The Protein Folding Network
Tài liệu tham khảo
Daggett, 2003, Is there a unifying mechanism for protein folding?, Trends Biochem. Sci., 28, 18, 10.1016/S0968-0004(02)00012-9
Bryngelson, 1989, Intermediates and barrier crossing in a random energy-model (with applications to protein folding), J. Phys. Chem., 93, 6902, 10.1021/j100356a007
Leopold, 1992, Protein folding funnels: a kinetic approach to the sequence-structure relationship, Proc. Natl Acad. Sci. USA, 89, 8721, 10.1073/pnas.89.18.8721
Karplus, 1997, The Levinthal paradox: yesterday and today, Fold. Des., 2, S69, 10.1016/S1359-0278(97)00067-9
Becker, 1997, The topology of multidimensional potential energy surfaces: theory and application to peptide structure and kinetics, J. Chem. Phys., 106, 1495, 10.1063/1.473299
Wales, 2000, Energy landscapes: from clusters to biomolecules, Advan. Chem. Phys., 115, 1, 10.1002/9780470141748.ch1
Krivov, 2002, Free energy disconnectivity graphs: application to peptide models, J. Chem. Phys., 117, 10894, 10.1063/1.1517606
Jeong, 2000, The large-scale organization of metabolic networks, Nature, 407, 651, 10.1038/35036627
Albert, 1999, Diameter of the World-Wide Web, Nature, 401, 130, 10.1038/43601
Vendruscolo, 2002, Small-world view of the amino acids that play a key role in protein folding, Phys. Rev. ser. E, 65, 061910.1, 10.1103/PhysRevE.65.061910
Greene, 2003, Uncovering network systems within protein structures, J. Mol. Biol., 334, 781, 10.1016/j.jmb.2003.08.061
Newman, 2003, The structure and function of complex networks, SIAM REV., 45, 167, 10.1137/S003614450342480
Scala, 2001, Small-world networks and the conformation space of a short lattice polymer chain, Europhys. Letters, 55, 594, 10.1209/epl/i2001-00457-7
Doye, 2002, Network topology of a potential energy landscape: a static scale-free network, Phys. Rev. Letters, 88, 238701, 10.1103/PhysRevLett.88.238701
De Alba, 1999, De novo, design of a monomeric three-stranded antiparallel β-sheet, Protein Sci., 8, 854, 10.1110/ps.8.4.854
Ferrara, 2002, Evaluation of a fast implicit solvent model for molecular dynamics simulations, Proteins: Struct., Funct. Genet., 46, 24, 10.1002/prot.10001
Ferrara, 2000, Folding simulations of a three-stranded antiparallel β-sheet peptide, Proc. Natl Acad. Sci. USA, 97, 10780, 10.1073/pnas.190324897
Cavalli, 2002, Weak temperature dependence of the free energy surface and folding pathways of structured peptides, Proteins: Struct., Funct. Genet., 47, 305, 10.1002/prot.10041
Cavalli, 2003, Fast protein folding on downhill energy landscape, Protein Sci., 12, 1801, 10.1110/ps.0366103
Ravasz, 2003, Hierarchical organization in complex networks, Phys. Rev. ser. E, 67, 026112, 10.1103/PhysRevE.67.026112
Brooks, 1983, CHARMM: a program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem., 4, 187, 10.1002/jcc.540040211
Gsponer, 2003, The role of side-chain interactions in the early steps of aggregation: molecular dynamics simulations of an amyloid-forming peptide from the yeast prion sup35, Proc. Natl Acad. Sci. USA, 100, 5154, 10.1073/pnas.0835307100
Hiltpold, 2000, Free energy surface of the helical peptide Y(MEARA)6, J. Phys. Chem. ser. B, 104, 10080, 10.1021/jp002207k
Gsponer, 2001, Role of native topology investigated by multiple unfolding simulations of four SH3 domains, J. Mol. Biol., 309, 285, 10.1006/jmbi.2001.4552
Gsponer, 2002, Molecular dynamics simulations of protein folding from the transition state, Proc. Natl Acad. Sci. USA, 99, 6719, 10.1073/pnas.092686399
Ferrara, 2000, Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations, J. Phys. Chem. ser. B, 104, 5000, 10.1021/jp994157t
Eaton, 2000, Fast kinetics and mechanisms in protein folding, Annu. Rev. Biophys. Biomol. Struct., 29, 327, 10.1146/annurev.biophys.29.1.327
Andersen, 2002, Continuum secondary structure captures protein flexibility, Structure, 10, 174, 10.1016/S0969-2126(02)00700-1
Du, 1998, On the transition coordinate for protein folding, J. Chem. Phys., 108, 334, 10.1063/1.475393
Onuchic, 1996, Protein folding funnels: the nature of the transition state ensemble, Fold. Des., 1, 441, 10.1016/S1359-0278(96)00060-0
Schonbrun, 2003, Fast protein folding kinetics, Proc. Natl Acad. Sci. USA, 100, 12678, 10.1073/pnas.1735417100
Griffiths-Jones, 2000, Structure, folding, and energetics of cooperative interactions between the β-strands of a de novo designed three-stranded antiparallel β-sheet peptide, J. Am. Chem. Soc., 122, 8350, 10.1021/ja000787t
Wright, 2003, Parallel protein-unfolding pathways revealed and mapped, Nature Struct. Biol., 10, 658, 10.1038/nsb947
Demarest, 1999, Local interactions drive the formation of nonnative structure in the denatured state of human alpha-lactalbumin: a high resolution structural characterization of a peptide model in aqueous solution, Biochemistry, 38, 7380, 10.1021/bi990320z
Barabási, 1999, Emergence of scaling in random networks, Science, 286, 509, 10.1126/science.286.5439.509
Newman, 2001, The structure of scientific collaboration networks, Proc. Natl Acad. Sci. USA, 98, 404, 10.1073/pnas.021544898
Chan, 1998, Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics, Proteins: Struct., Funct. Genet., 30, 2, 10.1002/(SICI)1097-0134(19980101)30:1<2::AID-PROT2>3.0.CO;2-R
Karplus, 2000, Aspects of protein reaction dynamics: deviations from simple behaivor, J. Phys. Chem. ser. B, 104, 11, 10.1021/jp993555t
Lazaridis, 1997, “New view” of protein folding reconciled with the old through multiple unfolding simulations, Science, 278, 1928, 10.1126/science.278.5345.1928
Koradi, 1996, MOLMOL: a program for display and analysis of macromolecular structures, J. Mol. Graph., 14, 51, 10.1016/0263-7855(96)00009-4