NMR Studies of Protein Side-Chain Dynamics

蛋白质侧链动力学的核磁共振研究

基本信息

批准号：
8299554
负责人：
MARK A RANCE
金额：
$ 33.21万
依托单位：
UNIVERSITY OF CINCINNATI
依托单位国家：
美国
项目类别：
财政年份：
2003
资助国家：
美国
起止时间：
2003-05-01 至 2014-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8299554
关键词：
Affinity Amino Acids Binding Binding Proteins Binding Sites Biochemical Biological Biological Models Biological Process Calcium Calcium Binding Calcium Signaling Calcium ion Calcium-Binding Proteins Cell Cycle Regulation Cell physiology Chemicals Communication Complement Complex Consensus Consensus Sequence DNA DNA Binding DNA Sequence DNA-Binding Proteins DNA-Protein Interaction Drosophila bicoid protein EF Hand Motifs EF-Hand Domain Entropy Exhibits Family Free Energy Genes Genetic Transcription Goals Health Homeodomain Proteins Human Immobilization Ions Knowledge Lysine Mediating Medical Modeling Molecular Muscle Contraction Play Positioning Attribute Property Protein Binding Protein Family Proteins Regulation Reporting Research Research Design Rieger syndrome Role SS DNA BP Side Signal Pathway Signal Transduction Single-Stranded DNA Site Solutions Specificity Structure System Techniques Testing Thermodynamics Variant Work base biological systems calbindin cooperative study driving force homeodomain improved innovation insight interest member molecular dynamics molecular recognition protein folding protein function recombinational repair research study response telomere

项目摘要

The overall goal of this project is to investigate the contribution of amino acid side-chain dynamics to the physico-chemical mechanisms that determine the thermodynamics of recognition and association in protein/DNA interactions and the molecular basis of cooperativity of ion binding in calcium-binding proteins (CaBPs). Side chains can make significant contributions to the configurational entropy of a protein, thereby modulating the thermodynamics of protein function. A fundamental understanding of how proteins work therefore requires an intimate knowledge of the dynamic properties of the side chains. Two model systems, protein/DNA complexes and the CaBP calbindin D9k, have been selected for study that will allow key insights to be obtained regarding the role of side-chain dynamics in protein/DNA binding/recognition and cooperativity of ion binding, respectively. Despite the large number of structural and thermodynamic studies that have been reported for a variety of protein/DNA systems, critical and substantial gaps exist in our knowledge and understanding of the role played by molecular dynamics in protein/DNA interactions. A general problem in the field of molecular recognition is that structural studies reveal relatively little about the entropic component of the free energy of complex formation. Thus, it is very important to complement structural information by undertaking studies to investigate side-chain dynamics in the protein/DNA interface. Cooperative ion binding is one of the fundamental properties of calcium signaling pathways. The readout of intracellular calcium signals must be very finely tuned to effect a rapid response to the transient and subtle variations in Ca2+ concentrations that constitute the calcium signals. The great importance of cooperative binding of Ca2+ by EF-hand CaBPs has motivated efforts to determine the molecular basis for cooperativity in specific members of this protein family. Calbindin D9k, a single domain EF-hand CaBP, is one of the primary model systems for studying the cooperative binding phenomenon. The general hypotheses of the proposed research are that modulation of protein side-chain dynamics plays important roles in establishing a complementary interface between consensus/non-consensus DNA sequences and a cognate DNA-binding protein, and in promoting allosteric communication between ion- binding sites that leads to cooperative calcium binding. To test these hypotheses the following specific aims are proposed: (1) determine the side-chain dynamics and thermodynamic properties of the K50-class homeodomains from the human Pitx2 and the Drosophila Bicoid proteins, bound to a consensus duplex DNA site; (2) determine the structure, dynamics and thermodynamics of the Pitx2 and Bicoid homeodomains bound to non-consensus DNA sites; (3) investigate the molecular basis and driving forces for cooperative binding of Ca2+ by the CaBP calbindin D9k; and (4) characterize the thermodynamic role of side-chain dynamics in the single-strand DNA-binding family of Telomere End Protection (TEP) proteins.

该项目的总体目标是研究氨基酸侧链动力学对确定识别和关联热力学的物理化学机制蛋白质/DNA相互作用和离子结合钙结合蛋白中离子结合的分子基础（驾驶室）。侧链可以为蛋白质的构型做出重大贡献，从而调节蛋白质功能的热力学。对蛋白质如何工作的基本了解因此，需要对侧链的动态特性有深入的了解。两个模型系统，蛋白质/DNA复合物和CABP Calbindin D9K已选择进行研究，这将允许关键见解可以获得侧链动力学在蛋白质/DNA结合/识别和合作性中的作用离子结合。尽管有大量的结构和热力学研究报告了各种蛋白质/DNA系统的报道，我们的知识中存在关键和实质性差距了解分子动力学在蛋白质/DNA相互作用中所起的作用。一个一般问题分子识别的领域是结构研究揭示了相对较小的关于复杂形成的自由能。因此，通过进行研究以研究蛋白质/DNA界面中的侧链动力学。合作离子结合是钙信号通路的基本特性之一。这细胞内钙信号的读数必须非常细微地调节，以对瞬态和瞬态产生快速响应构成钙信号的Ca2+浓度的细微变化。非常重要的 EF手CABP对Ca2+的合作结合已促进确定分子基础的努力该蛋白质家族的特定成员的合作性。 Calbindin D9K是一个单个域EF手，是一个研究合作结合现象的主要模型系统。拟议研究的一般假设是蛋白质侧链动力学的调节在建立共识/非共识DNA之间建立互补界面方面起着重要作用序列和同源DNA结合蛋白，并在离子之间促进变构通信结合位点，导致合作钙结合。为了检验这些假设以下特定目标提出：（1）确定K50级的侧链动力学和热力学特性来自人Pitx2和果蝇双聚体蛋白的同源域，与共识双链DNA结合地点; （2）确定pitx2和双域构成的结构，动力学和热力学结合到非共识DNA位点；（3）研究分子基础和驱动力的合作结合 Ca2+由Cabp Calbindin D9K; （4）表征侧链动力学在热力学作用中端粒保护（TEP）蛋白的单链DNA结合家族。

项目成果

期刊论文数量（8）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Structural mechanism for signal transduction in RXR nuclear receptor heterodimers.

DOI：
10.1038/ncomms9013
发表时间：
2015-08-20
期刊：
Nature communications
影响因子：
16.6
作者：
Kojetin DJ;Matta-Camacho E;Hughes TS;Srinivasan S;Nwachukwu JC;Cavett V;Nowak J;Chalmers MJ;Marciano DP;Kamenecka TM;Shulman AI;Rance M;Griffin PR;Bruning JB;Nettles KW
通讯作者：
Nettles KW

The N-terminal basolateral targeting signal unlikely acts alone in the differential trafficking of membrane transporters in MDCK cells.

DOI：
10.1021/bi4005914
发表时间：
2013-07-30
期刊：
BIOCHEMISTRY
影响因子：
2.9
作者：
Kuo, Shiu-Ming;Wang, Li-Yuan;Yu, Siyuan;Campbell, Christine E.;Valiyaparambil, Sujith A.;Rance, Mark;Blumenthal, Kenneth M.
通讯作者：
Blumenthal, Kenneth M.

Ligand and receptor dynamics contribute to the mechanism of graded PPARγ agonism.

DOI：
10.1016/j.str.2011.10.018
发表时间：
2012-01-11
期刊：
STRUCTURE
影响因子：
5.7
作者：
Hughes, Travis S.;Chalmers, Michael J.;Novick, Scott;Kuruvilla, Dana S.;Chang, Mi Ra;Kamenecka, Theodore M.;Rance, Mark;Johnson, Bruce A.;Burris, Thomas P.;Griffin, Patrick R.;Kojetin, Douglas J.
通讯作者：
Kojetin, Douglas J.

Effect of monovalent ion binding on molecular dynamics of the S100-family calcium-binding protein calbindin D9k.

单价离子结合对 S100 家族钙结合蛋白钙结合蛋白 D9k 分子动力学的影响。