Gibrat J F, Go N
Department of Chemistry, Faculty of Science, Kyoto University, Japan.
Proteins. 1990;8(3):258-79. doi: 10.1002/prot.340080308.
A normal mode analysis of human lysozyme has been carried out at room temperature. Human lysozyme is an enzyme constituted of two domains separated by an active site cleft, the motion of which is thought to be relevant for biological function. This motion has been described as a hinge bending motion. McCammon et al. have determined the characteristics of the hinge bending motion but they assumed a prior knowledge of the hinge axis. In this work we propose a method which is free from this assumption and determines the hinge axis and root mean square (rms) rotation angle which give the best agreement with the pattern of changes in all the distances between nonhydrogen atoms in the two domains, obtained by the normal mode analysis. The hinge axis we found is notably different from the one previously determined and goes, roughly, through the C alpha 55 and C alpha 76, i.e., it is located at the base of the beta-sheet of the second domain. The rms value for the rotation angle is also twice as large as the previous one: 3.37 degrees. It is shown that this hinge bending motion provides a fairly good approximation of the dynamics of human lysozyme and that the normal mode with the lowest frequency has a dominating contribution to this hinge bending motion. A study of the accessible surface area of the residues within the cleft reveals that the motion does not result in a better exposure to the solvent of these residues. A characterization of the thermally excited state (under the hypothesis of the harmonicity of the potential energy surface) has been done using the concept of topology of atom packing. Under this hypothesis the thermal fluctuations result only in a small change of the topology of atom packing, leading therefore to nearly elastic deformations of the protein.
已在室温下对人溶菌酶进行了正常模式分析。人溶菌酶是一种由两个结构域组成的酶，两个结构域由一个活性位点裂缝隔开，其运动被认为与生物学功能相关。这种运动被描述为铰链弯曲运动。麦卡蒙等人已经确定了铰链弯曲运动的特征，但他们预先假定了铰链轴的知识。在这项工作中，我们提出了一种方法，该方法无需这种假设，并确定了与通过正常模式分析获得的两个结构域中非氢原子之间所有距离的变化模式最吻合的铰链轴和均方根（rms）旋转角度。我们发现的铰链轴与先前确定的明显不同，大致穿过Cα55和Cα76，即它位于第二个结构域β折叠的底部。旋转角度的均方根值也是先前值的两倍：3.37度。结果表明，这种铰链弯曲运动为人类溶菌酶的动力学提供了相当好的近似，并且最低频率的正常模式对这种铰链弯曲运动有主要贡献。对裂缝内残基的可及表面积的研究表明，这种运动不会导致这些残基更好地暴露于溶剂中。利用原子堆积拓扑的概念对热激发态（在势能面谐波假设下）进行了表征。在这个假设下，热涨落仅导致原子堆积拓扑的微小变化，因此导致蛋白质几乎弹性变形。
