The protein folding problem has been extensively studied for decades, and hundreds of thousands of protein structures have been solved. Yet, how proteins fold from a linear peptide chain to their unique 3D structures is not fully understood. With key clues having emerged unexpectedly from the field of nanoscience, a “Confined Lowest Energy Fragment” (CLEF) hypothesis was proposed. The CLEF hypothesis states that a protein chain can be divided into CLEFs, the semi-independent folding units, by a small number of key residues that form key long-range interactions. The native structure of a CLEF is the lowest energy state under the constraints of the key long-range interactions, but the native structure of the whole protein is not necessary the lowest energy state as Anfinsen’s thermodynamic hypothesis suggested. The CLEF hypothesis proposes a unified CLEF mechanism for protein folding, basically a two-step process. In the first step, the favorable enthalpy of CLEFs for native structures quickly brings those residues for the key long-range interactions together, forming intermediates corresponding to the so-called hydrophobic collapse. In the second step, those collapsed key residues shuffle for the right combination to form the native key long-range interactions. The CLEF hypothesis provides a simple solution to all protein folding paradoxes, and proposes a “CLEF Age” or “Stone Age” for the prebiotic evolution of proteins.

蛋白质折叠问题已经被广泛研究了数十年，并且已经解决了成千上万的蛋白质结构。然而，蛋白质如何从线性肽链折叠到其独特的3D结构尚不完全清楚。有了来自纳米科学领域的意外线索，人们提出了“有限的最低能量碎片”（CLEF）假说。CLEF假设指出，蛋白质链可通过形成关键的长程相互作用的少量关键残基分为半独立的折叠单元CLEF。在关键的远程相互作用的约束下，CLEF的天然结构是最低能态，但是正如Anfinsen的热力学假设所建议的那样，整个蛋白质的天然结构不一定是最低能态。CLEF假设为蛋白质折叠提出了统一的CLEF机制，基本上是一个两步过程。第一步，CLEF对天然结构的有利焓使那些用于关键的远程相互作用的残基迅速聚集在一起，形成了与所谓的疏水塌陷相对应的中间体。在第二步中，那些折叠的键残基会按正确的组合进行混洗，以形成本机键远程交互。CLEF假设为所有蛋白质折叠悖论提供了简单的解决方案，并为蛋白质的益生元进化提出了“ CLEF年龄”或“石器时代”。形成对应于所谓的疏水塌陷的中间体。在第二步中，那些折叠的键残基会按正确的组合进行混洗，以形成本机键远程交互。CLEF假设为所有蛋白质折叠悖论提供了简单的解决方案，并为蛋白质的益生元进化提出了“ CLEF年龄”或“石器时代”。形成对应于所谓的疏水塌陷的中间体。在第二步中，那些折叠的键残基会按正确的组合进行混洗，以形成本机键远程交互。CLEF假设为所有蛋白质折叠悖论提供了简单的解决方案，并为蛋白质的益生元进化提出了“ CLEF年龄”或“石器时代”。