Bongini L, Piazza F, Casetti L, De Los Rios P
Departament de Fisica Fonamental, Facultat de Fisica, Universitat de Barcelona, E-08028 Barcelona, Spain.
Eur Phys J E Soft Matter. 2010 Sep;33(1):89-96. doi: 10.1140/epje/i2010-10653-8. Epub 2010 Sep 18.
In this paper we analyze the vibrational spectra of a large ensemble of non-homologous protein structures by means of a novel tool, that we coin Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the intrinsic heterogeneity of force constants displayed by protein arrangements and also incorporates side chain degrees of freedom. Our analysis shows that vibrational entropy per unit residue correlates with the content of secondary structure. Furthermore, we assess the individual contribution to vibrational entropy of the novel features of our scheme as compared with the predictions of state-of-the-art network models. This analysis highlights the importance of properly accounting for the intrinsic hierarchy in force strengths typical of the different atomic bonds that build up and stabilize protein scaffolds. Finally, we discuss possible implications of our findings in the context of protein aggregation phenomena.
在本文中，我们借助一种新颖的工具——我们称之为层次网络模型（HNM），分析了大量非同源蛋白质结构的振动光谱。我们的粗粒度方案考虑了蛋白质排列所显示的力常数的内在异质性，并且还纳入了侧链自由度。我们的分析表明，每单位残基的振动熵与二级结构的含量相关。此外，与最先进的网络模型的预测相比，我们评估了我们方案的新特征对振动熵的个体贡献。该分析突出了适当考虑构成并稳定蛋白质支架的不同原子键所特有的力强度中的内在层次结构的重要性。最后，我们在蛋白质聚集现象的背景下讨论了我们研究结果的可能含义。
