z. Guo, Biopolymers 0006-3525 35, 137 (1995). 10.1002/bip.360350114
    • (1995) Biopolymers , vol.35 , pp. 137
    • Thirumalai, D.1    Guo, Z.2
  • 9
    • 0029010695 scopus 로고
    • 0006-3525, 10.1002/bi360360108
    • Z. Guo and D. Thirumalai, Biopolymers 0006-3525 36, 83 (1995). 10.1002/bip.360360108
    • (1995) Biopolymers , vol.36 , pp. 83
    • Guo, Z.1    Thirumalai, D.2
  • 10
    • 0002689652 scopus 로고    scopus 로고
    • 0006-3525, 10.1002/(SICI)1097-0282(199712)42:7<745::AID-BIP1>3.0. CO;2-T
    • Z. Guo and C. L. Brooks, Biopolymers 0006-3525 42, 745 (1997). 10.1002/(SICI)1097-0282(199712)42:7<745::AID-BIP1>3.0.CO;2-T
    • (1997) Biopolymers , vol.42 , pp. 745
    • Guo, Z.1    Brooks, C.L.2
  • 11
    • 0031303354 scopus 로고    scopus 로고
    • 1359-0278, 10.1016/S1359-0278(97)00052-7
    • Z. Guo and D. Thirumalai, Folding Des. 1359-0278 2, 377 (1997). 10.1016/S1359-0278(97)00052-7
    • (1997) Folding Des. , vol.2 , pp. 377
    • Guo, Z.1    Thirumalai, D.2
  • 12
    • 0000870658 scopus 로고    scopus 로고
    • Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist β-barrel model
    • DOI 10.1063/1.476842, PII S0021960698508318
    • J. -E. Shea, Y. D. Nochomovitz, Z. Guo, and C. L. Brooks, J. Chem. Phys. 0021-9606 109, 2895 (1998). 10.1063/1.476842 (Pubitemid 128678183)
    • (1998) Journal of Chemical Physics , vol.109 , Issue.7 , pp. 2895-2903
    • Shea, J.-E.1    Nochomovitz, Y.D.2    Guo, Z.3    Brooks, C.L.4
  • 13
    • 33746881806 scopus 로고    scopus 로고
    • Local-structural diversity and protein folding: Application to all- β off-lattice protein models
    • DOI 10.1063/1.2151174, 024905
    • P. W. Pan, H. L. Gordon, and S. M. Rothstein, J. Chem. Phys. 0021-9606 124, 024905 (2006). 10.1063/1.2151174 (Pubitemid 43100254)
    • (2006) Journal of Chemical Physics , vol.124 , Issue.2 , pp. 1-13
    • Pan, P.W.1    Gordon, H.L.2    Rothstein, S.M.3
  • 14
    • 34047268552 scopus 로고    scopus 로고
    • Statistical temperature molecular dynamics: Application to coarse-grained Β -barrel-forming protein models
    • DOI 10.1063/1.2711812
    • J. Kim, J. E. Straub, and T. Keyes, J. Chem. Phys. 0021-9606 126, 135101 (2007). 10.1063/1.2711812 (Pubitemid 46550276)
    • (2007) Journal of Chemical Physics , vol.126 , Issue.13 , pp. 135101
    • Kim, J.1    Straub, J.E.2    Keyes, T.3
  • 18
    • 0000293127 scopus 로고    scopus 로고
    • 0021-9606, 10.1063/1.478992
    • N. Elmaci and R. S. Berry, J. Chem. Phys. 0021-9606 110, 10606 (1999). 10.1063/1.478992
    • (1999) J. Chem. Phys. , vol.110 , pp. 10606
    • Elmaci, N.1    Berry, R.S.2
  • 19
    • 0001764256 scopus 로고    scopus 로고
    • 0021-9606, 10.1063/1.480011
    • M. A. Miller and D. J. Wales, J. Chem. Phys. 0021-9606 111, 6610 (1999). 10.1063/1.480011
    • (1999) J. Chem. Phys. , vol.111 , pp. 6610
    • Miller, M.A.1    Wales, D.J.2
  • 20
    • 0001324734 scopus 로고    scopus 로고
    • Multicanonical jump walk annealing: An efficient method for geometric optimization
    • DOI 10.1063/1.480844
    • H. Xu and B. J. Berne, J. Chem. Phys. 0021-9606 112, 2701 (2000). 10.1063/1.480844 (Pubitemid 33640692)
    • (2000) Journal of Chemical Physics , vol.112 , Issue.6 , pp. 2701-2708
    • Xu, H.1    Berne, B.J.2
  • 21
    • 0035134004 scopus 로고    scopus 로고
    • Quantum thermal annealing with renormalization: application to a frustrated model protein
    • DOI 10.1021/jp002589u
    • Y. -H. Lee and B. J. Berne, J. Phys. Chem. A 1089-5639 105, 459 (2001). 10.1021/jp002589u (Pubitemid 32159179)
    • (2001) Journal of Physical Chemistry A , vol.105 , Issue.2 , pp. 459-464
    • Lee, Y.-H.1    Berne, B.J.2
  • 23
    • 0037460544 scopus 로고    scopus 로고
    • 0021-9606, 10.1063/1.1540099
    • D. A. Evans and D. J. Wales, J. Chem. Phys. 0021-9606 118, 3891 (2003). 10.1063/1.1540099
    • (2003) J. Chem. Phys. , vol.118 , pp. 3891
    • Evans, D.A.1    Wales, D.J.2
  • 24
    • 0344236093 scopus 로고    scopus 로고
    • 0021-9606, 10.1063/1.1616917
    • S. -Y. Kim, S. J. Lee, and J. Lee, J. Chem. Phys. 0021-9606 119, 10274 (2003). 10.1063/1.1616917
    • (2003) J. Chem. Phys. , vol.119 , pp. 10274
    • Kim, S.-Y.1    Lee, S.J.2    Lee, J.3
  • 25
    • 10844286223 scopus 로고    scopus 로고
    • Effect of salt bridges on the energy landscape of a model protein
    • DOI 10.1063/1.1810471
    • D. J. Wales and P. E. J. Dewsbury, J. Chem. Phys. 0021-9606 121, 10284 (2004). 10.1063/1.1810471 (Pubitemid 40001681)
    • (2004) Journal of Chemical Physics , vol.121 , Issue.20 , pp. 10284-10290
    • Wales, D.J.1    Dewsbury, P.E.J.2
  • 27
    • 0001176785 scopus 로고    scopus 로고
    • 0192-8651, 10.1002/(SICI)1096-987X(19970715)18:9<1222::AID-JCC10>3. 0.CO;2-7
    • J. Lee, H. A. Scheraga, and S. Rackovsky, J. Comput. Chem. 0192-8651 18, 1222 (1997). 10.1002/(SICI)1096-987X(19970715)18:9<1222::AID-JCC10>3.0. CO;2-7
    • (1997) J. Comput. Chem. , vol.18 , pp. 1222
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 30
    • 4043058565 scopus 로고    scopus 로고
    • Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing
    • DOI 10.1002/prot.20150
    • J. Lee, S. -Y. Kim, K. Joo, I. Kim, and J. Lee, Proteins 0887-3585 56, 704 (2004) 10.1002/prot.20150 (Pubitemid 39063314)
    • (2004) Proteins: Structure, Function and Genetics , vol.56 , Issue.4 , pp. 704-714
    • Lee, J.1    Kim, S.-Y.2    Joo, K.3    Kim, I.4    Lee, J.5
  • 31
    • 14744276882 scopus 로고    scopus 로고
    • Protein structure prediction based on fragment assembly and parameter optimization
    • DOI 10.1016/j.bpc.2004.12.046
    • J. Lee, S. -Y. Kim, and J. Lee, Biophys. Chem. 0301-4622 115, 209 (2005). 10.1016/j.bpc.2004.12.046 (Pubitemid 40327059)
    • (2005) Biophysical Chemistry , vol.115 , Issue.SPEC. ISS.2-3 , pp. 209-214
    • Lee, J.1    Kim, S.-Y.2    Lee, J.3
  • 33
    • 14744269544 scopus 로고    scopus 로고
    • Understanding the structural characteristics of compstatin by conformational space annealing
    • DOI 10.1016/j.bpc.2004.12.039
    • M. K. Song, S. -Y. Kim, and J. Lee, Biophys. Chem. 0301-4622 115, 201 (2005). 10.1016/j.bpc.2004.12.039 (Pubitemid 40327058)
    • (2005) Biophysical Chemistry , vol.115 , Issue.SPEC. ISS.2-3 , pp. 201-207
    • Song, M.K.1    Kim, S.-Y.2    Lee, J.3
  • 34
    • 33845323016 scopus 로고    scopus 로고
    • Protein folding using fragment assembly and physical energy function
    • DOI 10.1063/1.2364500
    • S. -Y. Kim, W. Lee, and J. Lee, J. Chem. Phys. 0021-9606 125, 194908 (2006). 10.1063/1.2364500 (Pubitemid 44867397)
    • (2006) Journal of Chemical Physics , vol.125 , Issue.19 , pp. 194908
    • Kim, S.-Y.1    Lee, W.2    Lee, J.3
  • 35
    • 69849109596 scopus 로고    scopus 로고
    • 0887-3585, (and references therein). 10.1002/prot.22312
    • K. Joo, J. Lee, J. -H. Seo, K. Lee, B. -G. Kim, and J. Lee, Proteins 0887-3585 75, 1010 (2009) (and references therein). 10.1002/prot.22312
    • (2009) Proteins , vol.75 , pp. 1010
    • Joo, K.1    Lee, J.2    Seo, J.-H.3    Lee, K.4    Kim, B.-G.5    Lee, J.6
  • 37
    • 0033610078 scopus 로고    scopus 로고
    • Global optimization of clusters, crystals, and biomolecules
    • DOI 10.1126/science.285.5432.1368
    • D. J. Wales and H. A. Scheraga, Science 0036-8075 285, 1368 (1999) (and references therein). 10.1126/science.285.5432.1368 (Pubitemid 29411661)
    • (1999) Science , vol.285 , Issue.5432 , pp. 1368-1372
    • Wales, D.J.1    Scheraga, H.A.2


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