메뉴 건너뛰기




Volumn 87, Issue 1, 2013, Pages

Generic folding and transition hierarchies for surface adsorption of hydrophobic-polar lattice model proteins

Author keywords

[No Author keywords available]

Indexed keywords

ATTRACTIVE SURFACES; CLASSIFICATION SCHEME; FOLDING BEHAVIOR; IDENTIFICATION SCHEME; LATTICE MODELS; LATTICE PROTEINS; SURFACE ADSORPTION; SURFACE CONTACT; SURFACE STRENGTHS; THERMODYNAMIC BEHAVIORS; WANG-LANDAU SAMPLING;

EID: 84872521576     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.87.012706     Document Type: Article
Times cited : (44)

References (64)
  • 1
    • 0030026989 scopus 로고    scopus 로고
    • Protein adsorption on solid surfaces
    • DOI 10.1016/S0958-1669(96)80098-X
    • V. Hlady and J. Buijs, Curr. Opin. Biotechnol. CUOBE3 0958-1669 10.1016/S0958-1669(96)80098-X 7, 72 (1996). (Pubitemid 26066591)
    • (1996) Current Opinion in Biotechnology , vol.7 , Issue.1 , pp. 72-77
    • Hlady, V.1    Buijs, J.2
  • 2
    • 1342302795 scopus 로고    scopus 로고
    • The interaction of proteins with solid surfaces
    • DOI 10.1016/j.sbi.2003.12.001
    • J. J. Gray, Curr. Opin. Struc. Biol. COSBEF 0959-440X 10.1016/j.sbi.2003.12.001 14, 110 (2004). (Pubitemid 38249599)
    • (2004) Current Opinion in Structural Biology , vol.14 , Issue.1 , pp. 110-115
    • Gray, J.J.1
  • 4
    • 0037435022 scopus 로고    scopus 로고
    • Protein analysis on a proteomic scale
    • DOI 10.1038/nature01512
    • E. Phizicky, P. I. Bastiaens, H. Zhu, M. Snyder, and S. Fields, Nature (London) NATUAS 0028-0836 10.1038/nature01512 422, 208 (2003). (Pubitemid 36362758)
    • (2003) Nature , vol.422 , Issue.6928 , pp. 208-215
    • Phizicky, E.1    Bastiaens, P.I.H.2    Zhu, H.3    Snyder, M.4    Fields, S.5
  • 5
    • 0030969778 scopus 로고    scopus 로고
    • NABIF9 1087-0156 10.1038/nbt0397-269
    • S. Brown, Nat. Biotechnol. NABIF9 1087-0156 10.1038/nbt0397-269 15, 269 (1997).
    • (1997) Nat. Biotechnol. , vol.15 , pp. 269
    • Brown, S.1
  • 6
    • 0034621827 scopus 로고    scopus 로고
    • Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly
    • DOI 10.1038/35015043
    • S. R. Whaley, D. S. English, E. L. Hu, P. F. Barbara, and A. M. Belcher, Nature (London) NATUAS 0028-0836 10.1038/35015043 405, 665 (2000). (Pubitemid 30428648)
    • (2000) Nature , vol.405 , Issue.6787 , pp. 665-668
    • Whaley, S.R.1    English, D.S.2    Hu, E.L.3    Barbara, P.F.4    Belcher, A.M.5
  • 7
    • 9744243512 scopus 로고    scopus 로고
    • NALEFD 1530-6984 10.1021/nl048829p
    • K. Goede, P. Busch, and M. Grundmann, Nano Lett. NALEFD 1530-6984 10.1021/nl048829p 4, 2115 (2004).
    • (2004) Nano Lett. , vol.4 , pp. 2115
    • Goede, K.1    Busch, P.2    Grundmann, M.3
  • 9
    • 0002125659 scopus 로고
    • 0065-3195 10.1007/3-540-16422-7-6
    • J. D. Andrade and V. Hlady, Adv. Polym. Sci. 0065-3195 10.1007/3-540-16422-7-6 79, 1 (1986).
    • (1986) Adv. Polym. Sci. , vol.79 , pp. 1
    • Andrade, J.D.1    Hlady, V.2
  • 10
    • 2942699751 scopus 로고    scopus 로고
    • in edited by M. Malmsten, Vol. 110 (Marcel Dekker, Inc., New York, USA
    • T. A. Horbett, in Biopolymers at Interfaces, 2nd ed., Surfactant Science Series, edited by, M. Malmsten, Vol. 110 (Marcel Dekker, Inc., New York, USA, 2003), Chap. 15, p. 393.
    • (2003) Biopolymers at Interfaces , pp. 393
    • Horbett, T.A.1
  • 11
    • 0029335538 scopus 로고
    • BCCHES 1043-1802 10.1021/bc00034a002
    • W. R. Gombotz and D. K. Pettit, Bioconjugate Chem. BCCHES 1043-1802 10.1021/bc00034a002 6, 332 (1995).
    • (1995) Bioconjugate Chem. , vol.6 , pp. 332
    • Gombotz, W.R.1    Pettit, D.K.2
  • 14
    • 0028050553 scopus 로고
    • QURBAW 0033-5835 10.1017/S0033583500002900
    • J. J. Ramsden, Q. Rev. Biophys. QURBAW 0033-5835 10.1017/ S0033583500002900 27, 41 (1994).
    • (1994) Q. Rev. Biophys. , vol.27 , pp. 41
    • Ramsden, J.J.1
  • 15
    • 0032848275 scopus 로고    scopus 로고
    • Methods for studying protein adsorption
    • DOI 10.1016/S0076-6879(99)09028-X
    • V. Hlady, J. Buijs, and H. P. Jennissen, Methods Enzymol. 0076-6879 10.1016/S0076-6879(99)09028-X 309, 402 (1999). (Pubitemid 29446463)
    • (1999) Methods in Enzymology , vol.309 , pp. 402-429
    • Hlady, V.1    Buijs, J.2    Jennissen, H.P.3
  • 17
    • 27844532645 scopus 로고    scopus 로고
    • Computer simulation of polypeptide adsorption on model biomaterials
    • DOI 10.1039/b506813d
    • F. Ganazzoli and G. Raffaini, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 10.1039/b506813d 7, 3651 (2005). (Pubitemid 41655942)
    • (2005) Physical Chemistry Chemical Physics , vol.7 , Issue.21 , pp. 3651-3663
    • Ganazzoli, F.1    Raffaini, G.2
  • 18
    • 0022423920 scopus 로고
    • 0006-2960 10.1021/bi00327a032
    • K. A. Dill, Biochemistry 0006-2960 10.1021/bi00327a032 24, 1501 (1985).
    • (1985) Biochemistry , vol.24 , pp. 1501
    • Dill, K.A.1
  • 19
    • 0024750637 scopus 로고
    • MAMOBX 0024-9297 10.1021/ma00200a030
    • K. F. Lau and K. A. Dill, Macromolecules MAMOBX 0024-9297 10.1021/ma00200a030 22, 3986 (1989).
    • (1989) Macromolecules , vol.22 , pp. 3986
    • Lau, K.F.1    Dill, K.A.2
  • 22
    • 0031897962 scopus 로고    scopus 로고
    • JCOBEM 1066-5277 10.1089/cmb.1998.5.27
    • B. Berger and T. Leighton, J. Comput. Biol. JCOBEM 1066-5277 10.1089/cmb.1998.5.27 5, 27 (1998).
    • (1998) J. Comput. Biol. , vol.5 , pp. 27
    • Berger, B.1    Leighton, T.2
  • 25
    • 84872547136 scopus 로고    scopus 로고
    • 1742-6588 10.1088/1742-6596/402/1/012046
    • Y. W. Li, T. Wüst, and D. P. Landau, J. Phys.: Conf. Ser. 1742-6588 10.1088/1742-6596/402/1/012046 402, 012046 (2012).
    • (2012) J. Phys.: Conf. Ser. , vol.402 , pp. 012046
    • Li, Y.W.1    Wüst, T.2    Landau, D.P.3
  • 26
    • 0027245418 scopus 로고
    • Genetic algorithms for protein folding simulations
    • DOI 10.1006/jmbi.1993.1258
    • R. Unger and J. Moult, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1993.1258 231, 75 (1993). (Pubitemid 23186599)
    • (1993) Journal of Molecular Biology , vol.231 , Issue.1 , pp. 75-81
    • Unger, R.1    Moult, J.2
  • 28
    • 0001635440 scopus 로고    scopus 로고
    • PRLTAO 0031-9007 10.1103/PhysRevLett.83.1886
    • G. Chikenji, M. Kikuchi, and Y. Iba, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.83.1886 83, 1886 (1999).
    • (1999) Phys. Rev. Lett. , vol.83 , pp. 1886
    • Chikenji, G.1    Kikuchi, M.2    Iba, Y.3
  • 31
    • 2342537648 scopus 로고    scopus 로고
    • PRLTAO 0031-9007 10.1103/PhysRevLett.92.120602
    • T. Prellberg and J. Krawczyk, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.92.120602 92, 120602 (2004).
    • (2004) Phys. Rev. Lett. , vol.92 , pp. 120602
    • Prellberg, T.1    Krawczyk, J.2
  • 32
    • 2342583504 scopus 로고    scopus 로고
    • JCPSA6 0021-9606 10.1063/1.1651055
    • M. Bachmann and W. Janke, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1651055 120, 6779 (2004).
    • (2004) J. Chem. Phys. , vol.120 , pp. 6779
    • Bachmann, M.1    Janke, W.2
  • 33
    • 33745602537 scopus 로고    scopus 로고
    • A study of density of states and ground states in hydrophobic-hydrophilic protein folding models by equi-energy sampling
    • DOI 10.1063/1.2208607
    • S. C. Kou, J. Oh, and W. H. Wong, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2208607 124, 244903 (2006). (Pubitemid 43993041)
    • (2006) Journal of Chemical Physics , vol.124 , Issue.24 , pp. 244903
    • Kou, S.C.1    Oh, J.2    Wong, W.H.3
  • 34
    • 34250701105 scopus 로고    scopus 로고
    • Biopolymer structure simulation and optimization via fragment regrowth Monte Carlo
    • DOI 10.1063/1.2736681
    • J. Zhang, S. C. Kou, and J. S. Liu, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2736681 126, 225101 (2007). (Pubitemid 46961611)
    • (2007) Journal of Chemical Physics , vol.126 , Issue.22 , pp. 225101
    • Zhang, J.1    Kou, S.C.2    Liu, J.S.3
  • 35
    • 14744289240 scopus 로고    scopus 로고
    • Energy landscapes for adsorption of a protein-like HP chain as a function of native-state stability
    • DOI 10.1016/j.jcis.2004.09.064, PII S0021979704009956
    • S. M. Liu and C. A. Haynes, J. Colloid Interface Sci. JCISA5 0021-9797 10.1016/j.jcis.2004.09.064 284, 7 (2005). (Pubitemid 40332442)
    • (2005) Journal of Colloid and Interface Science , vol.284 , Issue.1 , pp. 7-13
    • Liu, S.M.1    Haynes, C.A.2
  • 36
    • 10044225864 scopus 로고    scopus 로고
    • Mesoscopic dynamic Monte Carlo simulations of the adsorption of proteinlike HP chains within laterally constricted spaces
    • DOI 10.1016/j.jcis.2004.08.136, PII S0021979704008847
    • S. M. Liu and C. A. Haynes, J. Colloid Interface Sci. JCISA5 0021-9797 10.1016/j.jcis.2004.08.136 282, 283 (2005). (Pubitemid 39602650)
    • (2005) Journal of Colloid and Interface Science , vol.282 , Issue.2 , pp. 283-292
    • Liu, S.M.1    Haynes, C.A.2
  • 38
    • 33645942132 scopus 로고    scopus 로고
    • Conformational transition free energy profiles of an adsorbed, lattice model protein by multicanonical Monte Carlo simulation
    • DOI 10.1063/1.1849772, 084707
    • V. Castells and P. R. Van Tassel, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1849772 122, 084707 (2005). (Pubitemid 41047503)
    • (2005) Journal of Chemical Physics , vol.122 , Issue.8 , pp. 1-9
    • Castells, V.1    Van Tassel, P.R.2
  • 41
    • 6644221271 scopus 로고    scopus 로고
    • Efficient, multiple-range random walk algorithm to calculate the density of states
    • DOI 10.1103/PhysRevLett.86.2050
    • F. Wang and D. P. Landau, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.86.2050 86, 2050 (2001). (Pubitemid 32254758)
    • (2001) Physical Review Letters , vol.86 , Issue.10 , pp. 2050-2053
    • Wang, F.1    Landau, D.P.2
  • 42
    • 39749147672 scopus 로고    scopus 로고
    • PLEEE8 1539-3755 10.1103/PhysRevE.64.056101
    • F. Wang and D. P. Landau, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.64.056101 64, 056101 (2001).
    • (2001) Phys. Rev. e , vol.64 , pp. 056101
    • Wang, F.1    Landau, D.P.2
  • 43
    • 7444230388 scopus 로고    scopus 로고
    • A new approach to Monte Carlo simulations in statistical physics: Wang-Landau sampling
    • DOI 10.1119/1.1707017
    • D. P. Landau, S.-H. Tsai, and M. Exler, Am. J. Phys. AJPIAS 0002-9505 10.1119/1.1707017 72, 1294 (2004). (Pubitemid 39442970)
    • (2004) American Journal of Physics , vol.72 , Issue.10 , pp. 1294-1302
    • Landau, D.P.1    Tsai, S.-H.2    Exler, M.3
  • 45
    • 37549012605 scopus 로고    scopus 로고
    • 0075-8450 10.1007/978-3-540-74029-2-8
    • M. Bachmann and W. Janke, Lect. Notes Phys. 0075-8450 10.1007/978-3-540-74029-2-8 736, 203 (2008).
    • (2008) Lect. Notes Phys. , vol.736 , pp. 203
    • Bachmann, M.1    Janke, W.2
  • 47
    • 0000683715 scopus 로고    scopus 로고
    • JCPSA6 0021-9606 10.1063/1.473943
    • J. M. Deutsch, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.473943 106, 8849 (1997).
    • (1997) J. Chem. Phys. , vol.106 , pp. 8849
    • Deutsch, J.M.1
  • 48
    • 44649108481 scopus 로고    scopus 로고
    • CPHCBZ 0010-4655 10.1016/j.cpc.2008.01.028
    • T. Wüst and D. P. Landau, Comput. Phys. Commun. CPHCBZ 0010-4655 10.1016/j.cpc.2008.01.028 179, 124 (2008).
    • (2008) Comput. Phys. Commun. , vol.179 , pp. 124
    • Wüst, T.1    Landau, D.P.2
  • 49
    • 65549118844 scopus 로고    scopus 로고
    • PRLTAO 0031-9007 10.1103/PhysRevLett.102.178101
    • T. Wüst and D. P. Landau, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.102.178101 102, 178101 (2009).
    • (2009) Phys. Rev. Lett. , vol.102 , pp. 178101
    • Wüst, T.1    Landau, D.P.2
  • 50
    • 84865160719 scopus 로고    scopus 로고
    • JCPSA6 0021-9606 10.1063/1.4742969
    • T. Wüst and D. P. Landau, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.4742969 137, 064903 (2012).
    • (2012) J. Chem. Phys. , vol.137 , pp. 064903
    • Wüst, T.1    Landau, D.P.2
  • 52
    • 0028370962 scopus 로고
    • CPHCBZ 0010-4655 10.1016/0010-4655(94)90232-1
    • M. Lüscher, Comput. Phys. Commun. CPHCBZ 0010-4655 10.1016/0010-4655(94)90232-1 79, 100 (1994).
    • (1994) Comput. Phys. Commun. , vol.79 , pp. 100
    • Lüscher, M.1
  • 53
    • 79958130447 scopus 로고    scopus 로고
    • CPHCBZ 0010-4655 10.1016/j.cpc.2010.12.049
    • Y. W. Li, T. Wüst, and D. P. Landau, Comput. Phys. Commun. CPHCBZ 0010-4655 10.1016/j.cpc.2010.12.049 182, 1896 (2011).
    • (2011) Comput. Phys. Commun. , vol.182 , pp. 1896
    • Li, Y.W.1    Wüst, T.2    Landau, D.P.3
  • 54
    • 79951997262 scopus 로고    scopus 로고
    • JCCHDD 0192-8651 10.1002/jcc.21660
    • A. D. Swetnam and M. P. Allen, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.21660 32, 816 (2011).
    • (2011) J. Comput. Chem. , vol.32 , pp. 816
    • Swetnam, A.D.1    Allen, M.P.2
  • 55
    • 0000106469 scopus 로고
    • PYLBAJ 0370-2693 10.1016/0370-2693(91)91256-U
    • B. A. Berg and T. Neuhaus, Phys. Lett. B PYLBAJ 0370-2693 10.1016/0370-2693(91)91256-U 267, 249 (1991).
    • (1991) Phys. Lett. B , vol.267 , pp. 249
    • Berg, B.A.1    Neuhaus, T.2
  • 56
    • 4243613377 scopus 로고
    • PRLTAO 0031-9007 10.1103/PhysRevLett.68.9
    • B. A. Berg and T. Neuhaus, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.68.9 68, 9 (1992).
    • (1992) Phys. Rev. Lett. , vol.68 , pp. 9
    • Berg, B.A.1    Neuhaus, T.2
  • 58
    • 0028950075 scopus 로고
    • PNASA6 0027-8424 10.1073/pnas.92.1.146
    • K. Yue and K. A. Dill, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.92.1.146 92, 146 (1995).
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 146
    • Yue, K.1    Dill, K.A.2
  • 59
    • 0028224689 scopus 로고
    • Modeling compact denatured states of proteins
    • DOI 10.1021/bi00186a015
    • E. E. Lattman, K. M. Fiebig, and K. A. Dill, Biochemistry 0006-2960 10.1021/bi00186a015 33, 6158 (1994). (Pubitemid 24190767)
    • (1994) Biochemistry , vol.33 , Issue.20 , pp. 6158-6166
    • Lattman, E.E.1    Fiebig, K.M.2    Dill, K.A.3
  • 61
    • 80052035478 scopus 로고    scopus 로고
    • JSTPBS 0022-4715 10.1007/s10955-011-0266-z
    • T. Wüst, Y. W. Li, and D. P. Landau, J. Stat. Phys. JSTPBS 0022-4715 10.1007/s10955-011-0266-z 144, 638 (2011).
    • (2011) J. Stat. Phys. , vol.144 , pp. 638
    • Wüst, T.1    Li, Y.W.2    Landau, D.P.3
  • 62
    • 53449101250 scopus 로고    scopus 로고
    • JCPSA6 0021-9606 10.1063/1.2979142
    • S. Sharma and S. K. Kumar, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2979142 129, 134901 (2008).
    • (2008) J. Chem. Phys. , vol.129 , pp. 134901
    • Sharma, S.1    Kumar, S.K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.