Channeling Within Glycolysis: Steps Involving Nicotine Adenine Dinucleotide

糖酵解内的通道：涉及烟碱腺嘌呤二核苷酸的步骤

• 批准号: 8022695
• 负责人: KATHRYN A. THOMASSON
• 金额: $ 23.6万
• 依托单位: UNIVERSITY OF NORTH DAKOTA
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-08-15 至 2015-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8022695
• 关键词: Active Sites; Adenine; Aldehyde-Lyases; Brain; Cells; Chickens; Citric Acid Cycle; Collaborations; Communicable Diseases; Complex; Computer Simulation; Dinucleoside Phosphates; Disease; Electrophoresis; Electrostatics; Enzyme Interaction; Enzymes; Erythrocytes; Escherichia coli; Fluorescence; Fructose; Giardia; Glyceraldehyde 3-Phosphate; Glyceraldehyde-3-Phosphate Dehydrogenases; Glycolysis; Goals; Human; Lactate Dehydrogenase; Leishmania; Ligand Binding; Ligands; Liver; Methods; Modeling; Multienzyme Complexes; Muscle; Mycobacterium tuberculosis; Myocardium; Nature; Nicotine; Organism; Oryctolagus cuniculus; Pathway interactions; Plasmodium falciparum; Protein Isoforms; Pyruvate; Pyruvate Kinase; Rattus; Saccharomyces cerevisiae; Science; Sedimentation process; Solutions; Structure; System; Testing; Testis; Triose-Phosphate Isomerase; Trypanosoma; Work; Zebrafish; base; enzyme substrate; fetal; microorganism; models and simulation; professor; research study; simulation; trend

DESCRIPTION (provided by applicant): The channeling hypothesis (i.e., that substrates or co-enzymes may move from one active site to another without equilibrating with the bulk medium) is still controversial in glycolysis because glycolytic enzymes are large and have very dynamic interactions that are hard to detect. Channeling has been demonstrated in the tricarboxylic acid cycle where enzyme-enzyme complexes have been crystallized and electrostatic channeling pathways clearly modeled. A variety of experimental methods have provided evidence that channeling may occur in glycolysis including sedimentation, co-pelleting, and electrophoresis. There is also evidence of a metabolon, a functional multienzyme complex, for the glycolytic pathway. Computer modeling simulations can demonstrate potential enzyme-enzyme complexes and follow the trajectories of ligands as they move from one active site to another in such complexes. Herein, exploration of the channeling hypothesis in glycolysis will begin by using Brownian dynamics (BD) computer simulations on the enzymes that involve the co-factor nicotine adenine dinucleotide (NAD). The channeling hypothesis will be tested not only on the substrates of these enzymes, but also on the NAD itself. BD can explore the potential for forming enzyme-enzyme complexes, the potential pathways of ligands, and the efficiency of the ligand binding when compared to isolated enzymes in solution. The exportation will involve several enzymes and different species to see if there is a general trend observed throughout nature, including common vertebrate systems, disease causing organisms, and microorganisms. The initial focus will be on the parts of the pathway involving NAD because the enzymes can be well modeled based on known crystal structures and because it may be possible to follow the NAD through fluorescence experiments. Example channeling simulations include: NAD between glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and lactate dehydrogenase (LDH), glyceraldehyde-3- phosphate (GAP) between fructose-1,6-bisphosphate aldolase (aldolase) and GAPDH, GAP between triose phosphate isomerase (TPI) and GAPDH, GAP among aldolase, TPI and GAPDH, and finally pyruvate between pyruvate kinase and LDH. PUBLIC HEALTH RELEVANCE: The proposed work includes computer simulations useful not only for basic biomedical science (e.g, rabbit, human, rat, chicken, zebra fish, baker's yeast,) but also for infectious disease organisms (e.g., P. falciparum, trypanosomes, Leishmania, E. coli, M. tuberculosis) in an attempt to determine how ubiquitous the enzyme- enzyme interactions are and what kinds of channeling possibilities exist across species.

描述(由申请人提供)：通道假说(即底物或辅酶可以从一个活性部位移动到另一个活性部位而不与主体介质平衡)在糖酵解中仍然存在争议，因为糖酵解酶很大，并且具有很难检测到的非常动态的相互作用。在三羧酸循环中已经证实了通道作用，在那里酶-酶复合体已经结晶，静电通道被清楚地模拟出来。各种实验方法已经提供了证据表明，在糖酵解过程中可能会发生通道作用，包括沉淀法、共造粒和电泳法。也有证据表明糖酵解途径存在代谢蛋白，这是一种功能性的多酶复合体。计算机模拟模拟可以展示潜在的酶-酶复合体，并跟踪配体在这种复合体中从一个活性部位移动到另一个活性部位的轨迹。在这里，对糖酵解中的通道假说的探索将从使用布朗动力学(BD)计算机模拟涉及辅因子尼古丁腺嘌呤二核苷酸(NAD)的酶开始。通道假说不仅将在这些酶的底物上进行检验，而且还将在NAD本身上进行检验。BD可以探索形成酶-酶复合体的潜力，配体的潜在途径，以及与溶液中分离的酶相比，配体结合的效率。出口将涉及几种酶和不同的物种，以查看是否有在整个自然界观察到的普遍趋势，包括常见的脊椎动物系统、致病生物和微生物。最初的重点将放在涉及NAD的途径上，因为酶可以根据已知的晶体结构很好地建模，而且有可能通过荧光实验来跟踪NAD。沟道模拟的例子包括：甘油醛-3-磷酸脱氢酶(GAPDH)和乳酸脱氢酶(LDH)之间的NAD，果糖-1，6-二磷酸缩醛酶(ALDase)和GAPDH之间的GAP，磷酸三糖异构酶(TPI)和GAPDH之间的GAP，缩醛酶、TPI和GAPDH之间的GAP，以及最终丙酮酸激酶和LDH之间的丙酮酸。 与公共健康相关：拟议的工作包括计算机模拟，不仅对基础生物医学科学有用(例如兔子、人类、老鼠、鸡、斑马鱼、面包酵母)，而且还用于传染病生物(例如恶性疟原虫、锥虫、利什曼原虫、大肠杆菌、结核分枝杆菌)，以试图确定酶-酶相互作用的普遍程度以及存在何种跨物种的传导可能性。