Evolution of molecular complexes: genetic, structural, and functional mechanisms for the evolution of oligomers and allostery

分子复合物的进化：低聚物和变构进化的遗传、结构和功能机制

• 批准号: 10251124
• 负责人: Joseph W Thornton
• 金额: $ 29.91万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10251124
• 关键词: Address; Allosteric Regulation; Architecture; Bacteria; Binding; Biochemical; Biochemical Genetics; Biochemistry; Biological; Biological Process; Biology; Biophysical Process; Biophysics; Blood; Case Study; Cell physiology; Citrate (si)-Synthase; Complex; Development; Dimerization; Disease; Dissection; Energy Metabolism; Engineering; Enzymes; Evolution; Family; Family member; Foundations; Future; Gene Duplication; Gene Expression; Genetic; Genetic Structures; Genetic Variation; Globin; Goals; Hemoglobin; Hydrophobicity; Inherited; Jaw; Knowledge; Maintenance; Malignant Neoplasms; Mediating; Metabolic; Metabolic Diseases; Methodology; Modeling; Molecular; Molecular Evolution; Mutation; NADH; Oxygen; Pathway interactions; Phylogenetic Analysis; Physiology; Population Genetics; Process; Property; Protein Biochemistry; Protein Engineering; Protein Family; Proteins; Recording of previous events; Regulation; Regulator Genes; Reproduction; Resolution; Signal Transduction; Specificity; Steroid Receptors; Structural Biochemistry; Structure; Surface; Techniques; Testing; Time; Transducers; Vertebrates; Work; biological systems; biophysical analysis; design; dimer; experimental study; monomer; mutation screening; paralogous gene; protein complex; protein structure; reconstruction; small molecule inhibitor; steroid hormone receptor; stoichiometry; structural biology; transcription factor; virtual

We propose the first experimental studies of the historical origin and elaboration of molecular complexes. Virtually all proteins assemble with specific molecular partners into precise geometric arrangements, but we know little about the genetic and structural mechanisms by which these complexes evolved or the evolutionary forces that explain their origin, elaboration, and long-term persistence. We will combine ancestral protein reconstruction with biochemical, structural, and functional experiments to reconstruct the evolution of molecular complexes in three model protein families, enabling us to formulate and test general hypotheses about the evolutionary causes and consequences of changes in stoichiometry, allostery, and specificity. All three protein families are biologically essential, experimentally tractable, and exemplify distinct questions. The models are: 1) hemoglobin, the major oxygen carrier in vertebrates, a heterotetramer that is biochemistry's iconic case of an allosterically regulated molecular complex; 2) citrate synthase, an essential metabolic enzyme that is a dimer in some lineages and an allosterically regulated hexamer in others, which provides a rich case-study of the evolutionary relationship and long-term persistence of allostery and complexity; and 3) steroid hormone receptors, a family of transcription factors that regulate vertebrate reproduction and development and which evolved after gene duplication to specifically assemble as homodimers, each with distinct regulatory functions. The project will address these questions: 1) How and why do complexes originate and increase in stoichiometry from simpler forms? 2) What genetic and biophysical mechanisms mediate evolution of new and specific interfaces? 3) By what mechanisms did allostery evolve? 4) Does selection for oligomer-associated functions account entirely for the emergence and long-term persistence of molecular complexes? Or did substitutions compatible only with the assembled form occur neutrally and entrench the complex, creating an evolutionary ratchet towards greater complexity? And 5) After duplication, how did homomers evolve to selectively assemble with copies of themselves (excluding their sister paralogs), and was evolution of new functions constrained until this selectivity was achieved? By combining advanced techniques from protein biochemistry and evolutionary biology, the project will articulate and test at unprecedented resolution hypotheses about the evolutionary forces and biochemical mechanisms that underlie the physical and functional properties of molecular complexes. It will also help to explain why multimers are so widespread and, by revealing how evolution achieved specificity and allosteric regulation, enhance engineering efforts to design complexes with these properties. The project will also provide a methdological and conceptual template for future studies of other molecular complexes.

我们提出了第一个实验研究的历史起源和阐述的分子 配合物几乎所有的蛋白质都与特定的分子伴侣组装成精确的几何形状， 安排，但我们对这些安排的遗传和结构机制知之甚少。 复杂的进化或进化的力量，解释他们的起源，精心制作，和长期的 坚持不懈我们将把联合收割机祖先蛋白质的重建与生物化学、结构和功能相结合。 三种模型蛋白质分子复合物进化的功能实验 家庭，使我们能够制定和测试有关进化原因的一般假设， 化学计量、变构和特异性变化的后果。所有三种蛋白质家族都是 生物学上基本的，实验上易处理的，和不同的问题。这些模型是：1） 血红蛋白，脊椎动物中主要的氧载体，是生物化学的标志性异源四聚体 一个变构调节的分子复合物的情况下; 2）柠檬酸合酶，一个重要的代谢 一种酶，在某些谱系中是二聚体，在另一些谱系中是变构调节的六聚体， 提供了一个丰富的案例研究的进化关系和长期持久的变构， 复杂性;和3）类固醇激素受体，一个家族的转录因子，调节 脊椎动物的生殖和发育，并在基因复制后进化， 组装成同源二聚体，每个具有不同的调节功能。该项目将解决这些问题 问题：1）复合物是如何以及为什么从简单的形式产生并增加化学计量的？ 2)什么样的遗传和生物物理机制介导了新的和特定的界面的进化？3)通过 变构的进化机制是什么？4)寡聚体相关功能的选择是否考虑 完全是为了分子复合物的出现和长期存在？还是说替换 只与组装的形式兼容发生中立和巩固的复杂性，创造一个 进化的棘轮朝着更大的复杂性前进？5）复制后，同聚体是如何进化的 选择性地与自己的副本（不包括它们的姐妹旁系同源物）组装， 新功能的限制，直到这种选择性实现？通过结合先进的技术 从蛋白质生物化学和进化生物学，该项目将阐明和测试， 关于进化力量和生化机制的前所未有的解决假设， 构成了分子复合物的物理和功能特性的基础。这也有助于解释 为什么多聚体如此普遍，以及通过揭示进化如何实现特异性和变构， 监管，加强工程努力，设计具有这些特性的复合体。该项目将 也为今后研究其他分子复合物提供了方法和概念模板。