Chen Changjun, Li Lin, Xiao Yi
Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
Biopolymers. 2007 Jan;85(1):28-37. doi: 10.1002/bip.20600.
In this paper we use all-atom potential energy to define and analyze the inter-residue contacts in mesophilic and thermophilic proteins. Fifteen families of proteins are selected and each family has two representative proteins with greatly different preferred environmental temperatures. We find that both the number and energy of the contacts defined in this way show stronger correlations with the preferred temperatures of proteins than other factors used before. We also find that the charged-polar and charged-nonpolar residue contacts not only have larger contact numbers but also have lower single contact energies. Furthermore, the most important is that most of the thermophilic proteins have more charged-polar and charged-nonpolar residue contacts than their mesophilic counterparts. This suggests that they may play an important role in the thermostability of proteins, except usual charged-charged and nonpolar-nonpolar residue contacts. Charged residues may exert their profound influence by forming contacts not only with other charged residues but also with polar or nonpolar residues, thus further increasing the strength of contact network and then the thermostability of proteins.
在本文中，我们使用全原子势能来定义和分析中温蛋白和嗜热蛋白中的残基间相互作用。我们选择了15个蛋白家族，每个家族有两个具有显著不同偏好环境温度的代表性蛋白。我们发现，以这种方式定义的相互作用的数量和能量与蛋白的偏好温度的相关性比之前使用的其他因素更强。我们还发现，带电-极性和带电-非极性残基间相互作用不仅具有更大的相互作用数量，而且具有更低的单个相互作用能量。此外，最重要的是，大多数嗜热蛋白比它们的中温对应物具有更多的带电-极性和带电-非极性残基间相互作用。这表明，除了常见的带电-带电和非极性-非极性残基间相互作用外，它们可能在蛋白的热稳定性中发挥重要作用。带电残基可能不仅通过与其他带电残基形成相互作用，还通过与极性或非极性残基形成相互作用来发挥其深远影响，从而进一步增加相互作用网络的强度，进而提高蛋白的热稳定性。
