Frustration, Specificity and Function in the NfkB-IkB System

NfkB-IkB 系统中的挫败感、特异性和功能

• 批准号: 7806574
• 负责人: Diego Ulises Ferreiro
• 金额: $ 3.4万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-04-15 至 2012-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7806574
• 关键词: Acquired Immunodeficiency Syndrome; Affect; Amino Acids; Ankyrin Repeat; Architecture; Argentina; Arthritis; Asthma; Attention; Back; Behavior; Binding; Biochemistry; Bioinformatics; Biological; Biological Process; California; Chemistry; Code; Collaborations; Complex; Computer Analysis; Computer Simulation; Country; Coupled; Curiosities; DNA-Binding Proteins; Data; Diabetes Mellitus; Disease; Electronic Mail; Exhibits; Faculty; Family; Family member; Frustration; Genome; Grant; In Vitro; Individual; Intelligence; Interdisciplinary Study; International; Investigation; Joints; Kinetics; Laboratories; Language; Los Angeles; Malignant Neoplasms; Measures; Messenger RNA; Methods; Modeling; Motion; Mutation; Occupations; Parents; Pattern; Physics; Positioning Attribute; Postdoctoral Fellow; Process; Property; Proteins; Protons; Qualifying; Reaction; Research; Research Personnel; Residual state; Resolution; Role; San Francisco; Scheme; Signal Transduction; Simulate; Site; Specificity; Stretching; Structure; System; Telefacsimile; Thermodynamics; TimeLine; United States National Institutes of Health; Universities; Virus Diseases; Work; Writing; base; design; driving force; experience; inhibitor/antagonist; insight; novel strategies; parent grant; physical science; protein B; protein folding; protein function; protein structure; public health relevance; research study; simulation; skills; theories; three dimensional structure; transcription factor

DESCRIPTION (provided by applicant): Repeat proteins are found in all three phyla and present in some 6% of all eukaryotic protein coding sequences [1]. They are made up of tandem arrays of similar amino acid stretches that fold up into elongated architectures of repeating structural motifs that stack one upon the next producing extended superhelical structures [2]. Repeat proteins, by virtue of their inherent symmetries both in primary sequence and three dimensional structure, stand as remarkable models where the sequence-codes-folding-codes-function< hypothesis can be quantitatively evaluated. The energy landscape theory of protein folding is based on the principle of minimal frustration< [3]. This principle, however, does not rule out that some energetic frustration may be present in a folded protein. Moreover, the remaining frustration may facilitate motion of the protein around its native basin, and as such the residual frustration may be fundamental to protein function [4]. Recently developed methods for spatially localizing and quantifying the energetic frustration present in native protein structures reflects evolutionary constraints on a proteins< energy landscape and yields useful insights into their biological functions [5]. We focus our attention on the I:B proteins. These ankyrin-repeat (AR) containing proteins regulate the activity of the NF-:B transcription factor family, which is found misregulated in diseases such as cancer, arthritis, asthma, diabetes, AIDS and viral infections [6]. The Ankyrin-repeat region of I:B1 contains 6 ARs and displays a highly dynamic character when not complexed with NF-:B [7-9]. Moreover, it has been shown that its folding properties are clearly related to its function [10]. We envision a complementary approach to the following Aims presented in Project 3 of the parent grant: 1) characterize the overall kinetics of coupled folding and binding in the NF-:B/ I:B1 system. 2) characterize the residue specific dynamics of coupled folding and binding in the NF-:B/ I:B1 system. These require a joint theoretical and experimental effort that brings together computational analysis of the distributions of local frustration, its effect on the folding transitions (both simulated and measured), and how these affect the functional binding reactions. We will use bioinformatic methods to characterize the frustration patterns of various NF-:B and I:B family members [5], both in their free and bound states. We will use computational models to simulate the folding - binding reaction of I:B1 - NF-:B, using recently developed schemes that allow for energetic frustration [11]. We will design mutations that perturb the frustration distributions [11], realize those in the laboratory, and analyze how the structural transitions and the binding properties are affected by means of quantification of the appropriate thermodynamic observables [8,10,12]. This research will be done primarily in Buenos Aires, Argentina, at the Universidad Nacional de Quilmes, in collaboration with Dr Diego Ferreiro, as an extension of NIH Grant No P01-GM071862-01. PUBLIC HEALTH RELEVANCE: Transcription factors are proteins that control the synthesis of mRNA from genomes. Among transcription factors, the NF-:B transcription factor family, is found misregulated in diseases such as cancer, arthritis, asthma, diabetes, AIDS and viral infections [6]. This family is regulated by inhibitors called I:Bs and we have shown that I:B1 ;folds< upon binding to NF -:B [10]. The intricate folding transitions that this protein exhibits, the topic of the proposed research, may be a key to its biological functions, as they are likely to be related to its NF-:B recognition and inhibition rates [13], crucial processes in the overall behavior of the NF-:B signaling system [14].

描述(申请人提供)：在所有三个门中都发现了重复蛋白，并存在于所有真核蛋白编码序列中的约6%[1]。它们由相似氨基酸延伸的串联阵列组成，折叠成细长的结构，这些结构主题重复，一个堆叠在下一个之上，产生延伸的超螺旋结构[2]。重复蛋白，凭借其在一级序列和三维结构上的固有对称性，是一种引人注目的模型，在这里可以定量评估序列编码-折叠-编码-功能和功能假说。蛋白质折叠的能量景观理论基于最小挫折原理[3]。然而，这一原理并不排除折叠蛋白质中可能存在一些能量受挫。此外，剩余的挫折感可能会促进蛋白质在其天然盆地周围的运动，因此，残余挫折感可能是蛋白质功能的基础[4]。最近开发的空间定位和量化天然蛋白质结构中存在的能量挫折的方法反映了蛋白质能量格局的进化限制，并对其生物学功能产生了有用的见解[5]。我们把注意力集中在I：B蛋白上。这些含有Anankyrin-Repeat(AR)的蛋白质调节核因子-：B转录因子家族的活性，该转录因子家族在癌症、关节炎、哮喘、糖尿病、艾滋病和病毒感染等疾病中被发现调控不当[6]。I：B1的Ankyrin-Repeat区含有6个Ars，当不与NF-：B[7-9]络合时，表现出高度的动态特征。此外，还表明它的折叠性能与其功能有明显的关系[10]。我们设想了一种补充方法来实现父赠款项目3中提出的以下目标：1)表征NF-：B/I：B1系统中耦合折叠和结合的整体动力学。2)表征了NF-：B/I：B1体系中偶联折叠和结合的残基比动力学。这些需要联合理论和实验工作，将局部挫折的分布、其对折叠转变的影响(模拟和测量)以及这些如何影响功能结合反应的计算分析结合在一起。我们将使用生物信息学方法来描述不同的NF-：B和I：B家族成员在自由和结合状态下的挫折感模式[5]。我们将使用计算模型来模拟I：B1-NF-：B的折叠结合反应，使用最近开发的允许能量受挫的方案[11]。我们将设计扰乱挫折分布的突变[11]，在实验室中实现这些突变，并通过量化适当的热力学观测数据来分析结构转变和结合性质是如何受到影响的[8，10，12]。这项研究将主要在阿根廷布宜诺斯艾利斯的国家大学与迭戈·费雷罗博士合作进行，作为NIH第P01-GM071862-01号拨款的延伸。与公共健康相关：转录因子是控制基因组合成信使核糖核酸的蛋白质。在转录因子中，核因子-：B转录因子家族在癌症、关节炎、哮喘、糖尿病、艾滋病和病毒感染等疾病中被发现调控错误[6]。这个家族由称为I：BS的抑制剂调节，我们已经证明了I：B1；在与核因子-：B结合时折叠[10]。该蛋白质呈现的复杂的折叠转变可能是其生物学功能的关键，因为它们可能与其核因子-：B识别和抑制率有关[13]，这是核因子-：B信号系统整体行为的关键过程[14]。