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RNA Stability01:53

RNA Stability

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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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Mutations01:39

Mutations

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Overview
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Survival Tree01:19

Survival Tree

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Survival trees are a non-parametric method used in survival analysis to model the relationship between a set of covariates and the time until an event of interest occurs, often referred to as the "time-to-event" or "survival time." This method is particularly useful when dealing with censored data, where the event has not occurred for some individuals by the end of the study period, or when the exact time of the event is unknown.
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mRNA Stability and Gene Expression02:51

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The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.
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Protein Denaturation01:28

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The function of proteins depends on their native three-dimensional structure, which is dictated by the amino acid sequence of the specific protein. Folding of the polypeptide chain takes place under specific conditions that energetically favor the folded conformation. In contrast, protein denaturation occurs spontaneously under unfavorable conditions that disrupt the integrity of the folded conformation. Thus, the chemical and physical environment of a protein, such as significant changes in pH...
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Nonsense-mediated mRNA Decay

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The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
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DDMut:使用深度学习预测突变对蛋白质稳定性的影响.

Yunzhuo Zhou1,2, Qisheng Pan1,2, Douglas E V Pires3

  • 1School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.

Nucleic acids research
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DDMut是一种新的深度学习工具,可以准确预测突变导致的蛋白质稳定性变化. 它提供了一种快速可扩展的解决方案,用于理解蛋白质工程和变异解释中的突变效应.

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科学领域:

  • 计算生物学 计算生物学
  • 蛋白质工程是指蛋白质工程.
  • 生物信息学是一种生物信息学.

背景情况:

  • 预测突变对蛋白质稳定性的影响对生物技术和医学至关重要.
  • 现有的工具面临着速度,准确性和对破坏稳定的突变的偏差的限制.

研究的目的:

  • 开发一种快速准确的深度学习模型,用于预测单点和多点突变时的吉布斯自由能量 (ΔΔG) 的变化.
  • 通过解决计算时间,预测能力和预测偏差的局限性来改进现有方法.

主要方法:

  • 开发了DDMut,这是一个集成基于图形的3D环境表示与卷积层和变压器编码器的姆网络.
  • 利用前进和假设的反向突变来确保模型的反对称性.
  • 在广泛的蛋白质突变和它们的稳定性变化数据集上训练深度学习模型.

主要成果:

  • 对于单点 (RMSE: 1.37 kcal/mol) 和多点突变 (RMSE: 1.84 kcal/mol),DDMut获得了高精度,Pearson的相关性高达0.70.
  • 该模型在非冗余盲测试集上的现有方法相比,显示出更高的性能.
  • 对于稳定和不稳定突变,DDMut显示出出色的可扩展性和反对称性预测.

结论:

  • DDMut提供了一种计算效率高且准确的方法,用于预测突变引起的蛋白质稳定性的变化.
  • 这种工具可以在变异解释,蛋白质工程和理解突变驱动的功能后果方面发挥重要作用.
  • DDMut可以作为免费的Web服务器和API用于更广泛的科学用途.