NEW DELOCALIZED INTERACTION THAT EXISTS IN PROTEINS AND CONTROLS FOLDING

在过去的几年中，我们已经证明，RNase-（-118）缺乏6 核糖核酸酶A的羧基末端残基的吉布斯自由能不是最低的 能量和高度能动性，尽管天然结构 包括66%的螺旋结构。 我们认为，如果 传统的成对相互作用是为了共同解释 对于RNase-（1-118）的能量状态，衍生物应具有 自由能最低。 因此，为了解释观察结果， 假设一些离域相互作用存在于原生 核糖核酸酶A来稳定结构。 我们把这个新的 闭环交互假设闭环交互 由接触基团组成，将介导离域 互动 利用细胞色素c的碎片复合体系 在本节中，我们希望确定假设的 控制细胞色素c折叠的一个或多个闭环。 我们 已经研究了由血红素-和 马、金枪鱼、念珠菌和酵母的脱辅基片段（或脱辅基蛋白） 异-l-细胞色素c。 这些物种的碎片被发现 可以完全互换，但以下情况除外。 金枪鱼血红素片段（1-38）H和假丝酵母脱辅基片段的组合 （61-109），而不是假丝酵母血红素（1-44）H和金枪鱼脱辅基片段 （39-104），形成结合力急剧降低的复合物。 含有酵母脱辅基片段（44-108）的杂合复合物不被 研究了 比较氨基酸序列， 用苏氨酸取代亮氨酸9（马编号）， 和亮氨酸98与甲硫氨酸的弱结合负责 金枪鱼血红素-假丝酵母脱辅基片段复合物 这个和其他 与先前的观察结果一起，我们可以 将四个闭环1、2、3和4的位置指定为上方， 在血红素的左右两侧和下方， 分别 此外，先前发现的初始二阶 动力学阶段和随后的一级阶段被分配给 分别表示闭环1和3的形成。 回路 据推测，4是在真核生物进化过程中添加的。 细胞色素c来自原核物种。

In the previous years we have shown that RNase-(-118) lacking 6 carboxy terminal residues of RNase A is not of lowest Gibbs free energy and highly motile despite the native like structure including 66% of the helical structure. We argue that if the conventional pair-wise interactions were to collectively account for the energy state of RNase-(1-118) the derivative should have been of lowest free energy. Thus, to explain the observations we hypothesize that some delocalized interaction exists in native RNase A to stabilize the structure. We refer to this new interaction as closed loop interaction assuming that a closed loop consisting of contacting groups would mediate delocalized interaction. Using the fragment complex system of cytochrome c developed in this Section, we wish to identify the hypothetical closed loop or loops that controls folding of cytochrome c. We have investigated hybrid complexes formed from heme- and apofragments (or apoproteins) of horse, tuna, candida and yeast iso-l-cytochrome c. The fragments of these species are found to be completely exchangeable with the following exception. Combination of tuna heme fragment (1-38)H and candida apofragment (61-109), but not that of candida heme (1-44)H and tuna apofragment (39-104), forms a complex with drastically decreased binding force. Hybrid complexes containing yeast apofragment (44-108) were not investigated. Comparing the amino acid sequences it is proposed that substitutions of leucine 9 (horse numbering) with threonine and leucine 98 with methionine are responsible for the weak binding of tuna heme-candida apofragment complex. This and other observations taken together with those previous have allowed us to assign the locations of four closed loops 1,2,3 and 4 to be above, at the right and the left sides of, and below the heme, respectively. Further, the previously found initial second order kinetic phase and the following first order phase are assigned to represent formations of closed loops 1 and 3, respectively. Loop 4 is presumed to have been added during evolution of eukaryotic cytochrome c from prokaryotic species.