Biophysical and structural studies of protein and enzyme mechanism, evolution, and engineering

蛋白质和酶机制、进化和工程的生物物理和结构研究

• 批准号: 10550521
• 负责人: BARRY L. STODDARD
• 金额: $ 41.07万
• 依托单位: FRED HUTCHINSON CANCER CENTER
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-06-01 至 2028-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10550521
• 关键词: Address; Affinity; Binding; Biological; Biophysics; Complex; DNA; Endoribonucleases; Engineering; Enzymatic Biochemistry; Enzymes; Equilibrium; Evolution; Foundations; Gene Targeting; Genome engineering; Homing; Hydrogen Bonding; Laboratory Research; Laboratory Study; Ligands; Mission; Molecular; Nucleic Acids; Protein Engineering; Proteins; RNA; Regulation; Research; Retrotransposon; Role; Site; Specificity; Structure; System; Testing; Visualization; base; biological research; design; endonuclease; enzyme mechanism; experience; microbial; molecular recognition; novel; programs; protein folding; protein function; protein structure; small molecule; tool; transcriptomics

Project Summary/Abstract Among the several ongoing revolutions in biological research, two (the ability to visualize increasingly complex biomolecular machines and assemblages and the ability to create novel protein structures and corresponding functions) represent the foundation of our laboratory's research program. For many years, we have divided its activities between (i) determining the structures, mechanisms and biological roles of gene targeting proteins and base modifying enzymes, and (ii) employing protein engineering to create new protein folds, assemblages, and functions, and to test our understanding of protein form and function. We now plan to renew and expand upon our research mission by address several questions and problems in the fields of nucleic acid enzymology, molecular recognition, and protein engineering. The first two projects will build upon our experience studying and engineering homing endonucleases (also called `meganucleases'). In doing so, we will answer questions surrounding the evolution, recognition mechanisms and engineerability of (i) sequence-specific microbial RNA endonucleases and (ii) eukaryotic retrotransposons. We plan to leverage our basic studies of these systems to create new tools for transcriptomic analyses and genome engineering, respectively. The third project addresses a current challenge in protein engineering: the accurate design of biomolecular interfaces that rely heavily on stereospecific hydrogen-bond networks to facilitate the balance of affinity, specificity and reversibility that is a hallmark of biomolecular interactions and regulation. To do so, we will create and then couple together protein- protein and protein-small molecule binding functions through the creation of novel synthetic ligand-induced protein multimerization systems. The project will contribute to the field of molecular design and engineering by optimizing strategies for the accurate design of stereospecific hydrogen bond networks for that facilitate protein-protein and protein-ligand recognition and binding.

项目摘要/摘要 在生物学研究中的几项正在进行的革命中，有两个（能够可视化越来越复杂的能力 生物分子机器和组合以及创建新型蛋白质结构和相应的能力 功能）代表了我们实验室研究计划的基础。多年以来，我们已经分裂了 （i）确定靶向蛋白基因的结构，机制和生物学作用之间的活动 和基础修饰酶，以及（ii）采用蛋白质工程来创建新的蛋白质褶皱，组合， 和功能，并测试我们对蛋白质形式和功能的理解。我们现在计划更新和扩展 在我们的研究任务中，通过解决核酸领域的几个问题和问题 酶学，分子识别和蛋白质工程。 前两个项目将基于我们在研究和工程居住的核核的经验基础上（也是 称为“巨核”）。这样，我们将回答围绕进化，认可的问题 （i）序列特异性微生物RNA核酸内切酶和（ii）真核生物的机制和工程性 逆转座子。我们计划利用对这些系统的基础研究，为 转录组分析和基因组工程。第三个项目解决了当前 蛋白质工程中的挑战：严重依赖的生物分子界面的准确设计 立体氢键网络，以促进亲和力，特异性和可逆性的平衡 生物分子相互作用和调节的标志。为此，我们将创建然后将蛋白质 - 蛋白质和蛋白质 - 小分子结合函数通过创建新型合成配体诱导的 蛋白质多聚化系统。该项目将促进分子设计和工程领域 优化策略，以精确设计立体特定的氢键网络，以促进 蛋白质 - 蛋白质和蛋白质 - 配体识别和结合。