COMPUTER MODELING OF AN ATP-BINDING PROTEIN

ATP 结合蛋白的计算机建模

• 批准号: 7723521
• 负责人: ANDREW POHORILLE
• 金额: $ 0.58万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-07-01 至 2009-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7723521
• 关键词: Accidents; Adenine; Adenosine Diphosphate; Amino Acid Sequence; Amino Acids; Binding; Binding Proteins; Biological; Catalytic RNA; Cells; Complex; Computer Retrieval of Information on Scientific Projects Database; Computer Simulation; Cyclic AMP; Cysteine; Cytoplasmic Protein; Elements; Enzymes; Evolution; Exhibits; Family; Frequencies; Funding; Glycine; Grant; Guanosine Triphosphate; Hydrogen Bonding; In Vitro; Institution; Integral Membrane Protein; Ions; Lead; Membrane; Membrane Proteins; Modeling; Mutation; Numbers; Pattern; Phenylalanine; Protein Databases; Protein Family; Proteins; Research; Research Personnel; Resolution; Resources; Side; Source; Specificity; Standards of Weights and Measures; Techniques; Tyrosine; United States National Institutes of Health; Water; X-Ray Crystallography; Zinc; alpha helix; analog; beta pleated sheet; interest; novel; pointed protein; polypeptide; pressure; protein structure; size; three dimensional structure

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The origins of water-soluble proteins appear to be considerably more difficult to identify than the origins of membrane-bound proteins. Most transmembrane proteins, even those that are functionally and structurally complex, are built of a small number of structural elements that are shared across protein families. Moreover, there are simple, natural or synthetic models consisting of the same elements that can perform essential membrane-related functions. This is not the case with cytoplasmic proteins. In contemporary cells, they are usually quite large by protobiological standards, but in contrast to membrane proteins they cannot be significantly reduced in size without loss of activity. Using a novel in vitro technique, Keefe and Szostak selected ATP-binding proteins from six trillion random polypeptides. They found four new protein families, each containing proteins with highly similar amino acid sequences that were unrelated to each other or to anything found in the current protein databases. The frequency of finding ATP-binding proteins appears to be similar to the frequency of finding ATP-binding ribozymes. Proteins from one family have been characterized in fair detail. The originally selected protein contained 80 amino acids but deletion studies revealed that the minimal binding unit is less than 50 amino acids long and, thus, is the smallest known ATP-binding protein. The proteins are highly selective towards ATP and its close analog, adenosine diphosphate (ADP), as they bind neither guanosine triphosphate (GTP) nor cyclic AMP. However, their sequences do not contain any already identified ATP-binding motifs. To function, they require zinc ions and contain four conserved cysteine residues. More recently, the high resolution, three-dimensional structure of a protein from the family was solved using X-ray crystallography. As all biological, water-soluble proteins, this structure has a hydrophobic core, but exhibits a novel fold. It consists of a three-stranded antiparallel beta-sheet and two nonadjacent alpha-helices. ADP is stabilized in the binding pocket by stacking interactions with phenylalanine and tyrosine residues and by hydrogen bonds to several side chains in the protein. Selectivity of binding appears to be insured by hydrogen bonds between the N1, N3 and N6 of adenine and methianine-45 and glycine-63. A zinc ion is coordinated by the conserved cysteines in a region not adjacent to the binding pocket. The ATP-binding protein is a very interesting protobiological model because it is the first example of a simple, functional protein that has not been a subject of long evolutionary optimization. However, its folding pattern may be evolutionarily deficient. For example, it may not have the capability to acquire new specificity through mutations. We propose to examine the protein from this point of view and, if necessary, redesign its sequence in an attempt to eliminate the deficiencies without altering the fold. If this task were successful it would lead to the creation of a novel fold that appears to be suitable for evolution, thus providing an empirical argument supporting an "evolutionary accident" hypothesis of the origin of enzymes. If we found that the sequence could not be appropriately redesigned it would suggest that the fold, even if it were present among protobiological proteins, was not likely to survive subsequent evolutionary pressures. Although it would be clearly premature to draw conclusions from a single negative example, this result would hint that a hypothesis about evolutionary pruning of protein structures is worth serious considerations. In either case, we would gain an understanding how to construct and identify good candidate models for evolutionarily viable protobiological enzymes.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 与膜结合蛋白的起源相比，水溶性蛋白的起源似乎更难鉴定。大多数跨膜蛋白，即使是功能和结构复杂的蛋白，都由少数蛋白质家族共享的少数结构元素构建。此外，还有一个简单的，天然的或合成的模型，这些模型由相同的元素组成，这些元素可以执行必不可少的膜相关功能。细胞质蛋白不是这种情况。在当代细胞中，按原生生物学标准来看，它们通常很大，但是与膜蛋白相比，它们的大小不能显着降低而不会损失活性。 使用一种新型的体外技术，Keefe和Szostak从6万亿个随机多肽中选择了ATP结合蛋白。他们发现了四个新的蛋白质家族，每个蛋白质都包含具有高度相似的氨基酸序列的蛋白质，这些蛋白质彼此无关或与当前蛋白质数据库中发现的任何东西。查找ATP结合蛋白的频率似乎 与查找ATP结合核酶的频率相似。 一个家庭的蛋白质已被详细介绍。最初选择的蛋白质含有80个氨基酸，但缺失研究表明，最小结合单元的长度小于50氨基酸，因此是最小的已知ATP结合蛋白。蛋白质对ATP及其具有高度选择性 近距离类似物，腺苷二磷酸（ADP），因为它们既没有结合三磷酸鸟苷（GTP）也不结合环状AMP。但是，它们的序列不包含任何已经识别的ATP结合基序。为了发挥作用，它们需要锌离子并包含四个保守的半胱氨酸残基。最近，使用X射线晶体学求解了家族蛋白质的高分辨率，三维结构。与所有生物学的水溶性蛋白一样，该结构具有疏水性核心，但具有新颖的折叠。它由三链组成 反平行的beta表和两个非染色α-螺旋。 ADP稳定 通过与苯丙氨酸和酪氨酸残基的相互作用以及氢键与蛋白质中的多个侧链的氢键相互作用来结合口袋。结合的选择性似乎是由腺嘌呤和甲胺-45和甘氨酸63之间N1，N3和N6之间的氢键保险。锌离子由与结合口袋相邻的区域中的保守半胱氨酸协调。 ATP结合蛋白是一个非常有趣的原始生物学模型，因为它是一种简单的功能性蛋白质的第一个例子，它不是长期进化优化的主题。但是，其折叠模式在进化上可能不足。例如，它可能没有能力通过突变获得新的特异性。我们建议从这种角度检查蛋白质，并在必要时重新设计其序列，以消除不足而不改变折叠的缺陷。如果这项任务成功，将导致创建一个看起来适合进化的新颖折叠，从而提供了支持的经验论点 酶起源的“进化事故”假设。如果我们发现该序列无法适当地重新设计，它表明，即使折叠存在于原生生物学蛋白之间，它也无法在随后的进化压力下生存。尽管从单个负面的例子中得出结论显然为时过早，但该结果表明，关于蛋白质结构进化修剪的假设值得认真考虑。无论哪种情况，我们都将了解如何构建和确定进化可行的原始生物学酶的良好候选模型。