COMPUTER MODELING OF AN ATP-BINDING PROTEIN

ATP 结合蛋白的计算机建模

基本信息

批准号：
7955507
负责人：
ANDREW POHORILLE
金额：
$ 0.89万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-07-01 至 2010-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7955507
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 Imagery In Vitro Informatics Institution Integral Membrane Protein Ions Lead Membrane Membrane Proteins Modeling Mutation Pattern Phenylalanine Protein Databases Protein Family Proteins Research Research Personnel Resolution Resources Side Source Specificity Techniques Tyrosine United States National Institutes of Health Water X-Ray Crystallography Zinc alpha helix analog beta pleated sheet biocomputing interest novel pointed protein polypeptide premature pressure protein structure three dimensional structure

项目摘要

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.

该子项目是利用该技术的众多研究子项目之一资源由 NIH/NCRR 资助的中心拨款提供。子项目及研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金，因此可以在其他 CRISP 条目中表示。列出的机构是对于中心来说，它不一定是研究者的机构。水溶性蛋白质的起源似乎比膜结合蛋白质的起源更难鉴定。大多数跨膜蛋白，即使是那些功能和结构复杂的跨膜蛋白，也是由蛋白质家族共享的少量结构元件组成的。此外，还有由相同元素组成的简单、天然或合成模型，可以执行基本的膜相关功能。细胞质蛋白的情况并非如此。在当代细胞中，按照原始生物学标准，它们通常相当大，但与膜蛋白相比，它们不能在不丧失活性的情况下显着减小尺寸。 Keefe 和 Szostak 使用一种新颖的体外技术从 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，每个家族都含有氨基酸序列高度相似的蛋白质，这些蛋白质彼此无关，也与当前蛋白质数据库中发现的任何内容无关。发现 ATP 结合蛋白的频率似乎类似于发现 ATP 结合核酶的频率。来自一个家族的蛋白质已得到相当详细的表征。最初选择的蛋白质含有 80 个氨基酸，但删除研究表明最小结合单元的长度小于 50 个氨基酸，因此是已知最小的 ATP 结合蛋白。这些蛋白质对 ATP 及其紧密类似物二磷酸腺苷 (ADP)，因为它们既不结合三磷酸鸟苷 (GTP) 也不结合环 AMP。然而，它们的序列不包含任何已鉴定的 ATP 结合基序。为了发挥作用，它们需要锌离子并含有四个保守的半胱氨酸残基。最近，使用 X 射线晶体学解析了该家族蛋白质的高分辨率三维结构。与所有生物水溶性蛋白质一样，该结构具有疏水核心，但表现出新颖的折叠。它由三股线组成反平行的β-折叠和两个不相邻的α-螺旋。 ADP稳定在通过与苯丙氨酸和酪氨酸残基的堆积相互作用以及通过氢键与蛋白质中的几个侧链形成结合袋。结合的选择性似乎是由腺嘌呤、甲氨酸-45 和甘氨酸-63 的 N1、N3 和 N6 之间的氢键确保的。锌离子由不邻近结合袋的区域中的保守半胱氨酸配位。 ATP 结合蛋白是一个非常有趣的原始生物学模型，因为它是第一个没有经过长期进化优化的简单功能蛋白的例子。然而，它的折叠模式可能在进化上存在缺陷。例如，它可能没有能力通过突变获得新的特异性。我们建议从这个角度检查蛋白质，并在必要时重新设计其序列，以试图在不改变折叠的情况下消除缺陷。如果这项任务成功，它将导致创建一种似乎适合进化的新颖折叠，从而提供支持的经验论据酶起源的“进化偶然”假说。如果我们发现该序列无法适当地重新设计，则表明该折叠即使存在于原生生物蛋白质中，也不太可能在随后的进化压力中幸存下来。尽管从单个反面例子中得出结论显然还为时过早，但这一结果暗示有关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识别进化上可行的原生物酶的良好候选模型。