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Pradeep, Lovy,Shin, Hang-Cheol,Scheraga, Harold A. Elsevier 2006 FEBS letters Vol.580 No.21
<P><B>Abstract</B></P><P>Several studies attribute the slower phases in protein folding to prolyl isomerizations, and several others do not. A correlation exists between the number of prolines in a protein and the complexity of the mechanism with which it folds. In this study, we have demonstrated a direct correlation between the number of <I>cis</I>-prolyl bonds in a native protein and the complexity with which it folds via slower phases by studying the folding of three structurally homologous proteins of the ribonuclease family, namely RNase A, onconase and angiogenin, which differ in the number and isomerization states of their proline residues.</P>
Krupa, Paweł,Hałabis, Anna,Ż,mudziń,ska, Wioletta,Ołdziej, Stanisław,Scheraga, Harold A.,Liwo, Adam American Chemical Society 2017 JOURNAL OF CHEMICAL INFORMATION AND MODELING Vol.57 No.9
<P>By using the maximum likelihood method for force-field calibration recently developed in our laboratory, which is aimed at achieving the agreement between the simulated conformational ensembles of selected training proteins and the corresponding ensembles determined experimentally at various temperatures, the physics-based coarse-grained UNRES force field for simulations of protein structure and dynamics was optimized with seven small training proteins exhibiting a variety of secondary and tertiary structures. Four runs of optimization, in which the number of optimized force-field parameters was gradually increased, were carried out, and the resulting force fields were subsequently tested with a set of 22 alpha-, 12 beta-, and 12 alpha + beta-proteins not used in optimization. The variant in which energy-term weights, local, and correlation potentials, side-chain radii, and anisotropies were optimized turned out to be the most transferable and outperformed all previous versions of UNRES on the test set.</P>