Towards solution of the RNA folding problem
致力于解决RNA折叠问题
基本信息
- 批准号:8233539
- 负责人:
- 金额:$ 33.76万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2009
- 资助国家:美国
- 起止时间:2009-05-01 至 2015-02-28
- 项目状态:已结题
- 来源:
- 关键词:AffectBehaviorBiological ModelsBiological ProcessCatalytic DomainCationsCell physiologyCellsChemicalsComplexCouplingDataDevelopmentElementsEnvironmentGenetic TranscriptionGoalsHuman PathologyIn VitroIndividualIntronsKineticsLifeLinkMeasuresMediatingMessenger RNAMethodsMicroscopicModelingMolecular ChaperonesNatureNucleotidesPathologyPathway interactionsPhysical environmentPhysiologicalPolynucleotidesPopulationProcessProtein BindingProteinsRNARNA FoldingReactionRegulatory ElementResolutionShippingShipsSolutionsStructural ModelsStructureStudy modelsTemperatureTestingTimegroup I ribozymein vivomRNA Expressionmillisecondprotein structureresearch studysimulationthree dimensional structure
项目摘要
Project Summary
RNA molecules often must fold into distinct three-dimensional structures to exert their biological
function. These folded structures may be large or small, long-lived or transient, and/or stable or
unstable in nature. The kinetics of RNA folding is characterized by multiple pathways, the population
of intermediates and often (but not always) on- and/or off-pathway kinetically trapped species. Our
approach to understanding how the RNA is folded is to determine which folding pathways are possible
in vitro with the goal of determining the subset that occur in vivo. We computationally integrate local
and global measures of folding into `structural-kinetic' models that characterize folding reactions from
their earliest steps. Our development of high-throughput methods for the acquisition of time progress
curves with millisecond time and single nucleotide spatial resolution allows general hypotheses to be
tested against experimental data that is both deep and broad. The proposed studies of group I introns
seek to establish quantitative relationships between RNA structure, stability and folding kinetics by
critically comparing the folding of phylogenetically related RNA molecules and gentle systematic
perturbation of tertiary contacts. The folding of a riboswitch whose structure is homologous to the
catalytic core of group I intron is analyzed to determine if these different regulatory elements possess
a common folding mechanism. We explore the effect on the observed emergent folding behavior
solution variables such as temperature and ionic conditions that affect the microscopic environment
of RNA in order to understand the relationships between the physical environment and folding
environment. Lastly, we seek to understand how transcription affects RNA folding.
项目总结
项目成果
期刊论文数量(4)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Probing RNA-Protein Interactions and RNA Compaction by Sedimentation Velocity Analytical Ultracentrifugation.
通过沉降速度分析超速离心探测 RNA-蛋白质相互作用和 RNA 压实。
- DOI:10.1007/978-1-0716-0278-2_19
- 发表时间:2020
- 期刊:
- 影响因子:0
- 作者:Mitra,Somdeb;Demeler,Borries
- 通讯作者:Demeler,Borries
Using analytical ultracentrifugation (AUC) to measure global conformational changes accompanying equilibrium tertiary folding of RNA molecules.
使用分析超速离心 (AUC) 测量伴随 RNA 分子平衡三级折叠的整体构象变化。
- DOI:10.1016/s0076-6879(09)69010-8
- 发表时间:2009
- 期刊:
- 影响因子:0
- 作者:Mitra,Somdeb
- 通讯作者:Mitra,Somdeb
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Michael D. Brenowitz其他文献
Regulation of Nonmuscle Myosin IIA Assembly
- DOI:
10.1016/j.bpj.2009.12.869 - 发表时间:
2010-01-01 - 期刊:
- 影响因子:
- 作者:
K. Ilker Sen;Wendy Zencheck;Michael D. Brenowitz;Steven C. Almo;Anne R. Bresnick - 通讯作者:
Anne R. Bresnick
Regulation of Nonmuscle Myosin-IIA Filament Assembly/Disassembly
- DOI:
10.1016/j.bpj.2010.12.1003 - 发表时间:
2011-02-02 - 期刊:
- 影响因子:
- 作者:
K. Ilker Sen;Michael D. Brenowitz;Steven C. Almo;Gary G. Gerfen;Anne R. Bresnick - 通讯作者:
Anne R. Bresnick
Michael D. Brenowitz的其他文献
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{{ truncateString('Michael D. Brenowitz', 18)}}的其他基金
How MeCP2 discriminates epigenetic marks is still a mystery
MeCP2如何区分表观遗传标记仍然是个谜
- 批准号:
10201657 - 财政年份:2018
- 资助金额:
$ 33.76万 - 项目类别:
'Indirect Readout' Mediation of Protein-DNA Interactions
蛋白质-DNA 相互作用的“间接读出”介导
- 批准号:
6619789 - 财政年份:2001
- 资助金额:
$ 33.76万 - 项目类别:
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