Identifying determinants of specificity in yeast protein complexes

鉴定酵母蛋白复合物特异性的决定因素

• 批准号: BB/F007620/1
• 负责人: Simon Lovell
• 金额: $ 71.58万
• 依托单位: University of Manchester
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2008
• 资助国家: 英国
• 起止时间: 2008 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FF007620%2F1
• 关键词: Identifying; determinants; specificity; yeast; protein

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).

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;我们的目标是了解两个物种之间形成杂交时发生的细胞事件;我们还旨在在分子水平上了解物种之间的差异。蛋白质几乎总是一起工作以实现生物功能。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发挥作用。为了形成复合物，单个蛋白质必须与少量特定的伴侣接触（“结合”）。我们希望研究的是控制这种结合“特异性”的规则。因此，复合物中的结合是在蛋白质的三维蛋白质结构背景下的特异性接触的结果。我们建议确定结合的关键区域（称为“界面”），并在这些界面区域的氨基酸是最重要的结合。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进化提供的--物种从共同祖先进化（“分化”）的变化过程--它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，这些变化的性质是研究结合特异性的信息。例如，如果一个蛋白质序列中的一个关键氨基酸发生变化，那么其结合伴侣的序列中可能需要相关的变化。蛋白质之间的这种变化耦合被称为“共同进化”。在不同物种中，这一持续过程的结果是，在某个时候，蛋白质将成为物种特异性的，因此失去了结合姐妹物种伴侣的能力。我们项目的主要目标是了解这种变化过程的局限性，即，伴侣在什么时候不能再结合，哪些变化对结合的能力贡献最大。为了实现我们的目标，我们将结合联合收割机计算机（生物信息学）和实验室为基础的研究战略。这些相辅相成的办法将是我们成功的关键。在酵母中，杂种可以通过两个亲本细胞的融合形成。当这种情况发生时，子细胞将包含两个父母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，来自一个亲本的蛋白质复合物可以与另一个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存在的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将形成嵌合复合物，哪些不会。这将使我们能够了解不同物种蛋白质之间形成复合物的过程，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的差异程度（我们的主要目标）。我们的研究结果也将有影响的理解杂交种的物种形成的意义，允许洞察在分子水平上的过程中的“杂交优势”，增加成功或“健身”的杂交生物（我们的次要目标）。

项目成果

The effect of sequence evolution on protein structural divergence.

序列进化对蛋白质结构差异的影响。

• DOI: 10.1093/molbev/msp020
• 发表时间: 2009
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Williams SG

Evolvability of yeast protein-protein interaction interfaces.

酵母蛋白质-蛋白质相互作用界面的进化性。

• DOI: 10.1016/j.jmb.2012.03.021
• 发表时间: 2012
• 期刊: Journal of molecular biology
• 影响因子: 5.6
• 作者: Talavera D

Sequencing and characterisation of rearrangements in three S. pastorianus strains reveals the presence of chimeric genes and gives evidence of breakpoint reuse.

• DOI: 10.1371/journal.pone.0092203
• 发表时间: 2014
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Hewitt SK;Donaldson IJ;Lovell SC;Delneri D
• 通讯作者: Delneri D

Gene duplication and environmental adaptation within yeast populations.

• DOI: 10.1093/gbe/evq043
• 发表时间: 2010
• 期刊: Genome biology and evolution
• 影响因子: 3.3
• 作者: Ames RM;Rash BM;Hentges KE;Robertson DL;Delneri D;Lovell SC
• 通讯作者: Lovell SC

Evolution in protein interaction networks: co-evolution, rewiring and the role of duplication.

蛋白质相互作用网络的进化：共同进化、重新布线和复制的作用。

• DOI: 10.1042/bst0370768
• 发表时间: 2009
• 期刊: Biochemical Society transactions
• 影响因子: 3.9
• 作者: Robertson DL