Identifying determinants of specificity in yeast protein complexes

我们的目标是解决生物学中一些重要和基本的问题。具体来说，我们的目标是了解蛋白质如何相互作用以产生生物功能；我们的目标是了解当两个物种之间形成杂交时所发生的细胞事件；我们还旨在从分子水平上理解是什么导致了物种之间的差异。蛋白质几乎总是一起工作来实现生物功能。大约60%的蛋白质参与某种稳定的组装或“复合物”。这些蛋白质复合物在大多数细胞过程中起作用。为了形成复合物，单个蛋白质必须与少数特定的伙伴接触（“结合”）。我们希望研究的是控制这种绑定“特异性”的规则。因此，复合物中的结合是蛋白质三维结构背景下特定接触的结果。我们建议确定结合的关键区域（称为“界面”）以及在这些界面区域中对结合最重要的氨基酸。为了实现这一目标，我们将利用基于计算机的方法来预测单个蛋白质的哪些区域负责不同蛋白质之间的精确相互作用。我们将利用的一个生物信号是由进化提供的——物种从它们共同的祖先进化（“分化”）的变化过程——这表现为氨基酸序列的变化。由于蛋白质结构必须正确形成并保持其功能，这些变化的性质为研究结合特异性提供了信息。例如，如果一个蛋白质序列中的一个关键氨基酸发生了变化，那么它的结合伙伴的序列可能也会发生相应的变化。蛋白质之间的这种耦合变化被称为“共同进化”。在物种分化过程中，这一持续过程的结果是，在某种程度上，蛋白质将变得具有物种特异性，因此失去了与姐妹物种结合的能力。我们项目的主要目标是理解这个变化过程的限制，也就是说，在什么时候伙伴不再绑定，哪些变化对绑定的能力贡献最大。为了达到我们的目标，我们将结合计算机（生物信息学）和实验室为基础的研究策略。这些互补的方法将是我们成功的关键。在酵母中，杂交体可以由两个亲本细胞融合形成。当这种情况发生时，子细胞将包含两个亲本细胞的所有细胞成分的混合物。这将包括所有遗传物质和所有蛋白质。因此，来自一方亲本的蛋白质复合物可能与另一方亲本的蛋白质复合物结合，形成“嵌合”复合物，或者它们可能不结合，导致分子水平上的不相容性。我们将通过分析天然酵母和人工酵母杂交体来研究结合的规则。具体来说，我们将使用计算技术来开发可能的规则，使我们能够预测哪些蛋白质会形成嵌合复合物，哪些不会。这将使我们能够了解不同物种蛋白质之间复杂形成的过程，并量化物种在蛋白质结构水平上不相容之前在分子水平上必须不同的程度（我们的主要目标）。我们的研究结果也将对理解杂交物种形成的意义产生影响，允许在分子水平上深入了解“杂交活力”的过程；增加杂交生物的成功或“适应性”（我们的次要目标）。

We aim to tackle a number of important and fundamental questions in biology. Specifically, we aim to understand how proteins interact to produce biological function; we aim to understand the cellular events that take place when hybrids form between two species; we also aim to understand on a molecular level what gives rise to the differences between species. Proteins almost invariably work together to achieve biological function. Approximately 60% or proteins take part in some kind of stable assembly or 'complex'. These protein complexes play a role in the majority of cellular processes. In order to form complexes individual proteins must make contact with ('bind') to a small number of specific partners. It is the rules that control this 'specificity' for binding that we wish to investigate. Binding in complexes is, thus, the result of specific contacts in the context of proteins' three-dimensional protein structures. We propose to determine the key regions for binding (termed 'interfaces') and in these interface regions the amino acids that are most important for binding. In order to achieve this goal, we will make use of computer-based methodologies to predict which regions of an individual protein are responsible for the precise interactions between different proteins. A biological signal we will make use of is that provided by evolution - the process of change as species evolve away ('diverge') from their common ancestor - and that manifests itself as changes in amino acid sequences. As the protein structures must form correctly, and keep their function, the nature of these changes is informative for studying binding specificity. For example, if a key amino acid in one protein sequence changes, then an associated change might be necessary in the sequence of its binding partner. This coupling of change between proteins is termed 'co-evolution'. The consequence of this ongoing process in diverging species is that, at some point, proteins will become species-specific and so lose the ability to bind partners in their sister species. The primary objective of our project is to understand the limits of this process of change, i.e., at what point can partners no longer bind and which changes contribute most to the ability to bind. In order to achieve our objectives, we will combine computer (bioinformatics) and laboratory-based research strategies. These complementary approaches will be the key to our success. In yeast, hybrids can be formed by the fusion of two parent cells. When this happens, the daughter cell will contain a mixture of all of the cellular components of the two parents. This will include all genetic material and all proteins. Thus, protein complexes from one parent may bind to those of the other parent, making 'chimeric' complexes, or they may not bind resulting in incompatibilities at the molecular level. We will investigate the rules of binding by analysing both naturally occurring and artificial yeast hybrids. Specifically, we will use computational techniques to develop likely rules that will enable us to predict which proteins will form chimeric complexes, and which will not. This will allow us to understand the process of complex formation between proteins from different species and to quantify the extent to which species must be different at the molecular level before they are incompatible at the level of protein structure (our primary objective). Our results will also have implications for understanding the significance of hybrids in speciation by permitting insight at the molecular level into the process of 'hybrid vigour'; the increased success or 'fitness' of the hybrid organism (our secondary objective).