STATISTICAL MECHANICS OF PROTEIN FOLDING
蛋白质折叠的统计力学
基本信息
- 批准号:2822777
- 负责人:
- 金额:$ 13.09万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:1999
- 资助国家:美国
- 起止时间:1999-06-01 至 2002-05-31
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
Many theories have been proposed for the statistical mechanics of protein folding, typically derived from theories for less structured systems, such as random heteropolymers, diffusion-nucleation, random energies, or spin glasses. While these have certainly captured some important features of the physical chemistry of real proteins, such as cooperativity of folding and rapid folding from the random coil state, their derivation requires making some broad assumptions about the average behavior of polypeptides. In fact, the proteins of biological relevance consists of apparently very rare, moderately long amino acid sequences that permit the chain to fold rapidly- to a unique complicated native conformation, which depends greatly on the sequence. This suggests that theories focussing on average properties of long-chain heteropolymers may be over-generalizing and neglecting the important features of rare sequences folding to rare conformations. On the other hand, neither nature nor computer has sufficient time to exhaustively explore all conformations and all sequences for even small proteins. The idea here is to simply an otherwise realistic representation of polypeptides by reducing chain length, number of conformation states per residue, and choices of amino acid types until all sequences and all conformations can be exhaustively enumerated. By varying these parameters in the computationally feasible range, general conclusions can be detected and extrapolated to parameter values corresponding to real proteins. Since this model is so different from most theories, it is able to test their assumptions and conclusions about protein folding, such as the nature of the energy landscape and order parameters to describe the progress toward the native state. Questions to be addressed include: is there a general way to describe the folding of all proteins, or do some proceed by a recognizable pathway while others have innumerable routes? Can this model reproduce and explain the currently available experimental results on folding mechanisms and intermediates for certain particular proteins.
人们已经针对蛋白质折叠的统计力学提出了许多理论,通常源自结构较弱的系统的理论,例如随机杂聚物、扩散成核、随机能量或自旋玻璃。虽然这些确实捕获了真实蛋白质物理化学的一些重要特征,例如折叠的协同性和随机卷曲状态的快速折叠,但它们的推导需要对多肽的平均行为做出一些广泛的假设。事实上,具有生物相关性的蛋白质由明显非常罕见、中等长度的氨基酸序列组成,这些序列允许链快速折叠成独特的复杂天然构象,这在很大程度上取决于序列。这表明关注长链杂聚物平均性质的理论可能过度概括并忽略了稀有序列折叠成稀有构象的重要特征。另一方面,自然和计算机都没有足够的时间来彻底探索即使是小蛋白质的所有构象和所有序列。这里的想法是通过减少链长度、每个残基的构象状态数量以及氨基酸类型的选择来简单地表达多肽的实际表示,直到可以详尽地枚举所有序列和所有构象。通过在计算可行的范围内改变这些参数,可以检测一般结论并推断出与真实蛋白质相对应的参数值。由于该模型与大多数理论有很大不同,因此它能够测试他们关于蛋白质折叠的假设和结论,例如能量景观的性质和描述自然状态进展的顺序参数。需要解决的问题包括:是否有一个通用的方法来描述所有蛋白质的折叠,或者是否有些蛋白质通过可识别的途径进行,而另一些则有无数的途径?该模型能否重现并解释目前有关某些特定蛋白质的折叠机制和中间体的实验结果。
项目成果
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