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Volumn 15, Issue 2, 2005, Pages 144-150

Coarse-grained models for proteins

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN; PROTEIN;

EID: 17044393884     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2005.02.005     Document Type: Review
Times cited : (735)

References (82)
  • 1
    • 1242338103 scopus 로고    scopus 로고
    • Conformational sampling for the impatient
    • K. Tai Conformational sampling for the impatient Biophys Chem 107 2004 213 220
    • (2004) Biophys Chem , vol.107 , pp. 213-220
    • Tai, K.1
  • 2
    • 1442328108 scopus 로고    scopus 로고
    • Advances in biomolecular simulations: Methodology and recent applications
    • J. Norberg, and L. Nilsson Advances in biomolecular simulations: methodology and recent applications Q Rev Biophys 36 2003 257 306
    • (2003) Q Rev Biophys , vol.36 , pp. 257-306
    • Norberg, J.1    Nilsson, L.2
  • 3
    • 0037343308 scopus 로고    scopus 로고
    • Molecular dynamics of biological macromolecules: A brief history and perspective
    • M. Karplus Molecular dynamics of biological macromolecules: a brief history and perspective Biopolymers 68 2003 350 358
    • (2003) Biopolymers , vol.68 , pp. 350-358
    • Karplus, M.1
  • 4
    • 1642504223 scopus 로고    scopus 로고
    • Modeling and studying proteins with molecular dynamics
    • R. Schleif Modeling and studying proteins with molecular dynamics Methods Enzymol 383 2004 28 47
    • (2004) Methods Enzymol , vol.383 , pp. 28-47
    • Schleif, R.1
  • 5
    • 2942520968 scopus 로고    scopus 로고
    • Conformational flexibility in recombinant measles virus nucleocapsids visualised by cryo-negative stain electron microscopy and real-space helical reconstruction
    • D. Bhella, A. Ralph, and R.P. Yeo Conformational flexibility in recombinant measles virus nucleocapsids visualised by cryo-negative stain electron microscopy and real-space helical reconstruction J Mol Biol 340 2004 319 331
    • (2004) J Mol Biol , vol.340 , pp. 319-331
    • Bhella, D.1    Ralph, A.2    Yeo, R.P.3
  • 6
    • 4143101547 scopus 로고    scopus 로고
    • The machinery of membrane protein assembly
    • S.H. White, and G. von Heijne The machinery of membrane protein assembly Curr Opin Struct Biol 14 2004 397 404
    • (2004) Curr Opin Struct Biol , vol.14 , pp. 397-404
    • White, S.H.1    Von Heijne, G.2
  • 7
    • 0017157584 scopus 로고
    • A simplified representation of protein conformations for rapid simulation of protein folding
    • M. Levitt A simplified representation of protein conformations for rapid simulation of protein folding J Mol Biol 104 1976 59 107
    • (1976) J Mol Biol , vol.104 , pp. 59-107
    • Levitt, M.1
  • 8
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • M.M. Tirion Large amplitude elastic motions in proteins from a single-parameter, atomic analysis Phys Rev Lett 77 1996 1905 1908
    • (1996) Phys Rev Lett , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 9
    • 0017842051 scopus 로고
    • Studies on protein folding, unfolding and fluctuations by computer simulation. A three-dimensional lattice model of lysozyme
    • Y. Ueeda, H. Taketomi, and N. Gō Studies on protein folding, unfolding and fluctuations by computer simulation. A three-dimensional lattice model of lysozyme Biopolymers 17 1978 1531 1548
    • (1978) Biopolymers , vol.17 , pp. 1531-1548
    • Ueeda, Y.1    Taketomi, H.2    Go, N.3
  • 11
    • 10344230919 scopus 로고    scopus 로고
    • Automatic domain decomposition of proteins by Gaussian network model
    • S. Kundu, D.C. Sorensen, and G.N. Phillips Jr. Automatic domain decomposition of proteins by Gaussian network model Proteins 57 2004 725 733 A method is presented that uses ENM to automatically decompose a protein into structural domains, defined as portions of the protein that move independently. The accuracy of the method is verified for a large set of proteins and connections with graph theory are indicated.
    • (2004) Proteins , vol.57 , pp. 725-733
    • Kundu, S.1    Sorensen, D.C.2    Phillips Jr., G.N.3
  • 12
    • 0037830142 scopus 로고    scopus 로고
    • Universal behavior of localization of residue fluctuations in globular proteins
    • Y. Wu, X. Yuan, X. Gao, H. Fang, and J. Zi Universal behavior of localization of residue fluctuations in globular proteins Phys Rev E 67 2003 041909
    • (2003) Phys Rev e , vol.67 , pp. 041909
    • Wu, Y.1    Yuan, X.2    Gao, X.3    Fang, H.4    Zi, J.5
  • 13
    • 2442581510 scopus 로고    scopus 로고
    • Topological thermal instability and length of proteins
    • F. Burioni, D. Cassi, F. Cecconi, and A. Vulpiani Topological thermal instability and length of proteins Proteins 55 2004 529 535 ENM is used to analyze the relationship between topological thermal instability and the size of proteins. A general relationship is demonstrated between the size of the protein and the 'degree' of topological connectivity.
    • (2004) Proteins , vol.55 , pp. 529-535
    • Burioni, F.1    Cassi, D.2    Cecconi, F.3    Vulpiani, A.4
  • 14
    • 0037764042 scopus 로고    scopus 로고
    • Molecular dynamics simulations of peptides and proteins with amplified collective motions
    • Z. Zhang, Y. Shi, and H. Liu Molecular dynamics simulations of peptides and proteins with amplified collective motions Biophys J 84 2003 3583 3593 ENM is used to compute the principal modes along a full-atom MD trajectory and amplify them to better explore the phase space. The method is applied to T4 lysozyme and to the refolding of an S-peptide analog.
    • (2003) Biophys J , vol.84 , pp. 3583-3593
    • Zhang, Z.1    Shi, Y.2    Liu, H.3
  • 15
    • 0347379775 scopus 로고    scopus 로고
    • A comparison between elastic network interpolation and MD simulation of 16S ribosomal RNA
    • M.K. Kim, W. Li, B.A. Shapiro, and G.S. Chirikjian A comparison between elastic network interpolation and MD simulation of 16S ribosomal RNA J Biomol Struct Dyn 21 2003 395 405 An efficient method based on ENM for generating conformations that interpolate between two different conformations is demonstrated and applied to 16S rRNA. The resulting conformations are compared with an all-atom MD simulation.
    • (2003) J Biomol Struct Dyn , vol.21 , pp. 395-405
    • Kim, M.K.1    Li, W.2    Shapiro, B.A.3    Chirikjian, G.S.4
  • 16
    • 2442543557 scopus 로고    scopus 로고
    • Accurate description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models
    • C. Micheletti, P. Carloni, and A. Maritan Accurate description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models Proteins 55 2004 635 645 An ENM based on Cα and Cβ positions is proposed; it has the same computational complexity of a one-bead ENM and is proven to give a better accuracy.
    • (2004) Proteins , vol.55 , pp. 635-645
    • Micheletti, C.1    Carloni, P.2    Maritan, A.3
  • 17
    • 2342518038 scopus 로고    scopus 로고
    • On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models
    • M. Delarue, and P. Dumas On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models Proc Natl Acad Sci USA 101 2004 6957 6962
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 6957-6962
    • Delarue, M.1    Dumas, P.2
  • 18
    • 17044432465 scopus 로고    scopus 로고
    • Normal mode based fitting of atomic structure into electron density maps: Application to SR Ca-ATPase
    • K. Hinsen, N. Reuter, J. Navaza, D.L. Stokes, and J.-J. Lacapere Normal mode based fitting of atomic structure into electron density maps: application to SR Ca-ATPase Biophys J 88 2005 818 827 An ENM with distance-dependent elastic constants was used together with NMA to fit sarcoplasmic reticulum Ca-ATPase into electron density maps. Atomically detailed structures are obtained and conclusions are drawn about phosphorylation-induced conformational changes of the protein.
    • (2005) Biophys J , vol.88 , pp. 818-827
    • Hinsen, K.1    Reuter, N.2    Navaza, J.3    Stokes, D.L.4    Lacapere, J.-J.5
  • 19
    • 0037436340 scopus 로고    scopus 로고
    • Mega-dalton biomolecular motion captured from electron microscopy reconstructions
    • P. Chacon, F. Tama, and W. Wriggers Mega-dalton biomolecular motion captured from electron microscopy reconstructions J Mol Biol 326 2003 485 492 ENM and NMA are used to reconstruct the fundamental motions of bacterial RNA polymerase, the 30S and 50S subunits of the ribosome, and the chaperonin CCT.
    • (2003) J Mol Biol , vol.326 , pp. 485-492
    • Chacon, P.1    Tama, F.2    Wriggers, W.3
  • 20
    • 4344716056 scopus 로고    scopus 로고
    • Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM
    • F. Tama, O. Miyashita, and C.L. Brooks III Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM J Struct Biol 147 2004 315 326 A method for fitting high-resolution structures into low-resolution experimental data is shown. The method is based on ENM and NMA, and allows protein flexibility by taking into account conformational changes induced by interactions between structures. The method is applied to elongation factor G bound to the ribosome, Escherichia coli RNA polymerase and cowpea chlorotic mottle virus.
    • (2004) J Struct Biol , vol.147 , pp. 315-326
    • Tama, F.1    Miyashita, O.2    Brooks III, C.L.3
  • 21
    • 2942638203 scopus 로고    scopus 로고
    • Molecular mechanism of domain swapping in proteins: An analysis of slower motions
    • S. Kundy, and R.L. Jernigan Molecular mechanism of domain swapping in proteins: an analysis of slower motions Biophys J 86 2004 3846 3854
    • (2004) Biophys J , vol.86 , pp. 3846-3854
    • Kundy, S.1    Jernigan, R.L.2
  • 22
    • 0042424707 scopus 로고    scopus 로고
    • Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
    • F. Tama, M. Valle, J. Frank, and C.L. Brooks III Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy Proc Natl Acad Sci USA 100 2003 9319 9323 The slower motions of the 70S ribosome from T. thermophilus are analyzed with ENM and NMA. Mechanical rearrangements that appear to be related to function are highlighted and are shown to agree with cryo-EM data.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 9319-9323
    • Tama, F.1    Valle, M.2    Frank, J.3    Brooks III, C.L.4
  • 23
    • 0036154101 scopus 로고    scopus 로고
    • Functional motions of influenza virus hemagglutinin: A structure-based analytical approach
    • B. Isin, P. Doruker, and I. Bahar Functional motions of influenza virus hemagglutinin: a structure-based analytical approach Biophys J 82 2002 569 581
    • (2002) Biophys J , vol.82 , pp. 569-581
    • Isin, B.1    Doruker, P.2    Bahar, I.3
  • 25
    • 1042291214 scopus 로고    scopus 로고
    • Myosin flexibility: Structural domains and collective vibrations
    • I. Navizet, R. Lavery, and R.L. Jernigan Myosin flexibility: structural domains and collective vibrations Proteins 54 2004 384 393 An ENM of scallop myosin is reported and a method for the analysis of the rigid blocks of the protein is presented. Regions that have a key role in the change of rigidity of the protein are detected and analyzed.
    • (2004) Proteins , vol.54 , pp. 384-393
    • Navizet, I.1    Lavery, R.2    Jernigan, R.L.3
  • 26
    • 0345687171 scopus 로고    scopus 로고
    • A comparative study of motor-protein motions by using a simple elastic-network model
    • W. Zheng, and S. Doniach A comparative study of motor-protein motions by using a simple elastic-network model Proc Natl Acad Sci USA 100 2003 13253 13258
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 13253-13258
    • Zheng, W.1    Doniach, S.2
  • 27
    • 0037963159 scopus 로고    scopus 로고
    • Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: A structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations
    • N. Kurt, Scott WRP, C.A. Schiffer, and T. Haliloglu Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations Proteins 51 2003 409 422
    • (2003) Proteins , vol.51 , pp. 409-422
    • Kurt, N.1    Scott, W.R.P.2    Schiffer, C.A.3    Haliloglu, T.4
  • 29
    • 0034604105 scopus 로고    scopus 로고
    • A surprising simplicity to protein folding
    • D. Baker A surprising simplicity to protein folding Nature 405 2000 39 42
    • (2000) Nature , vol.405 , pp. 39-42
    • Baker, D.1
  • 30
    • 0035850732 scopus 로고    scopus 로고
    • Roles of native topology and chain-length scaling in protein folding: A simulation study with a Gō-like model
    • N. Koga, and S. Takada Roles of native topology and chain-length scaling in protein folding: a simulation study with a Gō-like model J Mol Biol 313 2001 171 180
    • (2001) J Mol Biol , vol.313 , pp. 171-180
    • Koga, N.1    Takada, S.2
  • 31
    • 0034685604 scopus 로고    scopus 로고
    • Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
    • C. Clementi, H. Nymeyer, and J.N. Onuchic Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins J Mol Biol 298 2000 937 953
    • (2000) J Mol Biol , vol.298 , pp. 937-953
    • Clementi, C.1    Nymeyer, H.2    Onuchic, J.N.3
  • 32
    • 0037154268 scopus 로고    scopus 로고
    • Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after structural collapse
    • M.S. Cheung, A.E. Garcia, and J. Onuchic Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after structural collapse Proc Natl Acad Sci USA 99 2000 685 690
    • (2000) Proc Natl Acad Sci USA , vol.99 , pp. 685-690
    • Cheung, M.S.1    Garcia, A.E.2    Onuchic, J.3
  • 33
    • 0037459035 scopus 로고    scopus 로고
    • Solvation effects and driving forces for protein thermodynamics and kinetic cooperativity: How adequate is native-centric topological modeling?
    • H. Kaya, and H.S. Chan Solvation effects and driving forces for protein thermodynamics and kinetic cooperativity: how adequate is native-centric topological modeling? J Mol Biol 326 2003 911 931
    • (2003) J Mol Biol , vol.326 , pp. 911-931
    • Kaya, H.1    Chan, H.S.2
  • 34
    • 0036156804 scopus 로고    scopus 로고
    • Folding thermodynamics of model four-strand antiparallel β-sheet protein
    • H. Jang, C.K. Hall, and Y. Zhou Folding thermodynamics of model four-strand antiparallel β-sheet protein Biophys J 82 2002 646 659
    • (2002) Biophys J , vol.82 , pp. 646-659
    • Jang, H.1    Hall, C.K.2    Zhou, Y.3
  • 35
    • 0347364624 scopus 로고    scopus 로고
    • Thermodynamics and stability of a β-sheet complex: Molecular dynamics simulations on simplified off-lattice protein models
    • H. Jang, C.K. Hall, and Y. Zhou Thermodynamics and stability of a β-sheet complex: molecular dynamics simulations on simplified off-lattice protein models Protein Sci 13 2004 40 53
    • (2004) Protein Sci , vol.13 , pp. 40-53
    • Jang, H.1    Hall, C.K.2    Zhou, Y.3
  • 36
    • 0346688724 scopus 로고    scopus 로고
    • Assembly and kinetic folding pathways of a tetrameric β sheet complex: Molecular dynamics simulations on simplified off-lattice protein model
    • H. Jang, C.K. Hall, and Y. Zhou Assembly and kinetic folding pathways of a tetrameric β sheet complex: molecular dynamics simulations on simplified off-lattice protein model Biophys J 86 2004 31 49 In this paper, a Gō-like model is used with discontinuous MD to investigate the folding dynamics and thermodynamic properties of the different kinds of intermediates that form during the folding process.
    • (2004) Biophys J , vol.86 , pp. 31-49
    • Jang, H.1    Hall, C.K.2    Zhou, Y.3
  • 37
    • 0037459022 scopus 로고    scopus 로고
    • Interplay among tertiary contacts, secondary structure formation and side chain packing in the protein folding mechanism: All-atom representation study of protein L
    • C. Clementi, A.E. Garcia, and J.N. Onuchic Interplay among tertiary contacts, secondary structure formation and side chain packing in the protein folding mechanism: all-atom representation study of protein L J Mol Biol 326 2003 933 954
    • (2003) J Mol Biol , vol.326 , pp. 933-954
    • Clementi, C.1    Garcia, A.E.2    Onuchic, J.N.3
  • 38
    • 2942590388 scopus 로고    scopus 로고
    • Simulation experiment and evolution: Understanding nucleation in protein S6 folding
    • I.A. Hubner, M. Oliveberg, and E.I. Shakhnovich Simulation experiment and evolution: understanding nucleation in protein S6 folding Proc Natl Acad Sci USA 101 2004 8354 8359
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 8354-8359
    • Hubner, I.A.1    Oliveberg, M.2    Shakhnovich, E.I.3
  • 39
    • 0345743709 scopus 로고    scopus 로고
    • Protein topology determines binding mechanism
    • Y. Levy, P.G. Wolynes, and J. Onuchic Protein topology determines binding mechanism Proc Natl Acad Sci USA 101 2004 511 516 A Gō model is used to investigate the binding of a variety of homodimeric proteins. Analysis of the free energy as a function of the intramonomer and intermonomer contacts allows discrimination between two-state obligate dimers (binding occurs together with folding) and three-state dimers (folding precedes binding and monomers are stable). The model reproduces the experimentally known association mechanisms.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 511-516
    • Levy, Y.1    Wolynes, P.G.2    Onuchic, J.3
  • 40
    • 2942615093 scopus 로고    scopus 로고
    • The folding and dimerization of HIV-1 protease: Evidence for a stable monomer from simulations
    • Y. Levy, A. Caflisch, J.N. Onuchic, and P.G. Wolynes The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations J Mol Biol 340 2004 67 79
    • (2004) J Mol Biol , vol.340 , pp. 67-79
    • Levy, Y.1    Caflisch, A.2    Onuchic, J.N.3    Wolynes, P.G.4
  • 41
    • 0141482088 scopus 로고    scopus 로고
    • How protein thermodynamics and folding mechanisms are altered by the chaperoning cage: Molecular simulations
    • F. Takagi, N. Koga, and S. Takada How protein thermodynamics and folding mechanisms are altered by the chaperoning cage: molecular simulations Proc Natl Acad Sci USA 100 2003 11367 11372 The folding of different substrate proteins confined within a model chaperonin cage is studied with Langevin dynamics and a Gō model of the proteins. It is shown that the folding kinetics are enhanced and that the native state is stabilized due to a reduction of the conformational entropy.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 11367-11372
    • Takagi, F.1    Koga, N.2    Takada, S.3
  • 44
    • 0031566950 scopus 로고    scopus 로고
    • Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
    • I. Bahar, and Jernigan Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation J Mol Biol 266 1997 195 214
    • (1997) J Mol Biol , vol.266 , pp. 195-214
    • Bahar, I.1    Jernigan2
  • 45
    • 1942423584 scopus 로고    scopus 로고
    • Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis
    • N.-V. Buchete, J.E. Straub, and D. Thirumalai Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis J Mol Graph Model 22 2004 441 450
    • (2004) J Mol Graph Model , vol.22 , pp. 441-450
    • Buchete, N.-V.1    Straub, J.E.2    Thirumalai, D.3
  • 46
    • 0141480046 scopus 로고    scopus 로고
    • Coarse grained sequences for protein folding and design
    • S. Brown, N.J. Fawzi, and T. Head-Gordon Coarse grained sequences for protein folding and design Proc Natl Acad Sci USA 100 2003 10712 10717 This is the last in a set of papers in which a one-bead minimalist model of protein folding is presented and optimized. The energy function includes bonded, dihedral and non-bonded terms, whose parameterization is dependent on the native topology and on the sequence via a 'three-letter' amino acid code (hydrophilic, hydrophobic and neutral). Angular parameters are designed to reproduce secondary structure, whereas non-bonded interactions are van der Waals like, and are set as attractive for hydrophobic-hydrophobic interactions, repulsive for hydrophobic-hydrophilic and strongly repulsive for hydrophilic-hydrophilic.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 10712-10717
    • Brown, S.1    Fawzi, N.J.2    Head-Gordon, T.3
  • 47
    • 0037799371 scopus 로고    scopus 로고
    • Effects of confinement and crowding on the thermodynamics and kinetics of folding of a minimalist β-barrel protein
    • M. Friedel, D.J. Scheeler, and J.-E. Shea Effects of confinement and crowding on the thermodynamics and kinetics of folding of a minimalist β-barrel protein J Chem Phys 118 2003 8106 8113
    • (2003) J Chem Phys , vol.118 , pp. 8106-8113
    • Friedel, M.1    Scheeler, D.J.2    Shea, J.-E.3
  • 48
    • 1942470951 scopus 로고    scopus 로고
    • Self-assembly of peptides into a beta-barrel motif
    • M. Friedel, and J.-E. Shea Self-assembly of peptides into a beta-barrel motif J Chem Phys 120 2004 5809 5823 By using a non-bonded interaction term with a parameter that adjusts the strength of non-native hydrophobic interactions, a continuous set of models with increasing frustration was used to study the aggregation of a β-barrel minimal protein. The frustration is shown to influence the aggregation process, stabilizing, in certain situations, amyloid-like aggregates.
    • (2004) J Chem Phys , vol.120 , pp. 5809-5823
    • Friedel, M.1    Shea, J.-E.2
  • 49
    • 17044374438 scopus 로고    scopus 로고
    • The dynamics of flap opening in HIV-1 protease: A coarse grained approach
    • V. Tozzini, and A. McCammon The dynamics of flap opening in HIV-1 protease: a coarse grained approach Protein Sci 13 suppl 1 2004 194
    • (2004) Protein Sci , vol.13 , Issue.1 SUPPL. , pp. 194
    • Tozzini, V.1    McCammon, A.2
  • 50
    • 17044415095 scopus 로고    scopus 로고
    • A coarse grained model for the ribosome: Molecular dynamics simulations
    • J. Trylska, V. Tozzini, and J.A. McCammon A coarse grained model for the ribosome: molecular dynamics simulations Protein Sci 13 2004 121
    • (2004) Protein Sci , vol.13 , pp. 121
    • Trylska, J.1    Tozzini, V.2    McCammon, J.A.3
  • 51
    • 0042783950 scopus 로고    scopus 로고
    • Deriving effective mesoscale potentials from atomistic simulations
    • D. Reith, M. Pütz, and F. Müller-Plathe Deriving effective mesoscale potentials from atomistic simulations J Comput Chem 24 2003 1624 1636
    • (2003) J Comput Chem , vol.24 , pp. 1624-1636
    • Reith, D.1    Pütz, M.2    Müller-Plathe, F.3
  • 52
    • 0042344862 scopus 로고    scopus 로고
    • Structure -based prediction of potential binding and non binding peptides to HIV-1 protease
    • ••] is used to evaluate the affinity of a test set of naturally occurring substrates of HIV-1 protease and to predict the binding affinity of new substrates. It is shown that the molecular flexibility and the specificity of sidechain short-range interactions are crucial in predicting the binding affinity.
    • (2003) Biophys J , vol.85 , pp. 853-863
    • Kurt, N.1    Haliloglu, T.2    Schiffer, C.A.3
  • 53
    • 1142279630 scopus 로고    scopus 로고
    • Contact pair dynamics during folding of two small proteins: Chicken villin head piece and the Alzheimer protein β-amyloid
    • A. Mukherjee, and B. Bagchi Contact pair dynamics during folding of two small proteins: chicken villin head piece and the Alzheimer protein β-amyloid J Chem Phys 120 2004 1602 1612 The authors present an analytical two-bead model with an interacting potential containing simplified bonded interactions between the backbone atoms, van der Waals terms including hydrophobicity, modeled following Levitt and based on the Boltzmann inversion of probability distributions of experimental structures. A term for helix propensity is added. The model was used with Brownian dynamics and applied to the folding of chicken villin head piece and the Alzheimer protein β-amyloid; it was shown to reproduce the different stages of folding.
    • (2004) J Chem Phys , vol.120 , pp. 1602-1612
    • Mukherjee, A.1    Bagchi, B.2
  • 54
    • 0037343371 scopus 로고    scopus 로고
    • Ab initio structure prediction of two alpha-helical oligomers with a multiple-chain united-residue force field and global search
    • J.A. Saunders, and H.A. Scheraga Ab initio structure prediction of two alpha-helical oligomers with a multiple-chain united-residue force field and global search Biopolymers 68 2003 300 317
    • (2003) Biopolymers , vol.68 , pp. 300-317
    • Saunders, J.A.1    Scheraga, H.A.2
  • 55
    • 4644264474 scopus 로고    scopus 로고
    • A united residue force-field for calcium-protein interactions
    • M. Khalili, J.A. Saunders, A. Liwo, S. Oldziej, and H.A. Scheraga A united residue force-field for calcium-protein interactions Protein Sci 13 2004 2725 2735 The last of a series of papers describing the development and optimization of the UNRES (united-residue) model, which was derived by Scheraga and co-workers over the past few years. The beads are located on the Cα atom, on the centroid of the sidechain and on a 'peptide' (p) center located midway between two Cα atoms. However, Cα is only used to calculate the position of p; thus, the degrees of freedom correspond to a two-bead model. The parameterization is based on the statistical analysis of structures and on fitting the free energy functions obtained from full-atom simulations of oligopeptides. Additional terms account for correlation between the degrees of freedom. The model has been recently optimized to include ellipsoid sidechains and interaction parameters with calcium, and used in protein structure and interaction prediction.
    • (2004) Protein Sci , vol.13 , pp. 2725-2735
    • Khalili, M.1    Saunders, J.A.2    Liwo, A.3    Oldziej, S.4    Scheraga, H.A.5
  • 56
    • 0038583687 scopus 로고    scopus 로고
    • Protein docking with a reduced protein model accounting for side-chain flexibility
    • M. Zacharias Protein docking with a reduced protein model accounting for side-chain flexibility Protein Sci 12 2003 1271 1282 A model with one bead for the Cα atom and up to two beads for the sidechains was used in a protein-protein docking approach. Size and hydrophilic/hydrophobic interactions are accounted for by van der Waals like amino-acid-specific terms. Sidechain conformational changes are taken into account by introducing several different rotamers of the sidechain during docking. This procedure is shown to generate more accurate complex structures than rigid docking.
    • (2003) Protein Sci , vol.12 , pp. 1271-1282
    • Zacharias, M.1
  • 57
    • 0035882559 scopus 로고    scopus 로고
    • α-helix formation: Discontinuous molecular dynamics on an intermediate-resolution protein model
    • A.V. Smith, and C.K. Hall α-helix formation: discontinuous molecular dynamics on an intermediate-resolution protein model Proteins 44 2001 344 360
    • (2001) Proteins , vol.44 , pp. 344-360
    • Smith, A.V.1    Hall, C.K.2
  • 58
    • 0035882537 scopus 로고    scopus 로고
    • Assembly of a tetrameric α-helical bundle: Computer simulations on an intermediate-resolution protein model
    • A.V. Smith, and C.K. Hall Assembly of a tetrameric α-helical bundle: computer simulations on an intermediate-resolution protein model Proteins 44 2001 376 391
    • (2001) Proteins , vol.44 , pp. 376-391
    • Smith, A.V.1    Hall, C.K.2
  • 60
    • 7244253280 scopus 로고    scopus 로고
    • Solvent effects on the conformational transition of a polyalanine peptide
    • H.D. Nguyen, A.J. Marchut, and C.K. Hall Solvent effects on the conformational transition of a polyalanine peptide Protein Sci 13 2004 2909 2924
    • (2004) Protein Sci , vol.13 , pp. 2909-2924
    • Nguyen, H.D.1    Marchut, A.J.2    Hall, C.K.3
  • 61
    • 10044280719 scopus 로고    scopus 로고
    • Phase diagrams describing fibrillization by polyalanine peptides
    • H.D. Nguyen, and C.K. Hall Phase diagrams describing fibrillization by polyalanine peptides Biophys J 87 2004 4122 4134
    • (2004) Biophys J , vol.87 , pp. 4122-4134
    • Nguyen, H.D.1    Hall, C.K.2
  • 62
    • 9244260521 scopus 로고    scopus 로고
    • Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
    • H.D. Nguyen, and C.K. Hall Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides Proc Natl Acad Sci USA 101 2004 16180 16185 The four-bead model described in [60] is used to study the aggregation of polyalanine in fibrils. Thermodynamic and environmental conditions (dis)favorable to fibril formation are indicated. The results are in qualitative agreement with experiments.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 16180-16185
    • Nguyen, H.D.1    Hall, C.K.2
  • 63
    • 0036681417 scopus 로고    scopus 로고
    • Pathway heterogeneity in protein folding
    • A. Fernandez, and A. Colubri Pathway heterogeneity in protein folding Proteins 48 2002 293 310
    • (2002) Proteins , vol.48 , pp. 293-310
    • Fernandez, A.1    Colubri, A.2
  • 64
    • 1542298146 scopus 로고    scopus 로고
    • Prediction of protein structure by simulating coarse-grained folding pathways: A preliminary report
    • A. Colubri Prediction of protein structure by simulating coarse-grained folding pathways: a preliminary report J Biomol Struct Dyn 21 2004 625 637
    • (2004) J Biomol Struct Dyn , vol.21 , pp. 625-637
    • Colubri, A.1
  • 65
    • 0032606941 scopus 로고    scopus 로고
    • Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and random heteropolymer
    • S. Takada, Z. Luthey-Schulten, and P.G. Wolynes Folding dynamics with nonadditive forces: a simulation study of a designed helical protein and random heteropolymer J Chem Phys 110 1999 11616 11628
    • (1999) J Chem Phys , vol.110 , pp. 11616-11628
    • Takada, S.1    Luthey-Schulten, Z.2    Wolynes, P.G.3
  • 66
    • 0035189984 scopus 로고    scopus 로고
    • Protein folding simulation with solvent-induced force field: Folding pathway ensemble of three-helix-bundle proteins
    • S. Takada Protein folding simulation with solvent-induced force field: folding pathway ensemble of three-helix-bundle proteins Proteins 42 2001 85 98
    • (2001) Proteins , vol.42 , pp. 85-98
    • Takada, S.1
  • 67
    • 0347417009 scopus 로고    scopus 로고
    • Optimizing physical energy functions for protein folding
    • Y. Fujisuka, S. Takada, Z.A. Luthey-Schulten, and P.G. Wolynes Optimizing physical energy functions for protein folding Proteins 54 2004 88 103 The latest version of the Takada model is presented. It uses constraints for bonds and bond angles, and sophisticated terms for dihedrals, van der Waals interactions and hydrogen bonds. Sequence-specific terms account for hydrophobicity, electrostatics, aromaticity and sidechain entropy loss due to secondary structure formation, allowing the accurate reproduction of Ramachandran plots. The parameters are optimized to minimize the folding frustration of a set of training structures.
    • (2004) Proteins , vol.54 , pp. 88-103
    • Fujisuka, Y.1    Takada, S.2    Luthey-Schulten, Z.A.3    Wolynes, P.G.4
  • 68
    • 1442300067 scopus 로고    scopus 로고
    • Roles of physical interactions in determining protein-folding mechanisms: Molecular simulation of protein G and alpha spectrin SH3
    • S.Y. Lee, Y. Fujitsuka, H. Kim do, and S. Takada Roles of physical interactions in determining protein-folding mechanisms: molecular simulation of protein G and alpha spectrin SH3 Proteins 55 2004 128 138
    • (2004) Proteins , vol.55 , pp. 128-138
    • Lee, S.Y.1    Fujitsuka, Y.2    Kim Do, H.3    Takada, S.4
  • 69
    • 0034610275 scopus 로고    scopus 로고
    • Three-helix-bundle protein in a Ramachandran model
    • A. Irbäck, F. Sjunesson, and S. Wallin Three-helix-bundle protein in a Ramachandran model Proc Natl Acad Sci USA 97 2000 13614 13618
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 13614-13618
    • Irbäck, A.1    Sjunesson, F.2    Wallin, S.3
  • 70
    • 0035681698 scopus 로고    scopus 로고
    • Hydrogen bonds, hydrophobicity forces and the character of the collapse transition
    • A. Irbäck, F. Sjunnesson, and S. Wallin Hydrogen bonds, hydrophobicity forces and the character of the collapse transition J Biol Phys 27 2001 169 179
    • (2001) J Biol Phys , vol.27 , pp. 169-179
    • Irbäck, A.1    Sjunnesson, F.2    Wallin, S.3
  • 71
    • 0036568327 scopus 로고    scopus 로고
    • Folding of a small helical protein using hydrogen bonds and hydrophobicity forces
    • G. Favrin, A. Irbäck, and S. Wallin Folding of a small helical protein using hydrogen bonds and hydrophobicity forces Proteins 47 2002 99 105
    • (2002) Proteins , vol.47 , pp. 99-105
    • Favrin, G.1    Irbäck, A.2    Wallin, S.3
  • 72
    • 0041629626 scopus 로고    scopus 로고
    • Thermodynamics of β and α structure formation in proteins
    • A. Irbäck, F. Sjunnesson, F. Sjunnesson, and S. Wallin Thermodynamics of β and α structure formation in proteins Biophys J 85 2003 1466 1473
    • (2003) Biophys J , vol.85 , pp. 1466-1473
    • Irbäck, A.1    Sjunnesson, F.2    Sjunnesson, F.3    Wallin, S.4
  • 73
    • 0035501804 scopus 로고    scopus 로고
    • Computer simulations aimed at structure prediction of supersecondary motifs in proteins
    • F. Forcellino, and P. Derremaux Computer simulations aimed at structure prediction of supersecondary motifs in proteins Proteins 45 2001 159 166
    • (2001) Proteins , vol.45 , pp. 159-166
    • Forcellino, F.1    Derremaux, P.2
  • 74
    • 3142737884 scopus 로고    scopus 로고
    • Complex folding pathways in a simple b-hairpin
    • G. Wei, N. Mosseau, and P. Derremaux Complex folding pathways in a simple b-hairpin Proteins 56 2003 464 474
    • (2003) Proteins , vol.56 , pp. 464-474
    • Wei, G.1    Mosseau, N.2    Derremaux, P.3
  • 75
    • 0037079578 scopus 로고    scopus 로고
    • Dynamics of large proteins through hierarchical levels of coarse-grained structures
    • P. Dorucker, R.L. Jernigan, and I. Bahar Dynamics of large proteins through hierarchical levels of coarse-grained structures J Comput Chem 23 2002 119 127
    • (2002) J Comput Chem , vol.23 , pp. 119-127
    • Dorucker, P.1    Jernigan, R.L.2    Bahar, I.3
  • 76
    • 0242558375 scopus 로고    scopus 로고
    • α coarse graining
    • α coarse graining J Mol Graph Model 22 2004 183 193 A new method for modeling a system as a set of rigid bodies connected by an elastic network is presented that reduces considerably the number of degrees of freedom with respect to conventional elastic network approaches. It is shown that the lowest modes of the system are reproduced with a good accuracy.
    • (2004) J Mol Graph Model , vol.22 , pp. 183-193
    • Schuyler, A.D.1    Chirikjan, G.S.2
  • 77
    • 0036840202 scopus 로고    scopus 로고
    • 2+-ATPase
    • 2+-ATPase Biophys J 83 2002 2457 2474
    • (2002) Biophys J , vol.83 , pp. 2457-2474
    • Li, G.1    Cui, Q.2
  • 78
    • 3042814575 scopus 로고    scopus 로고
    • A Brownian dynamics study: The effect of a membrane environment on an electron transfer system
    • D. Flock, and V. Helms A Brownian dynamics study: the effect of a membrane environment on an electron transfer system Biophys J 87 2004 65 74 A Brownian dynamics study of the association of cytochrome c with cytochrome c oxidase is presented, both in vacuo and as an all-atom model of the membrane. The membrane is shown to dramatically influence the association rates.
    • (2004) Biophys J , vol.87 , pp. 65-74
    • Flock, D.1    Helms, V.2
  • 79
    • 0037418340 scopus 로고    scopus 로고
    • Atomic-level observation of macromolecular crowding effects: Escape of a protein from the GroEL cage
    • A.H. Elcock Atomic-level observation of macromolecular crowding effects: escape of a protein from the GroEL cage Proc Natl Acad Sci USA 100 2003 2340 2344 A Brownian dynamics simulation of the interaction of a protein with the chaperonin GroEL cage in the presence of crowding agents is presented. A crowding agent is shown to be more effective if it forms favorable interactions with itself.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 2340-2344
    • Elcock, A.H.1
  • 80
    • 0042844593 scopus 로고    scopus 로고
    • The role of geometric complementarity in secondary structure packing: A systematic docking study
    • S. Jiang, A. Tovchicrechko, and I.A. Vakser The role of geometric complementarity in secondary structure packing: a systematic docking study Protein Sci 12 2003 1646 1651
    • (2003) Protein Sci , vol.12 , pp. 1646-1651
    • Jiang, S.1    Tovchicrechko, A.2    Vakser, I.A.3
  • 82
    • 0344982156 scopus 로고    scopus 로고
    • Competition between protein folding and aggregation with molecular chaperones in crowded solutions: Insight from mesoscopic simulations
    • A.R. Kinjo, and S. Takada Competition between protein folding and aggregation with molecular chaperones in crowded solutions: Insight from mesoscopic simulations Biophys J 85 2003 3521 3531
    • (2003) Biophys J , vol.85 , pp. 3521-3531
    • Kinjo, A.R.1    Takada, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.