Network and graph analyses of folding free energy surfaces

@article{citeulike:505393, abstract = {Protein folding is governed by a complex free energy surface whose entropic contributions are relevant because of the large number of degrees of freedom involved. Such complexity, in particular the conformational heterogeneity of the denatured state, is hidden in projections onto one or two order parameters (e.g. fraction of native contacts and/or radius of gyration), which usually results in relatively smooth surfaces. Recent approaches borrowed from network and graph theory have yielded quantitative unprojected representations of the free energy surfaces of a [beta]-hairpin and a three-stranded [beta]-sheet peptide using equilibrium folding-unfolding molecular dynamics simulations. Interestingly, the network and graph analyses of these structured peptides have revealed a very heterogeneous denatured state ensemble. It includes high-enthalpy, high-entropy conformations with fluctuating non-native secondary structure, as well as low-enthalpy, low-entropy traps.}, author = {Caflisch, Amedeo }, booktitle = {Protein-nucleic acid interactions/Folding and binding - Wei Yang and Gregory D Van Dyne/Mikael Oliveberg and Eugene I Shakhnovich}, citeulike-article-id = {505393}, doi = {10.1016/j.sbi.2006.01.002}, journal = {Current Opinion in Structural Biology}, keywords = {free-energy, protein\_dynamics}, month = {February}, number = {1}, pages = {71--78}, posted-at = {2008-04-11 19:59:28}, priority = {2}, title = {Network and graph analyses of folding free energy surfaces}, url = {http://dx.doi.org/10.1016/j.sbi.2006.01.002}, volume = {16}, year = {2006} }

TY - JOUR ID - citeulike:505393 L3 - citeulike-article-id:505393 TI - Network and graph analyses of folding free energy surfaces T2 - Protein-nucleic acid interactions/Folding and binding - Wei Yang and Gregory D Van Dyne/Mikael Oliveberg and Eugene I Shakhnovich JF - Current Opinion in Structural Biology VL - 16 IS - 1 SP - 71 EP - 78 N2 - Protein folding is governed by a complex free energy surface whose entropic contributions are relevant because of the large number of degrees of freedom involved. Such complexity, in particular the conformational heterogeneity of the denatured state, is hidden in projections onto one or two order parameters (e.g. fraction of native contacts and/or radius of gyration), which usually results in relatively smooth surfaces. Recent approaches borrowed from network and graph theory have yielded quantitative unprojected representations of the free energy surfaces of a [beta]-hairpin and a three-stranded [beta]-sheet peptide using equilibrium folding-unfolding molecular dynamics simulations. Interestingly, the network and graph analyses of these structured peptides have revealed a very heterogeneous denatured state ensemble. It includes high-enthalpy, high-entropy conformations with fluctuating non-native secondary structure, as well as low-enthalpy, low-entropy traps. KW - free-energy KW - protein_dynamics AU - Caflisch, Amedeo PY - 2006/02// UR - http://dx.doi.org/10.1016/j.sbi.2006.01.002 ER -