메뉴 건너뛰기




Volumn 45, Issue 2, 2004, Pages 707-716

The transfer matrix method for lattice proteins - An application with cooperative interactions

Author keywords

Helix coil transition; Transfer matrix method; Zimm Bragg theory

Indexed keywords

AMINO ACIDS; CONFORMATIONS; HYDROPHOBICITY; MATRIX ALGEBRA; POLYMERS;

EID: 0346492856     PISSN: 00323861     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.polymer.2003.10.072     Document Type: Article
Times cited : (7)

References (42)
  • 1
    • 0000668407 scopus 로고
    • Theory of the phase transition between helix and random coil in polypeptide chains
    • Zimm BH, Bragg JK. Theory of the phase transition between helix and random coil in polypeptide chains. J Chem Phys 1959;31:476-85.
    • (1959) J Chem Phys , vol.31 , pp. 476-485
    • Zimm, B.H.1    Bragg, J.K.2
  • 2
    • 36149030578 scopus 로고    scopus 로고
    • Enumeration of Hamiltonian walks on a cubic lattice
    • Pande VS, Joerg C, Grosberg AY, Tanaka T. Enumeration of Hamiltonian walks on a cubic lattice. J Phys A 2003;27:6231-6.
    • (2003) J Phys A , vol.27 , pp. 6231-6236
    • Pande, V.S.1    Joerg, C.2    Grosberg, A.Y.3    Tanaka, T.4
  • 3
    • 0001193711 scopus 로고
    • The effects of internal constraints on the configurations of chain molecules
    • Chan HS, Dill KA. The effects of internal constraints on the configurations of chain molecules. J Chem Phys 1990;92:3118-35.
    • (1990) J Chem Phys , vol.92 , pp. 3118-3135
    • Chan, H.S.1    Dill, K.A.2
  • 4
    • 0025906282 scopus 로고
    • Polymer principles in protein structure and stability
    • Chan HS, Dill KA. Polymer principles in protein structure and stability. Annu Rev Biophys Biophys Chem 1991;20:447-90.
    • (1991) Annu Rev Biophys Biophys Chem , vol.20 , pp. 447-490
    • Chan, H.S.1    Dill, K.A.2
  • 5
    • 33744825406 scopus 로고
    • Sequence space soup of proteins and copolymers
    • Chan HS, Dill KA. Sequence space soup of proteins and copolymers. J Chem Phys 1991;95:3775-87.
    • (1991) J Chem Phys , vol.95 , pp. 3775-3787
    • Chan, H.S.1    Dill, K.A.2
  • 6
    • 0000868733 scopus 로고
    • The protein folding problem
    • Chan HS, Dill KA. The protein folding problem. Phys Today 1993;46: 24-32.
    • (1993) Phys Today , vol.46 , pp. 24-32
    • Chan, H.S.1    Dill, K.A.2
  • 8
    • 36549094651 scopus 로고
    • Interchain loops in polymers-effects of excluded volume
    • Chan HS, Dill KA. Interchain loops in polymers-effects of excluded volume. J Chem Phys 1989;90:492-509.
    • (1989) J Chem Phys , vol.90 , pp. 492-509
    • Chan, H.S.1    Dill, K.A.2
  • 9
    • 0026519315 scopus 로고
    • A lattice model for protein-structure predicton at low resolution
    • Hinds DA, Levitt M. A lattice model for protein-structure predicton at low resolution. Proc Natl Acad Sci USA 1992;89:2536-40.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 2536-2540
    • Hinds, D.A.1    Levitt, M.2
  • 10
    • 0002698766 scopus 로고    scopus 로고
    • Modeling protein folding: The beauty and power of simplicity
    • Shakhnovich EI. Modeling protein folding: the beauty and power of simplicity. Fold Des 1996;1:R50-4.
    • (1996) Fold Des , vol.1
    • Shakhnovich, E.I.1
  • 12
    • 0031302932 scopus 로고    scopus 로고
    • High coordination lattice models of protein structure, dynamics and thermodynamics
    • Kolinski A, Skolnick J. High coordination lattice models of protein structure, dynamics and thermodynamics. Acta Biochim Pol 1997;44: 389-422.
    • (1997) Acta Biochim Pol , vol.44 , pp. 389-422
    • Kolinski, A.1    Skolnick, J.2
  • 14
    • 0012652364 scopus 로고
    • A combinatorial algorithm for effective generation of long maximally compact lattice chains
    • Ramakrishnan R, Pekny JF, Caruthers JM. A combinatorial algorithm for effective generation of long maximally compact lattice chains. J Chem Phys 1995;103:7592-604.
    • (1995) J Chem Phys , vol.103 , pp. 7592-7604
    • Ramakrishnan, R.1    Pekny, J.F.2    Caruthers, J.M.3
  • 15
    • 0028058107 scopus 로고
    • Stabilization of intermediate density states in globular- proteins by homogenous intramolecular attractive interactions
    • Bahar I, Jernigan RL. Stabilization of intermediate density states in globular-proteins by homogenous intramolecular attractive interactions. Biophys J 1994;66:454-66.
    • (1994) Biophys J , vol.66 , pp. 454-466
    • Bahar, I.1    Jernigan, R.L.2
  • 16
    • 0028085228 scopus 로고
    • Cooperative structural transitions induced by nonhomogenous intramolecular interactions in compact globular proteins
    • Bahar I, Jernigan RL. Cooperative structural transitions induced by nonhomogenous intramolecular interactions in compact globular proteins. Biophys J 1994;66:467-81.
    • (1994) Biophys J , vol.66 , pp. 467-481
    • Bahar, I.1    Jernigan, R.L.2
  • 17
    • 0025319917 scopus 로고
    • Conformations of folded proteins in restricted spaces
    • Covell DG, Jernigan RL. Conformations of folded proteins in restricted spaces. Biochemistry 1990;29:3287-94.
    • (1990) Biochemistry , vol.29 , pp. 3287-3294
    • Covell, D.G.1    Jernigan, R.L.2
  • 18
    • 36549097257 scopus 로고
    • Enumeration of all compact conformations of copolymers with random sequence of links
    • Shakhnovich E, Gutin A. Enumeration of all compact conformations of copolymers with random sequence of links. J Chem Phys 1990;93: 5967-71.
    • (1990) J Chem Phys , vol.93 , pp. 5967-5971
    • Shakhnovich, E.1    Gutin, A.2
  • 19
    • 0001942492 scopus 로고
    • Phenomenological renormalization of the self avoiding walk in 2 dimensions
    • Derrida B. Phenomenological renormalization of the self avoiding walk in 2 dimensions. J Phys A 1981;14:L5-L9.
    • (1981) J Phys A , vol.14
    • Derrida, B.1
  • 20
    • 0004560759 scopus 로고
    • Asymptotic distribution for self-avoiding walks constrained to s tips, cylinders, and tubes
    • Klein DJ. Asymptotic distribution for self-avoiding walks constrained to stips, cylinders, and tubes. J Stat Phys 1980;23:561-86.
    • (1980) J Stat Phys , vol.23 , pp. 561-586
    • Klein, D.J.1
  • 21
    • 36149040888 scopus 로고
    • Compact self-avoiding circuits on two dimensional lattices
    • Schmalz TG, Hite GE, Klein DJ. Compact self-avoiding circuits on two dimensional lattices. J Phys A 1984;17:445-53.
    • (1984) J Phys A , vol.17 , pp. 445-453
    • Schmalz, T.G.1    Hite, G.E.2    Klein, D.J.3
  • 22
    • 0031250872 scopus 로고    scopus 로고
    • Efficient method to count and generate compact protein lattice conformations
    • Kloczkowski A, Jernigan RL. Efficient method to count and generate compact protein lattice conformations. Macromolecules 1997;30: 6691-4.
    • (1997) Macromolecules , vol.30 , pp. 6691-6694
    • Kloczkowski, A.1    Jernigan, R.L.2
  • 23
    • 0000686163 scopus 로고    scopus 로고
    • Computer generation and enumeration of compact self-avoiding walks within simple geometries on lattices
    • Kloczkowski A, Jernigan RL. Computer generation and enumeration of compact self-avoiding walks within simple geometries on lattices. Comput Theor Polym Sci 1997;7:163-73.
    • (1997) Comput Theor Polym Sci , vol.7 , pp. 163-173
    • Kloczkowski, A.1    Jernigan, R.L.2
  • 24
    • 0342269221 scopus 로고    scopus 로고
    • Transfer matrix method for enumeration and generation of compact self-avoiding walks. II. Cubic lattice
    • Kloczkowski A, Jernigan RL. Transfer matrix method for enumeration and generation of compact self-avoiding walks. II. Cubic lattice. J Chem Phys 1998;109:5147-59.
    • (1998) J Chem Phys , vol.109 , pp. 5147-5159
    • Kloczkowski, A.1    Jernigan, R.L.2
  • 25
    • 0000763203 scopus 로고    scopus 로고
    • Transfer matrix method for enumeration ansi generation of compact self-avoiding walks. I. Square lattices
    • Kloczkowski A, Jernigan RL. Transfer matrix method for enumeration ansi generation of compact self-avoiding walks. I. Square lattices. J Chem Phys 1998;109:5134-46.
    • (1998) J Chem Phys , vol.109 , pp. 5134-5146
    • Kloczkowski, A.1    Jernigan, R.L.2
  • 26
    • 0035892853 scopus 로고    scopus 로고
    • Enumeration of compact self-avoiding walks
    • Jensen I. Enumeration of compact self-avoiding walks. Comput Phys Commun 2001;142:109-13.
    • (2001) Comput Phys Commun , vol.142 , pp. 109-113
    • Jensen, I.1
  • 29
    • 0037110580 scopus 로고    scopus 로고
    • Designability of protein structures: A lattice-model study using the Miyazawa-Jemigan matrix
    • Li H, Tang C, Wingreen NS. Designability of protein structures: a lattice-model study using the Miyazawa-Jemigan matrix. Prot: Struct Funct Genet 2002;49:403-12.
    • (2002) Prot: Struct Funct Genet , vol.49 , pp. 403-412
    • Li, H.1    Tang, C.2    Wingreen, N.S.3
  • 30
    • 0000713579 scopus 로고    scopus 로고
    • Designability, thermodynamic stability, and dynamics in protein folding: A lattice model study
    • Melin R, Li H, Wingreen NS, Tang C. Designability, thermodynamic stability, and dynamics in protein folding: a lattice model study. J Chem Phys 1999;110:1252-62.
    • (1999) J Chem Phys , vol.110 , pp. 1252-1262
    • Melin, R.1    Li, H.2    Wingreen, N.S.3    Tang, C.4
  • 31
    • 0036606863 scopus 로고    scopus 로고
    • Emergence of highly designable protein-backbone conformations in an off-lattice model
    • Miller J, Zeng C, Wingreen NS, Tang C. Emergence of highly designable protein-backbone conformations in an off-lattice model. Prot: Struct Funct Genet 2002;47:506-12.
    • (2002) Prot: Struct Funct Genet , vol.47 , pp. 506-512
    • Miller, J.1    Zeng, C.2    Wingreen, N.S.3    Tang, C.4
  • 33
    • 0029772552 scopus 로고    scopus 로고
    • Emergence of preferred structures in a simple model of protein folding
    • Li H, Helling R, Tang C, Wingreen N. Emergence of preferred structures in a simple model of protein folding. Science 1996;273: 666-9.
    • (1996) Science , vol.273 , pp. 666-669
    • Li, H.1    Helling, R.2    Tang, C.3    Wingreen, N.4
  • 35
    • 0013864421 scopus 로고
    • A general treatment of helix-coil equilibria in macromolecular systems
    • Flory PJ, Miller WG. A general treatment of helix-coil equilibria in macromolecular systems. J Mol Biol 1966;15:284-97.
    • (1966) J Mol Biol , vol.15 , pp. 284-297
    • Flory, P.J.1    Miller, W.G.2
  • 37
    • 0032190305 scopus 로고    scopus 로고
    • Analytical shape computing of macromolecules I: Molecular area and volume through alpha shape
    • Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. Analytical shape computing of macromolecules I: molecular area and volume through alpha shape. Proteins 1998;33:1-17.
    • (1998) Proteins , vol.33 , pp. 1-17
    • Liang, J.1    Edelsbrunner, H.2    Fu, P.3    Sudhakar, P.V.4    Subramaniam, S.5
  • 38
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
    • Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci 1998;7:1884-97.
    • (1998) Protein Sci , vol.7 , pp. 1884-1897
    • Liang, J.1    Edelsbrunner, H.2    Woodward, C.3
  • 39
    • 0032189626 scopus 로고    scopus 로고
    • Analytical shape computing of macromolecules II: Identification and computation of inaccessible cavities inside proteins
    • Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. Analytical shape computing of macromolecules II: identification and computation of inaccessible cavities inside proteins. Proteins 1998;33: 18-29.
    • (1998) Proteins , vol.33 , pp. 18-29
    • Liang, J.1    Edelsbrunner, H.2    Fu, P.3    Sudhakar, P.V.4    Subramaniam, S.5
  • 40
    • 0037103826 scopus 로고    scopus 로고
    • Statistical geometry of packing defects of lattice chain polymer from enumeration and sequential Monte Carlo method
    • Liang J, Zhang JF, Chen R. Statistical geometry of packing defects of lattice chain polymer from enumeration and sequential Monte Carlo method. J Chem Phys 2002;117:3511-21.
    • (2002) J Chem Phys , vol.117 , pp. 3511-3521
    • Liang, J.1    Zhang, J.F.2    Chen, R.3
  • 41
    • 0034901412 scopus 로고    scopus 로고
    • Are proteins well-packed?
    • Liang J, Dill KA. Are proteins well-packed? Biophys J 2001;81: 751-66.
    • (2001) Biophys J , vol.81 , pp. 751-766
    • Liang, J.1    Dill, K.A.2
  • 42
    • 0002052671 scopus 로고    scopus 로고
    • On the definition and the construction of pockets in macromolecules
    • Edelsbrunner H, Facello M, Liang J. On the definition and the construction of pockets in macromolecules. Dis Appl Math 1998;88: 83-102.
    • (1998) Dis Appl Math , vol.88 , pp. 83-102
    • Edelsbrunner, H.1    Facello, M.2    Liang, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.